From eduardobjacobi at gmail.com Thu Mar 1 14:57:53 2018 From: eduardobjacobi at gmail.com (Eduardo Bacelar) Date: Thu, 1 Mar 2018 10:57:53 -0300 Subject: [FieldTrip] Convert .PLX Message-ID: Hi, I am having problems with the conversion of .plx files, in my data I have spike and LFP data together, I now that is not possible to read this 2 types of data in the same function call, but is there any way were I am enable to only read LFP data and after that read Spike data? What I rely want to know is if is possible to read only a number of channels. Waiting for replay. Best rewards, -- Eduardo Bacelar Mestrando - Neuroengenharia Instituto Internacional de Neurociências - Edmond e Lily Safra . ------------------------------ Contact me: T: +55 (53) 8124-0032 Tw: @EddBacelar E: eduardobjacobi at gmail.com Fb: /eduardo.bacelar.89 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathalie.liegel at gmx.de Mon Mar 5 13:56:55 2018 From: nathalie.liegel at gmx.de (Nathalie Liegel) Date: Mon, 5 Mar 2018 13:56:55 +0100 Subject: [FieldTrip] Any German speaking cognitive neuroscientist interested in an exciting industry position? Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Anz-Stelle-A4-1802.pdf Type: application/pdf Size: 223494 bytes Desc: not available URL: From nelleke.van.wouwe at Vanderbilt.Edu Mon Mar 5 17:40:54 2018 From: nelleke.van.wouwe at Vanderbilt.Edu (Van Wouwe, Nelleke) Date: Mon, 5 Mar 2018 16:40:54 +0000 Subject: [FieldTrip] Postdoctoral Position University of Louisville Message-ID: <29540490A5680F42A88C5587547464E9F8CE83E2@ITS-HCWNEM108.ds.vanderbilt.edu> Postdoctoral Position A postdoctoral position is available in the Human Cognitive Neurophysiology Group (HCN) in the Department of Neurological Surgery at the University of Louisville School of Medicine. HCN (Drs. Neimat, van Wouwe, and Kaskan) investigates the neural correlates of cognition in the setting of human intraoperative recording and stimulation performed for the treatment of movement disorders and epilepsy. Our collaborative group pairs neuroscientists with physicians in a clinical research environment to provide rich opportunities for the novel exploration of brain function. Drs. Neimat and van Wouwe have recently been awarded a multi-site R01 (Louisville and Vanderbilt) entitled: Modulating Inhibitory Action Control Systems with Subthalamic Nucleus (STN) Stimulation. Dr. Kaskan has recently joined the group and is investigating the role of the STN in value-based decision-making. We are seeking to hire a postdoctoral fellow with a Ph.D. in neuroscience, engineering, computer science, cognitive psychology, the biomedical sciences, or a field related to neuroscience. Experience with the collection and analysis of single-unit neural recordings and/or local field potentials (human or animal) is required. Experience programming with MATLAB and familiarity with the Linux environment is highly encouraged. The best candidates will be experienced neurophysiologists interested in human cognition. The candidate is expected to be highly motivated, possess excellent presentation and interpersonal skills, an ability to troubleshoot technical neurophysiological issues, a demonstrated track record of publications and project completion, and the ability to work both independently and with others. Additional responsibilities include: manuscript and grant preparation, literature and manuscript review, presentations at local seminars and national meetings, and mentoring junior lab members. An initial appointment will be made for one year, with the possibility of extension based upon performance. Salary is commensurate with experience. The University of Louisville is a strong research environment and the postdoctoral fellow will have the opportunity to interact and collaborate with other departments including the Kentucky Spinal Cord Injury Research Center, the Department of Anatomical Sciences and Neurobiology, the Department of Psychological and Brain Sciences, and the JB Speed School of Engineering. The multi-site grant also provides the opportunity to work with the Neurology Department at Vanderbilt University Medical Center. The University of Louisville is an equal opportunity, affirmative action employer, and is committed to providing employment opportunities to all qualified applicants without regard to race, sex, age, color, national origin, ethnicity, creed, religion, disability, genetic information, sexual orientation, gender, gender identity and expression, marital status, pregnancy, or veteran status. Interested candidates should send a brief statement of research experience including interests and future objectives as well as a curriculum vitae, a reprint (.pdf) of an exemplar paper where they were an author, and the contact information for three professional references to peter.kaskan at ulp.org. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nico.boehler at ugent.be Tue Mar 6 08:31:18 2018 From: nico.boehler at ugent.be (=?Windows-1252?Q?Nico_B=F6hler?=) Date: Tue, 6 Mar 2018 07:31:18 +0000 Subject: [FieldTrip] 4 PhD student positions in Ghent, Belgium In-Reply-To: References: Message-ID: <1520321487503.74871@ugent.be> Four full-time PhD student positions are available at Ghent University. All are four-year positions (provided positive periodic evaluation), preferably starting in Sept or Oct 2018. Salary is according to standard Ghent University regulations for PhD students (starting at around €2000 per month net salary). Candidates should have a Master’s degree in Psychology, Cognitive Neuroscience, or similar. 1) Synchrony and coupling in procedural and declarative memory tasks This position is situated in the framework of an interuniversity project called “The journey of a memory: dynamics of learning and consolidation in maturation and ageing”, see www.eosprogramme.be Candidates are expected to carry out empirical work combining EEG, MEG, and computational modeling. Expertise in these methods is not required, but strong interest in cognitive neuroscience, data analysis, and computer programming are. As this is an interuniversity project it involves collaboration between three institutions. Supervisors will be Tom Verguts and Nico Boehler (Ghent University; main institution), in collaboration with Xavier De Tiège (Université Libre de Bruxelles) and Dante Mantini (KULeuven). More information about the project can be found here: https://sites.google.com/view/memodyn/homepage For applying, please send a CV (including two email addresses of academic referees) and motivation letter to Tom Verguts (tom.verguts at ugent.be). For further information on the project or details about the position, please also contact Tom Verguts. Applications will be considered until the position is filled. 2) Transfer of serial order information between working memory and long term memory This position is situated in the framework of an interuniversity project called “The journey of a memory: dynamics of learning and consolidation in maturation and ageing”, see www.eosprogramme.be Candidates are expected to carry out empirical work with fMRI and combined HD-EEG/MEG. Expertise in these methods is not required, but strong interest in cognitive neuroscience, data analysis, and computer programming are. As this is an interuniversity project it involves collaboration between three institutions. Supervisors at the Ghent University side is Wim Fias; at Université de Liège supervision is carried out by Steve Majerus at Université Libre de Bruxelles by Xavier De Tiège; at KULeuven, the supervisor is Dante Mantini. More information about the project can be found here: https://sites.google.com/view/memodyn/homepage For applying, please send a CV (including two email addresses of academic referees) and motivation letter to Wim Fias (wim.fias at ugent.be ; For further information on the project or details about the position, please also contact Wim Fias. Applications will be considered until the position is filled. 3) The role of the locus coeruleus in arousal regulation in ADHD This project is focused on arousal regulation in ADHD. There is a long tradition of explaining ADHD in terms of arousal regulation difficulties. While many studies found support for this, little is known about its underlying neurobiological substrates. The locus coeruleus (LC), a small nucleus in the brainstem, associated with arousal regulation, is a hypothesized candidate. In the current project, we will investigate the putative role of the LC in arousal regulation deficits in ADHD, by means of fMRI, EEG, and pupil measures. Expertise in these methods is not required but a great benefit. Strong interest in the combination of cognitive neuroscience and experimental-clinical research is required. Active knowledge of Dutch is a requirement (working with Flemish participants with ADHD). The main supervisor is Roeljan Wiersema (Dept. of Experimental Clinical and Health Psychology) and the co-supervisor is Nico Boehler (Department of Experimental Psychology). For applying, please send a CV (including two email addresses of academic referees, or referent letters) and motivation letter to Roeljan Wiersema (Roeljan.wiersema at ugent.be). For further information on the project or details about the position, please also contact Roeljan Wiersema. Applications will be considered until the position is filled. 4) Money well spent? A multi-modal investigation of context effects during and after a reward manipulation This project is focused on context effects of reward manipulations. Reward effects on cognitive functions have received a lot of scientific attention in the last years, usually finding that associating reward with a particular task ubiquitously improves performance. Yet, this work largely focused on transient reward effects using concurrent no-reward trials as the main comparison, and relatively little work has looked at potential costs of reward-based improvements. The present project aims at doing so by studying reward-context effects both during a reward manipulation (compared to no-reward trials from neutral task blocks) and after (most notably the “undermining effect”) to get a broader understanding of the costs and benefits of such manipulations. We will investigate the neurobiological implementation of these phenomena by using systematic behavioral testing in combination with electroencephalographic (EEG) and pupillometric measures. Experience with EEG and pupillometry are not required but would be a great benefit, as would be a background in programming experiments and analyzing experimental data. The main supervisor is Nico Boehler and the co-supervisor is Ruth Krebs. For applying, please send a CV (including two email addresses of academic referees) and motivation letter to Nico Boehler (nico.boehler at ugent.be), whom you can also contact for further information about the project or details about the position and procedure. Applications will be considered until the position is filled.? -------------- next part -------------- An HTML attachment was scrubbed... URL: From muthuraman10 at hotmail.com Fri Mar 9 16:20:08 2018 From: muthuraman10 at hotmail.com (Muthuraman Muthuraman) Date: Fri, 9 Mar 2018 15:20:08 +0000 Subject: [FieldTrip] PhD position on electrophysiology and cognition in multiple sclerosis patients! Message-ID: Doctoral Student Neuroscientist with focus on electrophysiology and cognition in multiple sclerosis The medical faculty of the University of Mainz, Germany, invites applications for a PhD Student for a functional translational neuroscience (FTN) scholarship three year position to work on electrophysiology and cognition in neuroimmunological disorders and multiple sclerosis. A project with multimodality usage of electroencephalography (EEG) and non-invasive brain stimulation technique like transcranial magnetic stimulation (TMS). The successful applicant holds a Master’s degree (or equivalent) in a relevant academic area such as basic life sciences, neuropsychology, applied mathematics or biomedical engineering or similar disciplines. German language proficiency is mandatory for communicating with the patients. The working language at the institute is English. Experience with electrophysiology and the analysis of brain signals is advantageous, but not essential. The applicant’s merits are assessed on the basis of the quality of Master’s level studies and thesis, previous experience with the brain imaging, motivation and research interests. The location for this research will mainly be the workgroups “Section of Movement Disorders, Neurostimulation and Neuroimaging“ of Prof. Sergiu Groppa at the Department of Neurology and “Multimodal Signal Processing and Statistical Analyses” of Prof. Muthuraman Muthuraman, both at the Focus Program Translational Neurosciences (http://www.ftn.uni-mainz.de/) and Neuroimaging Centre Mainz (http://www.ftn.nic.uni-mainz.de/). Expected close collaborations with national and international partners. The application should include a statement of research interests, a curriculum vitae (max. 4 pages) composed according to good scientific practice, a certificate of Master’s degree, copy of the master’s thesis and grades of Master’s level studies, the names and e-mail addresses of two referees and a proof of proficiency in English. The position will be open until filled. To apply for the position, please send the above documents as pdfs until 31.03.2018 to Prof. Sergiu Groppa, Department of Neurology, Section of movement disorders and neurostimulation, University of Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany, or by Email to segroppa(at)uni-mainz.de . For additional information please contact Sergiu Groppa. With regards M.Muthuraman Prof. Dr.- Ing. M.Muthuraman Biomedical statistics and multimodal signal processing unit Movement Disorders and Neurostimulation, Department of Neurology, Focus Program Translational Neuroscience (FTN) Johannes-Gutenberg-University Hospital, Langenbeckstr. 1 55131 Mainz, Germany Email: mmuthura at uni-mainz.de Website:http://www.tiefehirnstimulation.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From robpetrosino at gmail.com Sat Mar 10 22:28:56 2018 From: robpetrosino at gmail.com (Roberto Petrosino) Date: Sat, 10 Mar 2018 16:28:56 -0500 Subject: [FieldTrip] ft_definetrial() and ft_preprocessing() Message-ID: <50B52505-61C2-4807-9AB7-E7A21141765C@gmail.com> Hi all, I am trying to preprocess my eeg raw data (from BrainVision amplifiers), but I am having troubles with error I can’t figure out how to fix. Here’s the code: > clear; > clc; > > data_path = ‘/.../raw/'; > > %STEP 1: reading the data in > cfg = []; > cfg.dataset = [data_path ’subj1.vhdr']; > > %high-pass filter > cfg.preproc.hpfilter = 'yes'; > cfg.preproc.hpfiltord = 2; %known bug for filtering; can be avoided by changing the order of the filter (2 is random) > cfg.preproc.hpfreq = 0.1; %in Hz > > %rereference > cfg.preproc.reref = 'yes'; > cfg.preproc.channel = 'all'; > cfg.preproc.implicitref = ''; %on-line reference is empty > cfg.preproc.refchannel = {'M1', 'M2'}; %the channels we want to rereference our data against. In this > %case, we will rereference against the linked mastoids > > %updating channel locations; %% MPI/DCCN versions of actiCAP? > cfg.layout = '/Users/.../MATLAB/fieldtrip-master/template/layout/acticap-64ch-standard2.mat'; %the file we want to extract electrode coordinates from > > %demean > cfg.deman = 'yes'; > cfg.basewindow = [-.2 0]; > > %STEP 2: defining trials and epoching > cfg.trialdef.prestim = 0.2; > cfg.trialdef.poststim = 1; % epochs will be -200 1000 ms > cfg.trialdef.eventtype = 'Stimulus'; > cfg.trialfun = 'trialfun_congruency’; %customized function for the data > data_in = ft_definetrial(cfg); %this will create a trl structure field, which is a list > % of 3 columns, where every row describes a separate trial start, end and offset > data_prej = ft_preprocessing(cfg); This is the error that pops up: > Error using ft_preprocessing (line 387) > you must call FT_DEFINETRIAL prior to FT_PREPROCESSING which is weird, since ft_definetrial() is called right before ft_preprocessing(). Does anyone know what the problem could be? Thanks, -Roberto —— Roberto Petrosino PhD student in Linguistics CT Institute from Brain and Cognitive Sciences University of Connecticut -------------- next part -------------- An HTML attachment was scrubbed... URL: From ekenaykut at gmail.com Sat Mar 10 22:32:07 2018 From: ekenaykut at gmail.com (Aykut Eken) Date: Sun, 11 Mar 2018 00:32:07 +0300 Subject: [FieldTrip] ft_definetrial() and ft_preprocessing() In-Reply-To: <50B52505-61C2-4807-9AB7-E7A21141765C@gmail.com> References: <50B52505-61C2-4807-9AB7-E7A21141765C@gmail.com> Message-ID: >> data_in = ft_definetrial(cfg); %this will create a trl structure field, which is a list >> % of 3 columns, where every row describes a separate trial start, end and offset >> data_prej = ft_preprocessing(cfg); As far as I see, you must give the “data_in” as a input to ft_preprocessing. Regards Aykut Eken, PhD Düzce University Faculty of Engineering Biomedical Engineering Department Düzce University, Konuralp Campus, 81620, Konuralp, Düzce, Turkey Tel: +905366777364 Office Tel: +90380542 11 00 /4546 Mail address1: aykuteken at duzce.edu.tr Mail address2: ekenaykut at gmail.com > On 11 Mar 2018, at 00:28, Roberto Petrosino wrote: > > Hi all, > > I am trying to preprocess my eeg raw data (from BrainVision amplifiers), but I am having troubles with error I can’t figure out how to fix. Here’s the code: > >> clear; >> clc; >> >> data_path = ‘/.../raw/'; >> >> %STEP 1: reading the data in >> cfg = []; >> cfg.dataset = [data_path ’subj1.vhdr']; >> >> %high-pass filter >> cfg.preproc.hpfilter = 'yes'; >> cfg.preproc.hpfiltord = 2; %known bug for filtering; can be avoided by changing the order of the filter (2 is random) >> cfg.preproc.hpfreq = 0.1; %in Hz >> >> %rereference >> cfg.preproc.reref = 'yes'; >> cfg.preproc.channel = 'all'; >> cfg.preproc.implicitref = ''; %on-line reference is empty >> cfg.preproc.refchannel = {'M1', 'M2'}; %the channels we want to rereference our data against. In this >> %case, we will rereference against the linked mastoids >> >> %updating channel locations; %% MPI/DCCN versions of actiCAP? >> cfg.layout = '/Users/.../MATLAB/fieldtrip-master/template/layout/acticap-64ch-standard2.mat'; %the file we want to extract electrode coordinates from >> >> %demean >> cfg.deman = 'yes'; >> cfg.basewindow = [-.2 0]; >> >> %STEP 2: defining trials and epoching >> cfg.trialdef.prestim = 0.2; >> cfg.trialdef.poststim = 1; % epochs will be -200 1000 ms >> cfg.trialdef.eventtype = 'Stimulus'; >> cfg.trialfun = 'trialfun_congruency’; %customized function for the data >> data_in = ft_definetrial(cfg); %this will create a trl structure field, which is a list >> % of 3 columns, where every row describes a separate trial start, end and offset >> data_prej = ft_preprocessing(cfg); > > > This is the error that pops up: >> Error using ft_preprocessing (line 387) >> you must call FT_DEFINETRIAL prior to FT_PREPROCESSING > > > which is weird, since ft_definetrial() is called right before ft_preprocessing(). Does anyone know what the problem could be? > > Thanks, > -Roberto > > —— > Roberto Petrosino > PhD student in Linguistics > CT Institute from Brain and Cognitive Sciences > University of Connecticut > > _______________________________________________ > 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 a.stolk8 at gmail.com Sat Mar 10 22:35:24 2018 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Sat, 10 Mar 2018 13:35:24 -0800 Subject: [FieldTrip] ft_definetrial() and ft_preprocessing() In-Reply-To: References: <50B52505-61C2-4807-9AB7-E7A21141765C@gmail.com> Message-ID: Hi Roberto, ft_definetrial produces a cfg structure with a trl field that fr_preprocessing uses to read in the data segments of interest. conceptually, the order should be cfg = ft_definetrial(cfg) % do not clear cfg data = ft_preprocessing(cfg) Best, Arjen On Sat, Mar 10, 2018 at 1:32 PM, Aykut Eken wrote: > data_in = ft_definetrial(cfg); %this will create a > trl structure field, which is a list > % of 3 columns, where every row describes a separate trial start, end and > offset > data_prej = ft_preprocessing(cfg); > > > As far as I see, you must give the “data_in” as a input to > ft_preprocessing. > > Regards > > Aykut Eken, PhD > > Düzce University > Faculty of Engineering > Biomedical Engineering Department > > Düzce University, Konuralp Campus, > 81620, Konuralp, Düzce, Turkey > > Tel: +905366777364 <+90%20536%20677%2073%2064> > Office Tel: +90380542 11 00 /4546 > Mail address1: aykuteken at duzce.edu.tr > Mail address2: ekenaykut at gmail.com > > On 11 Mar 2018, at 00:28, Roberto Petrosino > wrote: > > Hi all, > > I am trying to preprocess my eeg raw data (from BrainVision amplifiers), > but I am having troubles with error I can’t figure out how to fix. Here’s > the code: > > clear; > clc; > > data_path = ‘/.../raw/'; > > %STEP 1: reading the data in > cfg = []; > cfg.dataset = [data_path ’subj1.vhdr']; > > %high-pass filter > cfg.preproc.hpfilter = 'yes'; > cfg.preproc.hpfiltord = 2; %known bug for filtering; can be avoided > by changing the order of the filter (2 is random) > cfg.preproc.hpfreq = 0.1; %in Hz > > %rereference > cfg.preproc.reref = 'yes'; > cfg.preproc.channel = 'all'; > cfg.preproc.implicitref = ''; %on-line reference is empty > cfg.preproc.refchannel = {'M1', 'M2'}; %the channels we want to > rereference our data against. In this > %case, we will rereference against the > linked mastoids > > %updating channel locations; %% MPI/DCCN versions of actiCAP? > cfg.layout = '/Users/.../MATLAB/fieldtrip-master/template/ > layout/acticap-64ch-standard2.mat'; %the file we want to extract > electrode coordinates from > > %demean > cfg.deman = 'yes'; > cfg.basewindow = [-.2 0]; > > %STEP 2: defining trials and epoching > cfg.trialdef.prestim = 0.2; > cfg.trialdef.poststim = 1; % epochs will be -200 1000 ms > cfg.trialdef.eventtype = 'Stimulus'; > cfg.trialfun = 'trialfun_congruency’; %customized > function for the data > data_in = ft_definetrial(cfg); %this will create a > trl structure field, which is a list > % of 3 columns, where every row describes a separate trial start, end and > offset > data_prej = ft_preprocessing(cfg); > > > > This is the error that pops up: > > Error using ft_preprocessing (line 387) > you must call FT_DEFINETRIAL prior to FT_PREPROCESSING > > > which is weird, since ft_definetrial() is called right *before * > ft_preprocessing(). Does anyone know what the problem could be? > > Thanks, > -Roberto > > —— > Roberto Petrosino > PhD student in Linguistics > CT Institute from Brain and Cognitive Sciences > University of Connecticut > > _______________________________________________ > 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 christine.blume at sbg.ac.at Sun Mar 11 18:21:20 2018 From: christine.blume at sbg.ac.at (Blume Christine) Date: Sun, 11 Mar 2018 17:21:20 +0000 Subject: [FieldTrip] Bayesian "follow-up" on Cluster-Based Permutation Tests Message-ID: Dear FT-Community, In the analysis of high-density EEG data for a recent manuscript (https://www.biorxiv.org/content/early/2017/12/06/187195) we have used the cluster-based permutation approach. While the reviewers commended the choice of this approach, one reviewer would like us to calculate a Bayesian measure in addition to the Monte Carlo p values. Does anyone have a recommendation how to best approach this, any "best practice" to share? It is quite easy to calculate a Bayes factor as a follow-up on classic t-tests for example (e.g. see here http://www.lifesci.sussex.ac.uk/home/Zoltan_Dienes/inference/Bayes.htm). However, even though the permutation approach uses a t-value as a test statistic, it is not a "t-test"... Best, Christine -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcarlapiastra at gmail.com Sun Mar 11 21:28:04 2018 From: mcarlapiastra at gmail.com (Maria Carla Piastra) Date: Sun, 11 Mar 2018 21:28:04 +0100 Subject: [FieldTrip] lh.volume not found Message-ID: Dear Fieldtrippers, I am running the pipeline described here: http://www.fieldtriptoolbox.org/tutorial/sourcemodel and it fails when running: /recon-all -finalsurfs -subjid Subject01/ lh.volume does not exist so far. How can I create it? Many thanks, Maria Carla -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.spaak at donders.ru.nl Mon Mar 12 10:19:24 2018 From: e.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 12 Mar 2018 10:19:24 +0100 Subject: [FieldTrip] Bayesian "follow-up" on Cluster-Based Permutation Tests In-Reply-To: References: Message-ID: Dear Christine, Bayes factors etc. are computed from the posterior distribution over some model parameters (e.g. means of Gaussians in the case analogous to the t-test). As the cluster-based permutation approach is inherently non-parametric (i.e. it tests the exchangeability of data beween conditions), I think it would be quite esoteric to try something Bayesian with the cluster test. I think your best bet would be to figure out *why* the reviewer wants this, and then come up with an alternative answer that does not depend on Bayesian measures. Of course, one could "zoom in" on the effect you found and compute parametric Bayesian stats for that region of interest, but that would constitute "double dipping" if you don't have an independent contrast. In case you find evidence in favour of a null effect (one circumstance under which reviewers might ask for Bayesian evidence), this approach and result might still be valid (as it goes against the bias introduced by the preselection). Best, Eelke On 11 March 2018 at 18:21, Blume Christine wrote: > Dear FT-Community, > > In the analysis of high-density EEG data for a recent manuscript > (https://www.biorxiv.org/content/early/2017/12/06/187195) we have used the > cluster-based permutation approach. While the reviewers commended the choice > of this approach, one reviewer would like us to calculate a Bayesian measure > in addition to the Monte Carlo p values. Does anyone have a recommendation > how to best approach this, any "best practice" to share? > > It is quite easy to calculate a Bayes factor as a follow-up on classic > t-tests for example (e.g. see here > http://www.lifesci.sussex.ac.uk/home/Zoltan_Dienes/inference/Bayes.htm). > However, even though the permutation approach uses a t-value as a test > statistic, it is not a "t-test"... > > Best, > Christine > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From abela.eugenio at gmail.com Mon Mar 12 11:10:55 2018 From: abela.eugenio at gmail.com (Eugenio Abela) Date: Mon, 12 Mar 2018 10:10:55 +0000 Subject: [FieldTrip] Bayesian "follow-up" on Cluster-Based Permutation Tests In-Reply-To: References: Message-ID: Hi Christine, If you want to try something Bayesian and only if you have strong a priori hypotheses for a particular effect in a specific data window of interest, you could extract values from that window and do Bayesian analyses in JASP (https://jasp-stats.org), which is really easy to use and has a range Bayesian alternatives for classical F- and t-tests available. Alternatively, but this is probably much more complicated and time-consuming, you could do full Bayesian analyses with SPM12 (http://www.fil.ion.ucl.ac.uk/spm/software/spm12/), which allows you to calculate posterior probabilities for scalp, scalp x frequency or scalp x time maps. This is a great way of assessing evidence in your data, but I think it’s less popular than permutation tests. You can convert between Fieldtrip and SPM formats using spm_eeg_ft2spm.m I totally agree with Eelke that doing Bayesian tests post-hoc, after you obtained convincing results with permutations, seems like unnecessary methodological flourish. Yet it’s often hard to argue with reviewers without compromising a bit. You might want to use one of the above e.g. for your most important analysis and show in the rebuttal that it doesn’t alter your conclusions (hopefully!). This should convince them that results are robust to methodological choices, and exempt you from having to recalculate the whole thing again. Hope that helps Eugenio On 12 Mar 2018, at 09:19, Eelke Spaak wrote: Dear Christine, Bayes factors etc. are computed from the posterior distribution over some model parameters (e.g. means of Gaussians in the case analogous to the t-test). As the cluster-based permutation approach is inherently non-parametric (i.e. it tests the exchangeability of data beween conditions), I think it would be quite esoteric to try something Bayesian with the cluster test. I think your best bet would be to figure out *why* the reviewer wants this, and then come up with an alternative answer that does not depend on Bayesian measures. Of course, one could "zoom in" on the effect you found and compute parametric Bayesian stats for that region of interest, but that would constitute "double dipping" if you don't have an independent contrast. In case you find evidence in favour of a null effect (one circumstance under which reviewers might ask for Bayesian evidence), this approach and result might still be valid (as it goes against the bias introduced by the preselection). Best, Eelke On 11 March 2018 at 18:21, Blume Christine wrote: > Dear FT-Community, > > In the analysis of high-density EEG data for a recent manuscript > (https://www.biorxiv.org/content/early/2017/12/06/187195) we have used the > cluster-based permutation approach. While the reviewers commended the choice > of this approach, one reviewer would like us to calculate a Bayesian measure > in addition to the Monte Carlo p values. Does anyone have a recommendation > how to best approach this, any "best practice" to share? > > It is quite easy to calculate a Bayes factor as a follow-up on classic > t-tests for example (e.g. see here > http://www.lifesci.sussex.ac.uk/home/Zoltan_Dienes/inference/Bayes.htm). > However, even though the permutation approach uses a t-value as a test > statistic, it is not a "t-test"... > > Best, > Christine > > > _______________________________________________ > 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 jasonseehochan at gmail.com Mon Mar 12 15:35:48 2018 From: jasonseehochan at gmail.com (Jason Chan) Date: Mon, 12 Mar 2018 14:35:48 +0000 Subject: [FieldTrip] EEG and shunts Message-ID: Dear Fieldtrippers, This is not a specific Frieldtrip question, but I am hoping you can answer it anyways. I am trying to design an eeg experiment with hydrocephalus patients. However, most will have multiple shunts. I realise this will likely have dramatic effects to the activation patterns. A quick Google search gave me some rather old papers. I am wondering what is the best way to compare their activity to controls? Also, I will have access to their MRIs. Can I use beamforming? Unfortunately, I don't have access to an MEG. Thanks in advance for any advise. Best, Jason -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsten.wolters at uni-muenster.de Mon Mar 12 16:39:36 2018 From: carsten.wolters at uni-muenster.de (Carsten Wolters) Date: Mon, 12 Mar 2018 16:39:36 +0100 Subject: [FieldTrip] EEG and shunts In-Reply-To: References: Message-ID: <1D143B1F-8649-49F6-9E90-7622E005F728@uni-muenster.de> Dear Jason, that is very interesting: (1) CSF: I would expect that in hydrocephalus you have a significant contribution of CSF, see https://www.ncbi.nlm.nih.gov/pubmed/23006805 and https://www.sciencedirect.com/science/article/pii/S1053811914005175?via%3Dihub (2) Effects of shunts have been investigated in this paper https://www.sciencedirect.com/science/article/pii/S1053811912004946?via%3Dihub You might then be interested to model your shunts and the possibly bigger CSF compartment by using e.g. the Fieldtrip-SimBio pipeline (corresponding paper has just been accepted): http://www.sci.utah.edu/~wolters/PaperWolters/2018/VorwerkOostenveldPiastraMagyariWolters_BiomedEngOnline_2018_accepted.pdf BR Carsten > Am 12.03.2018 um 15:35 schrieb Jason Chan : > > > Dear Fieldtrippers, > > This is not a specific Frieldtrip question, but I am hoping you can answer it anyways. I am trying to design an eeg experiment with hydrocephalus patients. However, most will have multiple shunts. I realise this will likely have dramatic effects to the activation patterns. A quick Google search gave me some rather old papers. I am wondering what is the best way to compare their activity to controls? Also, I will have access to their MRIs. Can I use beamforming? Unfortunately, I don't have access to an MEG. > > > Thanks in advance for any advise. > > Best, > Jason > > _______________________________________________ > 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 mcmackr at tcd.ie Tue Mar 13 00:24:02 2018 From: mcmackr at tcd.ie (Roisin McMackin) Date: Mon, 12 Mar 2018 23:24:02 +0000 Subject: [FieldTrip] Timecourse units in dipole fitting .dip.mom Message-ID: Hi, I'm wondering in the example given http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting what exactly do the x,y and z timecourses for each dipole represent if dip.mom is a combination of strength and orientation? In other words, what are the units of the .dip.mom field? Thanks for your help, Roisin -------------- next part -------------- An HTML attachment was scrubbed... URL: From pahran at gmail.com Tue Mar 13 22:30:35 2018 From: pahran at gmail.com (Junjie Wu) Date: Tue, 13 Mar 2018 17:30:35 -0400 Subject: [FieldTrip] FEM with DTI Message-ID: Hello Community, I am trying create an FEM model with anisotropic conductivity using DTI and T1 MPRAGE. I know we can use ft_prepare_headmodel by specifying method 'simbio' to achieve this. However, the tutorials on the FieldTrip website only provide an example using anatomical MRI. Any suggestions on how to use FieldTrip/Simbio for anisotropic modeling will be greatly appreciated. Thanks, Junjie -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.hindriks at vu.nl Wed Mar 14 10:26:53 2018 From: r.hindriks at vu.nl (Hindriks, R.) Date: Wed, 14 Mar 2018 09:26:53 +0000 Subject: [FieldTrip] PhD position in Statistics for Neuroscience Message-ID: PhD position in Statistics for Neuroscience at VU Amsterdam The Department of Mathematics of the Faculty of Science, Vrije Universiteit Amsterdam, invites applications for a PhD position in Statistics for Neuroscience (0.8/1.0 FTE). The position The department is seeking applicants for a PhD position in statistics for neuroscience. The PhD project concerns spatiotemporal modeling and analysis of resting-state brain dynamics and will be supervised by Dr. Rikkert Hindriks and Prof.dr. Mathisca de Gunst. The PhD position is co-funded by the national science foundation NWO. Tasks You will develop statistical methods for modeling and analysis of resting-state brain activity recorded with functional MRI, magnetoencephalography (MEG), electroencephalography (EEG), and electrocorticography (ECoG). The project focuses on spatiotemporal aspects of resting-state brain activity such as wave propagation and relevant mathematics includes Empirical Bayesian inference, simulation and analysis of large-scale biophysical models, and higher-order decomposition techniques. You will publish your results in quality peer-reviewed journals in the field, culminating in a PhD thesis to be defended in public. Aside from these research tasks, a minor part of the time will be spent on teaching duties within the Department of Mathematics. Requirements The candidate must be talented, ambitious and highly motivated, in possession of a MSc. degree in mathematics, physics, or a related area. Candidates should have a strong demonstrable background in mathematics, in particular in statistics. Experience with neuroimaging data (fMRI) or electrophysiology (EEG/MEG/ECoG) and programming (R, Matlab, Python) is considered an advantage. In addition, we require proficiency in reading and writing of scientific manuscripts in English. Further particulars The appointment will be initially for one year. After satisfactory evaluation of the initial appointment, it can be extended to a total duration of 4 years. The VU offers a broad and attractive package of employment conditions. The employment contract is governed by the Collective Labour Agreement (CAO) for Dutch universities. In addition to their salaries, staff members receive annual holiday pay and a year-end bonus. Staff members with a full-time contract (38 hours per week) are entitled to 29 days off. The VU also offers a good pension scheme via ABP. Further information about our employment conditions can be found on https://www.vu.nl/en/employment. Salary The salary will be in accordance with university regulations for academic personnel, and amounts to € 2.222,- gross per month in the first year up to € 2.840,- in the fourth year (salary scale 85) based on a full-time employment. Information For additional information please contact: Dr. Rikkert Hindriks phone: +31 20 59 87835 e-mail: r.hindriks at vu.nl website: https://research.vu.nl/en/persons/r-hindriks Application Applicants are requested to write a letter in which they describe their abilities and motivation, accompanied by a curriculum vitae, a list of courses plus their grades, and contact details of two or three references. Please send your application by e-mail before April 15, 2018 to: Dr. Rikkert Hindriks e-mail: r.hindriks at vu.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From annekathrinweise at gmail.com Thu Mar 15 12:50:46 2018 From: annekathrinweise at gmail.com (Annekathrin Weise) Date: Thu, 15 Mar 2018 12:50:46 +0100 Subject: [FieldTrip] Salzburg Mind Brain Annual Meeting - SAMBA2018 Message-ID: <858a5468-e2df-be7e-aca9-8732f3c1995f@gmail.com> Dear all, we are pleased to announce that the registration and abstract submission deadline for the *Salzburg Mind Brain Annual Meeting* (*SAMBA*) **has been extended to April 1st, 2018. The mission of SAMBA is to attract the most exciting researchers in the domain of cognitive neuroscience, including related fields (e.g., computational modeling, 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. Note that the *number of participants is limited* and only a *few places* are *left*. We encourage young (PhD) students and young Post Docs to take part in the**poster price competition. *Poster awards*, *worth EUR 250,- each*, are awarded to the *three best posters. * 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) For more information see the SAMBA website . 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 andrea.brovelli at univ-amu.fr Fri Mar 16 09:31:42 2018 From: andrea.brovelli at univ-amu.fr (Andrea Brovelli) Date: Fri, 16 Mar 2018 09:31:42 +0100 Subject: [FieldTrip] Call for PhD and Post-Doc positions at the Institute of Language, Communication and the Brain (Marseille, France) Message-ID: Three 2-year postdoc positions at Aix-Marseille/Avignon on Language, Communication and the Brain The Center of Excellence on Brain and Language (BLRI,www.blri.fr/ ) and the Institute of Language, Communication and the Brain (ILCB,http://www.ilcb.fr/) offer: *Three 2-year postdoc positions*on any topic that falls within the area of language, communication, brain and modelling. The BLRI-ILCB is located in Aix-en-Provence, Avignon and Marseille and regroups several research centers in linguistics, psychology, cognitive neuroscience, medicine, computer science, and mathematics. The scientific project, ideally interdisciplinary, should be supervised by at least one member of the BLRI/ILCB (seehttp://www.blri.fr/members.html) and should, if possible, involve two different laboratories of the institute. . Duration: 2 years (1 year, extendable for another year) . Monthly salary: ~2000 € net (depending on experience) HOW TO APPLY Candidates should first contact potential supervisor(s) among the members of the ILCB/BLRI. Below, you will finda list of potential projects and supervisors that will be given priority for this call. However , you can also apply to any subject, under the supervision of any ILCB/BLRI member (http://www.blri.fr/members.html.). When the research project is finalized and approved by the supervisor(s), the application must be sent to nadera.bureau at blri.fr . Two PhD grants at Aix-Marseille/Avignon on Language, Communication and the Brain The Center of Excellence on Brain and Language (BLRI,www.blri.fr/ ) and the Institute of Language, Communication and the Brain (ILCB,http://www.ilcb.fr/) award 2 PhD grants (3 years) on any topic that falls within the area of language, communication, brain and modelling. The BLRI-ILCB is located in Aix-en-Provence, Avignon and Marseille and regroups several research centers in linguistics, psychology, cognitive neuroscience, medicine, computer science, and mathematics. Interested candidates need to find one or more PhD supervisors amongst the members of the BRLI-ILCB Together with the supervisor(s), they would then need to write a 3-year PhD project. A priority is given to interdisciplinary co-directions and to projects that involve two different laboratories of the institute. Monthly salary: 1 685€ (1 368€ net) for a period of 3 years HOW TO APPLY Candidates should first contact potential supervisor(s) among the members of the ILCB/BLRI. Below, you will finda list of potential projects and supervisors that will be given priority for this call. However , you can also apply to any subject, under the supervision of any ILCB/BLRI member (http://www.blri.fr/members.html.). When the research project is finalized and approved by the supervisor(s), the application must be sent to nadera.bureau at blri.fr . -------------- next part -------------- An HTML attachment was scrubbed... URL: From jorn at artinis.com Mon Mar 19 09:07:49 2018 From: jorn at artinis.com (=?iso-8859-1?Q?J=F6rn_M._Horschig?=) Date: Mon, 19 Mar 2018 09:07:49 +0100 Subject: [FieldTrip] ESR / Doctoral student position in algorithm development Message-ID: <005f01d3bf59$5f82d280$1e887780$@artinis.com> Dear list, We have an open ESR position from a Marie Curie grant starting in September this year. The goal of the project is cleaning of fNIRS data from artefacts and extraction of physiological components such as heartbeat and respiration. We encourage of course publication of the algorithm and implementation of these algorithms in e.g. FieldTrip or other open source toolboxes to facilitate multimodal data analyses. The ESR will work in strong collaboration with the Donders Institute (Sabine Hunnius, Robert Oostenveld), but also with external universities in the EU and other companies (eye-tracking and motion-tracking). The ESR will be located at our company in the Netherlands. For more information, please see http://www.artinis.com/early-stage-researcher-esr-doctoral-student-1 If you have any questions regarding this position, please let me know. With best regards, Jörn -- Jörn M. Horschig, PhD Software Engineer & Project Leader NeuroGuard XS A Einsteinweg 17 6662PW Elst The Netherlands T +31 481 350 980 I www.artinis.com The information in this e-mail is confidential and intended solely for the person to whom it is addressed. If this message is not addressed to you, please be aware that you have no authorization to read this e-mail, to copy it, to furnish it to any person other than the addressee, or to use or misuse its content in any way whatsoever. Should you have received this e-mail by mistake, please bring this to the attention of the sender, after which you are kindly requested to destroy the original message. Sign up for our NIRS newsletter -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 9919 bytes Desc: not available URL: From noa1hc at gmail.com Mon Mar 19 21:51:08 2018 From: noa1hc at gmail.com (=?UTF-8?B?16DXldei15Qg15TXm9eU158=?=) Date: Mon, 19 Mar 2018 22:51:08 +0200 Subject: [FieldTrip] source grand average Message-ID: Hi all, I am working on source recognition. I used ft_sourcegrandavrage, but I could not plotting the results, because there is no 'anatomy' field. why is it happening? my code is- norm_source.pos=template_grid.pos norm_source.inside=template_grid.inside cfg.parameter = 'pow' cfg.keepindividual = 'yes' [grandavg] = ft_sourcegrandaverage(cfg, norm_source 1, norm_source 2) This generates a structure with the following fields: grandavg = pow: [2x7109137 double] coordsys: 'spm' dim: [181 217 181] inside: [6804x1 logical] pos: [6804x3 double] cfg: [1x1 struct] Thanks! Noa בלי וירוסים. www.avast.com <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Mon Mar 19 22:25:01 2018 From: julian.keil at gmail.com (Julian Keil) Date: Mon, 19 Mar 2018 22:25:01 +0100 Subject: [FieldTrip] source grand average In-Reply-To: References: Message-ID: <3188B927-9556-4575-B360-076E564C9296@gmail.com> Hi Noa, either use ft_sourceinterpolate to interpolate the grandaverage to a standard-MRI, or use the „surface“-option when plotting. Cheers, Julian ________________ Prof. Dr. Julian Keil Biologische Psychologie Olshausenstraße 62 - R. 306 24118 Kiel 0431 / 880 - 4872 http://www.biopsych.uni-kiel.de/ Klinik für Psychiatrie und Psychotherapie der Charité im St. Hedwig-Krankenhaus Große Hamburger Straße 5-11 10115 Berlin 030 / 2311 - 1879 www.multisensorymind.com > Am 19.03.2018 um 21:51 schrieb ⁨נועה הכהן⁩ <⁨noa1hc at gmail.com⁩>: > > Hi all, > I am working on source recognition. I used ft_sourcegrandavrage, but I could not plotting the results, because there is no 'anatomy' field. why is it happening? > > my code is- > norm_source.pos=template_grid.pos > norm_source.inside=template_grid.inside > cfg.parameter = 'pow' > cfg.keepindividual = 'yes' > [grandavg] = ft_sourcegrandaverage(cfg, norm_source 1, norm_source 2) > > This generates a structure with the following fields: > grandavg = > > pow: [2x7109137 double] > coordsys: 'spm' > dim: [181 217 181] > inside: [6804x1 logical] > pos: [6804x3 double] > cfg: [1x1 struct] > > Thanks! > Noa > > > בלי וירוסים. www.avast.com _______________________________________________ > 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: signature.asc Type: application/pgp-signature Size: 833 bytes Desc: Message signed with OpenPGP URL: From robpetrosino at gmail.com Tue Mar 20 02:56:16 2018 From: robpetrosino at gmail.com (Roberto Petrosino) Date: Mon, 19 Mar 2018 21:56:16 -0400 Subject: [FieldTrip] clarifications on the eeglab2fieldtrip function Message-ID: <512FE9BF-FFE5-4D4E-B961-B058729616EB@gmail.com> Hello fieldtrippers, can anyone clarify the usage of the argument fieldbox in the eeglab2fieldtrip function below? I don’t seem to find any relevant information anywhere. > eeglab2fieldtrip() - do this ... > > Usage: >> data = eeglab2fieldtrip( EEG, fieldbox, transform ); > > Inputs: > EEG - [struct] EEGLAB structure > fieldbox - ['preprocessing'|'freqanalysis'|'timelockanalysis'|'companalysis'] > transform - ['none'|'dipfit'] transform channel locations for DIPFIT > using the transformation matrix in the field > 'coord_transform' of the dipfit substructure of the EEG > structure. > Outputs: > data - FIELDTRIP structure Thanks, -Roberto ---------- Roberto Petrosino Ph.D. Student in Linguistics CT Institute for the Brain and Cognitive Sciences University of Connecticut -------------- next part -------------- An HTML attachment was scrubbed... URL: From noa1hc at gmail.com Tue Mar 20 06:33:21 2018 From: noa1hc at gmail.com (=?UTF-8?B?16DXldei15Qg15TXm9eU158=?=) Date: Tue, 20 Mar 2018 07:33:21 +0200 Subject: [FieldTrip] source grand average In-Reply-To: <3188B927-9556-4575-B360-076E564C9296@gmail.com> References: <3188B927-9556-4575-B360-076E564C9296@gmail.com> Message-ID: !Thanks :I tried to do this, and to used ft_sourcedescriptives but I got an error message Attempted to access sel(1); index out of bounds because numel(sel)=0. Error in ft_sourceinterpolate>my_interpn (line 688) ft_progress(sel(1)/num, 'interpolating %.1f%%\n', 100*sel(1)/num); Error in ft_sourceinterpolate (line 535) interp.inside( sel) = my_interpn(double(functional.inside), ax(sel), ay(sel), az(sel), 'nearest', cfg.feedback); Why? thanks, Noa. 2018-03-19 23:25 GMT+02:00 Julian Keil : > Hi Noa, > > either use ft_sourceinterpolate to interpolate the grandaverage to a > standard-MRI, or use the „surface“-option when plotting. > > Cheers, > > Julian > > ________________ > Prof. Dr. Julian Keil > > Biologische Psychologie > Olshausenstraße 62 - R. 306 > 24118 Kiel > > 0431 / 880 - 4872 > http://www.biopsych.uni-kiel.de/ > > Klinik für Psychiatrie und Psychotherapie > der Charité im St. Hedwig-Krankenhaus > Große Hamburger Straße 5-11 > 10115 Berlin > > 030 / 2311 - 1879 > www.multisensorymind.com > > Am 19.03.2018 um 21:51 schrieb ⁨נועה הכהן⁩ <⁨noa1hc at gmail.com⁩>: > > Hi all, > I am working on source recognition. I used ft_sourcegrandavrage, but I > could not plotting the results, because there is no 'anatomy' field. why is > it happening? > > my code is- > norm_source.pos=template_grid.pos > norm_source.inside=template_grid.inside > cfg.parameter = 'pow' > cfg.keepindividual = 'yes' > [grandavg] = ft_sourcegrandaverage(cfg, norm_source 1, norm_source 2) > > This generates a structure with the following fields: > > grandavg = > > pow: [2x7109137 double] > coordsys: 'spm' > dim: [181 217 181] > inside: [6804x1 logical] > pos: [6804x3 double] > cfg: [1x1 struct] > > > Thanks! > > Noa > > > > בלי > וירוסים. www.avast.com > > _______________________________________________ > 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 jan.schoffelen at donders.ru.nl Tue Mar 20 07:54:39 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 20 Mar 2018 06:54:39 +0000 Subject: [FieldTrip] clarifications on the eeglab2fieldtrip function In-Reply-To: <512FE9BF-FFE5-4D4E-B961-B058729616EB@gmail.com> References: <512FE9BF-FFE5-4D4E-B961-B058729616EB@gmail.com> Message-ID: <9205E207-C86E-4CC1-B407-5F612E8A431B@donders.ru.nl> I guess that this fieldbox should be string that specifies which type of data to return from the eeglab-structure. Best wishes, Jan-Mathijs On 20 Mar 2018, at 02:56, Roberto Petrosino > wrote: Hello fieldtrippers, can anyone clarify the usage of the argument fieldbox in the eeglab2fieldtrip function below? I don’t seem to find any relevant information anywhere. eeglab2fieldtrip() - do this ... Usage: >> data = eeglab2fieldtrip( EEG, fieldbox, transform ); Inputs: EEG - [struct] EEGLAB structure fieldbox - ['preprocessing'|'freqanalysis'|'timelockanalysis'|'companalysis'] transform - ['none'|'dipfit'] transform channel locations for DIPFIT using the transformation matrix in the field 'coord_transform' of the dipfit substructure of the EEG structure. Outputs: data - FIELDTRIP structure Thanks, -Roberto ---------- Roberto Petrosino Ph.D. Student in Linguistics CT Institute for the Brain and Cognitive Sciences University of Connecticut _______________________________________________ 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 M.Wimber at bham.ac.uk Tue Mar 20 10:01:38 2018 From: M.Wimber at bham.ac.uk (Maria Wimber) Date: Tue, 20 Mar 2018 09:01:38 +0000 Subject: [FieldTrip] 3-year postdoc at UoB, decoding mental states based on fMRI/EEG patterns Message-ID: Hi FieldTrip users We would like to bring this exciting postdoctoral position to the attention of potential applicants. Mindreading mindreading: Using multivariate pattern analysis to decode the neural basis of mental state ascription. The full time postdoctoral research fellow will work on this 3-year ESRC-funded project in the School of Psychology at the University of Birmingham, with Professor Ian Apperly and Dr Maria Wimber. The project will use advanced neuroimaging methods to test whether "social brain areas" that are active when we think about the minds of others actually encode information about what other people are thinking, or whether they control attention to information encoded elsewhere. Please address informal enquiries jointly to Ian Apperly and Maria Wimber. Online advert and application forms Centre for Human Brain Health Ian Apperly Maria Wimber -------------- next part -------------- An HTML attachment was scrubbed... URL: From panyl at psych.ac.cn Tue Mar 20 13:16:06 2018 From: panyl at psych.ac.cn (=?UTF-8?B?5r2Y5Lqa5Li9?=) Date: Tue, 20 Mar 2018 20:16:06 +0800 (GMT+08:00) Subject: [FieldTrip] fieldtrip Digest, Vol 88, Issue 12 In-Reply-To: References: Message-ID: <21109d8.a526.16243568722.Coremail.panyl@psych.ac.cn> > -----Original Messages----- > From: fieldtrip-request at science.ru.nl > Sent Time: 2018-03-20 19:00:02 (Tuesday) > To: fieldtrip at science.ru.nl > Cc: > Subject: fieldtrip Digest, Vol 88, Issue 12 > > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. source grand average (???? ????) > 2. Re: source grand average (Julian Keil) > 3. clarifications on the eeglab2fieldtrip function > (Roberto Petrosino) > 4. Re: source grand average (???? ????) > 5. Re: clarifications on the eeglab2fieldtrip function > (Schoffelen, J.M. (Jan Mathijs)) > 6. 3-year postdoc at UoB, decoding mental states based on > fMRI/EEG patterns (Maria Wimber) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 19 Mar 2018 22:51:08 +0200 > From: ???? ???? > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] source grand average > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi all, > I am working on source recognition. I used ft_sourcegrandavrage, but I > could not plotting the results, because there is no 'anatomy' field. why is > it happening? > > my code is- > norm_source.pos=template_grid.pos > norm_source.inside=template_grid.inside > cfg.parameter = 'pow' > cfg.keepindividual = 'yes' > [grandavg] = ft_sourcegrandaverage(cfg, norm_source 1, norm_source 2) > > This generates a structure with the following fields: > > grandavg = > > pow: [2x7109137 double] > coordsys: 'spm' > dim: [181 217 181] > inside: [6804x1 logical] > pos: [6804x3 double] > cfg: [1x1 struct] > > > Thanks! > > Noa > > > > ??? > ???????. www.avast.com > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 2 > Date: Mon, 19 Mar 2018 22:25:01 +0100 > From: Julian Keil > To: FieldTrip discussion list > Subject: Re: [FieldTrip] source grand average > Message-ID: <3188B927-9556-4575-B360-076E564C9296 at gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Noa, > > either use ft_sourceinterpolate to interpolate the grandaverage to a standard-MRI, or use the ?surface?-option when plotting. > > Cheers, > > Julian > > ________________ > Prof. Dr. Julian Keil > > Biologische Psychologie > Olshausenstra?e 62 - R. 306 > 24118 Kiel > > 0431 / 880 - 4872 > http://www.biopsych.uni-kiel.de/ > > Klinik f?r Psychiatrie und Psychotherapie > der Charit? im St. Hedwig-Krankenhaus > Gro?e Hamburger Stra?e 5-11 > 10115 Berlin > > 030 / 2311 - 1879 > www.multisensorymind.com > > > Am 19.03.2018 um 21:51 schrieb ????? ????? : > > > > Hi all, > > I am working on source recognition. I used ft_sourcegrandavrage, but I could not plotting the results, because there is no 'anatomy' field. why is it happening? > > > > my code is- > > norm_source.pos=template_grid.pos > > norm_source.inside=template_grid.inside > > cfg.parameter = 'pow' > > cfg.keepindividual = 'yes' > > [grandavg] = ft_sourcegrandaverage(cfg, norm_source 1, norm_source 2) > > > > This generates a structure with the following fields: > > grandavg = > > > > pow: [2x7109137 double] > > coordsys: 'spm' > > dim: [181 217 181] > > inside: [6804x1 logical] > > pos: [6804x3 double] > > cfg: [1x1 struct] > > > > Thanks! > > Noa > > > > > > ??? ???????. www.avast.com _______________________________________________ > > 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: signature.asc > Type: application/pgp-signature > Size: 833 bytes > Desc: Message signed with OpenPGP > URL: > > ------------------------------ > > Message: 3 > Date: Mon, 19 Mar 2018 21:56:16 -0400 > From: Roberto Petrosino > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] clarifications on the eeglab2fieldtrip function > Message-ID: <512FE9BF-FFE5-4D4E-B961-B058729616EB at gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello fieldtrippers, > > can anyone clarify the usage of the argument fieldbox in the eeglab2fieldtrip function below? I don?t seem to find any relevant information anywhere. > > > eeglab2fieldtrip() - do this ... > > > > Usage: >> data = eeglab2fieldtrip( EEG, fieldbox, transform ); > > > > Inputs: > > EEG - [struct] EEGLAB structure > > fieldbox - ['preprocessing'|'freqanalysis'|'timelockanalysis'|'companalysis'] > > transform - ['none'|'dipfit'] transform channel locations for DIPFIT > > using the transformation matrix in the field > > 'coord_transform' of the dipfit substructure of the EEG > > structure. > > Outputs: > > data - FIELDTRIP structure > > Thanks, > > -Roberto > > ---------- > Roberto Petrosino > Ph.D. Student in Linguistics > CT Institute for the Brain and Cognitive Sciences > University of Connecticut > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 4 > Date: Tue, 20 Mar 2018 07:33:21 +0200 > From: ???? ???? > To: FieldTrip discussion list > Subject: Re: [FieldTrip] source grand average > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > !Thanks > :I tried to do this, and to used ft_sourcedescriptives but I got an error > message > > Attempted to access sel(1); index out of bounds because numel(sel)=0. > > Error in ft_sourceinterpolate>my_interpn (line 688) > ft_progress(sel(1)/num, 'interpolating %.1f%%\n', 100*sel(1)/num); > > Error in ft_sourceinterpolate (line 535) > interp.inside( sel) = my_interpn(double(functional.inside), ax(sel), > ay(sel), az(sel), 'nearest', cfg.feedback); > > Why? > > thanks, Noa. > > > > 2018-03-19 23:25 GMT+02:00 Julian Keil : > > > Hi Noa, > > > > either use ft_sourceinterpolate to interpolate the grandaverage to a > > standard-MRI, or use the ?surface?-option when plotting. > > > > Cheers, > > > > Julian > > > > ________________ > > Prof. Dr. Julian Keil > > > > Biologische Psychologie > > Olshausenstra?e 62 - R. 306 > > 24118 Kiel > > > > 0431 / 880 - 4872 > > http://www.biopsych.uni-kiel.de/ > > > > Klinik f?r Psychiatrie und Psychotherapie > > der Charit? im St. Hedwig-Krankenhaus > > Gro?e Hamburger Stra?e 5-11 > > 10115 Berlin > > > > 030 / 2311 - 1879 > > www.multisensorymind.com > > > > Am 19.03.2018 um 21:51 schrieb ????? ????? : > > > > Hi all, > > I am working on source recognition. I used ft_sourcegrandavrage, but I > > could not plotting the results, because there is no 'anatomy' field. why is > > it happening? > > > > my code is- > > norm_source.pos=template_grid.pos > > norm_source.inside=template_grid.inside > > cfg.parameter = 'pow' > > cfg.keepindividual = 'yes' > > [grandavg] = ft_sourcegrandaverage(cfg, norm_source 1, norm_source 2) > > > > This generates a structure with the following fields: > > > > grandavg = > > > > pow: [2x7109137 double] > > coordsys: 'spm' > > dim: [181 217 181] > > inside: [6804x1 logical] > > pos: [6804x3 double] > > cfg: [1x1 struct] > > > > > > Thanks! > > > > Noa > > > > > > > > ??? > > ???????. www.avast.com > > > > _______________________________________________ > > 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: > > ------------------------------ > > Message: 5 > Date: Tue, 20 Mar 2018 06:54:39 +0000 > From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] clarifications on the eeglab2fieldtrip > function > Message-ID: <9205E207-C86E-4CC1-B407-5F612E8A431B at donders.ru.nl> > Content-Type: text/plain; charset="utf-8" > > I guess that this fieldbox should be string that specifies which type of data to return from the eeglab-structure. > Best wishes, > Jan-Mathijs > > > > > On 20 Mar 2018, at 02:56, Roberto Petrosino > wrote: > > Hello fieldtrippers, > > can anyone clarify the usage of the argument fieldbox in the eeglab2fieldtrip function below? I don?t seem to find any relevant information anywhere. > > eeglab2fieldtrip() - do this ... > > Usage: >> data = eeglab2fieldtrip( EEG, fieldbox, transform ); > > Inputs: > EEG - [struct] EEGLAB structure > fieldbox - ['preprocessing'|'freqanalysis'|'timelockanalysis'|'companalysis'] > transform - ['none'|'dipfit'] transform channel locations for DIPFIT > using the transformation matrix in the field > 'coord_transform' of the dipfit substructure of the EEG > structure. > Outputs: > data - FIELDTRIP structure > > Thanks, > > -Roberto > > ---------- > Roberto Petrosino > Ph.D. Student in Linguistics > CT Institute for the Brain and Cognitive Sciences > University of Connecticut > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 6 > Date: Tue, 20 Mar 2018 09:01:38 +0000 > From: Maria Wimber > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] 3-year postdoc at UoB, decoding mental states > based on fMRI/EEG patterns > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > Hi FieldTrip users > > We would like to bring this exciting postdoctoral position to the attention of potential applicants. > > Mindreading mindreading: Using multivariate pattern analysis to decode the neural basis of mental state ascription. The full time postdoctoral research fellow will work on this 3-year ESRC-funded project in the School of Psychology at the University of Birmingham, with Professor Ian Apperly and Dr Maria Wimber. The project will use advanced neuroimaging methods to test whether "social brain areas" that are active when we think about the minds of others actually encode information about what other people are thinking, or whether they control attention to information encoded elsewhere. Please address informal enquiries jointly to Ian Apperly and Maria Wimber. > > Online advert and application forms > Centre for Human Brain Health > Ian Apperly > Maria Wimber > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 88, Issue 12 > ***************************************** From diana-hime at yandex.ru Tue Mar 20 20:48:31 2018 From: diana-hime at yandex.ru (=?utf-8?B?LSDQlNC40LDQvdCw?=) Date: Tue, 20 Mar 2018 22:48:31 +0300 Subject: [FieldTrip] (no subject) Message-ID: <329671521575311@web9j.yandex.ru> An HTML attachment was scrubbed... URL: From davide.tabarelli at unitn.it Tue Mar 20 16:59:39 2018 From: davide.tabarelli at unitn.it (Davide Tabarelli) Date: Tue, 20 Mar 2018 16:59:39 +0100 Subject: [FieldTrip] Expressions of Interest for a Marie Sklodowksa - Curie Fellowship at CIMeC - University of Trento Message-ID: <690D12F4-748E-4389-888E-2D5D241B769A@unitn.it> Dear all, at this page a Call for Expressions of Interest in the Marie Sklodowksa - Curie Individual Fellowships has been published: https://www.unitn.it/ateneo/68640/cimec-call-for-expressions-of-interest-marie-sklodowksa-curie-individual-fellowships . The Center for Mind/Brain Sciences - CIMeC at the University of Trento (Italy) welcomes expressions of interest from excellent postdoctoral researchers to apply, jointly with a research supervisor from CIMeC, to the European Commission Marie Skłodowska- Curie Individual Fellowship. The Marie Skłodowska Curie Action is a funding scheme that supports researchers mobility: Individual Fellowships – European Fellowships may last 12-24 months involving a research project, advanced training and knowledge exchange at the host institution (CIMeC). It offers a competitive salary, mobility and family allowances plus a budget for research and training costs; applicants are expected to have an excellent CV and a strong publication record. Selected candidates will be offered both academic and administrative support from CIMeC faculty and the University of Trento Research Office with regards to the proposal development. Feel free to circulate this invitation to your networks. D. — Davide Tabarelli, Ph.D. MEG Physicist Center for Mind Brain Sciences (CIMeC) University of Trento, Via delle Regole, 101 38123 Mattarello (TN) Tel: +39 (0)461 283644 Italy From thomas.hartmann at th-ht.de Wed Mar 21 11:02:14 2018 From: thomas.hartmann at th-ht.de (Thomas Hartmann) Date: Wed, 21 Mar 2018 11:02:14 +0100 Subject: [FieldTrip] doing ica on magnetometers and gradiometers Message-ID: <10159d5d-525d-5769-ac9a-3bec4483ef38@th-ht.de> hi, we have had a vivid discussion in our group concerning whether apply ICA to magnetometers and gradiometers in one go (i.e. lumping them together) or whether it is necessary to apply the ICA on mags ands grads separately. most approaches that can be found on the internet seem to favor the do-it-in-one-go way. my main concern with applying it to both sensor types at the same time is that the resulting components will probably be a linear mixture of both sensor types. when i reject some components and the project the components back to the sensor space, gradiometer activity should "leak" into the magnetometer data and vice versa. or am i wrong with my thoughts? or does it just not matter at all? i am looking forward to reading your thoughts! best, thomas -- Dr. Thomas Hartmann Centre for Cognitive Neuroscience FB Psychologie Universität Salzburg Hellbrunnerstraße 34/II 5020 Salzburg Tel: +43 662 8044 5109 Email: thomas.hartmann at th-ht.de "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle) From diana-hime at yandex.ru Sat Mar 24 21:25:01 2018 From: diana-hime at yandex.ru (=?utf-8?B?LSDQlNC40LDQvdCw?=) Date: Sat, 24 Mar 2018 23:25:01 +0300 Subject: [FieldTrip] preprocessing error "Index exceeds matrix dimensions error" Message-ID: <3814791521923101@web25o.yandex.ru> An HTML attachment was scrubbed... URL: From weiwuneuro at gmail.com Mon Mar 26 02:55:14 2018 From: weiwuneuro at gmail.com (Wei Wu) Date: Sun, 25 Mar 2018 17:55:14 -0700 Subject: [FieldTrip] Faculty jobs in brain stimulation at Stanford University Message-ID: To whom it may concern, I wanted to share a link to this job posting for those who are interested: http://med.stanford.edu/content/dam/sm/psychiatry/documents/about_us/ FacultyJobs/BrainStimulation.pdf -------------- next part -------------- An HTML attachment was scrubbed... URL: From giulia.lioi at inria.fr Mon Mar 26 18:52:11 2018 From: giulia.lioi at inria.fr (Giulia Lioi) Date: Mon, 26 Mar 2018 18:52:11 +0200 (CEST) Subject: [FieldTrip] siemens_gui_streamer prisma scanner Message-ID: <1835860202.156994.1522083131598.JavaMail.zimbra@inria.fr> To whom it may concern, I am having some problems using the siemens_gui_streamer with a recently installed Siemens prisma scanner. I was using a custom script to extract the mrprot.txt and I tried to keep the same information I was getting from the mrprot of the verio scanner. When I try to run the gui_streamer with the new mrprot however it automatically closes after the first scan, while with the old protocol is working.., HAs anyone had a similar problem? Can you help with this? Many thanks Giulia Lioi, PhD | Engineer R&D Visages-Hybrid teams Univ Rennes, Inria, CNRS, IRISA F-35000 Rennes Tel: 0033 767466577 -------------- next part -------------- An HTML attachment was scrubbed... URL: From steva_fernandes at yahoo.com Tue Mar 27 07:31:22 2018 From: steva_fernandes at yahoo.com (steven fernandes) Date: Tue, 27 Mar 2018 05:31:22 +0000 (UTC) Subject: [FieldTrip] Source localization in 4D data References: <1446487794.148989.1522128682247.ref@mail.yahoo.com> Message-ID: <1446487794.148989.1522128682247@mail.yahoo.com> Dear Researchers, I have 4D data at resting state (link given below) https://www.dropbox.com/s/rwzbaz7ame99gt7/2.zip?dl=0 I want to use above data to perform source localization of the spikes that appear during resting state for epileptic patient. Can you please help me how could I implement it using FieldTrip.  I am new to FieldTrip and I would greatly appreciate your help. Regards,Steven  -------------- next part -------------- An HTML attachment was scrubbed... URL: From mathis.kaiser at charite.de Tue Mar 27 12:53:47 2018 From: mathis.kaiser at charite.de (Mathis Kaiser) Date: Tue, 27 Mar 2018 12:53:47 +0200 Subject: [FieldTrip] [ext] preprocessing error "Index exceeds matrix dimensions error" In-Reply-To: <3814791521923101@web25o.yandex.ru> References: <3814791521923101@web25o.yandex.ru> Message-ID: <34f5c673-ae4d-f279-01cd-5f2d8219ebb9@charite.de> Hi Diana, is it possible that you already segmented the data in NetStation? The header indicates 98 trials. I have no experience with EGI files, but is there an option to export the continuous data? If you want to define your trials in fieldtrip, this makes more sense. Best, Mathis On 24.03.2018 21:25, - Диана wrote: >   > Dear Fildtrippers, >      > My name is Diana, I'm new to Fieldtrip and curently trying to learn > how process eeg data >      > I have a .raw file, exported from NetStation > I'm using Matlab 2014b, and the latest version of fieldtrip. >   >   > [my definetria]: >   > events = ft_read_event('01 wordA 27-09.raw') > FileName = '01 wordA 27-09.raw'; >  cfg                         = []; >   cfg.dataset                 = FileName; >   cfg.trialdef.eventtype      = 'trigger'; >   cfg.trialdef.eventvalue     = 'tim0'; % здесь то значение, которое нужно >   cfg.trialdef.prestim        = 0.2; % интервал до стимула >   cfg.trialdef.poststim       = 0.8; % интервал после стимула >   >   cfg = ft_definetrial(cfg); >   >   > after this, I try >   > [preprocessing]: >   > cfg = [] > cfg.dataset = FileName > cfg.channel = 'EEG' > cfg.continuous   = 'no' > raw_data  = ft_preprocessing(cfg) >   > And get such error: >   > reading and preprocessing > reading and preprocessing trial 2 from 98 > Index exceeds matrix dimensions. >   > Error in read_sbin_data (line 121) >         eventData(:,1:NSamples)  = temp( >         (NChan+1):(NChan+NEvent), 1:NSamples); >   > Error in ft_read_data (line 737) >       dat = read_sbin_data(filename, hdr, begtrial, >       endtrial, chanindx); >   > Error in ft_preprocessing (line 573) >       dat = ft_read_data(cfg.datafile, 'header', hdr, >       'begsample', begsample, 'endsample', endsample, >       'chanindx', rawindx, 'checkboundary', >       strcmp(cfg.continuous, 'no'), 'dataformat', >       cfg.dataformat); >   > Error in preproc_try (line 3) > raw_data  = ft_preprocessing(cfg) >   > Error in run (line 63) > evalin('caller', [script ';']); >   > Could you help me to understand how to manage this, please? >   > Example file: > https://drive.google.com/open?id=1c5RYxL9Br1Q5LTkedBD_dR4Ns72Vb9J5 >   > Thank you for your answers! >   >   > With best wishes, Diana > Undergraduate Student > Department of Biology of MSU >   > P.S. Sorry for having this letter sent again, the first attempt failed > strangely. > > > _______________________________________________ > 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 diana-hime at yandex.ru Wed Mar 28 04:25:52 2018 From: diana-hime at yandex.ru (=?utf-8?B?LSDQlNC40LDQvdCw?=) Date: Wed, 28 Mar 2018 05:25:52 +0300 Subject: [FieldTrip] [ext] preprocessing error "Index exceeds matrix dimensions error" In-Reply-To: <34f5c673-ae4d-f279-01cd-5f2d8219ebb9@charite.de> References: <3814791521923101@web25o.yandex.ru> <34f5c673-ae4d-f279-01cd-5f2d8219ebb9@charite.de> Message-ID: <1472741522203952@web37j.yandex.ru> An HTML attachment was scrubbed... URL: From lindseyrtate at ou.edu Wed Mar 28 09:30:23 2018 From: lindseyrtate at ou.edu (Tate, Lindsey R.) Date: Wed, 28 Mar 2018 07:30:23 +0000 Subject: [FieldTrip] ft_read_header and ft_definetrial errors Message-ID: Hello fieldtrip community, I have a dataset I've been working with in EEGLAB, but I am now trying to use it in Fieldtrip. The dataset is a concatenation of extracted epochs from multiple participants. The data imports fine as an EDF. However, EEGLAB's formatting for epochs means that there aren't triggers in the data. I have made my own header and trigger files in BrainVision format (I did it this way because I had BrainVision files to mimic, and it's listed on http://www.fieldtriptoolbox.org/reference/ft_read_header as an acceptable format). My events read in fine with the *.vmrk file I have. My problem is that I haven't figured out how to read in the *.vhdr file I have successfully. When I've tried to read it in, it gives me an error that it can't identify the dataset that the header goes with. Without it, I get the error below that *.vmrk isn't an accepted header file format. I have two questions: (1) Am I right in my interpretation that the error I'm getting below is because I haven't read in the *.vhdr header file? If that's not correct, what does the error mean? (2) How can I read in the *.vhdr header file I have? The following is the code: %%file information AMBB = 'AM'; stimfreq = '6'; pathway = 'Z:\BB\Preprocessing\'; datafile = [pathway AMBB stimfreq '_3s_avgepoch_5.edf']; eventfile = [pathway AMBB stimfreq '_3s_avgepoch_5_ftevents.vmrk'] ; hdrfile = [pathway AMBB stimfreq '_3s_avgepoch_5_ftevents.vhdr']; output6 = [pathway AMBB stimfreq '_dics6.mat']; output12 = [pathway AMBB stimfreq '_dics12.mat']; output25 = [pathway AMBB stimfreq '_dics25.mat']; output50 = [pathway AMBB stimfreq '_dics50.mat']; %%read in events [event] = ft_read_event(eventfile); %%define trials cfg = []; cfg.trialdef.eventvalue = 2 ; cfg.trialdef.prestim = 1 ; cfg.trialdef.poststim = 3 ; cfg.dataset = eventfile ; cfg.trialfun = 'ft_trialfun_general'; [cfg] = ft_definetrial(cfg); The following is the output: evaluating trialfunction 'ft_trialfun_general' Error using ft_notification (line 340) unsupported header format "brainvision_vmrk" Error in ft_error (line 39) ft_notification(varargin{:}); Error in ft_read_header (line 2478) ft_error('unsupported header format "%s"', headerformat); Error in ft_trialfun_general (line 78) hdr = ft_read_header(cfg.headerfile, 'headerformat', cfg.headerformat); Error in ft_definetrial (line 178) [trl, event] = feval(cfg.trialfun, cfg); /// The *.vhdr and *.vmrk files are attached for reference. Thank you for any help or insight you can provide. Lindsey Tate PhD Candidate University of Oklahoma lindseyrtate at ou.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: AM6_3s_avgepoch_5_ftevents.vmrk Type: application/octet-stream Size: 42028 bytes Desc: AM6_3s_avgepoch_5_ftevents.vmrk URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: AM6_3s_avgepoch_5_ftevents.vhdr Type: application/octet-stream Size: 9763 bytes Desc: AM6_3s_avgepoch_5_ftevents.vhdr URL: From edauer1 at gmail.com Thu Mar 29 19:02:44 2018 From: edauer1 at gmail.com (Ed Auer) Date: Thu, 29 Mar 2018 13:02:44 -0400 Subject: [FieldTrip] Using a condition-average baseline normalization for display of TFR Message-ID: I am using Fieldtrip to conduct time frequency analyses on an EEG dataset that has 2 factors each with multiple levels. I would like be able to display the data within a factor/level relative to a baseline computed using the average over levels and factors. Currently, to plot relative to the condition/level specific baseline I am using. cfg = []; cfg.baseline = [-0.5 0.5]; cfg.baselinetype = 'relative'; cfg.zlim = 'maxmin'; cfg.ylim = [8 12]; cfg.layout = 'acticap-64ch-standard2.mat'; cfg.xlim = [-0.5:0.05:.5]; cfg.comment = 'xlim'; cfg.commentpos = 'title'; f1 = figure; ft_topoplotTFR(cfg, GABDCLRtfr) Reading through the documentation I do not see any way to specify a baseline from a different TFR. Have I missed something or is it necessary to compute the baseline normalization directly and then plot as absolute data? Thanks, --Ed Auer -------------- next part -------------- An HTML attachment was scrubbed... URL: From TaylorBealeR at cardiff.ac.uk Fri Mar 30 17:40:26 2018 From: TaylorBealeR at cardiff.ac.uk (Rosa Taylor Beale) Date: Fri, 30 Mar 2018 15:40:26 +0000 Subject: [FieldTrip] Empty array in coherence connectivity analysis Message-ID: Hi all, I'm a final year undergraduate in Cardiff working on pain networks. I have been trying to calculate coherence between 3 seed regions, however when I run the ft_connectivityanalysis, the labelcmb and cohspctrm arrays are empty (the channel labels don't look like they were read?). There is no error or warning messages that occur when running the command, so I am unsure why it is not running correctly. First, I run ft_freqanalysis which seems to run fine: cfg = [] cfg.method = 'wavelet'; cfg.output = 'pow'; cfg.toi = 0:0.05:2; cfg.foi = [30:1:100]; time_freq= ft_freqanalysis(cfg, virtualchannel_raw); time_freq = label: {3x1 cell} dimord: 'chan_freq_time' freq: [1x71 double] time: [1x41 double] powspctrm: [3x71x41 double] cfg: [1x1 struct] Then I run the connectivity analysis and up with the empty output: cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'pfcCont_seed' 'smc_seed' 'pfcIps_seed' 'smc_seed' 'pfcCont_seed' 'pfcIps_seed'}; coherence = ft_connectivityanalysis(cfg, time_freq); coherence = labelcmb: {0x2 cell} dimord: 'chancmb_freq_time' cohspctrm: [0x71x41 double] time: [1x41 double] freq: [1x71 double] cfg: [1x1 struct] >> coherence.labelcmb ans = Empty cell array: 0-by-2 >> coherence.cohspctrm ans = Empty array: 0-by-71-by-41 I have tried with fieldtrip versions 20161011 and 20171015 on matlab r2015a. I've shown this to various people much more experienced at fieldtrip than I and we've all been a bit stumped! Any ideas? Many thanks Rosa Taylor Beale -------------- next part -------------- An HTML attachment was scrubbed... URL: From TaylorBealeR at cardiff.ac.uk Fri Mar 30 17:52:14 2018 From: TaylorBealeR at cardiff.ac.uk (Rosa Taylor Beale) Date: Fri, 30 Mar 2018 15:52:14 +0000 Subject: [FieldTrip] Empty array in coherence connectivity analysis Message-ID: Hi all, I'm a final year undergraduate in Cardiff working on pain networks. I have been trying to calculate coherence between 3 seed regions, however when I run the ft_connectivityanalysis, the labelcmb and cohspctrm arrays are empty (the channel labels don't look like they were read?). There is no error or warning messages that occur when running the command, so I am unsure why it is not running correctly. First, I run ft_freqanalysis which seems to run fine: cfg = [] cfg.method = 'wavelet'; cfg.output = 'pow'; cfg.toi = 0:0.05:2; cfg.foi = [30:1:100]; time_freq= ft_freqanalysis(cfg, virtualchannel_raw); time_freq = label: {3x1 cell} dimord: 'chan_freq_time' freq: [1x71 double] time: [1x41 double] powspctrm: [3x71x41 double] cfg: [1x1 struct] Then I run the connectivity analysis and up with the empty output: cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'pfcCont_seed' 'smc_seed' 'pfcIps_seed' 'smc_seed' 'pfcCont_seed' 'pfcIps_seed'}; coherence = ft_connectivityanalysis(cfg, time_freq); coherence = labelcmb: {0x2 cell} dimord: 'chancmb_freq_time' cohspctrm: [0x71x41 double] time: [1x41 double] freq: [1x71 double] cfg: [1x1 struct] >> coherence.labelcmb ans = Empty cell array: 0-by-2 >> coherence.cohspctrm ans = Empty array: 0-by-71-by-41 I have tried with fieldtrip versions 20161011 and 20171015 on matlab r2015a. I've shown this to various people much more experienced at fieldtrip than I and we've all been a bit stumped! Any ideas? Many thanks Rosa Taylor Beale -------------- next part -------------- An HTML attachment was scrubbed... URL: From tobias.stdgl at gmail.com Fri Mar 30 18:00:49 2018 From: tobias.stdgl at gmail.com (Tobias Staudigl) Date: Fri, 30 Mar 2018 16:00:49 +0000 Subject: [FieldTrip] Empty array in coherence connectivity analysis In-Reply-To: References: Message-ID: Hi Taylor, First specify cfg.output = 'fourier' Or cfg.output ='powandcsd' in your ft_freqanalysis. Then try ft_connectivityanalysis again. Best, Tobias Am 30.03.2018 17:53 schrieb "Rosa Taylor Beale" : Hi all, I’m a final year undergraduate in Cardiff working on pain networks. I have been trying to calculate coherence between 3 seed regions, however when I run the ft_connectivityanalysis, the labelcmb and cohspctrm arrays are empty (the channel labels don’t look like they were read?). There is no error or warning messages that occur when running the command, so I am unsure why it is not running correctly. First, I run ft_freqanalysis which seems to run fine: cfg = [] cfg.method = 'wavelet'; cfg.output = 'pow'; cfg.toi = 0:0.05:2; cfg.foi = [30:1:100]; time_freq= ft_freqanalysis(cfg, virtualchannel_raw); time_freq = label: {3x1 cell} dimord: 'chan_freq_time' freq: [1x71 double] time: [1x41 double] powspctrm: [3x71x41 double] cfg: [1x1 struct] Then I run the connectivity analysis and up with the empty output: cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'pfcCont_seed' 'smc_seed' 'pfcIps_seed' 'smc_seed' 'pfcCont_seed' 'pfcIps_seed'}; coherence = ft_connectivityanalysis(cfg, time_freq); coherence = labelcmb: {0x2 cell} dimord: 'chancmb_freq_time' cohspctrm: [0x71x41 double] time: [1x41 double] freq: [1x71 double] cfg: [1x1 struct] >> coherence.labelcmb ans = Empty cell array: 0-by-2 >> coherence.cohspctrm ans = Empty array: 0-by-71-by-41 I have tried with fieldtrip versions 20161011 and 20171015 on matlab r2015a. I’ve shown this to various people much more experienced at fieldtrip than I and we’ve all been a bit stumped! Any ideas? Many thanks Rosa Taylor Beale _______________________________________________ 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 jan.schoffelen at donders.ru.nl Fri Mar 30 20:33:51 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 30 Mar 2018 18:33:51 +0000 Subject: [FieldTrip] Empty array in coherence connectivity analysis In-Reply-To: References: Message-ID: <90B1A8AF-87AA-480B-BEE7-DC9A7148780E@donders.ru.nl> Yes, and be sure that cfg.channelcmb is an Nx2 cell-array: {‘somechannel’ ‘someotherchannel’; ‘againsomechannel’ ‘someotherchannelaswell’; ‘etc’ ‘etc’} Best wishes, Jan-Mathijs On 30 Mar 2018, at 18:00, Tobias Staudigl > wrote: Hi Taylor, First specify cfg.output = 'fourier' Or cfg.output ='powandcsd' in your ft_freqanalysis. Then try ft_connectivityanalysis again. Best, Tobias Am 30.03.2018 17:53 schrieb "Rosa Taylor Beale" >: Hi all, I’m a final year undergraduate in Cardiff working on pain networks. I have been trying to calculate coherence between 3 seed regions, however when I run the ft_connectivityanalysis, the labelcmb and cohspctrm arrays are empty (the channel labels don’t look like they were read?). There is no error or warning messages that occur when running the command, so I am unsure why it is not running correctly. First, I run ft_freqanalysis which seems to run fine: cfg = [] cfg.method = 'wavelet'; cfg.output = 'pow'; cfg.toi = 0:0.05:2; cfg.foi = [30:1:100]; time_freq= ft_freqanalysis(cfg, virtualchannel_raw); time_freq = label: {3x1 cell} dimord: 'chan_freq_time' freq: [1x71 double] time: [1x41 double] powspctrm: [3x71x41 double] cfg: [1x1 struct] Then I run the connectivity analysis and up with the empty output: cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'pfcCont_seed' 'smc_seed' 'pfcIps_seed' 'smc_seed' 'pfcCont_seed' 'pfcIps_seed'}; coherence = ft_connectivityanalysis(cfg, time_freq); coherence = labelcmb: {0x2 cell} dimord: 'chancmb_freq_time' cohspctrm: [0x71x41 double] time: [1x41 double] freq: [1x71 double] cfg: [1x1 struct] >> coherence.labelcmb ans = Empty cell array: 0-by-2 >> coherence.cohspctrm ans = Empty array: 0-by-71-by-41 I have tried with fieldtrip versions 20161011 and 20171015 on matlab r2015a. I’ve shown this to various people much more experienced at fieldtrip than I and we’ve all been a bit stumped! Any ideas? Many thanks Rosa Taylor Beale _______________________________________________ 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 eduardobjacobi at gmail.com Thu Mar 1 14:57:53 2018 From: eduardobjacobi at gmail.com (Eduardo Bacelar) Date: Thu, 1 Mar 2018 10:57:53 -0300 Subject: [FieldTrip] Convert .PLX Message-ID: Hi, I am having problems with the conversion of .plx files, in my data I have spike and LFP data together, I now that is not possible to read this 2 types of data in the same function call, but is there any way were I am enable to only read LFP data and after that read Spike data? What I rely want to know is if is possible to read only a number of channels. Waiting for replay. Best rewards, -- Eduardo Bacelar Mestrando - Neuroengenharia Instituto Internacional de Neurociências - Edmond e Lily Safra . ------------------------------ Contact me: T: +55 (53) 8124-0032 Tw: @EddBacelar E: eduardobjacobi at gmail.com Fb: /eduardo.bacelar.89 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathalie.liegel at gmx.de Mon Mar 5 13:56:55 2018 From: nathalie.liegel at gmx.de (Nathalie Liegel) Date: Mon, 5 Mar 2018 13:56:55 +0100 Subject: [FieldTrip] Any German speaking cognitive neuroscientist interested in an exciting industry position? Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Anz-Stelle-A4-1802.pdf Type: application/pdf Size: 223494 bytes Desc: not available URL: From nelleke.van.wouwe at Vanderbilt.Edu Mon Mar 5 17:40:54 2018 From: nelleke.van.wouwe at Vanderbilt.Edu (Van Wouwe, Nelleke) Date: Mon, 5 Mar 2018 16:40:54 +0000 Subject: [FieldTrip] Postdoctoral Position University of Louisville Message-ID: <29540490A5680F42A88C5587547464E9F8CE83E2@ITS-HCWNEM108.ds.vanderbilt.edu> Postdoctoral Position A postdoctoral position is available in the Human Cognitive Neurophysiology Group (HCN) in the Department of Neurological Surgery at the University of Louisville School of Medicine. HCN (Drs. Neimat, van Wouwe, and Kaskan) investigates the neural correlates of cognition in the setting of human intraoperative recording and stimulation performed for the treatment of movement disorders and epilepsy. Our collaborative group pairs neuroscientists with physicians in a clinical research environment to provide rich opportunities for the novel exploration of brain function. Drs. Neimat and van Wouwe have recently been awarded a multi-site R01 (Louisville and Vanderbilt) entitled: Modulating Inhibitory Action Control Systems with Subthalamic Nucleus (STN) Stimulation. Dr. Kaskan has recently joined the group and is investigating the role of the STN in value-based decision-making. We are seeking to hire a postdoctoral fellow with a Ph.D. in neuroscience, engineering, computer science, cognitive psychology, the biomedical sciences, or a field related to neuroscience. Experience with the collection and analysis of single-unit neural recordings and/or local field potentials (human or animal) is required. Experience programming with MATLAB and familiarity with the Linux environment is highly encouraged. The best candidates will be experienced neurophysiologists interested in human cognition. The candidate is expected to be highly motivated, possess excellent presentation and interpersonal skills, an ability to troubleshoot technical neurophysiological issues, a demonstrated track record of publications and project completion, and the ability to work both independently and with others. Additional responsibilities include: manuscript and grant preparation, literature and manuscript review, presentations at local seminars and national meetings, and mentoring junior lab members. An initial appointment will be made for one year, with the possibility of extension based upon performance. Salary is commensurate with experience. The University of Louisville is a strong research environment and the postdoctoral fellow will have the opportunity to interact and collaborate with other departments including the Kentucky Spinal Cord Injury Research Center, the Department of Anatomical Sciences and Neurobiology, the Department of Psychological and Brain Sciences, and the JB Speed School of Engineering. The multi-site grant also provides the opportunity to work with the Neurology Department at Vanderbilt University Medical Center. The University of Louisville is an equal opportunity, affirmative action employer, and is committed to providing employment opportunities to all qualified applicants without regard to race, sex, age, color, national origin, ethnicity, creed, religion, disability, genetic information, sexual orientation, gender, gender identity and expression, marital status, pregnancy, or veteran status. Interested candidates should send a brief statement of research experience including interests and future objectives as well as a curriculum vitae, a reprint (.pdf) of an exemplar paper where they were an author, and the contact information for three professional references to peter.kaskan at ulp.org. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nico.boehler at ugent.be Tue Mar 6 08:31:18 2018 From: nico.boehler at ugent.be (=?Windows-1252?Q?Nico_B=F6hler?=) Date: Tue, 6 Mar 2018 07:31:18 +0000 Subject: [FieldTrip] 4 PhD student positions in Ghent, Belgium In-Reply-To: References: Message-ID: <1520321487503.74871@ugent.be> Four full-time PhD student positions are available at Ghent University. All are four-year positions (provided positive periodic evaluation), preferably starting in Sept or Oct 2018. Salary is according to standard Ghent University regulations for PhD students (starting at around €2000 per month net salary). Candidates should have a Master’s degree in Psychology, Cognitive Neuroscience, or similar. 1) Synchrony and coupling in procedural and declarative memory tasks This position is situated in the framework of an interuniversity project called “The journey of a memory: dynamics of learning and consolidation in maturation and ageing”, see www.eosprogramme.be Candidates are expected to carry out empirical work combining EEG, MEG, and computational modeling. Expertise in these methods is not required, but strong interest in cognitive neuroscience, data analysis, and computer programming are. As this is an interuniversity project it involves collaboration between three institutions. Supervisors will be Tom Verguts and Nico Boehler (Ghent University; main institution), in collaboration with Xavier De Tiège (Université Libre de Bruxelles) and Dante Mantini (KULeuven). More information about the project can be found here: https://sites.google.com/view/memodyn/homepage For applying, please send a CV (including two email addresses of academic referees) and motivation letter to Tom Verguts (tom.verguts at ugent.be). For further information on the project or details about the position, please also contact Tom Verguts. Applications will be considered until the position is filled. 2) Transfer of serial order information between working memory and long term memory This position is situated in the framework of an interuniversity project called “The journey of a memory: dynamics of learning and consolidation in maturation and ageing”, see www.eosprogramme.be Candidates are expected to carry out empirical work with fMRI and combined HD-EEG/MEG. Expertise in these methods is not required, but strong interest in cognitive neuroscience, data analysis, and computer programming are. As this is an interuniversity project it involves collaboration between three institutions. Supervisors at the Ghent University side is Wim Fias; at Université de Liège supervision is carried out by Steve Majerus at Université Libre de Bruxelles by Xavier De Tiège; at KULeuven, the supervisor is Dante Mantini. More information about the project can be found here: https://sites.google.com/view/memodyn/homepage For applying, please send a CV (including two email addresses of academic referees) and motivation letter to Wim Fias (wim.fias at ugent.be ; For further information on the project or details about the position, please also contact Wim Fias. Applications will be considered until the position is filled. 3) The role of the locus coeruleus in arousal regulation in ADHD This project is focused on arousal regulation in ADHD. There is a long tradition of explaining ADHD in terms of arousal regulation difficulties. While many studies found support for this, little is known about its underlying neurobiological substrates. The locus coeruleus (LC), a small nucleus in the brainstem, associated with arousal regulation, is a hypothesized candidate. In the current project, we will investigate the putative role of the LC in arousal regulation deficits in ADHD, by means of fMRI, EEG, and pupil measures. Expertise in these methods is not required but a great benefit. Strong interest in the combination of cognitive neuroscience and experimental-clinical research is required. Active knowledge of Dutch is a requirement (working with Flemish participants with ADHD). The main supervisor is Roeljan Wiersema (Dept. of Experimental Clinical and Health Psychology) and the co-supervisor is Nico Boehler (Department of Experimental Psychology). For applying, please send a CV (including two email addresses of academic referees, or referent letters) and motivation letter to Roeljan Wiersema (Roeljan.wiersema at ugent.be). For further information on the project or details about the position, please also contact Roeljan Wiersema. Applications will be considered until the position is filled. 4) Money well spent? A multi-modal investigation of context effects during and after a reward manipulation This project is focused on context effects of reward manipulations. Reward effects on cognitive functions have received a lot of scientific attention in the last years, usually finding that associating reward with a particular task ubiquitously improves performance. Yet, this work largely focused on transient reward effects using concurrent no-reward trials as the main comparison, and relatively little work has looked at potential costs of reward-based improvements. The present project aims at doing so by studying reward-context effects both during a reward manipulation (compared to no-reward trials from neutral task blocks) and after (most notably the “undermining effect”) to get a broader understanding of the costs and benefits of such manipulations. We will investigate the neurobiological implementation of these phenomena by using systematic behavioral testing in combination with electroencephalographic (EEG) and pupillometric measures. Experience with EEG and pupillometry are not required but would be a great benefit, as would be a background in programming experiments and analyzing experimental data. The main supervisor is Nico Boehler and the co-supervisor is Ruth Krebs. For applying, please send a CV (including two email addresses of academic referees) and motivation letter to Nico Boehler (nico.boehler at ugent.be), whom you can also contact for further information about the project or details about the position and procedure. Applications will be considered until the position is filled.? -------------- next part -------------- An HTML attachment was scrubbed... URL: From muthuraman10 at hotmail.com Fri Mar 9 16:20:08 2018 From: muthuraman10 at hotmail.com (Muthuraman Muthuraman) Date: Fri, 9 Mar 2018 15:20:08 +0000 Subject: [FieldTrip] PhD position on electrophysiology and cognition in multiple sclerosis patients! Message-ID: Doctoral Student Neuroscientist with focus on electrophysiology and cognition in multiple sclerosis The medical faculty of the University of Mainz, Germany, invites applications for a PhD Student for a functional translational neuroscience (FTN) scholarship three year position to work on electrophysiology and cognition in neuroimmunological disorders and multiple sclerosis. A project with multimodality usage of electroencephalography (EEG) and non-invasive brain stimulation technique like transcranial magnetic stimulation (TMS). The successful applicant holds a Master’s degree (or equivalent) in a relevant academic area such as basic life sciences, neuropsychology, applied mathematics or biomedical engineering or similar disciplines. German language proficiency is mandatory for communicating with the patients. The working language at the institute is English. Experience with electrophysiology and the analysis of brain signals is advantageous, but not essential. The applicant’s merits are assessed on the basis of the quality of Master’s level studies and thesis, previous experience with the brain imaging, motivation and research interests. The location for this research will mainly be the workgroups “Section of Movement Disorders, Neurostimulation and Neuroimaging“ of Prof. Sergiu Groppa at the Department of Neurology and “Multimodal Signal Processing and Statistical Analyses” of Prof. Muthuraman Muthuraman, both at the Focus Program Translational Neurosciences (http://www.ftn.uni-mainz.de/) and Neuroimaging Centre Mainz (http://www.ftn.nic.uni-mainz.de/). Expected close collaborations with national and international partners. The application should include a statement of research interests, a curriculum vitae (max. 4 pages) composed according to good scientific practice, a certificate of Master’s degree, copy of the master’s thesis and grades of Master’s level studies, the names and e-mail addresses of two referees and a proof of proficiency in English. The position will be open until filled. To apply for the position, please send the above documents as pdfs until 31.03.2018 to Prof. Sergiu Groppa, Department of Neurology, Section of movement disorders and neurostimulation, University of Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany, or by Email to segroppa(at)uni-mainz.de . For additional information please contact Sergiu Groppa. With regards M.Muthuraman Prof. Dr.- Ing. M.Muthuraman Biomedical statistics and multimodal signal processing unit Movement Disorders and Neurostimulation, Department of Neurology, Focus Program Translational Neuroscience (FTN) Johannes-Gutenberg-University Hospital, Langenbeckstr. 1 55131 Mainz, Germany Email: mmuthura at uni-mainz.de Website:http://www.tiefehirnstimulation.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From robpetrosino at gmail.com Sat Mar 10 22:28:56 2018 From: robpetrosino at gmail.com (Roberto Petrosino) Date: Sat, 10 Mar 2018 16:28:56 -0500 Subject: [FieldTrip] ft_definetrial() and ft_preprocessing() Message-ID: <50B52505-61C2-4807-9AB7-E7A21141765C@gmail.com> Hi all, I am trying to preprocess my eeg raw data (from BrainVision amplifiers), but I am having troubles with error I can’t figure out how to fix. Here’s the code: > clear; > clc; > > data_path = ‘/.../raw/'; > > %STEP 1: reading the data in > cfg = []; > cfg.dataset = [data_path ’subj1.vhdr']; > > %high-pass filter > cfg.preproc.hpfilter = 'yes'; > cfg.preproc.hpfiltord = 2; %known bug for filtering; can be avoided by changing the order of the filter (2 is random) > cfg.preproc.hpfreq = 0.1; %in Hz > > %rereference > cfg.preproc.reref = 'yes'; > cfg.preproc.channel = 'all'; > cfg.preproc.implicitref = ''; %on-line reference is empty > cfg.preproc.refchannel = {'M1', 'M2'}; %the channels we want to rereference our data against. In this > %case, we will rereference against the linked mastoids > > %updating channel locations; %% MPI/DCCN versions of actiCAP? > cfg.layout = '/Users/.../MATLAB/fieldtrip-master/template/layout/acticap-64ch-standard2.mat'; %the file we want to extract electrode coordinates from > > %demean > cfg.deman = 'yes'; > cfg.basewindow = [-.2 0]; > > %STEP 2: defining trials and epoching > cfg.trialdef.prestim = 0.2; > cfg.trialdef.poststim = 1; % epochs will be -200 1000 ms > cfg.trialdef.eventtype = 'Stimulus'; > cfg.trialfun = 'trialfun_congruency’; %customized function for the data > data_in = ft_definetrial(cfg); %this will create a trl structure field, which is a list > % of 3 columns, where every row describes a separate trial start, end and offset > data_prej = ft_preprocessing(cfg); This is the error that pops up: > Error using ft_preprocessing (line 387) > you must call FT_DEFINETRIAL prior to FT_PREPROCESSING which is weird, since ft_definetrial() is called right before ft_preprocessing(). Does anyone know what the problem could be? Thanks, -Roberto —— Roberto Petrosino PhD student in Linguistics CT Institute from Brain and Cognitive Sciences University of Connecticut -------------- next part -------------- An HTML attachment was scrubbed... URL: From ekenaykut at gmail.com Sat Mar 10 22:32:07 2018 From: ekenaykut at gmail.com (Aykut Eken) Date: Sun, 11 Mar 2018 00:32:07 +0300 Subject: [FieldTrip] ft_definetrial() and ft_preprocessing() In-Reply-To: <50B52505-61C2-4807-9AB7-E7A21141765C@gmail.com> References: <50B52505-61C2-4807-9AB7-E7A21141765C@gmail.com> Message-ID: >> data_in = ft_definetrial(cfg); %this will create a trl structure field, which is a list >> % of 3 columns, where every row describes a separate trial start, end and offset >> data_prej = ft_preprocessing(cfg); As far as I see, you must give the “data_in” as a input to ft_preprocessing. Regards Aykut Eken, PhD Düzce University Faculty of Engineering Biomedical Engineering Department Düzce University, Konuralp Campus, 81620, Konuralp, Düzce, Turkey Tel: +905366777364 Office Tel: +90380542 11 00 /4546 Mail address1: aykuteken at duzce.edu.tr Mail address2: ekenaykut at gmail.com > On 11 Mar 2018, at 00:28, Roberto Petrosino wrote: > > Hi all, > > I am trying to preprocess my eeg raw data (from BrainVision amplifiers), but I am having troubles with error I can’t figure out how to fix. Here’s the code: > >> clear; >> clc; >> >> data_path = ‘/.../raw/'; >> >> %STEP 1: reading the data in >> cfg = []; >> cfg.dataset = [data_path ’subj1.vhdr']; >> >> %high-pass filter >> cfg.preproc.hpfilter = 'yes'; >> cfg.preproc.hpfiltord = 2; %known bug for filtering; can be avoided by changing the order of the filter (2 is random) >> cfg.preproc.hpfreq = 0.1; %in Hz >> >> %rereference >> cfg.preproc.reref = 'yes'; >> cfg.preproc.channel = 'all'; >> cfg.preproc.implicitref = ''; %on-line reference is empty >> cfg.preproc.refchannel = {'M1', 'M2'}; %the channels we want to rereference our data against. In this >> %case, we will rereference against the linked mastoids >> >> %updating channel locations; %% MPI/DCCN versions of actiCAP? >> cfg.layout = '/Users/.../MATLAB/fieldtrip-master/template/layout/acticap-64ch-standard2.mat'; %the file we want to extract electrode coordinates from >> >> %demean >> cfg.deman = 'yes'; >> cfg.basewindow = [-.2 0]; >> >> %STEP 2: defining trials and epoching >> cfg.trialdef.prestim = 0.2; >> cfg.trialdef.poststim = 1; % epochs will be -200 1000 ms >> cfg.trialdef.eventtype = 'Stimulus'; >> cfg.trialfun = 'trialfun_congruency’; %customized function for the data >> data_in = ft_definetrial(cfg); %this will create a trl structure field, which is a list >> % of 3 columns, where every row describes a separate trial start, end and offset >> data_prej = ft_preprocessing(cfg); > > > This is the error that pops up: >> Error using ft_preprocessing (line 387) >> you must call FT_DEFINETRIAL prior to FT_PREPROCESSING > > > which is weird, since ft_definetrial() is called right before ft_preprocessing(). Does anyone know what the problem could be? > > Thanks, > -Roberto > > —— > Roberto Petrosino > PhD student in Linguistics > CT Institute from Brain and Cognitive Sciences > University of Connecticut > > _______________________________________________ > 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 a.stolk8 at gmail.com Sat Mar 10 22:35:24 2018 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Sat, 10 Mar 2018 13:35:24 -0800 Subject: [FieldTrip] ft_definetrial() and ft_preprocessing() In-Reply-To: References: <50B52505-61C2-4807-9AB7-E7A21141765C@gmail.com> Message-ID: Hi Roberto, ft_definetrial produces a cfg structure with a trl field that fr_preprocessing uses to read in the data segments of interest. conceptually, the order should be cfg = ft_definetrial(cfg) % do not clear cfg data = ft_preprocessing(cfg) Best, Arjen On Sat, Mar 10, 2018 at 1:32 PM, Aykut Eken wrote: > data_in = ft_definetrial(cfg); %this will create a > trl structure field, which is a list > % of 3 columns, where every row describes a separate trial start, end and > offset > data_prej = ft_preprocessing(cfg); > > > As far as I see, you must give the “data_in” as a input to > ft_preprocessing. > > Regards > > Aykut Eken, PhD > > Düzce University > Faculty of Engineering > Biomedical Engineering Department > > Düzce University, Konuralp Campus, > 81620, Konuralp, Düzce, Turkey > > Tel: +905366777364 <+90%20536%20677%2073%2064> > Office Tel: +90380542 11 00 /4546 > Mail address1: aykuteken at duzce.edu.tr > Mail address2: ekenaykut at gmail.com > > On 11 Mar 2018, at 00:28, Roberto Petrosino > wrote: > > Hi all, > > I am trying to preprocess my eeg raw data (from BrainVision amplifiers), > but I am having troubles with error I can’t figure out how to fix. Here’s > the code: > > clear; > clc; > > data_path = ‘/.../raw/'; > > %STEP 1: reading the data in > cfg = []; > cfg.dataset = [data_path ’subj1.vhdr']; > > %high-pass filter > cfg.preproc.hpfilter = 'yes'; > cfg.preproc.hpfiltord = 2; %known bug for filtering; can be avoided > by changing the order of the filter (2 is random) > cfg.preproc.hpfreq = 0.1; %in Hz > > %rereference > cfg.preproc.reref = 'yes'; > cfg.preproc.channel = 'all'; > cfg.preproc.implicitref = ''; %on-line reference is empty > cfg.preproc.refchannel = {'M1', 'M2'}; %the channels we want to > rereference our data against. In this > %case, we will rereference against the > linked mastoids > > %updating channel locations; %% MPI/DCCN versions of actiCAP? > cfg.layout = '/Users/.../MATLAB/fieldtrip-master/template/ > layout/acticap-64ch-standard2.mat'; %the file we want to extract > electrode coordinates from > > %demean > cfg.deman = 'yes'; > cfg.basewindow = [-.2 0]; > > %STEP 2: defining trials and epoching > cfg.trialdef.prestim = 0.2; > cfg.trialdef.poststim = 1; % epochs will be -200 1000 ms > cfg.trialdef.eventtype = 'Stimulus'; > cfg.trialfun = 'trialfun_congruency’; %customized > function for the data > data_in = ft_definetrial(cfg); %this will create a > trl structure field, which is a list > % of 3 columns, where every row describes a separate trial start, end and > offset > data_prej = ft_preprocessing(cfg); > > > > This is the error that pops up: > > Error using ft_preprocessing (line 387) > you must call FT_DEFINETRIAL prior to FT_PREPROCESSING > > > which is weird, since ft_definetrial() is called right *before * > ft_preprocessing(). Does anyone know what the problem could be? > > Thanks, > -Roberto > > —— > Roberto Petrosino > PhD student in Linguistics > CT Institute from Brain and Cognitive Sciences > University of Connecticut > > _______________________________________________ > 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 christine.blume at sbg.ac.at Sun Mar 11 18:21:20 2018 From: christine.blume at sbg.ac.at (Blume Christine) Date: Sun, 11 Mar 2018 17:21:20 +0000 Subject: [FieldTrip] Bayesian "follow-up" on Cluster-Based Permutation Tests Message-ID: Dear FT-Community, In the analysis of high-density EEG data for a recent manuscript (https://www.biorxiv.org/content/early/2017/12/06/187195) we have used the cluster-based permutation approach. While the reviewers commended the choice of this approach, one reviewer would like us to calculate a Bayesian measure in addition to the Monte Carlo p values. Does anyone have a recommendation how to best approach this, any "best practice" to share? It is quite easy to calculate a Bayes factor as a follow-up on classic t-tests for example (e.g. see here http://www.lifesci.sussex.ac.uk/home/Zoltan_Dienes/inference/Bayes.htm). However, even though the permutation approach uses a t-value as a test statistic, it is not a "t-test"... Best, Christine -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcarlapiastra at gmail.com Sun Mar 11 21:28:04 2018 From: mcarlapiastra at gmail.com (Maria Carla Piastra) Date: Sun, 11 Mar 2018 21:28:04 +0100 Subject: [FieldTrip] lh.volume not found Message-ID: Dear Fieldtrippers, I am running the pipeline described here: http://www.fieldtriptoolbox.org/tutorial/sourcemodel and it fails when running: /recon-all -finalsurfs -subjid Subject01/ lh.volume does not exist so far. How can I create it? Many thanks, Maria Carla -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.spaak at donders.ru.nl Mon Mar 12 10:19:24 2018 From: e.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 12 Mar 2018 10:19:24 +0100 Subject: [FieldTrip] Bayesian "follow-up" on Cluster-Based Permutation Tests In-Reply-To: References: Message-ID: Dear Christine, Bayes factors etc. are computed from the posterior distribution over some model parameters (e.g. means of Gaussians in the case analogous to the t-test). As the cluster-based permutation approach is inherently non-parametric (i.e. it tests the exchangeability of data beween conditions), I think it would be quite esoteric to try something Bayesian with the cluster test. I think your best bet would be to figure out *why* the reviewer wants this, and then come up with an alternative answer that does not depend on Bayesian measures. Of course, one could "zoom in" on the effect you found and compute parametric Bayesian stats for that region of interest, but that would constitute "double dipping" if you don't have an independent contrast. In case you find evidence in favour of a null effect (one circumstance under which reviewers might ask for Bayesian evidence), this approach and result might still be valid (as it goes against the bias introduced by the preselection). Best, Eelke On 11 March 2018 at 18:21, Blume Christine wrote: > Dear FT-Community, > > In the analysis of high-density EEG data for a recent manuscript > (https://www.biorxiv.org/content/early/2017/12/06/187195) we have used the > cluster-based permutation approach. While the reviewers commended the choice > of this approach, one reviewer would like us to calculate a Bayesian measure > in addition to the Monte Carlo p values. Does anyone have a recommendation > how to best approach this, any "best practice" to share? > > It is quite easy to calculate a Bayes factor as a follow-up on classic > t-tests for example (e.g. see here > http://www.lifesci.sussex.ac.uk/home/Zoltan_Dienes/inference/Bayes.htm). > However, even though the permutation approach uses a t-value as a test > statistic, it is not a "t-test"... > > Best, > Christine > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From abela.eugenio at gmail.com Mon Mar 12 11:10:55 2018 From: abela.eugenio at gmail.com (Eugenio Abela) Date: Mon, 12 Mar 2018 10:10:55 +0000 Subject: [FieldTrip] Bayesian "follow-up" on Cluster-Based Permutation Tests In-Reply-To: References: Message-ID: Hi Christine, If you want to try something Bayesian and only if you have strong a priori hypotheses for a particular effect in a specific data window of interest, you could extract values from that window and do Bayesian analyses in JASP (https://jasp-stats.org), which is really easy to use and has a range Bayesian alternatives for classical F- and t-tests available. Alternatively, but this is probably much more complicated and time-consuming, you could do full Bayesian analyses with SPM12 (http://www.fil.ion.ucl.ac.uk/spm/software/spm12/), which allows you to calculate posterior probabilities for scalp, scalp x frequency or scalp x time maps. This is a great way of assessing evidence in your data, but I think it’s less popular than permutation tests. You can convert between Fieldtrip and SPM formats using spm_eeg_ft2spm.m I totally agree with Eelke that doing Bayesian tests post-hoc, after you obtained convincing results with permutations, seems like unnecessary methodological flourish. Yet it’s often hard to argue with reviewers without compromising a bit. You might want to use one of the above e.g. for your most important analysis and show in the rebuttal that it doesn’t alter your conclusions (hopefully!). This should convince them that results are robust to methodological choices, and exempt you from having to recalculate the whole thing again. Hope that helps Eugenio On 12 Mar 2018, at 09:19, Eelke Spaak wrote: Dear Christine, Bayes factors etc. are computed from the posterior distribution over some model parameters (e.g. means of Gaussians in the case analogous to the t-test). As the cluster-based permutation approach is inherently non-parametric (i.e. it tests the exchangeability of data beween conditions), I think it would be quite esoteric to try something Bayesian with the cluster test. I think your best bet would be to figure out *why* the reviewer wants this, and then come up with an alternative answer that does not depend on Bayesian measures. Of course, one could "zoom in" on the effect you found and compute parametric Bayesian stats for that region of interest, but that would constitute "double dipping" if you don't have an independent contrast. In case you find evidence in favour of a null effect (one circumstance under which reviewers might ask for Bayesian evidence), this approach and result might still be valid (as it goes against the bias introduced by the preselection). Best, Eelke On 11 March 2018 at 18:21, Blume Christine wrote: > Dear FT-Community, > > In the analysis of high-density EEG data for a recent manuscript > (https://www.biorxiv.org/content/early/2017/12/06/187195) we have used the > cluster-based permutation approach. While the reviewers commended the choice > of this approach, one reviewer would like us to calculate a Bayesian measure > in addition to the Monte Carlo p values. Does anyone have a recommendation > how to best approach this, any "best practice" to share? > > It is quite easy to calculate a Bayes factor as a follow-up on classic > t-tests for example (e.g. see here > http://www.lifesci.sussex.ac.uk/home/Zoltan_Dienes/inference/Bayes.htm). > However, even though the permutation approach uses a t-value as a test > statistic, it is not a "t-test"... > > Best, > Christine > > > _______________________________________________ > 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 jasonseehochan at gmail.com Mon Mar 12 15:35:48 2018 From: jasonseehochan at gmail.com (Jason Chan) Date: Mon, 12 Mar 2018 14:35:48 +0000 Subject: [FieldTrip] EEG and shunts Message-ID: Dear Fieldtrippers, This is not a specific Frieldtrip question, but I am hoping you can answer it anyways. I am trying to design an eeg experiment with hydrocephalus patients. However, most will have multiple shunts. I realise this will likely have dramatic effects to the activation patterns. A quick Google search gave me some rather old papers. I am wondering what is the best way to compare their activity to controls? Also, I will have access to their MRIs. Can I use beamforming? Unfortunately, I don't have access to an MEG. Thanks in advance for any advise. Best, Jason -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsten.wolters at uni-muenster.de Mon Mar 12 16:39:36 2018 From: carsten.wolters at uni-muenster.de (Carsten Wolters) Date: Mon, 12 Mar 2018 16:39:36 +0100 Subject: [FieldTrip] EEG and shunts In-Reply-To: References: Message-ID: <1D143B1F-8649-49F6-9E90-7622E005F728@uni-muenster.de> Dear Jason, that is very interesting: (1) CSF: I would expect that in hydrocephalus you have a significant contribution of CSF, see https://www.ncbi.nlm.nih.gov/pubmed/23006805 and https://www.sciencedirect.com/science/article/pii/S1053811914005175?via%3Dihub (2) Effects of shunts have been investigated in this paper https://www.sciencedirect.com/science/article/pii/S1053811912004946?via%3Dihub You might then be interested to model your shunts and the possibly bigger CSF compartment by using e.g. the Fieldtrip-SimBio pipeline (corresponding paper has just been accepted): http://www.sci.utah.edu/~wolters/PaperWolters/2018/VorwerkOostenveldPiastraMagyariWolters_BiomedEngOnline_2018_accepted.pdf BR Carsten > Am 12.03.2018 um 15:35 schrieb Jason Chan : > > > Dear Fieldtrippers, > > This is not a specific Frieldtrip question, but I am hoping you can answer it anyways. I am trying to design an eeg experiment with hydrocephalus patients. However, most will have multiple shunts. I realise this will likely have dramatic effects to the activation patterns. A quick Google search gave me some rather old papers. I am wondering what is the best way to compare their activity to controls? Also, I will have access to their MRIs. Can I use beamforming? Unfortunately, I don't have access to an MEG. > > > Thanks in advance for any advise. > > Best, > Jason > > _______________________________________________ > 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 mcmackr at tcd.ie Tue Mar 13 00:24:02 2018 From: mcmackr at tcd.ie (Roisin McMackin) Date: Mon, 12 Mar 2018 23:24:02 +0000 Subject: [FieldTrip] Timecourse units in dipole fitting .dip.mom Message-ID: Hi, I'm wondering in the example given http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting what exactly do the x,y and z timecourses for each dipole represent if dip.mom is a combination of strength and orientation? In other words, what are the units of the .dip.mom field? Thanks for your help, Roisin -------------- next part -------------- An HTML attachment was scrubbed... URL: From pahran at gmail.com Tue Mar 13 22:30:35 2018 From: pahran at gmail.com (Junjie Wu) Date: Tue, 13 Mar 2018 17:30:35 -0400 Subject: [FieldTrip] FEM with DTI Message-ID: Hello Community, I am trying create an FEM model with anisotropic conductivity using DTI and T1 MPRAGE. I know we can use ft_prepare_headmodel by specifying method 'simbio' to achieve this. However, the tutorials on the FieldTrip website only provide an example using anatomical MRI. Any suggestions on how to use FieldTrip/Simbio for anisotropic modeling will be greatly appreciated. Thanks, Junjie -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.hindriks at vu.nl Wed Mar 14 10:26:53 2018 From: r.hindriks at vu.nl (Hindriks, R.) Date: Wed, 14 Mar 2018 09:26:53 +0000 Subject: [FieldTrip] PhD position in Statistics for Neuroscience Message-ID: PhD position in Statistics for Neuroscience at VU Amsterdam The Department of Mathematics of the Faculty of Science, Vrije Universiteit Amsterdam, invites applications for a PhD position in Statistics for Neuroscience (0.8/1.0 FTE). The position The department is seeking applicants for a PhD position in statistics for neuroscience. The PhD project concerns spatiotemporal modeling and analysis of resting-state brain dynamics and will be supervised by Dr. Rikkert Hindriks and Prof.dr. Mathisca de Gunst. The PhD position is co-funded by the national science foundation NWO. Tasks You will develop statistical methods for modeling and analysis of resting-state brain activity recorded with functional MRI, magnetoencephalography (MEG), electroencephalography (EEG), and electrocorticography (ECoG). The project focuses on spatiotemporal aspects of resting-state brain activity such as wave propagation and relevant mathematics includes Empirical Bayesian inference, simulation and analysis of large-scale biophysical models, and higher-order decomposition techniques. You will publish your results in quality peer-reviewed journals in the field, culminating in a PhD thesis to be defended in public. Aside from these research tasks, a minor part of the time will be spent on teaching duties within the Department of Mathematics. Requirements The candidate must be talented, ambitious and highly motivated, in possession of a MSc. degree in mathematics, physics, or a related area. Candidates should have a strong demonstrable background in mathematics, in particular in statistics. Experience with neuroimaging data (fMRI) or electrophysiology (EEG/MEG/ECoG) and programming (R, Matlab, Python) is considered an advantage. In addition, we require proficiency in reading and writing of scientific manuscripts in English. Further particulars The appointment will be initially for one year. After satisfactory evaluation of the initial appointment, it can be extended to a total duration of 4 years. The VU offers a broad and attractive package of employment conditions. The employment contract is governed by the Collective Labour Agreement (CAO) for Dutch universities. In addition to their salaries, staff members receive annual holiday pay and a year-end bonus. Staff members with a full-time contract (38 hours per week) are entitled to 29 days off. The VU also offers a good pension scheme via ABP. Further information about our employment conditions can be found on https://www.vu.nl/en/employment. Salary The salary will be in accordance with university regulations for academic personnel, and amounts to € 2.222,- gross per month in the first year up to € 2.840,- in the fourth year (salary scale 85) based on a full-time employment. Information For additional information please contact: Dr. Rikkert Hindriks phone: +31 20 59 87835 e-mail: r.hindriks at vu.nl website: https://research.vu.nl/en/persons/r-hindriks Application Applicants are requested to write a letter in which they describe their abilities and motivation, accompanied by a curriculum vitae, a list of courses plus their grades, and contact details of two or three references. Please send your application by e-mail before April 15, 2018 to: Dr. Rikkert Hindriks e-mail: r.hindriks at vu.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From annekathrinweise at gmail.com Thu Mar 15 12:50:46 2018 From: annekathrinweise at gmail.com (Annekathrin Weise) Date: Thu, 15 Mar 2018 12:50:46 +0100 Subject: [FieldTrip] Salzburg Mind Brain Annual Meeting - SAMBA2018 Message-ID: <858a5468-e2df-be7e-aca9-8732f3c1995f@gmail.com> Dear all, we are pleased to announce that the registration and abstract submission deadline for the *Salzburg Mind Brain Annual Meeting* (*SAMBA*) **has been extended to April 1st, 2018. The mission of SAMBA is to attract the most exciting researchers in the domain of cognitive neuroscience, including related fields (e.g., computational modeling, 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. Note that the *number of participants is limited* and only a *few places* are *left*. We encourage young (PhD) students and young Post Docs to take part in the**poster price competition. *Poster awards*, *worth EUR 250,- each*, are awarded to the *three best posters. * 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) For more information see the SAMBA website . 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 andrea.brovelli at univ-amu.fr Fri Mar 16 09:31:42 2018 From: andrea.brovelli at univ-amu.fr (Andrea Brovelli) Date: Fri, 16 Mar 2018 09:31:42 +0100 Subject: [FieldTrip] Call for PhD and Post-Doc positions at the Institute of Language, Communication and the Brain (Marseille, France) Message-ID: Three 2-year postdoc positions at Aix-Marseille/Avignon on Language, Communication and the Brain The Center of Excellence on Brain and Language (BLRI,www.blri.fr/ ) and the Institute of Language, Communication and the Brain (ILCB,http://www.ilcb.fr/) offer: *Three 2-year postdoc positions*on any topic that falls within the area of language, communication, brain and modelling. The BLRI-ILCB is located in Aix-en-Provence, Avignon and Marseille and regroups several research centers in linguistics, psychology, cognitive neuroscience, medicine, computer science, and mathematics. The scientific project, ideally interdisciplinary, should be supervised by at least one member of the BLRI/ILCB (seehttp://www.blri.fr/members.html) and should, if possible, involve two different laboratories of the institute. . Duration: 2 years (1 year, extendable for another year) . Monthly salary: ~2000 € net (depending on experience) HOW TO APPLY Candidates should first contact potential supervisor(s) among the members of the ILCB/BLRI. Below, you will finda list of potential projects and supervisors that will be given priority for this call. However , you can also apply to any subject, under the supervision of any ILCB/BLRI member (http://www.blri.fr/members.html.). When the research project is finalized and approved by the supervisor(s), the application must be sent to nadera.bureau at blri.fr . Two PhD grants at Aix-Marseille/Avignon on Language, Communication and the Brain The Center of Excellence on Brain and Language (BLRI,www.blri.fr/ ) and the Institute of Language, Communication and the Brain (ILCB,http://www.ilcb.fr/) award 2 PhD grants (3 years) on any topic that falls within the area of language, communication, brain and modelling. The BLRI-ILCB is located in Aix-en-Provence, Avignon and Marseille and regroups several research centers in linguistics, psychology, cognitive neuroscience, medicine, computer science, and mathematics. Interested candidates need to find one or more PhD supervisors amongst the members of the BRLI-ILCB Together with the supervisor(s), they would then need to write a 3-year PhD project. A priority is given to interdisciplinary co-directions and to projects that involve two different laboratories of the institute. Monthly salary: 1 685€ (1 368€ net) for a period of 3 years HOW TO APPLY Candidates should first contact potential supervisor(s) among the members of the ILCB/BLRI. Below, you will finda list of potential projects and supervisors that will be given priority for this call. However , you can also apply to any subject, under the supervision of any ILCB/BLRI member (http://www.blri.fr/members.html.). When the research project is finalized and approved by the supervisor(s), the application must be sent to nadera.bureau at blri.fr . -------------- next part -------------- An HTML attachment was scrubbed... URL: From jorn at artinis.com Mon Mar 19 09:07:49 2018 From: jorn at artinis.com (=?iso-8859-1?Q?J=F6rn_M._Horschig?=) Date: Mon, 19 Mar 2018 09:07:49 +0100 Subject: [FieldTrip] ESR / Doctoral student position in algorithm development Message-ID: <005f01d3bf59$5f82d280$1e887780$@artinis.com> Dear list, We have an open ESR position from a Marie Curie grant starting in September this year. The goal of the project is cleaning of fNIRS data from artefacts and extraction of physiological components such as heartbeat and respiration. We encourage of course publication of the algorithm and implementation of these algorithms in e.g. FieldTrip or other open source toolboxes to facilitate multimodal data analyses. The ESR will work in strong collaboration with the Donders Institute (Sabine Hunnius, Robert Oostenveld), but also with external universities in the EU and other companies (eye-tracking and motion-tracking). The ESR will be located at our company in the Netherlands. For more information, please see http://www.artinis.com/early-stage-researcher-esr-doctoral-student-1 If you have any questions regarding this position, please let me know. With best regards, Jörn -- Jörn M. Horschig, PhD Software Engineer & Project Leader NeuroGuard XS A Einsteinweg 17 6662PW Elst The Netherlands T +31 481 350 980 I www.artinis.com The information in this e-mail is confidential and intended solely for the person to whom it is addressed. If this message is not addressed to you, please be aware that you have no authorization to read this e-mail, to copy it, to furnish it to any person other than the addressee, or to use or misuse its content in any way whatsoever. Should you have received this e-mail by mistake, please bring this to the attention of the sender, after which you are kindly requested to destroy the original message. Sign up for our NIRS newsletter -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 9919 bytes Desc: not available URL: From noa1hc at gmail.com Mon Mar 19 21:51:08 2018 From: noa1hc at gmail.com (=?UTF-8?B?16DXldei15Qg15TXm9eU158=?=) Date: Mon, 19 Mar 2018 22:51:08 +0200 Subject: [FieldTrip] source grand average Message-ID: Hi all, I am working on source recognition. I used ft_sourcegrandavrage, but I could not plotting the results, because there is no 'anatomy' field. why is it happening? my code is- norm_source.pos=template_grid.pos norm_source.inside=template_grid.inside cfg.parameter = 'pow' cfg.keepindividual = 'yes' [grandavg] = ft_sourcegrandaverage(cfg, norm_source 1, norm_source 2) This generates a structure with the following fields: grandavg = pow: [2x7109137 double] coordsys: 'spm' dim: [181 217 181] inside: [6804x1 logical] pos: [6804x3 double] cfg: [1x1 struct] Thanks! Noa בלי וירוסים. www.avast.com <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Mon Mar 19 22:25:01 2018 From: julian.keil at gmail.com (Julian Keil) Date: Mon, 19 Mar 2018 22:25:01 +0100 Subject: [FieldTrip] source grand average In-Reply-To: References: Message-ID: <3188B927-9556-4575-B360-076E564C9296@gmail.com> Hi Noa, either use ft_sourceinterpolate to interpolate the grandaverage to a standard-MRI, or use the „surface“-option when plotting. Cheers, Julian ________________ Prof. Dr. Julian Keil Biologische Psychologie Olshausenstraße 62 - R. 306 24118 Kiel 0431 / 880 - 4872 http://www.biopsych.uni-kiel.de/ Klinik für Psychiatrie und Psychotherapie der Charité im St. Hedwig-Krankenhaus Große Hamburger Straße 5-11 10115 Berlin 030 / 2311 - 1879 www.multisensorymind.com > Am 19.03.2018 um 21:51 schrieb ⁨נועה הכהן⁩ <⁨noa1hc at gmail.com⁩>: > > Hi all, > I am working on source recognition. I used ft_sourcegrandavrage, but I could not plotting the results, because there is no 'anatomy' field. why is it happening? > > my code is- > norm_source.pos=template_grid.pos > norm_source.inside=template_grid.inside > cfg.parameter = 'pow' > cfg.keepindividual = 'yes' > [grandavg] = ft_sourcegrandaverage(cfg, norm_source 1, norm_source 2) > > This generates a structure with the following fields: > grandavg = > > pow: [2x7109137 double] > coordsys: 'spm' > dim: [181 217 181] > inside: [6804x1 logical] > pos: [6804x3 double] > cfg: [1x1 struct] > > Thanks! > Noa > > > בלי וירוסים. www.avast.com _______________________________________________ > 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: signature.asc Type: application/pgp-signature Size: 833 bytes Desc: Message signed with OpenPGP URL: From robpetrosino at gmail.com Tue Mar 20 02:56:16 2018 From: robpetrosino at gmail.com (Roberto Petrosino) Date: Mon, 19 Mar 2018 21:56:16 -0400 Subject: [FieldTrip] clarifications on the eeglab2fieldtrip function Message-ID: <512FE9BF-FFE5-4D4E-B961-B058729616EB@gmail.com> Hello fieldtrippers, can anyone clarify the usage of the argument fieldbox in the eeglab2fieldtrip function below? I don’t seem to find any relevant information anywhere. > eeglab2fieldtrip() - do this ... > > Usage: >> data = eeglab2fieldtrip( EEG, fieldbox, transform ); > > Inputs: > EEG - [struct] EEGLAB structure > fieldbox - ['preprocessing'|'freqanalysis'|'timelockanalysis'|'companalysis'] > transform - ['none'|'dipfit'] transform channel locations for DIPFIT > using the transformation matrix in the field > 'coord_transform' of the dipfit substructure of the EEG > structure. > Outputs: > data - FIELDTRIP structure Thanks, -Roberto ---------- Roberto Petrosino Ph.D. Student in Linguistics CT Institute for the Brain and Cognitive Sciences University of Connecticut -------------- next part -------------- An HTML attachment was scrubbed... URL: From noa1hc at gmail.com Tue Mar 20 06:33:21 2018 From: noa1hc at gmail.com (=?UTF-8?B?16DXldei15Qg15TXm9eU158=?=) Date: Tue, 20 Mar 2018 07:33:21 +0200 Subject: [FieldTrip] source grand average In-Reply-To: <3188B927-9556-4575-B360-076E564C9296@gmail.com> References: <3188B927-9556-4575-B360-076E564C9296@gmail.com> Message-ID: !Thanks :I tried to do this, and to used ft_sourcedescriptives but I got an error message Attempted to access sel(1); index out of bounds because numel(sel)=0. Error in ft_sourceinterpolate>my_interpn (line 688) ft_progress(sel(1)/num, 'interpolating %.1f%%\n', 100*sel(1)/num); Error in ft_sourceinterpolate (line 535) interp.inside( sel) = my_interpn(double(functional.inside), ax(sel), ay(sel), az(sel), 'nearest', cfg.feedback); Why? thanks, Noa. 2018-03-19 23:25 GMT+02:00 Julian Keil : > Hi Noa, > > either use ft_sourceinterpolate to interpolate the grandaverage to a > standard-MRI, or use the „surface“-option when plotting. > > Cheers, > > Julian > > ________________ > Prof. Dr. Julian Keil > > Biologische Psychologie > Olshausenstraße 62 - R. 306 > 24118 Kiel > > 0431 / 880 - 4872 > http://www.biopsych.uni-kiel.de/ > > Klinik für Psychiatrie und Psychotherapie > der Charité im St. Hedwig-Krankenhaus > Große Hamburger Straße 5-11 > 10115 Berlin > > 030 / 2311 - 1879 > www.multisensorymind.com > > Am 19.03.2018 um 21:51 schrieb ⁨נועה הכהן⁩ <⁨noa1hc at gmail.com⁩>: > > Hi all, > I am working on source recognition. I used ft_sourcegrandavrage, but I > could not plotting the results, because there is no 'anatomy' field. why is > it happening? > > my code is- > norm_source.pos=template_grid.pos > norm_source.inside=template_grid.inside > cfg.parameter = 'pow' > cfg.keepindividual = 'yes' > [grandavg] = ft_sourcegrandaverage(cfg, norm_source 1, norm_source 2) > > This generates a structure with the following fields: > > grandavg = > > pow: [2x7109137 double] > coordsys: 'spm' > dim: [181 217 181] > inside: [6804x1 logical] > pos: [6804x3 double] > cfg: [1x1 struct] > > > Thanks! > > Noa > > > > בלי > וירוסים. www.avast.com > > _______________________________________________ > 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 jan.schoffelen at donders.ru.nl Tue Mar 20 07:54:39 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 20 Mar 2018 06:54:39 +0000 Subject: [FieldTrip] clarifications on the eeglab2fieldtrip function In-Reply-To: <512FE9BF-FFE5-4D4E-B961-B058729616EB@gmail.com> References: <512FE9BF-FFE5-4D4E-B961-B058729616EB@gmail.com> Message-ID: <9205E207-C86E-4CC1-B407-5F612E8A431B@donders.ru.nl> I guess that this fieldbox should be string that specifies which type of data to return from the eeglab-structure. Best wishes, Jan-Mathijs On 20 Mar 2018, at 02:56, Roberto Petrosino > wrote: Hello fieldtrippers, can anyone clarify the usage of the argument fieldbox in the eeglab2fieldtrip function below? I don’t seem to find any relevant information anywhere. eeglab2fieldtrip() - do this ... Usage: >> data = eeglab2fieldtrip( EEG, fieldbox, transform ); Inputs: EEG - [struct] EEGLAB structure fieldbox - ['preprocessing'|'freqanalysis'|'timelockanalysis'|'companalysis'] transform - ['none'|'dipfit'] transform channel locations for DIPFIT using the transformation matrix in the field 'coord_transform' of the dipfit substructure of the EEG structure. Outputs: data - FIELDTRIP structure Thanks, -Roberto ---------- Roberto Petrosino Ph.D. Student in Linguistics CT Institute for the Brain and Cognitive Sciences University of Connecticut _______________________________________________ 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 M.Wimber at bham.ac.uk Tue Mar 20 10:01:38 2018 From: M.Wimber at bham.ac.uk (Maria Wimber) Date: Tue, 20 Mar 2018 09:01:38 +0000 Subject: [FieldTrip] 3-year postdoc at UoB, decoding mental states based on fMRI/EEG patterns Message-ID: Hi FieldTrip users We would like to bring this exciting postdoctoral position to the attention of potential applicants. Mindreading mindreading: Using multivariate pattern analysis to decode the neural basis of mental state ascription. The full time postdoctoral research fellow will work on this 3-year ESRC-funded project in the School of Psychology at the University of Birmingham, with Professor Ian Apperly and Dr Maria Wimber. The project will use advanced neuroimaging methods to test whether "social brain areas" that are active when we think about the minds of others actually encode information about what other people are thinking, or whether they control attention to information encoded elsewhere. Please address informal enquiries jointly to Ian Apperly and Maria Wimber. Online advert and application forms Centre for Human Brain Health Ian Apperly Maria Wimber -------------- next part -------------- An HTML attachment was scrubbed... URL: From panyl at psych.ac.cn Tue Mar 20 13:16:06 2018 From: panyl at psych.ac.cn (=?UTF-8?B?5r2Y5Lqa5Li9?=) Date: Tue, 20 Mar 2018 20:16:06 +0800 (GMT+08:00) Subject: [FieldTrip] fieldtrip Digest, Vol 88, Issue 12 In-Reply-To: References: Message-ID: <21109d8.a526.16243568722.Coremail.panyl@psych.ac.cn> > -----Original Messages----- > From: fieldtrip-request at science.ru.nl > Sent Time: 2018-03-20 19:00:02 (Tuesday) > To: fieldtrip at science.ru.nl > Cc: > Subject: fieldtrip Digest, Vol 88, Issue 12 > > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. source grand average (???? ????) > 2. Re: source grand average (Julian Keil) > 3. clarifications on the eeglab2fieldtrip function > (Roberto Petrosino) > 4. Re: source grand average (???? ????) > 5. Re: clarifications on the eeglab2fieldtrip function > (Schoffelen, J.M. (Jan Mathijs)) > 6. 3-year postdoc at UoB, decoding mental states based on > fMRI/EEG patterns (Maria Wimber) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 19 Mar 2018 22:51:08 +0200 > From: ???? ???? > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] source grand average > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi all, > I am working on source recognition. I used ft_sourcegrandavrage, but I > could not plotting the results, because there is no 'anatomy' field. why is > it happening? > > my code is- > norm_source.pos=template_grid.pos > norm_source.inside=template_grid.inside > cfg.parameter = 'pow' > cfg.keepindividual = 'yes' > [grandavg] = ft_sourcegrandaverage(cfg, norm_source 1, norm_source 2) > > This generates a structure with the following fields: > > grandavg = > > pow: [2x7109137 double] > coordsys: 'spm' > dim: [181 217 181] > inside: [6804x1 logical] > pos: [6804x3 double] > cfg: [1x1 struct] > > > Thanks! > > Noa > > > > ??? > ???????. www.avast.com > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 2 > Date: Mon, 19 Mar 2018 22:25:01 +0100 > From: Julian Keil > To: FieldTrip discussion list > Subject: Re: [FieldTrip] source grand average > Message-ID: <3188B927-9556-4575-B360-076E564C9296 at gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Noa, > > either use ft_sourceinterpolate to interpolate the grandaverage to a standard-MRI, or use the ?surface?-option when plotting. > > Cheers, > > Julian > > ________________ > Prof. Dr. Julian Keil > > Biologische Psychologie > Olshausenstra?e 62 - R. 306 > 24118 Kiel > > 0431 / 880 - 4872 > http://www.biopsych.uni-kiel.de/ > > Klinik f?r Psychiatrie und Psychotherapie > der Charit? im St. Hedwig-Krankenhaus > Gro?e Hamburger Stra?e 5-11 > 10115 Berlin > > 030 / 2311 - 1879 > www.multisensorymind.com > > > Am 19.03.2018 um 21:51 schrieb ????? ????? : > > > > Hi all, > > I am working on source recognition. I used ft_sourcegrandavrage, but I could not plotting the results, because there is no 'anatomy' field. why is it happening? > > > > my code is- > > norm_source.pos=template_grid.pos > > norm_source.inside=template_grid.inside > > cfg.parameter = 'pow' > > cfg.keepindividual = 'yes' > > [grandavg] = ft_sourcegrandaverage(cfg, norm_source 1, norm_source 2) > > > > This generates a structure with the following fields: > > grandavg = > > > > pow: [2x7109137 double] > > coordsys: 'spm' > > dim: [181 217 181] > > inside: [6804x1 logical] > > pos: [6804x3 double] > > cfg: [1x1 struct] > > > > Thanks! > > Noa > > > > > > ??? ???????. www.avast.com _______________________________________________ > > 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: signature.asc > Type: application/pgp-signature > Size: 833 bytes > Desc: Message signed with OpenPGP > URL: > > ------------------------------ > > Message: 3 > Date: Mon, 19 Mar 2018 21:56:16 -0400 > From: Roberto Petrosino > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] clarifications on the eeglab2fieldtrip function > Message-ID: <512FE9BF-FFE5-4D4E-B961-B058729616EB at gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello fieldtrippers, > > can anyone clarify the usage of the argument fieldbox in the eeglab2fieldtrip function below? I don?t seem to find any relevant information anywhere. > > > eeglab2fieldtrip() - do this ... > > > > Usage: >> data = eeglab2fieldtrip( EEG, fieldbox, transform ); > > > > Inputs: > > EEG - [struct] EEGLAB structure > > fieldbox - ['preprocessing'|'freqanalysis'|'timelockanalysis'|'companalysis'] > > transform - ['none'|'dipfit'] transform channel locations for DIPFIT > > using the transformation matrix in the field > > 'coord_transform' of the dipfit substructure of the EEG > > structure. > > Outputs: > > data - FIELDTRIP structure > > Thanks, > > -Roberto > > ---------- > Roberto Petrosino > Ph.D. Student in Linguistics > CT Institute for the Brain and Cognitive Sciences > University of Connecticut > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 4 > Date: Tue, 20 Mar 2018 07:33:21 +0200 > From: ???? ???? > To: FieldTrip discussion list > Subject: Re: [FieldTrip] source grand average > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > !Thanks > :I tried to do this, and to used ft_sourcedescriptives but I got an error > message > > Attempted to access sel(1); index out of bounds because numel(sel)=0. > > Error in ft_sourceinterpolate>my_interpn (line 688) > ft_progress(sel(1)/num, 'interpolating %.1f%%\n', 100*sel(1)/num); > > Error in ft_sourceinterpolate (line 535) > interp.inside( sel) = my_interpn(double(functional.inside), ax(sel), > ay(sel), az(sel), 'nearest', cfg.feedback); > > Why? > > thanks, Noa. > > > > 2018-03-19 23:25 GMT+02:00 Julian Keil : > > > Hi Noa, > > > > either use ft_sourceinterpolate to interpolate the grandaverage to a > > standard-MRI, or use the ?surface?-option when plotting. > > > > Cheers, > > > > Julian > > > > ________________ > > Prof. Dr. Julian Keil > > > > Biologische Psychologie > > Olshausenstra?e 62 - R. 306 > > 24118 Kiel > > > > 0431 / 880 - 4872 > > http://www.biopsych.uni-kiel.de/ > > > > Klinik f?r Psychiatrie und Psychotherapie > > der Charit? im St. Hedwig-Krankenhaus > > Gro?e Hamburger Stra?e 5-11 > > 10115 Berlin > > > > 030 / 2311 - 1879 > > www.multisensorymind.com > > > > Am 19.03.2018 um 21:51 schrieb ????? ????? : > > > > Hi all, > > I am working on source recognition. I used ft_sourcegrandavrage, but I > > could not plotting the results, because there is no 'anatomy' field. why is > > it happening? > > > > my code is- > > norm_source.pos=template_grid.pos > > norm_source.inside=template_grid.inside > > cfg.parameter = 'pow' > > cfg.keepindividual = 'yes' > > [grandavg] = ft_sourcegrandaverage(cfg, norm_source 1, norm_source 2) > > > > This generates a structure with the following fields: > > > > grandavg = > > > > pow: [2x7109137 double] > > coordsys: 'spm' > > dim: [181 217 181] > > inside: [6804x1 logical] > > pos: [6804x3 double] > > cfg: [1x1 struct] > > > > > > Thanks! > > > > Noa > > > > > > > > ??? > > ???????. www.avast.com > > > > _______________________________________________ > > 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: > > ------------------------------ > > Message: 5 > Date: Tue, 20 Mar 2018 06:54:39 +0000 > From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] clarifications on the eeglab2fieldtrip > function > Message-ID: <9205E207-C86E-4CC1-B407-5F612E8A431B at donders.ru.nl> > Content-Type: text/plain; charset="utf-8" > > I guess that this fieldbox should be string that specifies which type of data to return from the eeglab-structure. > Best wishes, > Jan-Mathijs > > > > > On 20 Mar 2018, at 02:56, Roberto Petrosino > wrote: > > Hello fieldtrippers, > > can anyone clarify the usage of the argument fieldbox in the eeglab2fieldtrip function below? I don?t seem to find any relevant information anywhere. > > eeglab2fieldtrip() - do this ... > > Usage: >> data = eeglab2fieldtrip( EEG, fieldbox, transform ); > > Inputs: > EEG - [struct] EEGLAB structure > fieldbox - ['preprocessing'|'freqanalysis'|'timelockanalysis'|'companalysis'] > transform - ['none'|'dipfit'] transform channel locations for DIPFIT > using the transformation matrix in the field > 'coord_transform' of the dipfit substructure of the EEG > structure. > Outputs: > data - FIELDTRIP structure > > Thanks, > > -Roberto > > ---------- > Roberto Petrosino > Ph.D. Student in Linguistics > CT Institute for the Brain and Cognitive Sciences > University of Connecticut > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 6 > Date: Tue, 20 Mar 2018 09:01:38 +0000 > From: Maria Wimber > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] 3-year postdoc at UoB, decoding mental states > based on fMRI/EEG patterns > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > Hi FieldTrip users > > We would like to bring this exciting postdoctoral position to the attention of potential applicants. > > Mindreading mindreading: Using multivariate pattern analysis to decode the neural basis of mental state ascription. The full time postdoctoral research fellow will work on this 3-year ESRC-funded project in the School of Psychology at the University of Birmingham, with Professor Ian Apperly and Dr Maria Wimber. The project will use advanced neuroimaging methods to test whether "social brain areas" that are active when we think about the minds of others actually encode information about what other people are thinking, or whether they control attention to information encoded elsewhere. Please address informal enquiries jointly to Ian Apperly and Maria Wimber. > > Online advert and application forms > Centre for Human Brain Health > Ian Apperly > Maria Wimber > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 88, Issue 12 > ***************************************** From diana-hime at yandex.ru Tue Mar 20 20:48:31 2018 From: diana-hime at yandex.ru (=?utf-8?B?LSDQlNC40LDQvdCw?=) Date: Tue, 20 Mar 2018 22:48:31 +0300 Subject: [FieldTrip] (no subject) Message-ID: <329671521575311@web9j.yandex.ru> An HTML attachment was scrubbed... URL: From davide.tabarelli at unitn.it Tue Mar 20 16:59:39 2018 From: davide.tabarelli at unitn.it (Davide Tabarelli) Date: Tue, 20 Mar 2018 16:59:39 +0100 Subject: [FieldTrip] Expressions of Interest for a Marie Sklodowksa - Curie Fellowship at CIMeC - University of Trento Message-ID: <690D12F4-748E-4389-888E-2D5D241B769A@unitn.it> Dear all, at this page a Call for Expressions of Interest in the Marie Sklodowksa - Curie Individual Fellowships has been published: https://www.unitn.it/ateneo/68640/cimec-call-for-expressions-of-interest-marie-sklodowksa-curie-individual-fellowships . The Center for Mind/Brain Sciences - CIMeC at the University of Trento (Italy) welcomes expressions of interest from excellent postdoctoral researchers to apply, jointly with a research supervisor from CIMeC, to the European Commission Marie Skłodowska- Curie Individual Fellowship. The Marie Skłodowska Curie Action is a funding scheme that supports researchers mobility: Individual Fellowships – European Fellowships may last 12-24 months involving a research project, advanced training and knowledge exchange at the host institution (CIMeC). It offers a competitive salary, mobility and family allowances plus a budget for research and training costs; applicants are expected to have an excellent CV and a strong publication record. Selected candidates will be offered both academic and administrative support from CIMeC faculty and the University of Trento Research Office with regards to the proposal development. Feel free to circulate this invitation to your networks. D. — Davide Tabarelli, Ph.D. MEG Physicist Center for Mind Brain Sciences (CIMeC) University of Trento, Via delle Regole, 101 38123 Mattarello (TN) Tel: +39 (0)461 283644 Italy From thomas.hartmann at th-ht.de Wed Mar 21 11:02:14 2018 From: thomas.hartmann at th-ht.de (Thomas Hartmann) Date: Wed, 21 Mar 2018 11:02:14 +0100 Subject: [FieldTrip] doing ica on magnetometers and gradiometers Message-ID: <10159d5d-525d-5769-ac9a-3bec4483ef38@th-ht.de> hi, we have had a vivid discussion in our group concerning whether apply ICA to magnetometers and gradiometers in one go (i.e. lumping them together) or whether it is necessary to apply the ICA on mags ands grads separately. most approaches that can be found on the internet seem to favor the do-it-in-one-go way. my main concern with applying it to both sensor types at the same time is that the resulting components will probably be a linear mixture of both sensor types. when i reject some components and the project the components back to the sensor space, gradiometer activity should "leak" into the magnetometer data and vice versa. or am i wrong with my thoughts? or does it just not matter at all? i am looking forward to reading your thoughts! best, thomas -- Dr. Thomas Hartmann Centre for Cognitive Neuroscience FB Psychologie Universität Salzburg Hellbrunnerstraße 34/II 5020 Salzburg Tel: +43 662 8044 5109 Email: thomas.hartmann at th-ht.de "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle) From diana-hime at yandex.ru Sat Mar 24 21:25:01 2018 From: diana-hime at yandex.ru (=?utf-8?B?LSDQlNC40LDQvdCw?=) Date: Sat, 24 Mar 2018 23:25:01 +0300 Subject: [FieldTrip] preprocessing error "Index exceeds matrix dimensions error" Message-ID: <3814791521923101@web25o.yandex.ru> An HTML attachment was scrubbed... URL: From weiwuneuro at gmail.com Mon Mar 26 02:55:14 2018 From: weiwuneuro at gmail.com (Wei Wu) Date: Sun, 25 Mar 2018 17:55:14 -0700 Subject: [FieldTrip] Faculty jobs in brain stimulation at Stanford University Message-ID: To whom it may concern, I wanted to share a link to this job posting for those who are interested: http://med.stanford.edu/content/dam/sm/psychiatry/documents/about_us/ FacultyJobs/BrainStimulation.pdf -------------- next part -------------- An HTML attachment was scrubbed... URL: From giulia.lioi at inria.fr Mon Mar 26 18:52:11 2018 From: giulia.lioi at inria.fr (Giulia Lioi) Date: Mon, 26 Mar 2018 18:52:11 +0200 (CEST) Subject: [FieldTrip] siemens_gui_streamer prisma scanner Message-ID: <1835860202.156994.1522083131598.JavaMail.zimbra@inria.fr> To whom it may concern, I am having some problems using the siemens_gui_streamer with a recently installed Siemens prisma scanner. I was using a custom script to extract the mrprot.txt and I tried to keep the same information I was getting from the mrprot of the verio scanner. When I try to run the gui_streamer with the new mrprot however it automatically closes after the first scan, while with the old protocol is working.., HAs anyone had a similar problem? Can you help with this? Many thanks Giulia Lioi, PhD | Engineer R&D Visages-Hybrid teams Univ Rennes, Inria, CNRS, IRISA F-35000 Rennes Tel: 0033 767466577 -------------- next part -------------- An HTML attachment was scrubbed... URL: From steva_fernandes at yahoo.com Tue Mar 27 07:31:22 2018 From: steva_fernandes at yahoo.com (steven fernandes) Date: Tue, 27 Mar 2018 05:31:22 +0000 (UTC) Subject: [FieldTrip] Source localization in 4D data References: <1446487794.148989.1522128682247.ref@mail.yahoo.com> Message-ID: <1446487794.148989.1522128682247@mail.yahoo.com> Dear Researchers, I have 4D data at resting state (link given below) https://www.dropbox.com/s/rwzbaz7ame99gt7/2.zip?dl=0 I want to use above data to perform source localization of the spikes that appear during resting state for epileptic patient. Can you please help me how could I implement it using FieldTrip.  I am new to FieldTrip and I would greatly appreciate your help. Regards,Steven  -------------- next part -------------- An HTML attachment was scrubbed... URL: From mathis.kaiser at charite.de Tue Mar 27 12:53:47 2018 From: mathis.kaiser at charite.de (Mathis Kaiser) Date: Tue, 27 Mar 2018 12:53:47 +0200 Subject: [FieldTrip] [ext] preprocessing error "Index exceeds matrix dimensions error" In-Reply-To: <3814791521923101@web25o.yandex.ru> References: <3814791521923101@web25o.yandex.ru> Message-ID: <34f5c673-ae4d-f279-01cd-5f2d8219ebb9@charite.de> Hi Diana, is it possible that you already segmented the data in NetStation? The header indicates 98 trials. I have no experience with EGI files, but is there an option to export the continuous data? If you want to define your trials in fieldtrip, this makes more sense. Best, Mathis On 24.03.2018 21:25, - Диана wrote: >   > Dear Fildtrippers, >      > My name is Diana, I'm new to Fieldtrip and curently trying to learn > how process eeg data >      > I have a .raw file, exported from NetStation > I'm using Matlab 2014b, and the latest version of fieldtrip. >   >   > [my definetria]: >   > events = ft_read_event('01 wordA 27-09.raw') > FileName = '01 wordA 27-09.raw'; >  cfg                         = []; >   cfg.dataset                 = FileName; >   cfg.trialdef.eventtype      = 'trigger'; >   cfg.trialdef.eventvalue     = 'tim0'; % здесь то значение, которое нужно >   cfg.trialdef.prestim        = 0.2; % интервал до стимула >   cfg.trialdef.poststim       = 0.8; % интервал после стимула >   >   cfg = ft_definetrial(cfg); >   >   > after this, I try >   > [preprocessing]: >   > cfg = [] > cfg.dataset = FileName > cfg.channel = 'EEG' > cfg.continuous   = 'no' > raw_data  = ft_preprocessing(cfg) >   > And get such error: >   > reading and preprocessing > reading and preprocessing trial 2 from 98 > Index exceeds matrix dimensions. >   > Error in read_sbin_data (line 121) >         eventData(:,1:NSamples)  = temp( >         (NChan+1):(NChan+NEvent), 1:NSamples); >   > Error in ft_read_data (line 737) >       dat = read_sbin_data(filename, hdr, begtrial, >       endtrial, chanindx); >   > Error in ft_preprocessing (line 573) >       dat = ft_read_data(cfg.datafile, 'header', hdr, >       'begsample', begsample, 'endsample', endsample, >       'chanindx', rawindx, 'checkboundary', >       strcmp(cfg.continuous, 'no'), 'dataformat', >       cfg.dataformat); >   > Error in preproc_try (line 3) > raw_data  = ft_preprocessing(cfg) >   > Error in run (line 63) > evalin('caller', [script ';']); >   > Could you help me to understand how to manage this, please? >   > Example file: > https://drive.google.com/open?id=1c5RYxL9Br1Q5LTkedBD_dR4Ns72Vb9J5 >   > Thank you for your answers! >   >   > With best wishes, Diana > Undergraduate Student > Department of Biology of MSU >   > P.S. Sorry for having this letter sent again, the first attempt failed > strangely. > > > _______________________________________________ > 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 diana-hime at yandex.ru Wed Mar 28 04:25:52 2018 From: diana-hime at yandex.ru (=?utf-8?B?LSDQlNC40LDQvdCw?=) Date: Wed, 28 Mar 2018 05:25:52 +0300 Subject: [FieldTrip] [ext] preprocessing error "Index exceeds matrix dimensions error" In-Reply-To: <34f5c673-ae4d-f279-01cd-5f2d8219ebb9@charite.de> References: <3814791521923101@web25o.yandex.ru> <34f5c673-ae4d-f279-01cd-5f2d8219ebb9@charite.de> Message-ID: <1472741522203952@web37j.yandex.ru> An HTML attachment was scrubbed... URL: From lindseyrtate at ou.edu Wed Mar 28 09:30:23 2018 From: lindseyrtate at ou.edu (Tate, Lindsey R.) Date: Wed, 28 Mar 2018 07:30:23 +0000 Subject: [FieldTrip] ft_read_header and ft_definetrial errors Message-ID: Hello fieldtrip community, I have a dataset I've been working with in EEGLAB, but I am now trying to use it in Fieldtrip. The dataset is a concatenation of extracted epochs from multiple participants. The data imports fine as an EDF. However, EEGLAB's formatting for epochs means that there aren't triggers in the data. I have made my own header and trigger files in BrainVision format (I did it this way because I had BrainVision files to mimic, and it's listed on http://www.fieldtriptoolbox.org/reference/ft_read_header as an acceptable format). My events read in fine with the *.vmrk file I have. My problem is that I haven't figured out how to read in the *.vhdr file I have successfully. When I've tried to read it in, it gives me an error that it can't identify the dataset that the header goes with. Without it, I get the error below that *.vmrk isn't an accepted header file format. I have two questions: (1) Am I right in my interpretation that the error I'm getting below is because I haven't read in the *.vhdr header file? If that's not correct, what does the error mean? (2) How can I read in the *.vhdr header file I have? The following is the code: %%file information AMBB = 'AM'; stimfreq = '6'; pathway = 'Z:\BB\Preprocessing\'; datafile = [pathway AMBB stimfreq '_3s_avgepoch_5.edf']; eventfile = [pathway AMBB stimfreq '_3s_avgepoch_5_ftevents.vmrk'] ; hdrfile = [pathway AMBB stimfreq '_3s_avgepoch_5_ftevents.vhdr']; output6 = [pathway AMBB stimfreq '_dics6.mat']; output12 = [pathway AMBB stimfreq '_dics12.mat']; output25 = [pathway AMBB stimfreq '_dics25.mat']; output50 = [pathway AMBB stimfreq '_dics50.mat']; %%read in events [event] = ft_read_event(eventfile); %%define trials cfg = []; cfg.trialdef.eventvalue = 2 ; cfg.trialdef.prestim = 1 ; cfg.trialdef.poststim = 3 ; cfg.dataset = eventfile ; cfg.trialfun = 'ft_trialfun_general'; [cfg] = ft_definetrial(cfg); The following is the output: evaluating trialfunction 'ft_trialfun_general' Error using ft_notification (line 340) unsupported header format "brainvision_vmrk" Error in ft_error (line 39) ft_notification(varargin{:}); Error in ft_read_header (line 2478) ft_error('unsupported header format "%s"', headerformat); Error in ft_trialfun_general (line 78) hdr = ft_read_header(cfg.headerfile, 'headerformat', cfg.headerformat); Error in ft_definetrial (line 178) [trl, event] = feval(cfg.trialfun, cfg); /// The *.vhdr and *.vmrk files are attached for reference. Thank you for any help or insight you can provide. Lindsey Tate PhD Candidate University of Oklahoma lindseyrtate at ou.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: AM6_3s_avgepoch_5_ftevents.vmrk Type: application/octet-stream Size: 42028 bytes Desc: AM6_3s_avgepoch_5_ftevents.vmrk URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: AM6_3s_avgepoch_5_ftevents.vhdr Type: application/octet-stream Size: 9763 bytes Desc: AM6_3s_avgepoch_5_ftevents.vhdr URL: From edauer1 at gmail.com Thu Mar 29 19:02:44 2018 From: edauer1 at gmail.com (Ed Auer) Date: Thu, 29 Mar 2018 13:02:44 -0400 Subject: [FieldTrip] Using a condition-average baseline normalization for display of TFR Message-ID: I am using Fieldtrip to conduct time frequency analyses on an EEG dataset that has 2 factors each with multiple levels. I would like be able to display the data within a factor/level relative to a baseline computed using the average over levels and factors. Currently, to plot relative to the condition/level specific baseline I am using. cfg = []; cfg.baseline = [-0.5 0.5]; cfg.baselinetype = 'relative'; cfg.zlim = 'maxmin'; cfg.ylim = [8 12]; cfg.layout = 'acticap-64ch-standard2.mat'; cfg.xlim = [-0.5:0.05:.5]; cfg.comment = 'xlim'; cfg.commentpos = 'title'; f1 = figure; ft_topoplotTFR(cfg, GABDCLRtfr) Reading through the documentation I do not see any way to specify a baseline from a different TFR. Have I missed something or is it necessary to compute the baseline normalization directly and then plot as absolute data? Thanks, --Ed Auer -------------- next part -------------- An HTML attachment was scrubbed... URL: From TaylorBealeR at cardiff.ac.uk Fri Mar 30 17:40:26 2018 From: TaylorBealeR at cardiff.ac.uk (Rosa Taylor Beale) Date: Fri, 30 Mar 2018 15:40:26 +0000 Subject: [FieldTrip] Empty array in coherence connectivity analysis Message-ID: Hi all, I'm a final year undergraduate in Cardiff working on pain networks. I have been trying to calculate coherence between 3 seed regions, however when I run the ft_connectivityanalysis, the labelcmb and cohspctrm arrays are empty (the channel labels don't look like they were read?). There is no error or warning messages that occur when running the command, so I am unsure why it is not running correctly. First, I run ft_freqanalysis which seems to run fine: cfg = [] cfg.method = 'wavelet'; cfg.output = 'pow'; cfg.toi = 0:0.05:2; cfg.foi = [30:1:100]; time_freq= ft_freqanalysis(cfg, virtualchannel_raw); time_freq = label: {3x1 cell} dimord: 'chan_freq_time' freq: [1x71 double] time: [1x41 double] powspctrm: [3x71x41 double] cfg: [1x1 struct] Then I run the connectivity analysis and up with the empty output: cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'pfcCont_seed' 'smc_seed' 'pfcIps_seed' 'smc_seed' 'pfcCont_seed' 'pfcIps_seed'}; coherence = ft_connectivityanalysis(cfg, time_freq); coherence = labelcmb: {0x2 cell} dimord: 'chancmb_freq_time' cohspctrm: [0x71x41 double] time: [1x41 double] freq: [1x71 double] cfg: [1x1 struct] >> coherence.labelcmb ans = Empty cell array: 0-by-2 >> coherence.cohspctrm ans = Empty array: 0-by-71-by-41 I have tried with fieldtrip versions 20161011 and 20171015 on matlab r2015a. I've shown this to various people much more experienced at fieldtrip than I and we've all been a bit stumped! Any ideas? Many thanks Rosa Taylor Beale -------------- next part -------------- An HTML attachment was scrubbed... URL: From TaylorBealeR at cardiff.ac.uk Fri Mar 30 17:52:14 2018 From: TaylorBealeR at cardiff.ac.uk (Rosa Taylor Beale) Date: Fri, 30 Mar 2018 15:52:14 +0000 Subject: [FieldTrip] Empty array in coherence connectivity analysis Message-ID: Hi all, I'm a final year undergraduate in Cardiff working on pain networks. I have been trying to calculate coherence between 3 seed regions, however when I run the ft_connectivityanalysis, the labelcmb and cohspctrm arrays are empty (the channel labels don't look like they were read?). There is no error or warning messages that occur when running the command, so I am unsure why it is not running correctly. First, I run ft_freqanalysis which seems to run fine: cfg = [] cfg.method = 'wavelet'; cfg.output = 'pow'; cfg.toi = 0:0.05:2; cfg.foi = [30:1:100]; time_freq= ft_freqanalysis(cfg, virtualchannel_raw); time_freq = label: {3x1 cell} dimord: 'chan_freq_time' freq: [1x71 double] time: [1x41 double] powspctrm: [3x71x41 double] cfg: [1x1 struct] Then I run the connectivity analysis and up with the empty output: cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'pfcCont_seed' 'smc_seed' 'pfcIps_seed' 'smc_seed' 'pfcCont_seed' 'pfcIps_seed'}; coherence = ft_connectivityanalysis(cfg, time_freq); coherence = labelcmb: {0x2 cell} dimord: 'chancmb_freq_time' cohspctrm: [0x71x41 double] time: [1x41 double] freq: [1x71 double] cfg: [1x1 struct] >> coherence.labelcmb ans = Empty cell array: 0-by-2 >> coherence.cohspctrm ans = Empty array: 0-by-71-by-41 I have tried with fieldtrip versions 20161011 and 20171015 on matlab r2015a. I've shown this to various people much more experienced at fieldtrip than I and we've all been a bit stumped! Any ideas? Many thanks Rosa Taylor Beale -------------- next part -------------- An HTML attachment was scrubbed... URL: From tobias.stdgl at gmail.com Fri Mar 30 18:00:49 2018 From: tobias.stdgl at gmail.com (Tobias Staudigl) Date: Fri, 30 Mar 2018 16:00:49 +0000 Subject: [FieldTrip] Empty array in coherence connectivity analysis In-Reply-To: References: Message-ID: Hi Taylor, First specify cfg.output = 'fourier' Or cfg.output ='powandcsd' in your ft_freqanalysis. Then try ft_connectivityanalysis again. Best, Tobias Am 30.03.2018 17:53 schrieb "Rosa Taylor Beale" : Hi all, I’m a final year undergraduate in Cardiff working on pain networks. I have been trying to calculate coherence between 3 seed regions, however when I run the ft_connectivityanalysis, the labelcmb and cohspctrm arrays are empty (the channel labels don’t look like they were read?). There is no error or warning messages that occur when running the command, so I am unsure why it is not running correctly. First, I run ft_freqanalysis which seems to run fine: cfg = [] cfg.method = 'wavelet'; cfg.output = 'pow'; cfg.toi = 0:0.05:2; cfg.foi = [30:1:100]; time_freq= ft_freqanalysis(cfg, virtualchannel_raw); time_freq = label: {3x1 cell} dimord: 'chan_freq_time' freq: [1x71 double] time: [1x41 double] powspctrm: [3x71x41 double] cfg: [1x1 struct] Then I run the connectivity analysis and up with the empty output: cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'pfcCont_seed' 'smc_seed' 'pfcIps_seed' 'smc_seed' 'pfcCont_seed' 'pfcIps_seed'}; coherence = ft_connectivityanalysis(cfg, time_freq); coherence = labelcmb: {0x2 cell} dimord: 'chancmb_freq_time' cohspctrm: [0x71x41 double] time: [1x41 double] freq: [1x71 double] cfg: [1x1 struct] >> coherence.labelcmb ans = Empty cell array: 0-by-2 >> coherence.cohspctrm ans = Empty array: 0-by-71-by-41 I have tried with fieldtrip versions 20161011 and 20171015 on matlab r2015a. I’ve shown this to various people much more experienced at fieldtrip than I and we’ve all been a bit stumped! Any ideas? Many thanks Rosa Taylor Beale _______________________________________________ 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 jan.schoffelen at donders.ru.nl Fri Mar 30 20:33:51 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 30 Mar 2018 18:33:51 +0000 Subject: [FieldTrip] Empty array in coherence connectivity analysis In-Reply-To: References: Message-ID: <90B1A8AF-87AA-480B-BEE7-DC9A7148780E@donders.ru.nl> Yes, and be sure that cfg.channelcmb is an Nx2 cell-array: {‘somechannel’ ‘someotherchannel’; ‘againsomechannel’ ‘someotherchannelaswell’; ‘etc’ ‘etc’} Best wishes, Jan-Mathijs On 30 Mar 2018, at 18:00, Tobias Staudigl > wrote: Hi Taylor, First specify cfg.output = 'fourier' Or cfg.output ='powandcsd' in your ft_freqanalysis. Then try ft_connectivityanalysis again. Best, Tobias Am 30.03.2018 17:53 schrieb "Rosa Taylor Beale" >: Hi all, I’m a final year undergraduate in Cardiff working on pain networks. I have been trying to calculate coherence between 3 seed regions, however when I run the ft_connectivityanalysis, the labelcmb and cohspctrm arrays are empty (the channel labels don’t look like they were read?). There is no error or warning messages that occur when running the command, so I am unsure why it is not running correctly. First, I run ft_freqanalysis which seems to run fine: cfg = [] cfg.method = 'wavelet'; cfg.output = 'pow'; cfg.toi = 0:0.05:2; cfg.foi = [30:1:100]; time_freq= ft_freqanalysis(cfg, virtualchannel_raw); time_freq = label: {3x1 cell} dimord: 'chan_freq_time' freq: [1x71 double] time: [1x41 double] powspctrm: [3x71x41 double] cfg: [1x1 struct] Then I run the connectivity analysis and up with the empty output: cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'pfcCont_seed' 'smc_seed' 'pfcIps_seed' 'smc_seed' 'pfcCont_seed' 'pfcIps_seed'}; coherence = ft_connectivityanalysis(cfg, time_freq); coherence = labelcmb: {0x2 cell} dimord: 'chancmb_freq_time' cohspctrm: [0x71x41 double] time: [1x41 double] freq: [1x71 double] cfg: [1x1 struct] >> coherence.labelcmb ans = Empty cell array: 0-by-2 >> coherence.cohspctrm ans = Empty array: 0-by-71-by-41 I have tried with fieldtrip versions 20161011 and 20171015 on matlab r2015a. I’ve shown this to various people much more experienced at fieldtrip than I and we’ve all been a bit stumped! Any ideas? Many thanks Rosa Taylor Beale _______________________________________________ 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 eduardobjacobi at gmail.com Thu Mar 1 14:57:53 2018 From: eduardobjacobi at gmail.com (Eduardo Bacelar) Date: Thu, 1 Mar 2018 10:57:53 -0300 Subject: [FieldTrip] Convert .PLX Message-ID: Hi, I am having problems with the conversion of .plx files, in my data I have spike and LFP data together, I now that is not possible to read this 2 types of data in the same function call, but is there any way were I am enable to only read LFP data and after that read Spike data? What I rely want to know is if is possible to read only a number of channels. Waiting for replay. Best rewards, -- Eduardo Bacelar Mestrando - Neuroengenharia Instituto Internacional de Neurociências - Edmond e Lily Safra . ------------------------------ Contact me: T: +55 (53) 8124-0032 Tw: @EddBacelar E: eduardobjacobi at gmail.com Fb: /eduardo.bacelar.89 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathalie.liegel at gmx.de Mon Mar 5 13:56:55 2018 From: nathalie.liegel at gmx.de (Nathalie Liegel) Date: Mon, 5 Mar 2018 13:56:55 +0100 Subject: [FieldTrip] Any German speaking cognitive neuroscientist interested in an exciting industry position? Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Anz-Stelle-A4-1802.pdf Type: application/pdf Size: 223494 bytes Desc: not available URL: From nelleke.van.wouwe at Vanderbilt.Edu Mon Mar 5 17:40:54 2018 From: nelleke.van.wouwe at Vanderbilt.Edu (Van Wouwe, Nelleke) Date: Mon, 5 Mar 2018 16:40:54 +0000 Subject: [FieldTrip] Postdoctoral Position University of Louisville Message-ID: <29540490A5680F42A88C5587547464E9F8CE83E2@ITS-HCWNEM108.ds.vanderbilt.edu> Postdoctoral Position A postdoctoral position is available in the Human Cognitive Neurophysiology Group (HCN) in the Department of Neurological Surgery at the University of Louisville School of Medicine. HCN (Drs. Neimat, van Wouwe, and Kaskan) investigates the neural correlates of cognition in the setting of human intraoperative recording and stimulation performed for the treatment of movement disorders and epilepsy. Our collaborative group pairs neuroscientists with physicians in a clinical research environment to provide rich opportunities for the novel exploration of brain function. Drs. Neimat and van Wouwe have recently been awarded a multi-site R01 (Louisville and Vanderbilt) entitled: Modulating Inhibitory Action Control Systems with Subthalamic Nucleus (STN) Stimulation. Dr. Kaskan has recently joined the group and is investigating the role of the STN in value-based decision-making. We are seeking to hire a postdoctoral fellow with a Ph.D. in neuroscience, engineering, computer science, cognitive psychology, the biomedical sciences, or a field related to neuroscience. Experience with the collection and analysis of single-unit neural recordings and/or local field potentials (human or animal) is required. Experience programming with MATLAB and familiarity with the Linux environment is highly encouraged. The best candidates will be experienced neurophysiologists interested in human cognition. The candidate is expected to be highly motivated, possess excellent presentation and interpersonal skills, an ability to troubleshoot technical neurophysiological issues, a demonstrated track record of publications and project completion, and the ability to work both independently and with others. Additional responsibilities include: manuscript and grant preparation, literature and manuscript review, presentations at local seminars and national meetings, and mentoring junior lab members. An initial appointment will be made for one year, with the possibility of extension based upon performance. Salary is commensurate with experience. The University of Louisville is a strong research environment and the postdoctoral fellow will have the opportunity to interact and collaborate with other departments including the Kentucky Spinal Cord Injury Research Center, the Department of Anatomical Sciences and Neurobiology, the Department of Psychological and Brain Sciences, and the JB Speed School of Engineering. The multi-site grant also provides the opportunity to work with the Neurology Department at Vanderbilt University Medical Center. The University of Louisville is an equal opportunity, affirmative action employer, and is committed to providing employment opportunities to all qualified applicants without regard to race, sex, age, color, national origin, ethnicity, creed, religion, disability, genetic information, sexual orientation, gender, gender identity and expression, marital status, pregnancy, or veteran status. Interested candidates should send a brief statement of research experience including interests and future objectives as well as a curriculum vitae, a reprint (.pdf) of an exemplar paper where they were an author, and the contact information for three professional references to peter.kaskan at ulp.org. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nico.boehler at ugent.be Tue Mar 6 08:31:18 2018 From: nico.boehler at ugent.be (=?Windows-1252?Q?Nico_B=F6hler?=) Date: Tue, 6 Mar 2018 07:31:18 +0000 Subject: [FieldTrip] 4 PhD student positions in Ghent, Belgium In-Reply-To: References: Message-ID: <1520321487503.74871@ugent.be> Four full-time PhD student positions are available at Ghent University. All are four-year positions (provided positive periodic evaluation), preferably starting in Sept or Oct 2018. Salary is according to standard Ghent University regulations for PhD students (starting at around €2000 per month net salary). Candidates should have a Master’s degree in Psychology, Cognitive Neuroscience, or similar. 1) Synchrony and coupling in procedural and declarative memory tasks This position is situated in the framework of an interuniversity project called “The journey of a memory: dynamics of learning and consolidation in maturation and ageing”, see www.eosprogramme.be Candidates are expected to carry out empirical work combining EEG, MEG, and computational modeling. Expertise in these methods is not required, but strong interest in cognitive neuroscience, data analysis, and computer programming are. As this is an interuniversity project it involves collaboration between three institutions. Supervisors will be Tom Verguts and Nico Boehler (Ghent University; main institution), in collaboration with Xavier De Tiège (Université Libre de Bruxelles) and Dante Mantini (KULeuven). More information about the project can be found here: https://sites.google.com/view/memodyn/homepage For applying, please send a CV (including two email addresses of academic referees) and motivation letter to Tom Verguts (tom.verguts at ugent.be). For further information on the project or details about the position, please also contact Tom Verguts. Applications will be considered until the position is filled. 2) Transfer of serial order information between working memory and long term memory This position is situated in the framework of an interuniversity project called “The journey of a memory: dynamics of learning and consolidation in maturation and ageing”, see www.eosprogramme.be Candidates are expected to carry out empirical work with fMRI and combined HD-EEG/MEG. Expertise in these methods is not required, but strong interest in cognitive neuroscience, data analysis, and computer programming are. As this is an interuniversity project it involves collaboration between three institutions. Supervisors at the Ghent University side is Wim Fias; at Université de Liège supervision is carried out by Steve Majerus at Université Libre de Bruxelles by Xavier De Tiège; at KULeuven, the supervisor is Dante Mantini. More information about the project can be found here: https://sites.google.com/view/memodyn/homepage For applying, please send a CV (including two email addresses of academic referees) and motivation letter to Wim Fias (wim.fias at ugent.be ; For further information on the project or details about the position, please also contact Wim Fias. Applications will be considered until the position is filled. 3) The role of the locus coeruleus in arousal regulation in ADHD This project is focused on arousal regulation in ADHD. There is a long tradition of explaining ADHD in terms of arousal regulation difficulties. While many studies found support for this, little is known about its underlying neurobiological substrates. The locus coeruleus (LC), a small nucleus in the brainstem, associated with arousal regulation, is a hypothesized candidate. In the current project, we will investigate the putative role of the LC in arousal regulation deficits in ADHD, by means of fMRI, EEG, and pupil measures. Expertise in these methods is not required but a great benefit. Strong interest in the combination of cognitive neuroscience and experimental-clinical research is required. Active knowledge of Dutch is a requirement (working with Flemish participants with ADHD). The main supervisor is Roeljan Wiersema (Dept. of Experimental Clinical and Health Psychology) and the co-supervisor is Nico Boehler (Department of Experimental Psychology). For applying, please send a CV (including two email addresses of academic referees, or referent letters) and motivation letter to Roeljan Wiersema (Roeljan.wiersema at ugent.be). For further information on the project or details about the position, please also contact Roeljan Wiersema. Applications will be considered until the position is filled. 4) Money well spent? A multi-modal investigation of context effects during and after a reward manipulation This project is focused on context effects of reward manipulations. Reward effects on cognitive functions have received a lot of scientific attention in the last years, usually finding that associating reward with a particular task ubiquitously improves performance. Yet, this work largely focused on transient reward effects using concurrent no-reward trials as the main comparison, and relatively little work has looked at potential costs of reward-based improvements. The present project aims at doing so by studying reward-context effects both during a reward manipulation (compared to no-reward trials from neutral task blocks) and after (most notably the “undermining effect”) to get a broader understanding of the costs and benefits of such manipulations. We will investigate the neurobiological implementation of these phenomena by using systematic behavioral testing in combination with electroencephalographic (EEG) and pupillometric measures. Experience with EEG and pupillometry are not required but would be a great benefit, as would be a background in programming experiments and analyzing experimental data. The main supervisor is Nico Boehler and the co-supervisor is Ruth Krebs. For applying, please send a CV (including two email addresses of academic referees) and motivation letter to Nico Boehler (nico.boehler at ugent.be), whom you can also contact for further information about the project or details about the position and procedure. Applications will be considered until the position is filled.? -------------- next part -------------- An HTML attachment was scrubbed... URL: From muthuraman10 at hotmail.com Fri Mar 9 16:20:08 2018 From: muthuraman10 at hotmail.com (Muthuraman Muthuraman) Date: Fri, 9 Mar 2018 15:20:08 +0000 Subject: [FieldTrip] PhD position on electrophysiology and cognition in multiple sclerosis patients! Message-ID: Doctoral Student Neuroscientist with focus on electrophysiology and cognition in multiple sclerosis The medical faculty of the University of Mainz, Germany, invites applications for a PhD Student for a functional translational neuroscience (FTN) scholarship three year position to work on electrophysiology and cognition in neuroimmunological disorders and multiple sclerosis. A project with multimodality usage of electroencephalography (EEG) and non-invasive brain stimulation technique like transcranial magnetic stimulation (TMS). The successful applicant holds a Master’s degree (or equivalent) in a relevant academic area such as basic life sciences, neuropsychology, applied mathematics or biomedical engineering or similar disciplines. German language proficiency is mandatory for communicating with the patients. The working language at the institute is English. Experience with electrophysiology and the analysis of brain signals is advantageous, but not essential. The applicant’s merits are assessed on the basis of the quality of Master’s level studies and thesis, previous experience with the brain imaging, motivation and research interests. The location for this research will mainly be the workgroups “Section of Movement Disorders, Neurostimulation and Neuroimaging“ of Prof. Sergiu Groppa at the Department of Neurology and “Multimodal Signal Processing and Statistical Analyses” of Prof. Muthuraman Muthuraman, both at the Focus Program Translational Neurosciences (http://www.ftn.uni-mainz.de/) and Neuroimaging Centre Mainz (http://www.ftn.nic.uni-mainz.de/). Expected close collaborations with national and international partners. The application should include a statement of research interests, a curriculum vitae (max. 4 pages) composed according to good scientific practice, a certificate of Master’s degree, copy of the master’s thesis and grades of Master’s level studies, the names and e-mail addresses of two referees and a proof of proficiency in English. The position will be open until filled. To apply for the position, please send the above documents as pdfs until 31.03.2018 to Prof. Sergiu Groppa, Department of Neurology, Section of movement disorders and neurostimulation, University of Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany, or by Email to segroppa(at)uni-mainz.de . For additional information please contact Sergiu Groppa. With regards M.Muthuraman Prof. Dr.- Ing. M.Muthuraman Biomedical statistics and multimodal signal processing unit Movement Disorders and Neurostimulation, Department of Neurology, Focus Program Translational Neuroscience (FTN) Johannes-Gutenberg-University Hospital, Langenbeckstr. 1 55131 Mainz, Germany Email: mmuthura at uni-mainz.de Website:http://www.tiefehirnstimulation.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From robpetrosino at gmail.com Sat Mar 10 22:28:56 2018 From: robpetrosino at gmail.com (Roberto Petrosino) Date: Sat, 10 Mar 2018 16:28:56 -0500 Subject: [FieldTrip] ft_definetrial() and ft_preprocessing() Message-ID: <50B52505-61C2-4807-9AB7-E7A21141765C@gmail.com> Hi all, I am trying to preprocess my eeg raw data (from BrainVision amplifiers), but I am having troubles with error I can’t figure out how to fix. Here’s the code: > clear; > clc; > > data_path = ‘/.../raw/'; > > %STEP 1: reading the data in > cfg = []; > cfg.dataset = [data_path ’subj1.vhdr']; > > %high-pass filter > cfg.preproc.hpfilter = 'yes'; > cfg.preproc.hpfiltord = 2; %known bug for filtering; can be avoided by changing the order of the filter (2 is random) > cfg.preproc.hpfreq = 0.1; %in Hz > > %rereference > cfg.preproc.reref = 'yes'; > cfg.preproc.channel = 'all'; > cfg.preproc.implicitref = ''; %on-line reference is empty > cfg.preproc.refchannel = {'M1', 'M2'}; %the channels we want to rereference our data against. In this > %case, we will rereference against the linked mastoids > > %updating channel locations; %% MPI/DCCN versions of actiCAP? > cfg.layout = '/Users/.../MATLAB/fieldtrip-master/template/layout/acticap-64ch-standard2.mat'; %the file we want to extract electrode coordinates from > > %demean > cfg.deman = 'yes'; > cfg.basewindow = [-.2 0]; > > %STEP 2: defining trials and epoching > cfg.trialdef.prestim = 0.2; > cfg.trialdef.poststim = 1; % epochs will be -200 1000 ms > cfg.trialdef.eventtype = 'Stimulus'; > cfg.trialfun = 'trialfun_congruency’; %customized function for the data > data_in = ft_definetrial(cfg); %this will create a trl structure field, which is a list > % of 3 columns, where every row describes a separate trial start, end and offset > data_prej = ft_preprocessing(cfg); This is the error that pops up: > Error using ft_preprocessing (line 387) > you must call FT_DEFINETRIAL prior to FT_PREPROCESSING which is weird, since ft_definetrial() is called right before ft_preprocessing(). Does anyone know what the problem could be? Thanks, -Roberto —— Roberto Petrosino PhD student in Linguistics CT Institute from Brain and Cognitive Sciences University of Connecticut -------------- next part -------------- An HTML attachment was scrubbed... URL: From ekenaykut at gmail.com Sat Mar 10 22:32:07 2018 From: ekenaykut at gmail.com (Aykut Eken) Date: Sun, 11 Mar 2018 00:32:07 +0300 Subject: [FieldTrip] ft_definetrial() and ft_preprocessing() In-Reply-To: <50B52505-61C2-4807-9AB7-E7A21141765C@gmail.com> References: <50B52505-61C2-4807-9AB7-E7A21141765C@gmail.com> Message-ID: >> data_in = ft_definetrial(cfg); %this will create a trl structure field, which is a list >> % of 3 columns, where every row describes a separate trial start, end and offset >> data_prej = ft_preprocessing(cfg); As far as I see, you must give the “data_in” as a input to ft_preprocessing. Regards Aykut Eken, PhD Düzce University Faculty of Engineering Biomedical Engineering Department Düzce University, Konuralp Campus, 81620, Konuralp, Düzce, Turkey Tel: +905366777364 Office Tel: +90380542 11 00 /4546 Mail address1: aykuteken at duzce.edu.tr Mail address2: ekenaykut at gmail.com > On 11 Mar 2018, at 00:28, Roberto Petrosino wrote: > > Hi all, > > I am trying to preprocess my eeg raw data (from BrainVision amplifiers), but I am having troubles with error I can’t figure out how to fix. Here’s the code: > >> clear; >> clc; >> >> data_path = ‘/.../raw/'; >> >> %STEP 1: reading the data in >> cfg = []; >> cfg.dataset = [data_path ’subj1.vhdr']; >> >> %high-pass filter >> cfg.preproc.hpfilter = 'yes'; >> cfg.preproc.hpfiltord = 2; %known bug for filtering; can be avoided by changing the order of the filter (2 is random) >> cfg.preproc.hpfreq = 0.1; %in Hz >> >> %rereference >> cfg.preproc.reref = 'yes'; >> cfg.preproc.channel = 'all'; >> cfg.preproc.implicitref = ''; %on-line reference is empty >> cfg.preproc.refchannel = {'M1', 'M2'}; %the channels we want to rereference our data against. In this >> %case, we will rereference against the linked mastoids >> >> %updating channel locations; %% MPI/DCCN versions of actiCAP? >> cfg.layout = '/Users/.../MATLAB/fieldtrip-master/template/layout/acticap-64ch-standard2.mat'; %the file we want to extract electrode coordinates from >> >> %demean >> cfg.deman = 'yes'; >> cfg.basewindow = [-.2 0]; >> >> %STEP 2: defining trials and epoching >> cfg.trialdef.prestim = 0.2; >> cfg.trialdef.poststim = 1; % epochs will be -200 1000 ms >> cfg.trialdef.eventtype = 'Stimulus'; >> cfg.trialfun = 'trialfun_congruency’; %customized function for the data >> data_in = ft_definetrial(cfg); %this will create a trl structure field, which is a list >> % of 3 columns, where every row describes a separate trial start, end and offset >> data_prej = ft_preprocessing(cfg); > > > This is the error that pops up: >> Error using ft_preprocessing (line 387) >> you must call FT_DEFINETRIAL prior to FT_PREPROCESSING > > > which is weird, since ft_definetrial() is called right before ft_preprocessing(). Does anyone know what the problem could be? > > Thanks, > -Roberto > > —— > Roberto Petrosino > PhD student in Linguistics > CT Institute from Brain and Cognitive Sciences > University of Connecticut > > _______________________________________________ > 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 a.stolk8 at gmail.com Sat Mar 10 22:35:24 2018 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Sat, 10 Mar 2018 13:35:24 -0800 Subject: [FieldTrip] ft_definetrial() and ft_preprocessing() In-Reply-To: References: <50B52505-61C2-4807-9AB7-E7A21141765C@gmail.com> Message-ID: Hi Roberto, ft_definetrial produces a cfg structure with a trl field that fr_preprocessing uses to read in the data segments of interest. conceptually, the order should be cfg = ft_definetrial(cfg) % do not clear cfg data = ft_preprocessing(cfg) Best, Arjen On Sat, Mar 10, 2018 at 1:32 PM, Aykut Eken wrote: > data_in = ft_definetrial(cfg); %this will create a > trl structure field, which is a list > % of 3 columns, where every row describes a separate trial start, end and > offset > data_prej = ft_preprocessing(cfg); > > > As far as I see, you must give the “data_in” as a input to > ft_preprocessing. > > Regards > > Aykut Eken, PhD > > Düzce University > Faculty of Engineering > Biomedical Engineering Department > > Düzce University, Konuralp Campus, > 81620, Konuralp, Düzce, Turkey > > Tel: +905366777364 <+90%20536%20677%2073%2064> > Office Tel: +90380542 11 00 /4546 > Mail address1: aykuteken at duzce.edu.tr > Mail address2: ekenaykut at gmail.com > > On 11 Mar 2018, at 00:28, Roberto Petrosino > wrote: > > Hi all, > > I am trying to preprocess my eeg raw data (from BrainVision amplifiers), > but I am having troubles with error I can’t figure out how to fix. Here’s > the code: > > clear; > clc; > > data_path = ‘/.../raw/'; > > %STEP 1: reading the data in > cfg = []; > cfg.dataset = [data_path ’subj1.vhdr']; > > %high-pass filter > cfg.preproc.hpfilter = 'yes'; > cfg.preproc.hpfiltord = 2; %known bug for filtering; can be avoided > by changing the order of the filter (2 is random) > cfg.preproc.hpfreq = 0.1; %in Hz > > %rereference > cfg.preproc.reref = 'yes'; > cfg.preproc.channel = 'all'; > cfg.preproc.implicitref = ''; %on-line reference is empty > cfg.preproc.refchannel = {'M1', 'M2'}; %the channels we want to > rereference our data against. In this > %case, we will rereference against the > linked mastoids > > %updating channel locations; %% MPI/DCCN versions of actiCAP? > cfg.layout = '/Users/.../MATLAB/fieldtrip-master/template/ > layout/acticap-64ch-standard2.mat'; %the file we want to extract > electrode coordinates from > > %demean > cfg.deman = 'yes'; > cfg.basewindow = [-.2 0]; > > %STEP 2: defining trials and epoching > cfg.trialdef.prestim = 0.2; > cfg.trialdef.poststim = 1; % epochs will be -200 1000 ms > cfg.trialdef.eventtype = 'Stimulus'; > cfg.trialfun = 'trialfun_congruency’; %customized > function for the data > data_in = ft_definetrial(cfg); %this will create a > trl structure field, which is a list > % of 3 columns, where every row describes a separate trial start, end and > offset > data_prej = ft_preprocessing(cfg); > > > > This is the error that pops up: > > Error using ft_preprocessing (line 387) > you must call FT_DEFINETRIAL prior to FT_PREPROCESSING > > > which is weird, since ft_definetrial() is called right *before * > ft_preprocessing(). Does anyone know what the problem could be? > > Thanks, > -Roberto > > —— > Roberto Petrosino > PhD student in Linguistics > CT Institute from Brain and Cognitive Sciences > University of Connecticut > > _______________________________________________ > 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 christine.blume at sbg.ac.at Sun Mar 11 18:21:20 2018 From: christine.blume at sbg.ac.at (Blume Christine) Date: Sun, 11 Mar 2018 17:21:20 +0000 Subject: [FieldTrip] Bayesian "follow-up" on Cluster-Based Permutation Tests Message-ID: Dear FT-Community, In the analysis of high-density EEG data for a recent manuscript (https://www.biorxiv.org/content/early/2017/12/06/187195) we have used the cluster-based permutation approach. While the reviewers commended the choice of this approach, one reviewer would like us to calculate a Bayesian measure in addition to the Monte Carlo p values. Does anyone have a recommendation how to best approach this, any "best practice" to share? It is quite easy to calculate a Bayes factor as a follow-up on classic t-tests for example (e.g. see here http://www.lifesci.sussex.ac.uk/home/Zoltan_Dienes/inference/Bayes.htm). However, even though the permutation approach uses a t-value as a test statistic, it is not a "t-test"... Best, Christine -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcarlapiastra at gmail.com Sun Mar 11 21:28:04 2018 From: mcarlapiastra at gmail.com (Maria Carla Piastra) Date: Sun, 11 Mar 2018 21:28:04 +0100 Subject: [FieldTrip] lh.volume not found Message-ID: Dear Fieldtrippers, I am running the pipeline described here: http://www.fieldtriptoolbox.org/tutorial/sourcemodel and it fails when running: /recon-all -finalsurfs -subjid Subject01/ lh.volume does not exist so far. How can I create it? Many thanks, Maria Carla -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.spaak at donders.ru.nl Mon Mar 12 10:19:24 2018 From: e.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 12 Mar 2018 10:19:24 +0100 Subject: [FieldTrip] Bayesian "follow-up" on Cluster-Based Permutation Tests In-Reply-To: References: Message-ID: Dear Christine, Bayes factors etc. are computed from the posterior distribution over some model parameters (e.g. means of Gaussians in the case analogous to the t-test). As the cluster-based permutation approach is inherently non-parametric (i.e. it tests the exchangeability of data beween conditions), I think it would be quite esoteric to try something Bayesian with the cluster test. I think your best bet would be to figure out *why* the reviewer wants this, and then come up with an alternative answer that does not depend on Bayesian measures. Of course, one could "zoom in" on the effect you found and compute parametric Bayesian stats for that region of interest, but that would constitute "double dipping" if you don't have an independent contrast. In case you find evidence in favour of a null effect (one circumstance under which reviewers might ask for Bayesian evidence), this approach and result might still be valid (as it goes against the bias introduced by the preselection). Best, Eelke On 11 March 2018 at 18:21, Blume Christine wrote: > Dear FT-Community, > > In the analysis of high-density EEG data for a recent manuscript > (https://www.biorxiv.org/content/early/2017/12/06/187195) we have used the > cluster-based permutation approach. While the reviewers commended the choice > of this approach, one reviewer would like us to calculate a Bayesian measure > in addition to the Monte Carlo p values. Does anyone have a recommendation > how to best approach this, any "best practice" to share? > > It is quite easy to calculate a Bayes factor as a follow-up on classic > t-tests for example (e.g. see here > http://www.lifesci.sussex.ac.uk/home/Zoltan_Dienes/inference/Bayes.htm). > However, even though the permutation approach uses a t-value as a test > statistic, it is not a "t-test"... > > Best, > Christine > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From abela.eugenio at gmail.com Mon Mar 12 11:10:55 2018 From: abela.eugenio at gmail.com (Eugenio Abela) Date: Mon, 12 Mar 2018 10:10:55 +0000 Subject: [FieldTrip] Bayesian "follow-up" on Cluster-Based Permutation Tests In-Reply-To: References: Message-ID: Hi Christine, If you want to try something Bayesian and only if you have strong a priori hypotheses for a particular effect in a specific data window of interest, you could extract values from that window and do Bayesian analyses in JASP (https://jasp-stats.org), which is really easy to use and has a range Bayesian alternatives for classical F- and t-tests available. Alternatively, but this is probably much more complicated and time-consuming, you could do full Bayesian analyses with SPM12 (http://www.fil.ion.ucl.ac.uk/spm/software/spm12/), which allows you to calculate posterior probabilities for scalp, scalp x frequency or scalp x time maps. This is a great way of assessing evidence in your data, but I think it’s less popular than permutation tests. You can convert between Fieldtrip and SPM formats using spm_eeg_ft2spm.m I totally agree with Eelke that doing Bayesian tests post-hoc, after you obtained convincing results with permutations, seems like unnecessary methodological flourish. Yet it’s often hard to argue with reviewers without compromising a bit. You might want to use one of the above e.g. for your most important analysis and show in the rebuttal that it doesn’t alter your conclusions (hopefully!). This should convince them that results are robust to methodological choices, and exempt you from having to recalculate the whole thing again. Hope that helps Eugenio On 12 Mar 2018, at 09:19, Eelke Spaak wrote: Dear Christine, Bayes factors etc. are computed from the posterior distribution over some model parameters (e.g. means of Gaussians in the case analogous to the t-test). As the cluster-based permutation approach is inherently non-parametric (i.e. it tests the exchangeability of data beween conditions), I think it would be quite esoteric to try something Bayesian with the cluster test. I think your best bet would be to figure out *why* the reviewer wants this, and then come up with an alternative answer that does not depend on Bayesian measures. Of course, one could "zoom in" on the effect you found and compute parametric Bayesian stats for that region of interest, but that would constitute "double dipping" if you don't have an independent contrast. In case you find evidence in favour of a null effect (one circumstance under which reviewers might ask for Bayesian evidence), this approach and result might still be valid (as it goes against the bias introduced by the preselection). Best, Eelke On 11 March 2018 at 18:21, Blume Christine wrote: > Dear FT-Community, > > In the analysis of high-density EEG data for a recent manuscript > (https://www.biorxiv.org/content/early/2017/12/06/187195) we have used the > cluster-based permutation approach. While the reviewers commended the choice > of this approach, one reviewer would like us to calculate a Bayesian measure > in addition to the Monte Carlo p values. Does anyone have a recommendation > how to best approach this, any "best practice" to share? > > It is quite easy to calculate a Bayes factor as a follow-up on classic > t-tests for example (e.g. see here > http://www.lifesci.sussex.ac.uk/home/Zoltan_Dienes/inference/Bayes.htm). > However, even though the permutation approach uses a t-value as a test > statistic, it is not a "t-test"... > > Best, > Christine > > > _______________________________________________ > 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 jasonseehochan at gmail.com Mon Mar 12 15:35:48 2018 From: jasonseehochan at gmail.com (Jason Chan) Date: Mon, 12 Mar 2018 14:35:48 +0000 Subject: [FieldTrip] EEG and shunts Message-ID: Dear Fieldtrippers, This is not a specific Frieldtrip question, but I am hoping you can answer it anyways. I am trying to design an eeg experiment with hydrocephalus patients. However, most will have multiple shunts. I realise this will likely have dramatic effects to the activation patterns. A quick Google search gave me some rather old papers. I am wondering what is the best way to compare their activity to controls? Also, I will have access to their MRIs. Can I use beamforming? Unfortunately, I don't have access to an MEG. Thanks in advance for any advise. Best, Jason -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsten.wolters at uni-muenster.de Mon Mar 12 16:39:36 2018 From: carsten.wolters at uni-muenster.de (Carsten Wolters) Date: Mon, 12 Mar 2018 16:39:36 +0100 Subject: [FieldTrip] EEG and shunts In-Reply-To: References: Message-ID: <1D143B1F-8649-49F6-9E90-7622E005F728@uni-muenster.de> Dear Jason, that is very interesting: (1) CSF: I would expect that in hydrocephalus you have a significant contribution of CSF, see https://www.ncbi.nlm.nih.gov/pubmed/23006805 and https://www.sciencedirect.com/science/article/pii/S1053811914005175?via%3Dihub (2) Effects of shunts have been investigated in this paper https://www.sciencedirect.com/science/article/pii/S1053811912004946?via%3Dihub You might then be interested to model your shunts and the possibly bigger CSF compartment by using e.g. the Fieldtrip-SimBio pipeline (corresponding paper has just been accepted): http://www.sci.utah.edu/~wolters/PaperWolters/2018/VorwerkOostenveldPiastraMagyariWolters_BiomedEngOnline_2018_accepted.pdf BR Carsten > Am 12.03.2018 um 15:35 schrieb Jason Chan : > > > Dear Fieldtrippers, > > This is not a specific Frieldtrip question, but I am hoping you can answer it anyways. I am trying to design an eeg experiment with hydrocephalus patients. However, most will have multiple shunts. I realise this will likely have dramatic effects to the activation patterns. A quick Google search gave me some rather old papers. I am wondering what is the best way to compare their activity to controls? Also, I will have access to their MRIs. Can I use beamforming? Unfortunately, I don't have access to an MEG. > > > Thanks in advance for any advise. > > Best, > Jason > > _______________________________________________ > 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 mcmackr at tcd.ie Tue Mar 13 00:24:02 2018 From: mcmackr at tcd.ie (Roisin McMackin) Date: Mon, 12 Mar 2018 23:24:02 +0000 Subject: [FieldTrip] Timecourse units in dipole fitting .dip.mom Message-ID: Hi, I'm wondering in the example given http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting what exactly do the x,y and z timecourses for each dipole represent if dip.mom is a combination of strength and orientation? In other words, what are the units of the .dip.mom field? Thanks for your help, Roisin -------------- next part -------------- An HTML attachment was scrubbed... URL: From pahran at gmail.com Tue Mar 13 22:30:35 2018 From: pahran at gmail.com (Junjie Wu) Date: Tue, 13 Mar 2018 17:30:35 -0400 Subject: [FieldTrip] FEM with DTI Message-ID: Hello Community, I am trying create an FEM model with anisotropic conductivity using DTI and T1 MPRAGE. I know we can use ft_prepare_headmodel by specifying method 'simbio' to achieve this. However, the tutorials on the FieldTrip website only provide an example using anatomical MRI. Any suggestions on how to use FieldTrip/Simbio for anisotropic modeling will be greatly appreciated. Thanks, Junjie -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.hindriks at vu.nl Wed Mar 14 10:26:53 2018 From: r.hindriks at vu.nl (Hindriks, R.) Date: Wed, 14 Mar 2018 09:26:53 +0000 Subject: [FieldTrip] PhD position in Statistics for Neuroscience Message-ID: PhD position in Statistics for Neuroscience at VU Amsterdam The Department of Mathematics of the Faculty of Science, Vrije Universiteit Amsterdam, invites applications for a PhD position in Statistics for Neuroscience (0.8/1.0 FTE). The position The department is seeking applicants for a PhD position in statistics for neuroscience. The PhD project concerns spatiotemporal modeling and analysis of resting-state brain dynamics and will be supervised by Dr. Rikkert Hindriks and Prof.dr. Mathisca de Gunst. The PhD position is co-funded by the national science foundation NWO. Tasks You will develop statistical methods for modeling and analysis of resting-state brain activity recorded with functional MRI, magnetoencephalography (MEG), electroencephalography (EEG), and electrocorticography (ECoG). The project focuses on spatiotemporal aspects of resting-state brain activity such as wave propagation and relevant mathematics includes Empirical Bayesian inference, simulation and analysis of large-scale biophysical models, and higher-order decomposition techniques. You will publish your results in quality peer-reviewed journals in the field, culminating in a PhD thesis to be defended in public. Aside from these research tasks, a minor part of the time will be spent on teaching duties within the Department of Mathematics. Requirements The candidate must be talented, ambitious and highly motivated, in possession of a MSc. degree in mathematics, physics, or a related area. Candidates should have a strong demonstrable background in mathematics, in particular in statistics. Experience with neuroimaging data (fMRI) or electrophysiology (EEG/MEG/ECoG) and programming (R, Matlab, Python) is considered an advantage. In addition, we require proficiency in reading and writing of scientific manuscripts in English. Further particulars The appointment will be initially for one year. After satisfactory evaluation of the initial appointment, it can be extended to a total duration of 4 years. The VU offers a broad and attractive package of employment conditions. The employment contract is governed by the Collective Labour Agreement (CAO) for Dutch universities. In addition to their salaries, staff members receive annual holiday pay and a year-end bonus. Staff members with a full-time contract (38 hours per week) are entitled to 29 days off. The VU also offers a good pension scheme via ABP. Further information about our employment conditions can be found on https://www.vu.nl/en/employment. Salary The salary will be in accordance with university regulations for academic personnel, and amounts to € 2.222,- gross per month in the first year up to € 2.840,- in the fourth year (salary scale 85) based on a full-time employment. Information For additional information please contact: Dr. Rikkert Hindriks phone: +31 20 59 87835 e-mail: r.hindriks at vu.nl website: https://research.vu.nl/en/persons/r-hindriks Application Applicants are requested to write a letter in which they describe their abilities and motivation, accompanied by a curriculum vitae, a list of courses plus their grades, and contact details of two or three references. Please send your application by e-mail before April 15, 2018 to: Dr. Rikkert Hindriks e-mail: r.hindriks at vu.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From annekathrinweise at gmail.com Thu Mar 15 12:50:46 2018 From: annekathrinweise at gmail.com (Annekathrin Weise) Date: Thu, 15 Mar 2018 12:50:46 +0100 Subject: [FieldTrip] Salzburg Mind Brain Annual Meeting - SAMBA2018 Message-ID: <858a5468-e2df-be7e-aca9-8732f3c1995f@gmail.com> Dear all, we are pleased to announce that the registration and abstract submission deadline for the *Salzburg Mind Brain Annual Meeting* (*SAMBA*) **has been extended to April 1st, 2018. The mission of SAMBA is to attract the most exciting researchers in the domain of cognitive neuroscience, including related fields (e.g., computational modeling, 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. Note that the *number of participants is limited* and only a *few places* are *left*. We encourage young (PhD) students and young Post Docs to take part in the**poster price competition. *Poster awards*, *worth EUR 250,- each*, are awarded to the *three best posters. * 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) For more information see the SAMBA website . 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 andrea.brovelli at univ-amu.fr Fri Mar 16 09:31:42 2018 From: andrea.brovelli at univ-amu.fr (Andrea Brovelli) Date: Fri, 16 Mar 2018 09:31:42 +0100 Subject: [FieldTrip] Call for PhD and Post-Doc positions at the Institute of Language, Communication and the Brain (Marseille, France) Message-ID: Three 2-year postdoc positions at Aix-Marseille/Avignon on Language, Communication and the Brain The Center of Excellence on Brain and Language (BLRI,www.blri.fr/ ) and the Institute of Language, Communication and the Brain (ILCB,http://www.ilcb.fr/) offer: *Three 2-year postdoc positions*on any topic that falls within the area of language, communication, brain and modelling. The BLRI-ILCB is located in Aix-en-Provence, Avignon and Marseille and regroups several research centers in linguistics, psychology, cognitive neuroscience, medicine, computer science, and mathematics. The scientific project, ideally interdisciplinary, should be supervised by at least one member of the BLRI/ILCB (seehttp://www.blri.fr/members.html) and should, if possible, involve two different laboratories of the institute. . Duration: 2 years (1 year, extendable for another year) . Monthly salary: ~2000 € net (depending on experience) HOW TO APPLY Candidates should first contact potential supervisor(s) among the members of the ILCB/BLRI. Below, you will finda list of potential projects and supervisors that will be given priority for this call. However , you can also apply to any subject, under the supervision of any ILCB/BLRI member (http://www.blri.fr/members.html.). When the research project is finalized and approved by the supervisor(s), the application must be sent to nadera.bureau at blri.fr . Two PhD grants at Aix-Marseille/Avignon on Language, Communication and the Brain The Center of Excellence on Brain and Language (BLRI,www.blri.fr/ ) and the Institute of Language, Communication and the Brain (ILCB,http://www.ilcb.fr/) award 2 PhD grants (3 years) on any topic that falls within the area of language, communication, brain and modelling. The BLRI-ILCB is located in Aix-en-Provence, Avignon and Marseille and regroups several research centers in linguistics, psychology, cognitive neuroscience, medicine, computer science, and mathematics. Interested candidates need to find one or more PhD supervisors amongst the members of the BRLI-ILCB Together with the supervisor(s), they would then need to write a 3-year PhD project. A priority is given to interdisciplinary co-directions and to projects that involve two different laboratories of the institute. Monthly salary: 1 685€ (1 368€ net) for a period of 3 years HOW TO APPLY Candidates should first contact potential supervisor(s) among the members of the ILCB/BLRI. Below, you will finda list of potential projects and supervisors that will be given priority for this call. However , you can also apply to any subject, under the supervision of any ILCB/BLRI member (http://www.blri.fr/members.html.). When the research project is finalized and approved by the supervisor(s), the application must be sent to nadera.bureau at blri.fr . -------------- next part -------------- An HTML attachment was scrubbed... URL: From jorn at artinis.com Mon Mar 19 09:07:49 2018 From: jorn at artinis.com (=?iso-8859-1?Q?J=F6rn_M._Horschig?=) Date: Mon, 19 Mar 2018 09:07:49 +0100 Subject: [FieldTrip] ESR / Doctoral student position in algorithm development Message-ID: <005f01d3bf59$5f82d280$1e887780$@artinis.com> Dear list, We have an open ESR position from a Marie Curie grant starting in September this year. The goal of the project is cleaning of fNIRS data from artefacts and extraction of physiological components such as heartbeat and respiration. We encourage of course publication of the algorithm and implementation of these algorithms in e.g. FieldTrip or other open source toolboxes to facilitate multimodal data analyses. The ESR will work in strong collaboration with the Donders Institute (Sabine Hunnius, Robert Oostenveld), but also with external universities in the EU and other companies (eye-tracking and motion-tracking). The ESR will be located at our company in the Netherlands. For more information, please see http://www.artinis.com/early-stage-researcher-esr-doctoral-student-1 If you have any questions regarding this position, please let me know. With best regards, Jörn -- Jörn M. Horschig, PhD Software Engineer & Project Leader NeuroGuard XS A Einsteinweg 17 6662PW Elst The Netherlands T +31 481 350 980 I www.artinis.com The information in this e-mail is confidential and intended solely for the person to whom it is addressed. If this message is not addressed to you, please be aware that you have no authorization to read this e-mail, to copy it, to furnish it to any person other than the addressee, or to use or misuse its content in any way whatsoever. Should you have received this e-mail by mistake, please bring this to the attention of the sender, after which you are kindly requested to destroy the original message. Sign up for our NIRS newsletter -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 9919 bytes Desc: not available URL: From noa1hc at gmail.com Mon Mar 19 21:51:08 2018 From: noa1hc at gmail.com (=?UTF-8?B?16DXldei15Qg15TXm9eU158=?=) Date: Mon, 19 Mar 2018 22:51:08 +0200 Subject: [FieldTrip] source grand average Message-ID: Hi all, I am working on source recognition. I used ft_sourcegrandavrage, but I could not plotting the results, because there is no 'anatomy' field. why is it happening? my code is- norm_source.pos=template_grid.pos norm_source.inside=template_grid.inside cfg.parameter = 'pow' cfg.keepindividual = 'yes' [grandavg] = ft_sourcegrandaverage(cfg, norm_source 1, norm_source 2) This generates a structure with the following fields: grandavg = pow: [2x7109137 double] coordsys: 'spm' dim: [181 217 181] inside: [6804x1 logical] pos: [6804x3 double] cfg: [1x1 struct] Thanks! Noa בלי וירוסים. www.avast.com <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Mon Mar 19 22:25:01 2018 From: julian.keil at gmail.com (Julian Keil) Date: Mon, 19 Mar 2018 22:25:01 +0100 Subject: [FieldTrip] source grand average In-Reply-To: References: Message-ID: <3188B927-9556-4575-B360-076E564C9296@gmail.com> Hi Noa, either use ft_sourceinterpolate to interpolate the grandaverage to a standard-MRI, or use the „surface“-option when plotting. Cheers, Julian ________________ Prof. Dr. Julian Keil Biologische Psychologie Olshausenstraße 62 - R. 306 24118 Kiel 0431 / 880 - 4872 http://www.biopsych.uni-kiel.de/ Klinik für Psychiatrie und Psychotherapie der Charité im St. Hedwig-Krankenhaus Große Hamburger Straße 5-11 10115 Berlin 030 / 2311 - 1879 www.multisensorymind.com > Am 19.03.2018 um 21:51 schrieb ⁨נועה הכהן⁩ <⁨noa1hc at gmail.com⁩>: > > Hi all, > I am working on source recognition. I used ft_sourcegrandavrage, but I could not plotting the results, because there is no 'anatomy' field. why is it happening? > > my code is- > norm_source.pos=template_grid.pos > norm_source.inside=template_grid.inside > cfg.parameter = 'pow' > cfg.keepindividual = 'yes' > [grandavg] = ft_sourcegrandaverage(cfg, norm_source 1, norm_source 2) > > This generates a structure with the following fields: > grandavg = > > pow: [2x7109137 double] > coordsys: 'spm' > dim: [181 217 181] > inside: [6804x1 logical] > pos: [6804x3 double] > cfg: [1x1 struct] > > Thanks! > Noa > > > בלי וירוסים. www.avast.com _______________________________________________ > 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: signature.asc Type: application/pgp-signature Size: 833 bytes Desc: Message signed with OpenPGP URL: From robpetrosino at gmail.com Tue Mar 20 02:56:16 2018 From: robpetrosino at gmail.com (Roberto Petrosino) Date: Mon, 19 Mar 2018 21:56:16 -0400 Subject: [FieldTrip] clarifications on the eeglab2fieldtrip function Message-ID: <512FE9BF-FFE5-4D4E-B961-B058729616EB@gmail.com> Hello fieldtrippers, can anyone clarify the usage of the argument fieldbox in the eeglab2fieldtrip function below? I don’t seem to find any relevant information anywhere. > eeglab2fieldtrip() - do this ... > > Usage: >> data = eeglab2fieldtrip( EEG, fieldbox, transform ); > > Inputs: > EEG - [struct] EEGLAB structure > fieldbox - ['preprocessing'|'freqanalysis'|'timelockanalysis'|'companalysis'] > transform - ['none'|'dipfit'] transform channel locations for DIPFIT > using the transformation matrix in the field > 'coord_transform' of the dipfit substructure of the EEG > structure. > Outputs: > data - FIELDTRIP structure Thanks, -Roberto ---------- Roberto Petrosino Ph.D. Student in Linguistics CT Institute for the Brain and Cognitive Sciences University of Connecticut -------------- next part -------------- An HTML attachment was scrubbed... URL: From noa1hc at gmail.com Tue Mar 20 06:33:21 2018 From: noa1hc at gmail.com (=?UTF-8?B?16DXldei15Qg15TXm9eU158=?=) Date: Tue, 20 Mar 2018 07:33:21 +0200 Subject: [FieldTrip] source grand average In-Reply-To: <3188B927-9556-4575-B360-076E564C9296@gmail.com> References: <3188B927-9556-4575-B360-076E564C9296@gmail.com> Message-ID: !Thanks :I tried to do this, and to used ft_sourcedescriptives but I got an error message Attempted to access sel(1); index out of bounds because numel(sel)=0. Error in ft_sourceinterpolate>my_interpn (line 688) ft_progress(sel(1)/num, 'interpolating %.1f%%\n', 100*sel(1)/num); Error in ft_sourceinterpolate (line 535) interp.inside( sel) = my_interpn(double(functional.inside), ax(sel), ay(sel), az(sel), 'nearest', cfg.feedback); Why? thanks, Noa. 2018-03-19 23:25 GMT+02:00 Julian Keil : > Hi Noa, > > either use ft_sourceinterpolate to interpolate the grandaverage to a > standard-MRI, or use the „surface“-option when plotting. > > Cheers, > > Julian > > ________________ > Prof. Dr. Julian Keil > > Biologische Psychologie > Olshausenstraße 62 - R. 306 > 24118 Kiel > > 0431 / 880 - 4872 > http://www.biopsych.uni-kiel.de/ > > Klinik für Psychiatrie und Psychotherapie > der Charité im St. Hedwig-Krankenhaus > Große Hamburger Straße 5-11 > 10115 Berlin > > 030 / 2311 - 1879 > www.multisensorymind.com > > Am 19.03.2018 um 21:51 schrieb ⁨נועה הכהן⁩ <⁨noa1hc at gmail.com⁩>: > > Hi all, > I am working on source recognition. I used ft_sourcegrandavrage, but I > could not plotting the results, because there is no 'anatomy' field. why is > it happening? > > my code is- > norm_source.pos=template_grid.pos > norm_source.inside=template_grid.inside > cfg.parameter = 'pow' > cfg.keepindividual = 'yes' > [grandavg] = ft_sourcegrandaverage(cfg, norm_source 1, norm_source 2) > > This generates a structure with the following fields: > > grandavg = > > pow: [2x7109137 double] > coordsys: 'spm' > dim: [181 217 181] > inside: [6804x1 logical] > pos: [6804x3 double] > cfg: [1x1 struct] > > > Thanks! > > Noa > > > > בלי > וירוסים. www.avast.com > > _______________________________________________ > 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 jan.schoffelen at donders.ru.nl Tue Mar 20 07:54:39 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 20 Mar 2018 06:54:39 +0000 Subject: [FieldTrip] clarifications on the eeglab2fieldtrip function In-Reply-To: <512FE9BF-FFE5-4D4E-B961-B058729616EB@gmail.com> References: <512FE9BF-FFE5-4D4E-B961-B058729616EB@gmail.com> Message-ID: <9205E207-C86E-4CC1-B407-5F612E8A431B@donders.ru.nl> I guess that this fieldbox should be string that specifies which type of data to return from the eeglab-structure. Best wishes, Jan-Mathijs On 20 Mar 2018, at 02:56, Roberto Petrosino > wrote: Hello fieldtrippers, can anyone clarify the usage of the argument fieldbox in the eeglab2fieldtrip function below? I don’t seem to find any relevant information anywhere. eeglab2fieldtrip() - do this ... Usage: >> data = eeglab2fieldtrip( EEG, fieldbox, transform ); Inputs: EEG - [struct] EEGLAB structure fieldbox - ['preprocessing'|'freqanalysis'|'timelockanalysis'|'companalysis'] transform - ['none'|'dipfit'] transform channel locations for DIPFIT using the transformation matrix in the field 'coord_transform' of the dipfit substructure of the EEG structure. Outputs: data - FIELDTRIP structure Thanks, -Roberto ---------- Roberto Petrosino Ph.D. Student in Linguistics CT Institute for the Brain and Cognitive Sciences University of Connecticut _______________________________________________ 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 M.Wimber at bham.ac.uk Tue Mar 20 10:01:38 2018 From: M.Wimber at bham.ac.uk (Maria Wimber) Date: Tue, 20 Mar 2018 09:01:38 +0000 Subject: [FieldTrip] 3-year postdoc at UoB, decoding mental states based on fMRI/EEG patterns Message-ID: Hi FieldTrip users We would like to bring this exciting postdoctoral position to the attention of potential applicants. Mindreading mindreading: Using multivariate pattern analysis to decode the neural basis of mental state ascription. The full time postdoctoral research fellow will work on this 3-year ESRC-funded project in the School of Psychology at the University of Birmingham, with Professor Ian Apperly and Dr Maria Wimber. The project will use advanced neuroimaging methods to test whether "social brain areas" that are active when we think about the minds of others actually encode information about what other people are thinking, or whether they control attention to information encoded elsewhere. Please address informal enquiries jointly to Ian Apperly and Maria Wimber. Online advert and application forms Centre for Human Brain Health Ian Apperly Maria Wimber -------------- next part -------------- An HTML attachment was scrubbed... URL: From panyl at psych.ac.cn Tue Mar 20 13:16:06 2018 From: panyl at psych.ac.cn (=?UTF-8?B?5r2Y5Lqa5Li9?=) Date: Tue, 20 Mar 2018 20:16:06 +0800 (GMT+08:00) Subject: [FieldTrip] fieldtrip Digest, Vol 88, Issue 12 In-Reply-To: References: Message-ID: <21109d8.a526.16243568722.Coremail.panyl@psych.ac.cn> > -----Original Messages----- > From: fieldtrip-request at science.ru.nl > Sent Time: 2018-03-20 19:00:02 (Tuesday) > To: fieldtrip at science.ru.nl > Cc: > Subject: fieldtrip Digest, Vol 88, Issue 12 > > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. source grand average (???? ????) > 2. Re: source grand average (Julian Keil) > 3. clarifications on the eeglab2fieldtrip function > (Roberto Petrosino) > 4. Re: source grand average (???? ????) > 5. Re: clarifications on the eeglab2fieldtrip function > (Schoffelen, J.M. (Jan Mathijs)) > 6. 3-year postdoc at UoB, decoding mental states based on > fMRI/EEG patterns (Maria Wimber) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 19 Mar 2018 22:51:08 +0200 > From: ???? ???? > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] source grand average > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi all, > I am working on source recognition. I used ft_sourcegrandavrage, but I > could not plotting the results, because there is no 'anatomy' field. why is > it happening? > > my code is- > norm_source.pos=template_grid.pos > norm_source.inside=template_grid.inside > cfg.parameter = 'pow' > cfg.keepindividual = 'yes' > [grandavg] = ft_sourcegrandaverage(cfg, norm_source 1, norm_source 2) > > This generates a structure with the following fields: > > grandavg = > > pow: [2x7109137 double] > coordsys: 'spm' > dim: [181 217 181] > inside: [6804x1 logical] > pos: [6804x3 double] > cfg: [1x1 struct] > > > Thanks! > > Noa > > > > ??? > ???????. www.avast.com > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 2 > Date: Mon, 19 Mar 2018 22:25:01 +0100 > From: Julian Keil > To: FieldTrip discussion list > Subject: Re: [FieldTrip] source grand average > Message-ID: <3188B927-9556-4575-B360-076E564C9296 at gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Noa, > > either use ft_sourceinterpolate to interpolate the grandaverage to a standard-MRI, or use the ?surface?-option when plotting. > > Cheers, > > Julian > > ________________ > Prof. Dr. Julian Keil > > Biologische Psychologie > Olshausenstra?e 62 - R. 306 > 24118 Kiel > > 0431 / 880 - 4872 > http://www.biopsych.uni-kiel.de/ > > Klinik f?r Psychiatrie und Psychotherapie > der Charit? im St. Hedwig-Krankenhaus > Gro?e Hamburger Stra?e 5-11 > 10115 Berlin > > 030 / 2311 - 1879 > www.multisensorymind.com > > > Am 19.03.2018 um 21:51 schrieb ????? ????? : > > > > Hi all, > > I am working on source recognition. I used ft_sourcegrandavrage, but I could not plotting the results, because there is no 'anatomy' field. why is it happening? > > > > my code is- > > norm_source.pos=template_grid.pos > > norm_source.inside=template_grid.inside > > cfg.parameter = 'pow' > > cfg.keepindividual = 'yes' > > [grandavg] = ft_sourcegrandaverage(cfg, norm_source 1, norm_source 2) > > > > This generates a structure with the following fields: > > grandavg = > > > > pow: [2x7109137 double] > > coordsys: 'spm' > > dim: [181 217 181] > > inside: [6804x1 logical] > > pos: [6804x3 double] > > cfg: [1x1 struct] > > > > Thanks! > > Noa > > > > > > ??? ???????. www.avast.com _______________________________________________ > > 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: signature.asc > Type: application/pgp-signature > Size: 833 bytes > Desc: Message signed with OpenPGP > URL: > > ------------------------------ > > Message: 3 > Date: Mon, 19 Mar 2018 21:56:16 -0400 > From: Roberto Petrosino > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] clarifications on the eeglab2fieldtrip function > Message-ID: <512FE9BF-FFE5-4D4E-B961-B058729616EB at gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello fieldtrippers, > > can anyone clarify the usage of the argument fieldbox in the eeglab2fieldtrip function below? I don?t seem to find any relevant information anywhere. > > > eeglab2fieldtrip() - do this ... > > > > Usage: >> data = eeglab2fieldtrip( EEG, fieldbox, transform ); > > > > Inputs: > > EEG - [struct] EEGLAB structure > > fieldbox - ['preprocessing'|'freqanalysis'|'timelockanalysis'|'companalysis'] > > transform - ['none'|'dipfit'] transform channel locations for DIPFIT > > using the transformation matrix in the field > > 'coord_transform' of the dipfit substructure of the EEG > > structure. > > Outputs: > > data - FIELDTRIP structure > > Thanks, > > -Roberto > > ---------- > Roberto Petrosino > Ph.D. Student in Linguistics > CT Institute for the Brain and Cognitive Sciences > University of Connecticut > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 4 > Date: Tue, 20 Mar 2018 07:33:21 +0200 > From: ???? ???? > To: FieldTrip discussion list > Subject: Re: [FieldTrip] source grand average > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > !Thanks > :I tried to do this, and to used ft_sourcedescriptives but I got an error > message > > Attempted to access sel(1); index out of bounds because numel(sel)=0. > > Error in ft_sourceinterpolate>my_interpn (line 688) > ft_progress(sel(1)/num, 'interpolating %.1f%%\n', 100*sel(1)/num); > > Error in ft_sourceinterpolate (line 535) > interp.inside( sel) = my_interpn(double(functional.inside), ax(sel), > ay(sel), az(sel), 'nearest', cfg.feedback); > > Why? > > thanks, Noa. > > > > 2018-03-19 23:25 GMT+02:00 Julian Keil : > > > Hi Noa, > > > > either use ft_sourceinterpolate to interpolate the grandaverage to a > > standard-MRI, or use the ?surface?-option when plotting. > > > > Cheers, > > > > Julian > > > > ________________ > > Prof. Dr. Julian Keil > > > > Biologische Psychologie > > Olshausenstra?e 62 - R. 306 > > 24118 Kiel > > > > 0431 / 880 - 4872 > > http://www.biopsych.uni-kiel.de/ > > > > Klinik f?r Psychiatrie und Psychotherapie > > der Charit? im St. Hedwig-Krankenhaus > > Gro?e Hamburger Stra?e 5-11 > > 10115 Berlin > > > > 030 / 2311 - 1879 > > www.multisensorymind.com > > > > Am 19.03.2018 um 21:51 schrieb ????? ????? : > > > > Hi all, > > I am working on source recognition. I used ft_sourcegrandavrage, but I > > could not plotting the results, because there is no 'anatomy' field. why is > > it happening? > > > > my code is- > > norm_source.pos=template_grid.pos > > norm_source.inside=template_grid.inside > > cfg.parameter = 'pow' > > cfg.keepindividual = 'yes' > > [grandavg] = ft_sourcegrandaverage(cfg, norm_source 1, norm_source 2) > > > > This generates a structure with the following fields: > > > > grandavg = > > > > pow: [2x7109137 double] > > coordsys: 'spm' > > dim: [181 217 181] > > inside: [6804x1 logical] > > pos: [6804x3 double] > > cfg: [1x1 struct] > > > > > > Thanks! > > > > Noa > > > > > > > > ??? > > ???????. www.avast.com > > > > _______________________________________________ > > 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: > > ------------------------------ > > Message: 5 > Date: Tue, 20 Mar 2018 06:54:39 +0000 > From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] clarifications on the eeglab2fieldtrip > function > Message-ID: <9205E207-C86E-4CC1-B407-5F612E8A431B at donders.ru.nl> > Content-Type: text/plain; charset="utf-8" > > I guess that this fieldbox should be string that specifies which type of data to return from the eeglab-structure. > Best wishes, > Jan-Mathijs > > > > > On 20 Mar 2018, at 02:56, Roberto Petrosino > wrote: > > Hello fieldtrippers, > > can anyone clarify the usage of the argument fieldbox in the eeglab2fieldtrip function below? I don?t seem to find any relevant information anywhere. > > eeglab2fieldtrip() - do this ... > > Usage: >> data = eeglab2fieldtrip( EEG, fieldbox, transform ); > > Inputs: > EEG - [struct] EEGLAB structure > fieldbox - ['preprocessing'|'freqanalysis'|'timelockanalysis'|'companalysis'] > transform - ['none'|'dipfit'] transform channel locations for DIPFIT > using the transformation matrix in the field > 'coord_transform' of the dipfit substructure of the EEG > structure. > Outputs: > data - FIELDTRIP structure > > Thanks, > > -Roberto > > ---------- > Roberto Petrosino > Ph.D. Student in Linguistics > CT Institute for the Brain and Cognitive Sciences > University of Connecticut > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 6 > Date: Tue, 20 Mar 2018 09:01:38 +0000 > From: Maria Wimber > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] 3-year postdoc at UoB, decoding mental states > based on fMRI/EEG patterns > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > Hi FieldTrip users > > We would like to bring this exciting postdoctoral position to the attention of potential applicants. > > Mindreading mindreading: Using multivariate pattern analysis to decode the neural basis of mental state ascription. The full time postdoctoral research fellow will work on this 3-year ESRC-funded project in the School of Psychology at the University of Birmingham, with Professor Ian Apperly and Dr Maria Wimber. The project will use advanced neuroimaging methods to test whether "social brain areas" that are active when we think about the minds of others actually encode information about what other people are thinking, or whether they control attention to information encoded elsewhere. Please address informal enquiries jointly to Ian Apperly and Maria Wimber. > > Online advert and application forms > Centre for Human Brain Health > Ian Apperly > Maria Wimber > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 88, Issue 12 > ***************************************** From diana-hime at yandex.ru Tue Mar 20 20:48:31 2018 From: diana-hime at yandex.ru (=?utf-8?B?LSDQlNC40LDQvdCw?=) Date: Tue, 20 Mar 2018 22:48:31 +0300 Subject: [FieldTrip] (no subject) Message-ID: <329671521575311@web9j.yandex.ru> An HTML attachment was scrubbed... URL: From davide.tabarelli at unitn.it Tue Mar 20 16:59:39 2018 From: davide.tabarelli at unitn.it (Davide Tabarelli) Date: Tue, 20 Mar 2018 16:59:39 +0100 Subject: [FieldTrip] Expressions of Interest for a Marie Sklodowksa - Curie Fellowship at CIMeC - University of Trento Message-ID: <690D12F4-748E-4389-888E-2D5D241B769A@unitn.it> Dear all, at this page a Call for Expressions of Interest in the Marie Sklodowksa - Curie Individual Fellowships has been published: https://www.unitn.it/ateneo/68640/cimec-call-for-expressions-of-interest-marie-sklodowksa-curie-individual-fellowships . The Center for Mind/Brain Sciences - CIMeC at the University of Trento (Italy) welcomes expressions of interest from excellent postdoctoral researchers to apply, jointly with a research supervisor from CIMeC, to the European Commission Marie Skłodowska- Curie Individual Fellowship. The Marie Skłodowska Curie Action is a funding scheme that supports researchers mobility: Individual Fellowships – European Fellowships may last 12-24 months involving a research project, advanced training and knowledge exchange at the host institution (CIMeC). It offers a competitive salary, mobility and family allowances plus a budget for research and training costs; applicants are expected to have an excellent CV and a strong publication record. Selected candidates will be offered both academic and administrative support from CIMeC faculty and the University of Trento Research Office with regards to the proposal development. Feel free to circulate this invitation to your networks. D. — Davide Tabarelli, Ph.D. MEG Physicist Center for Mind Brain Sciences (CIMeC) University of Trento, Via delle Regole, 101 38123 Mattarello (TN) Tel: +39 (0)461 283644 Italy From thomas.hartmann at th-ht.de Wed Mar 21 11:02:14 2018 From: thomas.hartmann at th-ht.de (Thomas Hartmann) Date: Wed, 21 Mar 2018 11:02:14 +0100 Subject: [FieldTrip] doing ica on magnetometers and gradiometers Message-ID: <10159d5d-525d-5769-ac9a-3bec4483ef38@th-ht.de> hi, we have had a vivid discussion in our group concerning whether apply ICA to magnetometers and gradiometers in one go (i.e. lumping them together) or whether it is necessary to apply the ICA on mags ands grads separately. most approaches that can be found on the internet seem to favor the do-it-in-one-go way. my main concern with applying it to both sensor types at the same time is that the resulting components will probably be a linear mixture of both sensor types. when i reject some components and the project the components back to the sensor space, gradiometer activity should "leak" into the magnetometer data and vice versa. or am i wrong with my thoughts? or does it just not matter at all? i am looking forward to reading your thoughts! best, thomas -- Dr. Thomas Hartmann Centre for Cognitive Neuroscience FB Psychologie Universität Salzburg Hellbrunnerstraße 34/II 5020 Salzburg Tel: +43 662 8044 5109 Email: thomas.hartmann at th-ht.de "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle) From diana-hime at yandex.ru Sat Mar 24 21:25:01 2018 From: diana-hime at yandex.ru (=?utf-8?B?LSDQlNC40LDQvdCw?=) Date: Sat, 24 Mar 2018 23:25:01 +0300 Subject: [FieldTrip] preprocessing error "Index exceeds matrix dimensions error" Message-ID: <3814791521923101@web25o.yandex.ru> An HTML attachment was scrubbed... URL: From weiwuneuro at gmail.com Mon Mar 26 02:55:14 2018 From: weiwuneuro at gmail.com (Wei Wu) Date: Sun, 25 Mar 2018 17:55:14 -0700 Subject: [FieldTrip] Faculty jobs in brain stimulation at Stanford University Message-ID: To whom it may concern, I wanted to share a link to this job posting for those who are interested: http://med.stanford.edu/content/dam/sm/psychiatry/documents/about_us/ FacultyJobs/BrainStimulation.pdf -------------- next part -------------- An HTML attachment was scrubbed... URL: From giulia.lioi at inria.fr Mon Mar 26 18:52:11 2018 From: giulia.lioi at inria.fr (Giulia Lioi) Date: Mon, 26 Mar 2018 18:52:11 +0200 (CEST) Subject: [FieldTrip] siemens_gui_streamer prisma scanner Message-ID: <1835860202.156994.1522083131598.JavaMail.zimbra@inria.fr> To whom it may concern, I am having some problems using the siemens_gui_streamer with a recently installed Siemens prisma scanner. I was using a custom script to extract the mrprot.txt and I tried to keep the same information I was getting from the mrprot of the verio scanner. When I try to run the gui_streamer with the new mrprot however it automatically closes after the first scan, while with the old protocol is working.., HAs anyone had a similar problem? Can you help with this? Many thanks Giulia Lioi, PhD | Engineer R&D Visages-Hybrid teams Univ Rennes, Inria, CNRS, IRISA F-35000 Rennes Tel: 0033 767466577 -------------- next part -------------- An HTML attachment was scrubbed... URL: From steva_fernandes at yahoo.com Tue Mar 27 07:31:22 2018 From: steva_fernandes at yahoo.com (steven fernandes) Date: Tue, 27 Mar 2018 05:31:22 +0000 (UTC) Subject: [FieldTrip] Source localization in 4D data References: <1446487794.148989.1522128682247.ref@mail.yahoo.com> Message-ID: <1446487794.148989.1522128682247@mail.yahoo.com> Dear Researchers, I have 4D data at resting state (link given below) https://www.dropbox.com/s/rwzbaz7ame99gt7/2.zip?dl=0 I want to use above data to perform source localization of the spikes that appear during resting state for epileptic patient. Can you please help me how could I implement it using FieldTrip.  I am new to FieldTrip and I would greatly appreciate your help. Regards,Steven  -------------- next part -------------- An HTML attachment was scrubbed... URL: From mathis.kaiser at charite.de Tue Mar 27 12:53:47 2018 From: mathis.kaiser at charite.de (Mathis Kaiser) Date: Tue, 27 Mar 2018 12:53:47 +0200 Subject: [FieldTrip] [ext] preprocessing error "Index exceeds matrix dimensions error" In-Reply-To: <3814791521923101@web25o.yandex.ru> References: <3814791521923101@web25o.yandex.ru> Message-ID: <34f5c673-ae4d-f279-01cd-5f2d8219ebb9@charite.de> Hi Diana, is it possible that you already segmented the data in NetStation? The header indicates 98 trials. I have no experience with EGI files, but is there an option to export the continuous data? If you want to define your trials in fieldtrip, this makes more sense. Best, Mathis On 24.03.2018 21:25, - Диана wrote: >   > Dear Fildtrippers, >      > My name is Diana, I'm new to Fieldtrip and curently trying to learn > how process eeg data >      > I have a .raw file, exported from NetStation > I'm using Matlab 2014b, and the latest version of fieldtrip. >   >   > [my definetria]: >   > events = ft_read_event('01 wordA 27-09.raw') > FileName = '01 wordA 27-09.raw'; >  cfg                         = []; >   cfg.dataset                 = FileName; >   cfg.trialdef.eventtype      = 'trigger'; >   cfg.trialdef.eventvalue     = 'tim0'; % здесь то значение, которое нужно >   cfg.trialdef.prestim        = 0.2; % интервал до стимула >   cfg.trialdef.poststim       = 0.8; % интервал после стимула >   >   cfg = ft_definetrial(cfg); >   >   > after this, I try >   > [preprocessing]: >   > cfg = [] > cfg.dataset = FileName > cfg.channel = 'EEG' > cfg.continuous   = 'no' > raw_data  = ft_preprocessing(cfg) >   > And get such error: >   > reading and preprocessing > reading and preprocessing trial 2 from 98 > Index exceeds matrix dimensions. >   > Error in read_sbin_data (line 121) >         eventData(:,1:NSamples)  = temp( >         (NChan+1):(NChan+NEvent), 1:NSamples); >   > Error in ft_read_data (line 737) >       dat = read_sbin_data(filename, hdr, begtrial, >       endtrial, chanindx); >   > Error in ft_preprocessing (line 573) >       dat = ft_read_data(cfg.datafile, 'header', hdr, >       'begsample', begsample, 'endsample', endsample, >       'chanindx', rawindx, 'checkboundary', >       strcmp(cfg.continuous, 'no'), 'dataformat', >       cfg.dataformat); >   > Error in preproc_try (line 3) > raw_data  = ft_preprocessing(cfg) >   > Error in run (line 63) > evalin('caller', [script ';']); >   > Could you help me to understand how to manage this, please? >   > Example file: > https://drive.google.com/open?id=1c5RYxL9Br1Q5LTkedBD_dR4Ns72Vb9J5 >   > Thank you for your answers! >   >   > With best wishes, Diana > Undergraduate Student > Department of Biology of MSU >   > P.S. Sorry for having this letter sent again, the first attempt failed > strangely. > > > _______________________________________________ > 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 diana-hime at yandex.ru Wed Mar 28 04:25:52 2018 From: diana-hime at yandex.ru (=?utf-8?B?LSDQlNC40LDQvdCw?=) Date: Wed, 28 Mar 2018 05:25:52 +0300 Subject: [FieldTrip] [ext] preprocessing error "Index exceeds matrix dimensions error" In-Reply-To: <34f5c673-ae4d-f279-01cd-5f2d8219ebb9@charite.de> References: <3814791521923101@web25o.yandex.ru> <34f5c673-ae4d-f279-01cd-5f2d8219ebb9@charite.de> Message-ID: <1472741522203952@web37j.yandex.ru> An HTML attachment was scrubbed... URL: From lindseyrtate at ou.edu Wed Mar 28 09:30:23 2018 From: lindseyrtate at ou.edu (Tate, Lindsey R.) Date: Wed, 28 Mar 2018 07:30:23 +0000 Subject: [FieldTrip] ft_read_header and ft_definetrial errors Message-ID: Hello fieldtrip community, I have a dataset I've been working with in EEGLAB, but I am now trying to use it in Fieldtrip. The dataset is a concatenation of extracted epochs from multiple participants. The data imports fine as an EDF. However, EEGLAB's formatting for epochs means that there aren't triggers in the data. I have made my own header and trigger files in BrainVision format (I did it this way because I had BrainVision files to mimic, and it's listed on http://www.fieldtriptoolbox.org/reference/ft_read_header as an acceptable format). My events read in fine with the *.vmrk file I have. My problem is that I haven't figured out how to read in the *.vhdr file I have successfully. When I've tried to read it in, it gives me an error that it can't identify the dataset that the header goes with. Without it, I get the error below that *.vmrk isn't an accepted header file format. I have two questions: (1) Am I right in my interpretation that the error I'm getting below is because I haven't read in the *.vhdr header file? If that's not correct, what does the error mean? (2) How can I read in the *.vhdr header file I have? The following is the code: %%file information AMBB = 'AM'; stimfreq = '6'; pathway = 'Z:\BB\Preprocessing\'; datafile = [pathway AMBB stimfreq '_3s_avgepoch_5.edf']; eventfile = [pathway AMBB stimfreq '_3s_avgepoch_5_ftevents.vmrk'] ; hdrfile = [pathway AMBB stimfreq '_3s_avgepoch_5_ftevents.vhdr']; output6 = [pathway AMBB stimfreq '_dics6.mat']; output12 = [pathway AMBB stimfreq '_dics12.mat']; output25 = [pathway AMBB stimfreq '_dics25.mat']; output50 = [pathway AMBB stimfreq '_dics50.mat']; %%read in events [event] = ft_read_event(eventfile); %%define trials cfg = []; cfg.trialdef.eventvalue = 2 ; cfg.trialdef.prestim = 1 ; cfg.trialdef.poststim = 3 ; cfg.dataset = eventfile ; cfg.trialfun = 'ft_trialfun_general'; [cfg] = ft_definetrial(cfg); The following is the output: evaluating trialfunction 'ft_trialfun_general' Error using ft_notification (line 340) unsupported header format "brainvision_vmrk" Error in ft_error (line 39) ft_notification(varargin{:}); Error in ft_read_header (line 2478) ft_error('unsupported header format "%s"', headerformat); Error in ft_trialfun_general (line 78) hdr = ft_read_header(cfg.headerfile, 'headerformat', cfg.headerformat); Error in ft_definetrial (line 178) [trl, event] = feval(cfg.trialfun, cfg); /// The *.vhdr and *.vmrk files are attached for reference. Thank you for any help or insight you can provide. Lindsey Tate PhD Candidate University of Oklahoma lindseyrtate at ou.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: AM6_3s_avgepoch_5_ftevents.vmrk Type: application/octet-stream Size: 42028 bytes Desc: AM6_3s_avgepoch_5_ftevents.vmrk URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: AM6_3s_avgepoch_5_ftevents.vhdr Type: application/octet-stream Size: 9763 bytes Desc: AM6_3s_avgepoch_5_ftevents.vhdr URL: From edauer1 at gmail.com Thu Mar 29 19:02:44 2018 From: edauer1 at gmail.com (Ed Auer) Date: Thu, 29 Mar 2018 13:02:44 -0400 Subject: [FieldTrip] Using a condition-average baseline normalization for display of TFR Message-ID: I am using Fieldtrip to conduct time frequency analyses on an EEG dataset that has 2 factors each with multiple levels. I would like be able to display the data within a factor/level relative to a baseline computed using the average over levels and factors. Currently, to plot relative to the condition/level specific baseline I am using. cfg = []; cfg.baseline = [-0.5 0.5]; cfg.baselinetype = 'relative'; cfg.zlim = 'maxmin'; cfg.ylim = [8 12]; cfg.layout = 'acticap-64ch-standard2.mat'; cfg.xlim = [-0.5:0.05:.5]; cfg.comment = 'xlim'; cfg.commentpos = 'title'; f1 = figure; ft_topoplotTFR(cfg, GABDCLRtfr) Reading through the documentation I do not see any way to specify a baseline from a different TFR. Have I missed something or is it necessary to compute the baseline normalization directly and then plot as absolute data? Thanks, --Ed Auer -------------- next part -------------- An HTML attachment was scrubbed... URL: From TaylorBealeR at cardiff.ac.uk Fri Mar 30 17:40:26 2018 From: TaylorBealeR at cardiff.ac.uk (Rosa Taylor Beale) Date: Fri, 30 Mar 2018 15:40:26 +0000 Subject: [FieldTrip] Empty array in coherence connectivity analysis Message-ID: Hi all, I'm a final year undergraduate in Cardiff working on pain networks. I have been trying to calculate coherence between 3 seed regions, however when I run the ft_connectivityanalysis, the labelcmb and cohspctrm arrays are empty (the channel labels don't look like they were read?). There is no error or warning messages that occur when running the command, so I am unsure why it is not running correctly. First, I run ft_freqanalysis which seems to run fine: cfg = [] cfg.method = 'wavelet'; cfg.output = 'pow'; cfg.toi = 0:0.05:2; cfg.foi = [30:1:100]; time_freq= ft_freqanalysis(cfg, virtualchannel_raw); time_freq = label: {3x1 cell} dimord: 'chan_freq_time' freq: [1x71 double] time: [1x41 double] powspctrm: [3x71x41 double] cfg: [1x1 struct] Then I run the connectivity analysis and up with the empty output: cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'pfcCont_seed' 'smc_seed' 'pfcIps_seed' 'smc_seed' 'pfcCont_seed' 'pfcIps_seed'}; coherence = ft_connectivityanalysis(cfg, time_freq); coherence = labelcmb: {0x2 cell} dimord: 'chancmb_freq_time' cohspctrm: [0x71x41 double] time: [1x41 double] freq: [1x71 double] cfg: [1x1 struct] >> coherence.labelcmb ans = Empty cell array: 0-by-2 >> coherence.cohspctrm ans = Empty array: 0-by-71-by-41 I have tried with fieldtrip versions 20161011 and 20171015 on matlab r2015a. I've shown this to various people much more experienced at fieldtrip than I and we've all been a bit stumped! Any ideas? Many thanks Rosa Taylor Beale -------------- next part -------------- An HTML attachment was scrubbed... URL: From TaylorBealeR at cardiff.ac.uk Fri Mar 30 17:52:14 2018 From: TaylorBealeR at cardiff.ac.uk (Rosa Taylor Beale) Date: Fri, 30 Mar 2018 15:52:14 +0000 Subject: [FieldTrip] Empty array in coherence connectivity analysis Message-ID: Hi all, I'm a final year undergraduate in Cardiff working on pain networks. I have been trying to calculate coherence between 3 seed regions, however when I run the ft_connectivityanalysis, the labelcmb and cohspctrm arrays are empty (the channel labels don't look like they were read?). There is no error or warning messages that occur when running the command, so I am unsure why it is not running correctly. First, I run ft_freqanalysis which seems to run fine: cfg = [] cfg.method = 'wavelet'; cfg.output = 'pow'; cfg.toi = 0:0.05:2; cfg.foi = [30:1:100]; time_freq= ft_freqanalysis(cfg, virtualchannel_raw); time_freq = label: {3x1 cell} dimord: 'chan_freq_time' freq: [1x71 double] time: [1x41 double] powspctrm: [3x71x41 double] cfg: [1x1 struct] Then I run the connectivity analysis and up with the empty output: cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'pfcCont_seed' 'smc_seed' 'pfcIps_seed' 'smc_seed' 'pfcCont_seed' 'pfcIps_seed'}; coherence = ft_connectivityanalysis(cfg, time_freq); coherence = labelcmb: {0x2 cell} dimord: 'chancmb_freq_time' cohspctrm: [0x71x41 double] time: [1x41 double] freq: [1x71 double] cfg: [1x1 struct] >> coherence.labelcmb ans = Empty cell array: 0-by-2 >> coherence.cohspctrm ans = Empty array: 0-by-71-by-41 I have tried with fieldtrip versions 20161011 and 20171015 on matlab r2015a. I've shown this to various people much more experienced at fieldtrip than I and we've all been a bit stumped! Any ideas? Many thanks Rosa Taylor Beale -------------- next part -------------- An HTML attachment was scrubbed... URL: From tobias.stdgl at gmail.com Fri Mar 30 18:00:49 2018 From: tobias.stdgl at gmail.com (Tobias Staudigl) Date: Fri, 30 Mar 2018 16:00:49 +0000 Subject: [FieldTrip] Empty array in coherence connectivity analysis In-Reply-To: References: Message-ID: Hi Taylor, First specify cfg.output = 'fourier' Or cfg.output ='powandcsd' in your ft_freqanalysis. Then try ft_connectivityanalysis again. Best, Tobias Am 30.03.2018 17:53 schrieb "Rosa Taylor Beale" : Hi all, I’m a final year undergraduate in Cardiff working on pain networks. I have been trying to calculate coherence between 3 seed regions, however when I run the ft_connectivityanalysis, the labelcmb and cohspctrm arrays are empty (the channel labels don’t look like they were read?). There is no error or warning messages that occur when running the command, so I am unsure why it is not running correctly. First, I run ft_freqanalysis which seems to run fine: cfg = [] cfg.method = 'wavelet'; cfg.output = 'pow'; cfg.toi = 0:0.05:2; cfg.foi = [30:1:100]; time_freq= ft_freqanalysis(cfg, virtualchannel_raw); time_freq = label: {3x1 cell} dimord: 'chan_freq_time' freq: [1x71 double] time: [1x41 double] powspctrm: [3x71x41 double] cfg: [1x1 struct] Then I run the connectivity analysis and up with the empty output: cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'pfcCont_seed' 'smc_seed' 'pfcIps_seed' 'smc_seed' 'pfcCont_seed' 'pfcIps_seed'}; coherence = ft_connectivityanalysis(cfg, time_freq); coherence = labelcmb: {0x2 cell} dimord: 'chancmb_freq_time' cohspctrm: [0x71x41 double] time: [1x41 double] freq: [1x71 double] cfg: [1x1 struct] >> coherence.labelcmb ans = Empty cell array: 0-by-2 >> coherence.cohspctrm ans = Empty array: 0-by-71-by-41 I have tried with fieldtrip versions 20161011 and 20171015 on matlab r2015a. I’ve shown this to various people much more experienced at fieldtrip than I and we’ve all been a bit stumped! Any ideas? Many thanks Rosa Taylor Beale _______________________________________________ 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 jan.schoffelen at donders.ru.nl Fri Mar 30 20:33:51 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 30 Mar 2018 18:33:51 +0000 Subject: [FieldTrip] Empty array in coherence connectivity analysis In-Reply-To: References: Message-ID: <90B1A8AF-87AA-480B-BEE7-DC9A7148780E@donders.ru.nl> Yes, and be sure that cfg.channelcmb is an Nx2 cell-array: {‘somechannel’ ‘someotherchannel’; ‘againsomechannel’ ‘someotherchannelaswell’; ‘etc’ ‘etc’} Best wishes, Jan-Mathijs On 30 Mar 2018, at 18:00, Tobias Staudigl > wrote: Hi Taylor, First specify cfg.output = 'fourier' Or cfg.output ='powandcsd' in your ft_freqanalysis. Then try ft_connectivityanalysis again. Best, Tobias Am 30.03.2018 17:53 schrieb "Rosa Taylor Beale" >: Hi all, I’m a final year undergraduate in Cardiff working on pain networks. I have been trying to calculate coherence between 3 seed regions, however when I run the ft_connectivityanalysis, the labelcmb and cohspctrm arrays are empty (the channel labels don’t look like they were read?). There is no error or warning messages that occur when running the command, so I am unsure why it is not running correctly. First, I run ft_freqanalysis which seems to run fine: cfg = [] cfg.method = 'wavelet'; cfg.output = 'pow'; cfg.toi = 0:0.05:2; cfg.foi = [30:1:100]; time_freq= ft_freqanalysis(cfg, virtualchannel_raw); time_freq = label: {3x1 cell} dimord: 'chan_freq_time' freq: [1x71 double] time: [1x41 double] powspctrm: [3x71x41 double] cfg: [1x1 struct] Then I run the connectivity analysis and up with the empty output: cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'pfcCont_seed' 'smc_seed' 'pfcIps_seed' 'smc_seed' 'pfcCont_seed' 'pfcIps_seed'}; coherence = ft_connectivityanalysis(cfg, time_freq); coherence = labelcmb: {0x2 cell} dimord: 'chancmb_freq_time' cohspctrm: [0x71x41 double] time: [1x41 double] freq: [1x71 double] cfg: [1x1 struct] >> coherence.labelcmb ans = Empty cell array: 0-by-2 >> coherence.cohspctrm ans = Empty array: 0-by-71-by-41 I have tried with fieldtrip versions 20161011 and 20171015 on matlab r2015a. I’ve shown this to various people much more experienced at fieldtrip than I and we’ve all been a bit stumped! Any ideas? Many thanks Rosa Taylor Beale _______________________________________________ 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: