From michak at is.umk.pl Fri Dec 1 15:57:57 2017 From: michak at is.umk.pl (=?UTF-8?Q?Micha=C5=82_Komorowski?=) Date: Fri, 1 Dec 2017 23:57:57 +0900 Subject: [FieldTrip] non-existent mat in BEM headmodel Message-ID: When I had a problem with dipoli I have done this: If there is a problem with not finding file dipoli.glnx86 even if it exist in proper location, just install gcc-multilib package. refer to: - https://bbs.archlinux.org/viewtopic.php?id=131156 (about problem) - https://stackoverflow.com/questions/23970684/how-to-install-32-bit-glibc-on-64-bit-ubuntu (installing) So maybe try to install it and run again. Michał Komorowski -------------- next part -------------- An HTML attachment was scrubbed... URL: From boukje.habets at uni-bielefeld.de Tue Dec 5 10:55:28 2017 From: boukje.habets at uni-bielefeld.de (Boukje Habets) Date: Tue, 05 Dec 2017 10:55:28 +0100 Subject: [FieldTrip] Question about segmentation Message-ID: <71c0e7f647c8c.5a267b20@uni-bielefeld.de> Dear Fieldtrippers, Im new to Fieldtrip and have a question about segmentation. I want to do a freqanalysis on EEG data (Brainvision Recorder). I have one file per condition (so only containing one trigger code, and a start code at the beginning of the file) that i want to segment into 2sec pieces. Ive been trying to find a way to add a trigger with Fieldtrip, so that I can segment around a new trigger. Using a pre- and poststim timewindow around the trigger code is not a solution, as this gives me overlapping segments, which i do not want. This doesnt seem possible? After reading about cfg.trialfun, I saw that i can segment a continuous file into segments that i can define in terms of length (sec/samples). I guess this is the easiest way for me to segment my file. However, i want to be able to define the start and end point of segmentation, as my file contains a part in the beginning without codes (EEG was being recorded, but experiment was running yet). I have been playing around with the commands begsample and endsample, but that didnt change the window of segmentation (meaning it always segments my whole file, giving me 'empty' segments). Does anybody know how to solve this? Thanks for your time, Boukje Habets -- Dr. Boukje Habets Biopsychology & Cognitive Neuroscience (AE14) Faculty of Psychology and Sports Science | Bielefeld University PO-Box 100131 | D-33501 Bielefeld, Germany Phone: (49) 521 - 106 67 533 | Fax: (49) 521 - 106 15 67 530 Office: UHG T3-250 ---------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Tue Dec 5 11:52:16 2017 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Tue, 5 Dec 2017 11:52:16 +0100 Subject: [FieldTrip] Question about segmentation In-Reply-To: <71c0e7f647c8c.5a267b20@uni-bielefeld.de> References: <71c0e7f647c8c.5a267b20@uni-bielefeld.de> Message-ID: Hi Boukje, Your question is not totally clear to me, so apologies if this is not what you mean. I gather that you want to segment your data into non-overlapping 2-sec intervals, starting at a single trigger in your data? In any case, everything is possible, it just relies on understanding of the trl structure (always defined in samplenumbers) and the use of ft_preprocessing (in your case to read data and replace samples into a time-axis) and ft_redefinetrial (can be done afterwards) It you only want to segment your data into non-overlapping 2-sec intervals you could do something like this: 1. Use ft_preprocessing to read all your data as one long trial relative to your first trigger. For this you will need to enter a .trl field that has a single row with start, end, and offset in samplenr. You can get the sample number of your trigger (as well as the (relative) beginning and end sample numbers) using ft_read_events. The output of ft_preprocessing will give you a single trial defined in time around your trigger. 2. You can then use ft_redefinetrial to segment the data into short (non-overlapping) segments. Check it's help for details. But realize you will now define segments in terms of time, not samples. The benefit of this order of things is that in the first preprocessing step you can do things like filtering on the whole dataset, if you can spare the RAM. Hope this helps, Stephen Virus-free. www.avast.com <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On 5 December 2017 at 10:55, Boukje Habets wrote: > Dear Fieldtrippers, > > Im new to Fieldtrip and have a question about segmentation. I want to do a > freqanalysis on EEG data (Brainvision Recorder). > I have one file per condition (so only containing one trigger code, and a > start code at the beginning of the file) that i want to segment into 2sec > pieces. Ive been trying to find a way to add a trigger with Fieldtrip, so > that I can segment around a new trigger. Using a pre- and poststim > timewindow around the trigger code is not a solution, as this gives me > overlapping segments, which i do not want. > This doesnt seem possible? > > After reading about cfg.trialfun, I saw that i can segment a continuous > file into segments that i can define in terms of length (sec/samples). I > guess this is the easiest way for me to segment my file. However, i want to > be able to define the start and end point of segmentation, as my file > contains a part in the beginning without codes (EEG was being recorded, but > experiment was running yet). I have been playing around with the commands > begsample and endsample, but that didnt change the window of segmentation > (meaning it always segments my whole file, giving me 'empty' segments). > > Does anybody know how to solve this? > > Thanks for your time, > > Boukje Habets > > -- > > Dr. Boukje Habets > Biopsychology & Cognitive Neuroscience (AE14) > Faculty of Psychology and Sports Science | Bielefeld University > PO-Box 100131 | D-33501 Bielefeld, Germany > Phone: (49) 521 - 106 67 533 | Fax: (49) 521 - 106 15 67 530 > Office: UHG T3-250 > ---------------------------------------------------------------- > _______________________________________________ > 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 Dec 5 11:57:33 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 5 Dec 2017 10:57:33 +0000 Subject: [FieldTrip] Question about segmentation In-Reply-To: <71c0e7f647c8c.5a267b20@uni-bielefeld.de> References: <71c0e7f647c8c.5a267b20@uni-bielefeld.de> Message-ID: <851A8ED2-B8C9-4889-A997-F34090596BE5@donders.ru.nl> Dear Boukje, I don’t think that ‘adding a trigger’ is necessary. Instead, I think you should be able to do something like this: start_idx = X*fsample; end_idx = Y*fsample; (X and Y are the intended start and end points of the data, in seconds relative to the onset of the data recording, fsample is the sampling frequency in Hz) cfg = []; cfg.datafile = ‘the-name-of-your-datafile’; cfg.trl = [start_idx end_idx 0]; cfg = … (some other optional parameters to be defined here) data =ft_preprocessing(cfg); cfg = []; cfg.length = 2; data_segmented = ft_redefinetrial(cfg, data); best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > On 5 Dec 2017, at 10:55, Boukje Habets wrote: > > Dear Fieldtrippers, > > Im new to Fieldtrip and have a question about segmentation. I want to do a freqanalysis on EEG data (Brainvision Recorder). > I have one file per condition (so only containing one trigger code, and a start code at the beginning of the file) that i want to segment into 2sec pieces. Ive been trying to find a way to add a trigger with Fieldtrip, so that I can segment around a new trigger. Using a pre- and poststim timewindow around the trigger code is not a solution, as this gives me overlapping segments, which i do not want. > This doesnt seem possible? > > After reading about cfg.trialfun, I saw that i can segment a continuous file into segments that i can define in terms of length (sec/samples). I guess this is the easiest way for me to segment my file. However, i want to be able to define the start and end point of segmentation, as my file contains a part in the beginning without codes (EEG was being recorded, but experiment was running yet). I have been playing around with the commands begsample and endsample, but that didnt change the window of segmentation (meaning it always segments my whole file, giving me 'empty' segments). > > Does anybody know how to solve this? > > Thanks for your time, > > Boukje Habets > > -- > > Dr. Boukje Habets > Biopsychology & Cognitive Neuroscience (AE14) > Faculty of Psychology and Sports Science | Bielefeld University > PO-Box 100131 | D-33501 Bielefeld, Germany > Phone: (49) 521 - 106 67 533 | Fax: (49) 521 - 106 15 67 530 > Office: UHG T3-250 > ---------------------------------------------------------------- _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From boukje.habets at uni-bielefeld.de Thu Dec 7 10:09:56 2017 From: boukje.habets at uni-bielefeld.de (Boukje Habets) Date: Thu, 07 Dec 2017 10:09:56 +0100 Subject: [FieldTrip] Question about segmentation In-Reply-To: References: Message-ID: <7170d1644abcb.5a291374@uni-bielefeld.de> Hi Stephen and Jan-Mathijs, Thanks for your replies! I indeed did not need to add a trigger, i just didnt define the timewindow (with respect to the first trigger code) correctly before. Now its working just fine Thanks for your help, Boukje Am 05.12.17 12:12 schrieb fieldtrip-request at science.ru.nl: > > 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. Question about segmentation (Boukje Habets) > 2. Re: Question about segmentation (Stephen Whitmarsh) > 3. Re: Question about segmentation (Schoffelen, J.M. (Jan Mathijs)) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 05 Dec 2017 10:55:28 +0100 > From: Boukje Habets > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Question about segmentation > Message-ID: <71c0e7f647c8c.5a267b20 at uni-bielefeld.de> > Content-Type: text/plain; charset="us-ascii" > > Dear Fieldtrippers, > > Im new to Fieldtrip and have a question about segmentation. I want to do a freqanalysis on EEG data (Brainvision Recorder). > I have one file per condition (so only containing one trigger code, and a start code at the beginning of the file) that i want to segment into 2sec pieces. Ive been trying to find a way to add a trigger with Fieldtrip, so that I can segment around a new trigger. Using a pre- and poststim timewindow around the trigger code is not a solution, as this gives me overlapping segments, which i do not want. > This doesnt seem possible? > > After reading about cfg.trialfun, I saw that i can segment a continuous file into segments that i can define in terms of length (sec/samples). I guess this is the easiest way for me to segment my file. However, i want to be able to define the start and end point of segmentation, as my file contains a part in the beginning without codes (EEG was being recorded, but experiment was running yet). I have been playing around with the commands begsample and endsample, but that didnt change the window of segmentation (meaning it always segments my whole file, giving me 'empty' segments). > > Does anybody know how to solve this? > > Thanks for your time, > > Boukje Habets > > -- > > Dr. Boukje Habets > Biopsychology & Cognitive Neuroscience (AE14) > Faculty of Psychology and Sports Science | Bielefeld University > PO-Box 100131 | D-33501 Bielefeld, Germany > Phone: (49) 521 - 106 67 533 | Fax: (49) 521 - 106 15 67 530 > Office: UHG T3-250 > ---------------------------------------------------------------- > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 2 > Date: Tue, 5 Dec 2017 11:52:16 +0100 > From: Stephen Whitmarsh > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Question about segmentation > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi Boukje, > > Your question is not totally clear to me, so apologies if this is not what > you mean. I gather that you want to segment your data into non-overlapping > 2-sec intervals, starting at a single trigger in your data? > > In any case, everything is possible, it just relies on understanding of the > trl structure (always defined in samplenumbers) and the use of > ft_preprocessing (in your case to read data and replace samples into a > time-axis) and ft_redefinetrial (can be done afterwards) > > It you only want to segment your data into non-overlapping 2-sec intervals > you could do something like this: > > 1. Use ft_preprocessing to read all your data as one long trial relative > to your first trigger. For this you will need to enter a .trl field that > has a single row with start, end, and offset in samplenr. You can get the > sample number of your trigger (as well as the (relative) beginning and end > sample numbers) using ft_read_events. The output of ft_preprocessing will > give you a single trial defined in time around your trigger. > 2. You can then use ft_redefinetrial to segment the data into short > (non-overlapping) segments. Check it's help for details. But realize you > will now define segments in terms of time, not samples. > > The benefit of this order of things is that in the first preprocessing step > you can do things like filtering on the whole dataset, if you can spare the > RAM. > > Hope this helps, > Stephen > > > > > > > Virus-free. > www.avast.com > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > On 5 December 2017 at 10:55, Boukje Habets > wrote: > > > Dear Fieldtrippers, > > > > Im new to Fieldtrip and have a question about segmentation. I want to do a > > freqanalysis on EEG data (Brainvision Recorder). > > I have one file per condition (so only containing one trigger code, and a > > start code at the beginning of the file) that i want to segment into 2sec > > pieces. Ive been trying to find a way to add a trigger with Fieldtrip, so > > that I can segment around a new trigger. Using a pre- and poststim > > timewindow around the trigger code is not a solution, as this gives me > > overlapping segments, which i do not want. > > This doesnt seem possible? > > > > After reading about cfg.trialfun, I saw that i can segment a continuous > > file into segments that i can define in terms of length (sec/samples). I > > guess this is the easiest way for me to segment my file. However, i want to > > be able to define the start and end point of segmentation, as my file > > contains a part in the beginning without codes (EEG was being recorded, but > > experiment was running yet). I have been playing around with the commands > > begsample and endsample, but that didnt change the window of segmentation > > (meaning it always segments my whole file, giving me 'empty' segments). > > > > Does anybody know how to solve this? > > > > Thanks for your time, > > > > Boukje Habets > > > > -- > > > > Dr. Boukje Habets > > Biopsychology & Cognitive Neuroscience (AE14) > > Faculty of Psychology and Sports Science | Bielefeld University > > PO-Box 100131 | D-33501 Bielefeld, Germany > > Phone: (49) 521 - 106 67 533 | Fax: (49) 521 - 106 15 67 530 > > Office: UHG T3-250 > > ---------------------------------------------------------------- > > _______________________________________________ > > 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: 3 > Date: Tue, 5 Dec 2017 10:57:33 +0000 > From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Question about segmentation > Message-ID: <851A8ED2-B8C9-4889-A997-F34090596BE5 at donders.ru.nl> > Content-Type: text/plain; charset="utf-8" > > Dear Boukje, > > I don?t think that ?adding a trigger? is necessary. > > Instead, I think you should be able to do something like this: > > start_idx = X*fsample; > end_idx = Y*fsample; > > (X and Y are the intended start and end points of the data, in seconds relative to the onset of the data recording, fsample is the sampling frequency in Hz) > > cfg = []; > cfg.datafile = ?the-name-of-your-datafile?; > cfg.trl = [start_idx end_idx 0]; > cfg = ? (some other optional parameters to be defined here) > data =ft_preprocessing(cfg); > > cfg = []; > cfg.length = 2; > data_segmented = ft_redefinetrial(cfg, data); > > best wishes, > Jan-Mathijs > > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > > > > > > On 5 Dec 2017, at 10:55, Boukje Habets wrote: > > > > Dear Fieldtrippers, > > > > Im new to Fieldtrip and have a question about segmentation. I want to do a freqanalysis on EEG data (Brainvision Recorder). > > I have one file per condition (so only containing one trigger code, and a start code at the beginning of the file) that i want to segment into 2sec pieces. Ive been trying to find a way to add a trigger with Fieldtrip, so that I can segment around a new trigger. Using a pre- and poststim timewindow around the trigger code is not a solution, as this gives me overlapping segments, which i do not want. > > This doesnt seem possible? > > > > After reading about cfg.trialfun, I saw that i can segment a continuous file into segments that i can define in terms of length (sec/samples). I guess this is the easiest way for me to segment my file. However, i want to be able to define the start and end point of segmentation, as my file contains a part in the beginning without codes (EEG was being recorded, but experiment was running yet). I have been playing around with the commands begsample and endsample, but that didnt change the window of segmentation (meaning it always segments my whole file, giving me 'empty' segments). > > > > Does anybody know how to solve this? > > > > Thanks for your time, > > > > Boukje Habets > > > > -- > > > > Dr. Boukje Habets > > Biopsychology & Cognitive Neuroscience (AE14) > > Faculty of Psychology and Sports Science | Bielefeld University > > PO-Box 100131 | D-33501 Bielefeld, Germany > > Phone: (49) 521 - 106 67 533 | Fax: (49) 521 - 106 15 67 530 > > Office: UHG T3-250 > > ---------------------------------------------------------------- _______________________________________________ > > 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 > > End of fieldtrip Digest, Vol 85, Issue 3 > **************************************** > -- Dr. Boukje Habets Biopsychology & Cognitive Neuroscience (AE14) Faculty of Psychology and Sports Science | Bielefeld University PO-Box 100131 | D-33501 Bielefeld, Germany Phone: (49) 521 - 106 67 533 | Fax: (49) 521 - 106 15 67 530 Office: UHG T3-250 ---------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From akoles01 at mail.bbk.ac.uk Thu Dec 7 16:02:44 2017 From: akoles01 at mail.bbk.ac.uk (Anna Kolesnik) Date: Thu, 7 Dec 2017 15:02:44 +0000 Subject: [FieldTrip] Fwd: Netstation >> Fieldtrip conversion References: Message-ID: <3EDA86DB-659F-4ACA-AEA7-7F601A56AECD@mail.bbk.ac.uk> Dear members of the discussion list, I am looking for advice on how best to export pre-processed data from Netstation (version 5+) to Fieldtrip. We have data that is already filtered, segmented, and cleaned for artefacts that needs to be imported into Fieldtrip to run the time-frequency analysis. I know that it is possible to export the processed file to EEGLAB (although I know of some bugs), but has anyone successfully attempted to export to Fieldtrip? If so, what processing stage was it at and what was the format most suitable for this operation? Thank you in advance! Anna Kolesnik PhD student at the Centre for Brain and Cognitive Development Birkbeck College, University of London The BMA House, Tavistock Square WC1H 9JP From dariashn at ugr.es Thu Dec 7 20:24:30 2017 From: dariashn at ugr.es (=?utf-8?Q?Dar=C3=ADas_Manuel_Holgado_Nu=C3=B1ez?=) Date: Thu, 7 Dec 2017 20:24:30 +0100 Subject: [FieldTrip] Dependant samples F multivariate Message-ID: <9F7CADE9-5655-4686-B5E2-672D2CF82B08@ugr.es> Dear list My name is Darias Holgado and I am working in the Mind, Brain and Behaviour Research Centre in Granada on tDCS, EEG and Sport performance. I am analysing data of a project, where we recorded EEG under three tDCS’ stimulation. I have carried out a tDCS’s study in a within-subjects fashion. I have 3 conditions (anodal, cathodal and sham) x one measure (3x1). I am performing permutation test with the montecarlo approach and the ft_statfun_dsamplesFmultivariate. After having specified the design and running the script, it seems that it is ok, but in the output the total number of variables appears as 2, when it is supposed it should say 3. is it that correct? The design I specified it seems correct and it is working but this data is confusing. The cfg and design I use are as follows: %Within-Subject design 3 condition x 1 measure cfg.design(1,1:3*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub) 3*ones(1,Nsub)]; cfg.design(2,1:3*Nsub) = [1:Nsub 1:Nsub 1:Nsub]; cfg.ivar = 1; cfg.uvar = 2; cfg.channel = chanlocs; cfg.method = 'montecarlo'; cfg.statistic = 'ft_statfun_depsamplesFmultivariate'; cfg.correctm = 'cluster'; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.numrandomization = 5000; cfg.tail = 1; % cfg.clustertail = 1; cfg.alpha = 0.025; %cfg.frequency = freqrange; %cfg.avgoverfreq = 'yes'; cfg.neighbours = neighbours; Thank you for your time Best regards, --------------------------------------------------------------------------------- Darías Holgado Nuñez Mind, Brain and Behaviour Research Centre. University of Granada (Spain) https://www.researchgate.net/profile/Darias_Holgado -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at me.com Fri Dec 8 07:46:48 2017 From: nathanweisz at me.com (Nathan Weisz) Date: Fri, 08 Dec 2017 07:46:48 +0100 Subject: [FieldTrip] Postdoc Position @Blechert-lab Message-ID: FYI. Post-doc and PhD position focusing on the cognitive neuroscience of eating behavior at the center for cognitive neuroscience, Salzburg University, advertized on www.eat.sbg.ac.at -------------- next part -------------- An HTML attachment was scrubbed... URL: From i.charest at bham.ac.uk Fri Dec 8 13:58:00 2017 From: i.charest at bham.ac.uk (Ian Charest (School of Psychology)) Date: Fri, 8 Dec 2017 12:58:00 +0000 Subject: [FieldTrip] PhD position on the neurocognitive mechanisms of conscious access Message-ID: <97F95B166F2157409BE1EC68292F25AC4360AA19@EX13.adf.bham.ac.uk> Dear Fieldtrip discussion list, see below for details of a fully funded PhD position in Birmingham, UK. Best wishes, Ian Charest Lecturer, School of Psychology, University of Birmingham, UK iancharest.com _________________________ Advert: The School of Psychology at the University of Birmingham is looking for a bright and motivated PhD student to join the Charest Laboratory (iancharest.com). The PhD position to be filled is part of a project recently funded by a European Research Council Starting Grant entitled: "Spatio-Temporal Attention and Representation Tracking: the precise neural architecture of conscious object perception" (START). The Project: START is an ambitious programme of work that will make use of cutting-edge multivariate pattern analyses (MVPA) techniques to reveal the brain mechanisms that are critical for consciously perceiving visual objects in tasks that manipulate conscious access to visual information. The ability to consciously recognise faces, objects, or sounds is crucial for adaptive behaviour and survival. Yet, how our conscious experience of the world emerges in our brain remains unknown. The overall aim of the START programme is to fill an important gap in our understanding of consciousness by elucidating the neural underpinnings of conscious access. How does the brain select relevant information among distractors, and keep this information in mind? Why does our ability to consciously recognise salient objects sometimes fail under pressure and exhibit variability across days and individuals? START will try to address these important questions by precisely tracking where in the brain and when in time the representations critical for conscious access are established, by using novel approaches of Representational Similarity Analyses which combines the strengths of EEG, fMRI, and Deep Convolutional Neuronal Networks. This project will provide new insights on the precise spatio-temporal dynamics of conscious access, the mechanisms governing it, and the idiosyncratic subtleties behind the meanderings of consciousness. The candidate: The successful candidate will have (or be in the process of obtaining) a Masters degree in cognitive neuroscience or a related field. Previous experience with psychophysical tasks that manipulate conscious access in vision is desirable. Given the nature of the project, good understanding of and experience with fMRI, EEG/MEG and data analysis is desirable. Experience in using matlab or python (and Psychtoolbox or PsychoPy) is a requirement. The successful applicant will have experience with multivariate pattern analyses (Representational Similarity Analysis, Fisher linear discriminants, etc) of neuroimaging data. This post will require designing experiments, collecting and analysing data associated with the project, preparing manuscripts for publication, presenting results at national and international conferences and the possible supervision of research assistants and students. The School: The School of Psychology at the University of Birmingham (http://www.birmingham.ac.uk/schools/psychology/index.aspx) is one of the largest and most successful in the UK, currently ranked in the top 5 Schools in the country (REF 2014). The School is soon to move to new accommodation in the form of a fully refurbished, purpose-designed space and a new-build Centre for Human Brain Health that will house our new MRI, MEG, EEG, NIRS, sleep lab, and the recently appointed Chair in Translational Neuroscience. The University of Birmingham is an equal opportunities employer. The School of Psychology has a Bronze Athena SWAN award and strives to maintain a flexible and supportive environment that enables its staff to flourish. For informal enquiries about the project please contact Dr. Ian Charest (i.charest at bham.ac.uk). Formal applications must be made via the postgraduate admissions system in the School of Psychology. Applicants are encouraged to attach to their application a short and original project proposal (500 words). http://www.birmingham.ac.uk/students/courses/postgraduate/research/psych/psychology.aspx#CourseDetailsTab Full advert of the position on find a phd: https://www.findaphd.com/search/projectdetails.aspx?PJID=92145 -------------- next part -------------- An HTML attachment was scrubbed... URL: From omerxsharon at gmail.com Sat Dec 9 13:12:48 2017 From: omerxsharon at gmail.com (Omer Sharon) Date: Sat, 9 Dec 2017 14:12:48 +0200 Subject: [FieldTrip] Netstation >> Fieldtrip conversion Message-ID: Hi Anna Fieltrip could read the MFF file directly using ft_preprocessing(), use the folder like it was a file. In NS5 there is an issue with the triggers' files and the spaces should be replaces with underscores (fix it if you get an error). I move to field-trip in a very early stage, but you can export to fieldtrip in any stage you like. Good luck Omer Sharon PhD student at NirLab Department of physiology and pharmacology Sackler Faculty of Medicine Tel Aviv University, Israel On Fri, Dec 8, 2017 at 1:00 PM, wrote: > 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. Fwd: Netstation >> Fieldtrip conversion (Anna Kolesnik) > 2. Dependant samples F multivariate (Dar?as Manuel Holgado Nu?ez) > 3. Postdoc Position @Blechert-lab (Nathan Weisz) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 7 Dec 2017 15:02:44 +0000 > From: Anna Kolesnik > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Fwd: Netstation >> Fieldtrip conversion > Message-ID: <3EDA86DB-659F-4ACA-AEA7-7F601A56AECD at mail.bbk.ac.uk> > Content-Type: text/plain; charset=us-ascii > > Dear members of the discussion list, > > I am looking for advice on how best to export pre-processed data from > Netstation (version 5+) to Fieldtrip. We have data that is already > filtered, segmented, and cleaned for artefacts that needs to be imported > into Fieldtrip to run the time-frequency analysis. > I know that it is possible to export the processed file to EEGLAB > (although I know of some bugs), but has anyone successfully attempted to > export to Fieldtrip? If so, what processing stage was it at and what was > the format most suitable for this operation? > > > Thank you in advance! > > > Anna Kolesnik > PhD student at the Centre for Brain and Cognitive Development > Birkbeck College, University of London > The BMA House, Tavistock Square > WC1H 9JP > > > ------------------------------ > > Message: 2 > Date: Thu, 7 Dec 2017 20:24:30 +0100 > From: Dar?as Manuel Holgado Nu?ez > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Dependant samples F multivariate > Message-ID: <9F7CADE9-5655-4686-B5E2-672D2CF82B08 at ugr.es> > Content-Type: text/plain; charset="utf-8" > > Dear list > > My name is Darias Holgado and I am working in the Mind, Brain and > Behaviour Research Centre in Granada on tDCS, EEG and Sport performance. I > am analysing data of a project, where we recorded EEG under three tDCS? > stimulation. > > I have carried out a tDCS?s study in a within-subjects fashion. I have 3 > conditions (anodal, cathodal and sham) x one measure (3x1). I am performing > permutation test with the montecarlo approach and the ft_statfun_ > dsamplesFmultivariate. > After having specified the design and running the script, it seems that it > is ok, but in the output the total number of variables appears as 2, when > it is supposed it should say 3. is it that correct? The design I specified > it seems correct and it is working but this data is confusing. > > The cfg and design I use are as follows: > > %Within-Subject design 3 condition x 1 measure > cfg.design(1,1:3*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub) 3*ones(1,Nsub)]; > cfg.design(2,1:3*Nsub) = [1:Nsub 1:Nsub 1:Nsub]; > cfg.ivar = 1; > cfg.uvar = 2; > > cfg.channel = chanlocs; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_depsamplesFmultivariate'; > cfg.correctm = 'cluster'; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.numrandomization = 5000; > cfg.tail = 1; > % cfg.clustertail = 1; > cfg.alpha = 0.025; > %cfg.frequency = freqrange; > %cfg.avgoverfreq = 'yes'; > cfg.neighbours = neighbours; > > > Thank you for your time > > > Best regards, > ------------------------------------------------------------ > --------------------- > Dar?as Holgado Nu?ez > Mind, Brain and Behaviour Research Centre. > University of Granada (Spain) > https://www.researchgate.net/profile/Darias_Holgado > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20171207/96780d19/attachment-0001.html> > > ------------------------------ > > Message: 3 > Date: Fri, 08 Dec 2017 07:46:48 +0100 > From: Nathan Weisz > To: FieldTrip discussion list > Subject: [FieldTrip] Postdoc Position @Blechert-lab > Message-ID: > Content-Type: text/plain; charset="us-ascii" > > FYI. > > Post-doc and PhD position focusing on the cognitive neuroscience of > eating behavior at the center for cognitive neuroscience, Salzburg > University, advertized on > www.eat.sbg.ac.at > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20171208/0634be20/attachment-0001.html> > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 85, Issue 5 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From xiew1202 at gmail.com Sat Dec 9 13:23:48 2017 From: xiew1202 at gmail.com (Xie Wanze) Date: Sat, 09 Dec 2017 12:23:48 +0000 Subject: [FieldTrip] Netstation >> Fieldtrip conversion In-Reply-To: References: Message-ID: Anna, You may also read in the segmented data into Eeglab, and then use eeglab2fieldtrip function to export them into field trip format. Wanze Omer Sharon 于2017年12月9日 周六上午7:13写道: > Hi Anna > > Fieltrip could read the MFF file directly using ft_preprocessing(), use > the folder like it was a file. In NS5 there is an issue with the triggers' > files and the spaces should be replaces with underscores (fix it if you get > an error). > > I move to field-trip in a very early stage, but you can export to > fieldtrip in any stage you like. > > Good luck > > Omer Sharon > PhD student at NirLab > Department of physiology and pharmacology > Sackler Faculty of Medicine > Tel Aviv University, Israel > > > On Fri, Dec 8, 2017 at 1:00 PM, wrote: > >> 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. Fwd: Netstation >> Fieldtrip conversion (Anna Kolesnik) >> 2. Dependant samples F multivariate (Dar?as Manuel Holgado Nu?ez) >> 3. Postdoc Position @Blechert-lab (Nathan Weisz) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Thu, 7 Dec 2017 15:02:44 +0000 >> From: Anna Kolesnik >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] Fwd: Netstation >> Fieldtrip conversion >> Message-ID: <3EDA86DB-659F-4ACA-AEA7-7F601A56AECD at mail.bbk.ac.uk> >> Content-Type: text/plain; charset=us-ascii > > >> >> Dear members of the discussion list, >> >> I am looking for advice on how best to export pre-processed data from >> Netstation (version 5+) to Fieldtrip. We have data that is already >> filtered, segmented, and cleaned for artefacts that needs to be imported >> into Fieldtrip to run the time-frequency analysis. >> I know that it is possible to export the processed file to EEGLAB >> (although I know of some bugs), but has anyone successfully attempted to >> export to Fieldtrip? If so, what processing stage was it at and what was >> the format most suitable for this operation? >> >> >> Thank you in advance! >> >> >> Anna Kolesnik >> PhD student at the Centre for Brain and Cognitive Development >> Birkbeck College, University of London >> The BMA House, Tavistock Square >> WC1H 9JP >> >> >> ------------------------------ >> >> Message: 2 >> Date: Thu, 7 Dec 2017 20:24:30 +0100 >> From: Dar?as Manuel Holgado Nu?ez >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] Dependant samples F multivariate >> Message-ID: <9F7CADE9-5655-4686-B5E2-672D2CF82B08 at ugr.es> >> Content-Type: text/plain; charset="utf-8" >> >> Dear list >> >> My name is Darias Holgado and I am working in the Mind, Brain and >> Behaviour Research Centre in Granada on tDCS, EEG and Sport performance. I >> am analysing data of a project, where we recorded EEG under three tDCS? >> stimulation. >> >> I have carried out a tDCS?s study in a within-subjects fashion. I have 3 >> conditions (anodal, cathodal and sham) x one measure (3x1). I am performing >> permutation test with the montecarlo approach and the >> ft_statfun_dsamplesFmultivariate. >> After having specified the design and running the script, it seems that >> it is ok, but in the output the total number of variables appears as 2, >> when it is supposed it should say 3. is it that correct? The design I >> specified it seems correct and it is working but this data is confusing. >> >> The cfg and design I use are as follows: >> >> %Within-Subject design 3 condition x 1 measure >> cfg.design(1,1:3*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub) 3*ones(1,Nsub)]; >> cfg.design(2,1:3*Nsub) = [1:Nsub 1:Nsub 1:Nsub]; >> cfg.ivar = 1; >> cfg.uvar = 2; >> >> cfg.channel = chanlocs; >> cfg.method = 'montecarlo'; >> cfg.statistic = 'ft_statfun_depsamplesFmultivariate'; >> cfg.correctm = 'cluster'; >> cfg.clusterstatistic = 'maxsum'; >> cfg.minnbchan = 2; >> cfg.numrandomization = 5000; >> cfg.tail = 1; >> % cfg.clustertail = 1; >> cfg.alpha = 0.025; >> %cfg.frequency = freqrange; >> %cfg.avgoverfreq = 'yes'; >> cfg.neighbours = neighbours; >> >> >> Thank you for your time >> >> >> Best regards, >> >> --------------------------------------------------------------------------------- >> Dar?as Holgado Nu?ez >> Mind, Brain and Behaviour Research Centre. >> University of Granada (Spain) >> https://www.researchgate.net/profile/Darias_Holgado >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20171207/96780d19/attachment-0001.html >> > >> >> ------------------------------ >> >> Message: 3 >> Date: Fri, 08 Dec 2017 07:46:48 +0100 >> From: Nathan Weisz >> To: FieldTrip discussion list >> Subject: [FieldTrip] Postdoc Position @Blechert-lab >> Message-ID: >> Content-Type: text/plain; charset="us-ascii" >> >> FYI. >> >> Post-doc and PhD position focusing on the cognitive neuroscience of >> eating behavior at the center for cognitive neuroscience, Salzburg >> University, advertized on >> www.eat.sbg.ac.at >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20171208/0634be20/attachment-0001.html >> > >> >> ------------------------------ > > >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> End of fieldtrip Digest, Vol 85, Issue 5 >> **************************************** >> > > _______________________________________________ > 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 mikexcohen at gmail.com Sat Dec 9 22:14:41 2017 From: mikexcohen at gmail.com (Mike X Cohen) Date: Sat, 9 Dec 2017 22:14:41 +0100 Subject: [FieldTrip] Neuroscience data analysis summer-school announcements Message-ID: Dear colleagues, I am happy to announce *two week-long neuroscience data analysis courses* at the Radboud University in Netherlands in August 2018: One about time-frequency/synchronization/statistics, and one about linear algebra and source-separation. Below are the direct links to the course pages with application information. You can also find more information, including syllabi, on mikexcohen.com (scroll down to "In-vivo teaching"). *Please pass these links around to your colleagues/students who might be interested in one or both of these courses!* Analyzing neural time series data (6-10 August). Fourier transform, convolution, time-frequency analysis, synchronization, nonparametric statistics, simulating time series data. Linear algebra for neuroscientists (13-17 August). Matrix algebra, least-squares model fitting, eigendecomposition, multivariate source separation, state-space analyses, simulating multicomponent and multichannal time series data. Please note that applications, if approved, are selected on a first-come-first-serve basis, and that the number of participants for each course is limited. If you have questions about the courses, please feel free to contact me. Mike -- Mike X Cohen, PhD New online courses: mikexcohen.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From urieduardo at gmail.com Tue Dec 12 14:38:42 2017 From: urieduardo at gmail.com (=?UTF-8?Q?Uri_Eduardo_Ram=C3=ADrez_Pasos?=) Date: Tue, 12 Dec 2017 14:38:42 +0100 Subject: [FieldTrip] ft_sourcestatistics Message-ID: Dear fieldtrippers, I have a couple questions regarding source reconstruction that I hope you can help me with. 1. What is the best way to 'normalize' the position values in each forward model across my subjects so that I can run ft_sourcestatistics with cfg.statistic = 'ft_statfun_depsamplesT' ? 2. For one of my subjects, their leadfield keeps containing only NaNs. What could be the source (no pun intended) of the problem? 3. If my experiment's design has three 'levels' (say A1, A2, A3) for one 'factor', is it valid to subtract source values (obtained using method 'dics') for a comparison (e.g. A1-A3 vs A2-A3)? 4. What could have gone wrong when i get the warning “matrix is singular, close to singular or badly scaled. Results may be inaccurate.” How does one go about solving this? Best regards, Eduardo Ramírez, PhD candidate University of Würzburg -------------- next part -------------- An HTML attachment was scrubbed... URL: From mi_mayer at gmx.de Tue Dec 12 17:24:36 2017 From: mi_mayer at gmx.de (Irene Sophia Mayer) Date: Tue, 12 Dec 2017 17:24:36 +0100 Subject: [FieldTrip] Forward model EEG no MRI Message-ID: An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Tue Dec 12 17:37:51 2017 From: julian.keil at gmail.com (Julian Keil) Date: Tue, 12 Dec 2017 17:37:51 +0100 Subject: [FieldTrip] Forward model EEG no MRI In-Reply-To: References: Message-ID: <6EA73EED-F0B6-4676-99A0-FE1723A6578A@gmail.com> Dear Sophia, Fieldtrip comes with a number of precomputed Headmodels as well as standard MRIs which you can use (take a look into the „forward“-folder in the FT directory). You just have to make sure, your electrodes fit to the headmodels, but you would have to do this with a „real“ MRI as well. Good luck, Julian > Am 12.12.2017 um 17:24 schrieb Irene Sophia Mayer : > > Dear Fieldtrippers, > > I am attempting to do source reconstruction with Fieldtrip for the first time. I have EEG data but no MRI, just measurements of the electrode positions (with Zebris). However, I got already stuck at creating the forward model. > > Do I need to prepare my own sourcemodel with ft_prepare_sourcemodel or can I use the default options in ft_prepare_leadfield? > > All tutorials for creating a headmodel use an MRI, how can I do it without MRI images of my subjects? > > I have tried to use ft_prepare_headmodel with > headmodel = ft_prepare_headmodel(cfg, elec) with the output of FT_READ_SENS headmo > elec = > chanpos: [62x3 double] > elecpos: [62x3 double] > label: {62x1 cell} > type: 'eeg1005' > unit: 'mm' > > Unfortunately, it first told me: Either a segmentated MRI or data with closed triangulated mesh is required as data > input for the bemcp, dipoli or openmeeg method, and when I tried other methods, I got: The data input might already be a sensor description. Reference to non-existent field 'outputfile' > > I would be thankful for tips on how to do this! > > Best, > Sophia > _______________________________________________ > 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 julian.keil at gmail.com Tue Dec 12 17:49:01 2017 From: julian.keil at gmail.com (Julian Keil) Date: Tue, 12 Dec 2017 17:49:01 +0100 Subject: [FieldTrip] ft_sourcestatistics In-Reply-To: References: Message-ID: <6E37C718-06F7-439B-87B1-329FEFFACFF8@gmail.com> Dear Eduardo, @1: Do you mean normalize across the group? What you could do is interpolate the source-level data to an MRI and then use ft_volumenormalise to normalize all images to a common standard MRI. Check the FT site here: http://www.fieldtriptoolbox.org/tutorial/sourcemodel?s[]=warp Alternatively, you could take care that a common source grid is warped to the individual headmodel prior to the source analysis. In this case, you don’t need to normalize, as all subjects have the same number of sources. Check the tutorials on the FT-website for hints (e.g. http://www.fieldtriptoolbox.org/tutorial/salzburg?s[]=warp or http://www.fieldtriptoolbox.org/tutorial/beamformingextended?s[]=warp ) @2: Did you build your own headmodel? It might be that the elements of the headmodel intersect. I would go back and double check all steps leading up to the leadfield computation for errors. @3: I have no idea. @4: When does this happen? Good luck, Julian > Am 12.12.2017 um 14:38 schrieb Uri Eduardo Ramírez Pasos : > > Dear fieldtrippers, > > I have a couple questions regarding source reconstruction that I hope you can help me with. > > 1. What is the best way to 'normalize' the position values in each forward model across my subjects so that I can run ft_sourcestatistics with cfg.statistic = 'ft_statfun_depsamplesT' ? > > 2. For one of my subjects, their leadfield keeps containing only NaNs. What could be the source (no pun intended) of the problem? > > 3. If my experiment's design has three 'levels' (say A1, A2, A3) for one 'factor', is it valid to subtract source values (obtained using method 'dics') for a comparison (e.g. A1-A3 vs A2-A3)? > > 4. What could have gone wrong when i get the warning “matrix is singular, close to singular or badly scaled. Results may be inaccurate.” How does one go about solving this? > > Best regards, > Eduardo Ramírez, PhD candidate > University of Würzburg > _______________________________________________ > 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 cmista at bioingenieria.edu.ar Wed Dec 13 14:16:17 2017 From: cmista at bioingenieria.edu.ar (Christian Mista) Date: Wed, 13 Dec 2017 10:16:17 -0300 Subject: [FieldTrip] About connectivity and ft_topoplotCC Message-ID: Hi all, I'm starting with EEG analysis and Fiedltrip, and I'll would like to plot topographical maps of the connectivity (using imaginary part of coherence). I tried ft_topoplotCC to make a connection line/arrow graph, but I think I'm doing something wrong because the graph at 10 hz seems to be the same at 50 hz (attached some images). In addition, I was wondering if there is any way to set a threshold, so only fewer lines are plotted in the connection map. Below the code I'm using in matlab. %CODE %calculate coherence cfg = []; cfg.method = 'mtmfft'; cfg.taper = 'hanning'; %connectivity analysis needs power and phase -> 'pownadcsd' cfg.output = 'powandcsd'; % windows of frequency of interest foilim cfg.foilim = [1 60]; freq1 = ft_freqanalysis(cfg, data); %calculating the imaginary part of the coherence cfg = []; cfg.method = 'coh'; cfg.complex = 'absimag'; conn1 = ft_connectivityanalysis(cfg, freq1); %The conectome %figure;imagesc(conn1.cohspctrm); cfg = []; %my layout cfg.layout = layout; cfg.foi = 10; ft_topoplotCC(cfg, conn1) cfg = []; cfg.layout = layout; cfg.foi = 50; ft_topoplotCC(cfg, conn1) Best regards / Cordiales saludos Christian -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: connections10Hz.jpg Type: image/jpeg Size: 35441 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: connections50Hz.jpg Type: image/jpeg Size: 37955 bytes Desc: not available URL: From urieduardo at gmail.com Thu Dec 14 15:09:36 2017 From: urieduardo at gmail.com (=?UTF-8?Q?Uri_Eduardo_Ram=C3=ADrez_Pasos?=) Date: Thu, 14 Dec 2017 15:09:36 +0100 Subject: [FieldTrip] ft_sourcestatistics In-Reply-To: <6E37C718-06F7-439B-87B1-329FEFFACFF8@gmail.com> References: <6E37C718-06F7-439B-87B1-329FEFFACFF8@gmail.com> Message-ID: Dear Julian, Thanks a lot for your advice! Some follow-up questions and clarifications. 1a. I've looked at both approaches suggested in http://www.fieldtriptoolbox.org/tutorial/sourcemodel?s%5B%5D=warp. For the first approach (interpolate then normalize volumes), I used the following code (for EEG data), where I compute source values from two conditions, ON and OFF: cfg = []; cfg.method = 'dics'; cfg.frequency = 18; cfg.grid = grid; cfg.headmodel = headmodel; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.keepfilter = 'yes'; cfg.dics.realfilter = 'yes'; sourceAllneg_pos = ft_sourceanalysis(cfg, freqAll); cfg.grid.filter = sourceAllneg_pos.avg.filter; sourceOFF_con = ft_sourceanalysis(cfg, freqOFF); sourceON_con = ft_sourceanalysis(cfg, freqON); atlas = ft_read_atlas( '~/Documents/MATLAB/fieldtrip-20170618/template/atlas/aal/ROI_MNI_V4.nii'); cfg=[]; cfg.parameter='pow'; cont_sources{pat,1,1}=ft_sourceinterpolate(cfg, sourceOFF_con, atlas); cont_sources{pat,1,2}=ft_sourceinterpolate(cfg, sourceON_con, atlas); cfg=[]; cfg.parameter='pow'; [mri] = ft_volumenormalise(cfg, mri) Using ft_sourceinterpolate normalized the .pos values across my subjects, however I'm not sure what to do with the MRI variable created with ft_volumenormalize, but I'm guessing it should be integrated somewhere for results to be valid. 1b. I also tried the second method in the tutorial (Subject-specific grids), but the standard_sourcemodel3dxmm.mat files are based on the single shell method, and hence only relevant for MEG. When inputting cfg.grid.template= 'cortex_xxxx.surf.gii' (the other templates, which I hope are for EEG), I get the error using load: 'Number of columns on line 2 of ASCII file cortex_xxxx.surf.gii must be the same as previous lines. 2. Yes, I just used %get mri mri = ft_read_mri('0001.dcm'); %segment mri cfg=[]; cfg.output={'brain','skull','scalp'}; segmentedmri=ft_volumesegment(cfg,mri); % Y % r % a % s % n cfg=[]; cfg.tissue={'brain','skull','scalp'}; cfg.numvertices=[3000 2000 1000]; cfg.method='projectmesh';% or 'iso2mesh', 'isosurface', bnd=ft_prepare_mesh(cfg,segmentedmri); cfg=[]; cfg.method='bemcp';%or dipoli on a mac, or openmeeg headmodel = ft_prepare_headmodel(cfg,bnd); I'm using a mac, though I can't get dipoli to work. I've used this for the other subjects without every problem. I have no fiducials, not sure if this has any influence. 3. I've thought about this further, it doesn't make much sense to do this at the source level. 4. The warning occurs after running cfg=[]; cfg.method='bemcp';%or dipoli on a mac, or openmeeg headmodel = ft_prepare_headmodel(cfg,bnd); , though I also get this when running sample data from fieldtrip tutorials. Again, thank you immensely for your pointers! Uri 2017-12-12 17:49 GMT+01:00 Julian Keil : > Dear Eduardo, > > @1: Do you mean normalize across the group? What you could do is > interpolate the source-level data to an MRI and then use ft_volumenormalise > to normalize all images to a common standard MRI. Check the FT site here: > http://www.fieldtriptoolbox.org/tutorial/sourcemodel?s[]=warp > Alternatively, you could take care that a common source grid is warped to > the individual headmodel prior to the source analysis. In this case, you > don’t need to normalize, as all subjects have the same number of sources. > Check the tutorials on the FT-website for hints (e.g. http://www. > fieldtriptoolbox.org/tutorial/salzburg?s[]=warp or http:// > www.fieldtriptoolbox.org/tutorial/beamformingextended?s[]=warp) > > @2: Did you build your own headmodel? It might be that the elements of the > headmodel intersect. I would go back and double check all steps leading up > to the leadfield computation for errors. > > @3: I have no idea. > > @4: When does this happen? > > Good luck, > > Julian > > Am 12.12.2017 um 14:38 schrieb Uri Eduardo Ramírez Pasos < > urieduardo at gmail.com>: > > Dear fieldtrippers, > > I have a couple questions regarding source reconstruction that I hope you > can help me with. > > 1. What is the best way to 'normalize' the position values in each forward > model across my subjects so that I can run ft_sourcestatistics with > cfg.statistic = 'ft_statfun_depsamplesT' ? > > 2. For one of my subjects, their leadfield keeps containing only NaNs. > What could be the source (no pun intended) of the problem? > > 3. If my experiment's design has three 'levels' (say A1, A2, A3) for one > 'factor', is it valid to subtract source values (obtained using method > 'dics') for a comparison (e.g. A1-A3 vs A2-A3)? > > 4. What could have gone wrong when i get the warning “matrix is singular, > close to singular or badly scaled. Results may be inaccurate.” How does one > go about solving this? > > Best regards, > Eduardo Ramírez, PhD candidate > University of Würzburg > _______________________________________________ > 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 caschera at dis.uniroma1.it Fri Dec 15 10:51:20 2017 From: caschera at dis.uniroma1.it (Stefano Caschera) Date: Fri, 15 Dec 2017 10:51:20 +0100 Subject: [FieldTrip] Including brain lesion - OpenMeeg Message-ID: Hi, I would like to include a brain lesion to obtain a leadfield through openmeeg. I have already computed the meshes. Is it possible to use ft_prepare_headmodel and openmeeg_dsm ? And how? I tried but I've got strange results. As I know openmeeg can handle four layers but probably the brain has to be the inner one. If it is not possible using openmeeg, can you suggest me another method? Thank you, Stefano -- Stefano Caschera, PhD Student *Neuroelectrical Imaging and BCI lab* Fondazione Santa Lucia, IRCCS Via Ardeatina, 306 I-00179, Rome, Italy *Department of Computer, Control, andManagement Engineering "Antonio Ruberti"* Sapienza, University of Rome V. Ariosto, 25 00185, Rome, Italy Tel +39 06 5150 1165 Email: stefano.caschera at uniroma1.it caschera at dis.uniroma1.it s.caschera at hsantalucia.it ___________________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.homolle at donders.ru.nl Fri Dec 15 11:12:49 2017 From: s.homolle at donders.ru.nl (Simon Homolle) Date: Fri, 15 Dec 2017 11:12:49 +0100 Subject: [FieldTrip] Including brain lesion - OpenMeeg In-Reply-To: References: Message-ID: <92ED8BAC-B04F-4AF0-B989-46E94B2CD8F9@donders.ru.nl> Dear Stefano, What do you mean by strange results? Some figures describing the results would help to give you further help. You talked about 4 layers so i presume you used Skin, Skull, Brain and Lesion? Are these nested compartments? Could you show some visualisation of the meshes/segmentations you used? seg_i = ft_datatype_segmentation(segmentedmri,'segmentationstyle','indexed'); cfg = []; cfg.funparameter = 'seg'; cfg.funcolormap = lines(6); % distinct color per tissue cfg.location = 'center'; cfg.atlas = seg_i; % the segmentation can also be used as atlas ft_sourceplot(cfg, seg_i); Best regards, Simon Homölle PhD Candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Phone: +31-(0)24-36-65059 > On 15 Dec 2017, at 10:51, Stefano Caschera wrote: > > Hi, > I would like to include a brain lesion to obtain a leadfield through openmeeg. > > I have already computed the meshes. > > Is it possible to use ft_prepare_headmodel and openmeeg_dsm ? > And how? I tried but I've got strange results. As I know openmeeg can handle four layers but probably the brain has to be the inner one. > > If it is not possible using openmeeg, can you suggest me another method? > > Thank you, > Stefano > > -- > Stefano Caschera, PhD Student > > Neuroelectrical Imaging and BCI lab > Fondazione Santa Lucia, IRCCS > Via Ardeatina, 306 > I-00179, Rome, Italy > > Department of Computer, Control, and > Management Engineering "Antonio Ruberti" > Sapienza, University of Rome > V. Ariosto, 25 > 00185, Rome, Italy > > Tel +39 06 5150 1165 > Email: stefano.caschera at uniroma1.it > caschera at dis.uniroma1.it > s.caschera at hsantalucia.it > ___________________________________________________ > _______________________________________________ > 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 sarang at cfin.au.dk Fri Dec 15 23:11:17 2017 From: sarang at cfin.au.dk (Sarang S. Dalal) Date: Fri, 15 Dec 2017 22:11:17 +0000 Subject: [FieldTrip] Including brain lesion - OpenMeeg In-Reply-To: <92ED8BAC-B04F-4AF0-B989-46E94B2CD8F9@donders.ru.nl> References: <92ED8BAC-B04F-4AF0-B989-46E94B2CD8F9@donders.ru.nl> Message-ID: <1513375868.2120.25.camel@cfin.au.dk> Dear Stefano, OpenMEEG can do what you need. We wrote the function in FieldTrip that sets up the OpenMEEG parameters (fieldtrip/forward/private/leadfield_openmeeg.m) with the assumption that there would be either 3 layers (scalp, skull, brain) or 4 layers (scalp, skull, csf, brain). These layers are assumed to be nested from outside to inside, with no surfaces crossing or touching. As Simon suggested, you probably have lesion nested within brain. So, if you don't have a CSF layer, you could use the 4-layer functionality that is already there, with the order [scalp skull brain lesion]. You will have to configure cfg.conductivity appropriately with the same order. You may also take a look at the examples from my group where we script MRI segmentations and set up OpenMEEG computations in practice (for 3- and 4-layer nested geometries): https://github.com/meeg-cfin/nemolab/blob/master/basics/nemo_mriproc.m https://github.com/meeg-cfin/nemolab/blob/master/basics/nemo_makeleadfield.m OpenMEEG will also support non-nested configurations, but you will have to adapt leadfield_openmeeg.m to get it to work with FieldTrip. You can have a look at the documentation on the OpenMEEG website for a description of how to write the parameter files for that situation. Cheers, Sarang On Fri, 2017-12-15 at 11:12 +0100, Simon Homolle wrote: Dear Stefano, What do you mean by strange results? Some figures describing the results would help to give you further help. You talked about 4 layers so i presume you used Skin, Skull, Brain and Lesion? Are these nested compartments? Could you show some visualisation of the meshes/segmentations you used? seg_i = ft_datatype_segmentation(segmentedmri,'segmentationstyle','indexed'); cfg = []; cfg.funparameter = 'seg'; cfg.funcolormap = lines(6); % distinct color per tissue cfg.location = 'center'; cfg.atlas = seg_i; % the segmentation can also be used as atlas ft_sourceplot(cfg, seg_i); Best regards, Simon Homölle PhD Candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Phone: +31-(0)24-36-65059 On 15 Dec 2017, at 10:51, Stefano Caschera > wrote: Hi, I would like to include a brain lesion to obtain a leadfield through openmeeg. I have already computed the meshes. Is it possible to use ft_prepare_headmodel and openmeeg_dsm ? And how? I tried but I've got strange results. As I know openmeeg can handle four layers but probably the brain has to be the inner one. If it is not possible using openmeeg, can you suggest me another method? Thank you, Stefano -- Stefano Caschera, PhD Student Neuroelectrical Imaging and BCI lab Fondazione Santa Lucia, IRCCS Via Ardeatina, 306 I-00179, Rome, Italy Department of Computer, Control, and Management Engineering "Antonio Ruberti" Sapienza, University of Rome V. Ariosto, 25 00185, Rome, Italy Tel +39 06 5150 1165 Email: stefano.caschera at uniroma1.it caschera at dis.uniroma1.it s.caschera at hsantalucia.it ___________________________________________________ _______________________________________________ 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 pascualm at key.uzh.ch Tue Dec 19 16:32:49 2017 From: pascualm at key.uzh.ch (pascualm at key.uzh.ch) Date: Wed, 20 Dec 2017 00:32:49 +0900 Subject: [FieldTrip] Measures of time series coupling based on generalized weighted multiple regression Message-ID: Dear Colleagues, The pre-print at: https://doi.org/10.1101/235721 entitled "Measures of time series coupling based on generalized weighted multiple regression" might be of interest to those working in the field of brain connectivity based on signals of electric neuronal activity. The abstract can be found below, under the signature. Cordially, Roberto ... Roberto D. Pascual-Marqui, PhD, PD The KEY Institute for Brain-Mind Research, University of Zurich Visiting Professor at Neuropsychiatry, Kansai Medical University, Osaka [www.keyinst.uzh.ch/loreta] [scholar.google.com/citations?user=pascualmarqui] /////////////// Abstract: The sharing and the transmission of information between cortical brain regions is carried out by mechanisms that are still not fully understood. A deeper understanding should shed light on how consciousness and cognition are implemented in the brain. Research activity in this field has recently been focusing on the discovery of non-conventional coupling mechanisms, such as all forms of cross-frequency couplings between diverse combinations of amplitudes and phases, applied to measured or estimated cortical signals of electric neuronal activity. However, all coupling measures that involve phase computation have poor statistical properties. In this work, the conventional estimators for the well-known phase-phase (phase synchronization or locking), phase-amplitude, and phase-amplitude-amplitude couplings are generalized by means of the weighted multiple regression model. The choice of appropriate weights produces estimators that bypass the need for computing the complex-valued phase. In addition, a new coupling, denoted as the inhibitory coupling (InhCo), is introduced and defined as the dependence of one complex-valued variable on the inverse and on the conjugate inverse of another complex-valued variable. A weighted version denoted as wInhCo is also introduced, bypassing the need for computing the inverse of a complex variable, which has very poor statistical properties. The importance of this form of inhibitory coupling is that it may capture well-known processes, such as the observed inverse alpha/gamma relation within the same cortical region, or the inverse alpha/alpha relation between distant cortical regions. /////////////// From a.stolk8 at gmail.com Thu Dec 21 04:40:38 2017 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Wed, 20 Dec 2017 19:40:38 -0800 Subject: [FieldTrip] iEEG analysis protocol Message-ID: For those of you who work with human intracranial data (iEEG), see here for a preprint of our analysis protocol (directly integrated with FieldTrip): https://www.biorxiv.org/content/early/2017/12/08/230912 *Integrated analysis of anatomical and electrophysiological human intracranial data* The exquisite spatiotemporal precision of human intracranial EEG recordings (iEEG) permits characterizing neural processing with a level of detail that is inaccessible to scalp-EEG, MEG, or fMRI. However, the same qualities that make iEEG an exceptionally powerful tool also present unique challenges. Until now, the fusion of anatomical data (MRI and CT images) with the electrophysiological data and its subsequent analysis has relied on technologically and conceptually challenging combinations of software. Here, we describe a comprehensive protocol that addresses the complexities associated with human iEEG, providing complete transparency and flexibility in the evolution of raw data into illustrative representations. The protocol is directly integrated with an open source toolbox for electrophysiological data analysis (FieldTrip). This allows iEEG researchers to build on a continuously growing body of scriptable and reproducible analysis methods that, over the past decade, have been developed and employed by a large research community. We demonstrate the protocol for an example complex iEEG data set to provide an intuitive and rapid approach to dealing with both neuroanatomical information and large electrophysiological data sets. We explain how the protocol can be largely automated, taking under an hour to complete, and readily adjusted to iEEG data sets with other characteristics. -------------- next part -------------- An HTML attachment was scrubbed... URL: From prabodh.sontakke at gmail.com Thu Dec 21 06:41:02 2017 From: prabodh.sontakke at gmail.com (prabodh sontakke) Date: Thu, 21 Dec 2017 11:11:02 +0530 Subject: [FieldTrip] help Message-ID: Dear Sir/Madam, I am doing a MTech project on "Study of complex network on EEG time series", doing so I need to calculate the connectivity measures .In the fieldtrip I don't know what value of Input and varagin to take and I am using the 23 electrodes location of Alzheimer patient with 400 sampling frequency and 124000 instances of each electrode location. Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From christoph.kayser at uni-bielefeld.de Fri Dec 22 21:48:33 2017 From: christoph.kayser at uni-bielefeld.de (Christoph Kayser) Date: Fri, 22 Dec 2017 21:48:33 +0100 Subject: [FieldTrip] PhD / Postdoc position Bielefeld, Germany Message-ID: <7130e2be26f92.5a3d7db1@uni-bielefeld.de> The Department of Cognitive Neuroscience at Bielefeld University, Germany, is advertising a 3-year Postdoctoral position, and a 3-year PhD position in auditory and multisensory neuroimaging studies. We are looking to fill two 3-year positions to complement our research on auditory or multisensory perception based on a combination of behavioural, neuroimaging (EEG) and statistical modelling techniques. The Department for Cognitive Neuroscience is dedicated to understanding the integration of sensory information in the brain. The planned studies use state of the art EEG imaging, combined with eyetracking, psychophysical paradigms, and substantive quantitative data analysis to better understand when and how the brain transforms sensory information into a conscious percept. Further details about our research can be found on our website http://www.uni-bielefeld.de/biologie/cns/ The positions involve all aspects of study design, implementation, data collection, data analysis and the write up of results. Contributions to the supervision of student projects or the preparation of practical courses are expected. Applicants should have a background in neuroscience, cognitive science, psychology, mathematics, or a relevant discipline. Applicants for the post-doc position should have a doctoral degree or equivalent title in a relevant discipline. We are especially interested in devotion to advanced quantitative data analysis including the capabilities to program or modify analysis code. The ideal applicant will have a strong analytical background and direct experience using MATLAB software. Applicants should have enthusiasm, and a clear, demonstrable capacity for acquiring expertise in these techniques. The positions are funded for 3 years starting ideally in April 2018, at Germany salary grades TV-L E13 (100% for post-doc, 65% for PhD student). The official adverts with all relevant details (in German) can be found here, under references ‘wiss17359’ and ‘wiss17356’: https://www.uni-bielefeld.de/Universitaet/Aktuelles/Stellenausschreibungen/auswiss_2013.html Questions and applications (cover letter, CV) should be directed until 31st of January 2018 to the PI: Christoph.Kayser at uni-bielefeld.de. -- ------------------------------------------------------------------------- Prof. Christoph Kayser Research Group Cognitive Neuroscience, Faculty of Biology UHG W3-110, Bielefeld University Universitätsstr. 25 33615 Bielefeld, Germany Tel. +49 (521) 106-5700 -------------- next part -------------- An HTML attachment was scrubbed... URL: From bick35 at gmail.com Fri Dec 29 17:24:01 2017 From: bick35 at gmail.com (steph) Date: Fri, 29 Dec 2017 11:24:01 -0500 Subject: [FieldTrip] Research Assistant Positions in ECoG Lab in New York Message-ID: Dear all, The ECoG Laboratory for Human Brain Mapping at the Feinstein Institute for Medical Research – Hofstra Northwell School of Medicine is looking for two research assistants. The successful candidates will help with the lab’s research into (1) improving the identification of functional and pathological brain regions in individuals suffering from epilepsy, (2) the neural mechanisms of cognition, and (3) characterization of macroscale human brain networks. The lab works exclusively with patients being evaluated for epilepsy surgery using methods such as electrocorticography (ECoG), MRI, fMRI, DTI, and direct electrical brain stimulation. The start date is as soon as possible. The responsibilities of both research assistants include assisting with the collection and analysis of the aforementioned data, managing lab equipment, and helping to present lab findings at conferences and in journals. One position will further focus on project management and administration, working with a research coordinator on IRB matters, and assistance with preparing progress reports and grant applications. The second position is more computationally focused and will require more in-depth analysis of neural and behavioral data, database management, and the development of analysis scripts (depending on proficiency with coding and signal processing). Both RAs will have their own scientific projects with dedicated time to work on them. Past research assistants in the lab have presented their work at clinical and basic research conferences, co-authored publications, and are working on first author publications. They have gone on to medical schools or PhD programs after spending 1-3 years in the lab. These unique positions will expose the successful applicant to basic and clinical neuroscience as well as neurosurgery, neurology, and neuropsychology. The location of the institute allows living either in the suburban neighborhoods of Long Island, or in vibrant Brooklyn or Queens. Some employees also commute from Manhattan. It is a great opportunity for recent post-bacs interested in medical school or graduate school in neuroscience/biomedical engineering. ------------- Qualifications ------------- Minimum: -B.A./B.S./B.E. in an appropriate discipline (e.g., neuroscience, psychology, biomedical engineering, computer science, physics) -For the second RA position: Experience with at least one programming language (MATLAB, R, or Python) and statistical analyses -1 year commitment Desirable: -Prior experience working with neuroimaging, EEG/MEG, or brain stimulation data -Previous experience working with patients -Previous work in a research laboratory that shows evidence of independent scholarship, problem solving, and motivation -2 year commitment preferred For more information about the position please send your CV along with your questions to Drs. Stephan Bickel (sbickel at northwell.edu ) and Ashesh Mehta (amehta.northwell.edu ). We are looking forward to hearing from you! -------------- next part -------------- An HTML attachment was scrubbed... URL: From michak at is.umk.pl Fri Dec 1 15:57:57 2017 From: michak at is.umk.pl (=?UTF-8?Q?Micha=C5=82_Komorowski?=) Date: Fri, 1 Dec 2017 23:57:57 +0900 Subject: [FieldTrip] non-existent mat in BEM headmodel Message-ID: When I had a problem with dipoli I have done this: If there is a problem with not finding file dipoli.glnx86 even if it exist in proper location, just install gcc-multilib package. refer to: - https://bbs.archlinux.org/viewtopic.php?id=131156 (about problem) - https://stackoverflow.com/questions/23970684/how-to-install-32-bit-glibc-on-64-bit-ubuntu (installing) So maybe try to install it and run again. Michał Komorowski -------------- next part -------------- An HTML attachment was scrubbed... URL: From boukje.habets at uni-bielefeld.de Tue Dec 5 10:55:28 2017 From: boukje.habets at uni-bielefeld.de (Boukje Habets) Date: Tue, 05 Dec 2017 10:55:28 +0100 Subject: [FieldTrip] Question about segmentation Message-ID: <71c0e7f647c8c.5a267b20@uni-bielefeld.de> Dear Fieldtrippers, Im new to Fieldtrip and have a question about segmentation. I want to do a freqanalysis on EEG data (Brainvision Recorder). I have one file per condition (so only containing one trigger code, and a start code at the beginning of the file) that i want to segment into 2sec pieces. Ive been trying to find a way to add a trigger with Fieldtrip, so that I can segment around a new trigger. Using a pre- and poststim timewindow around the trigger code is not a solution, as this gives me overlapping segments, which i do not want. This doesnt seem possible? After reading about cfg.trialfun, I saw that i can segment a continuous file into segments that i can define in terms of length (sec/samples). I guess this is the easiest way for me to segment my file. However, i want to be able to define the start and end point of segmentation, as my file contains a part in the beginning without codes (EEG was being recorded, but experiment was running yet). I have been playing around with the commands begsample and endsample, but that didnt change the window of segmentation (meaning it always segments my whole file, giving me 'empty' segments). Does anybody know how to solve this? Thanks for your time, Boukje Habets -- Dr. Boukje Habets Biopsychology & Cognitive Neuroscience (AE14) Faculty of Psychology and Sports Science | Bielefeld University PO-Box 100131 | D-33501 Bielefeld, Germany Phone: (49) 521 - 106 67 533 | Fax: (49) 521 - 106 15 67 530 Office: UHG T3-250 ---------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Tue Dec 5 11:52:16 2017 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Tue, 5 Dec 2017 11:52:16 +0100 Subject: [FieldTrip] Question about segmentation In-Reply-To: <71c0e7f647c8c.5a267b20@uni-bielefeld.de> References: <71c0e7f647c8c.5a267b20@uni-bielefeld.de> Message-ID: Hi Boukje, Your question is not totally clear to me, so apologies if this is not what you mean. I gather that you want to segment your data into non-overlapping 2-sec intervals, starting at a single trigger in your data? In any case, everything is possible, it just relies on understanding of the trl structure (always defined in samplenumbers) and the use of ft_preprocessing (in your case to read data and replace samples into a time-axis) and ft_redefinetrial (can be done afterwards) It you only want to segment your data into non-overlapping 2-sec intervals you could do something like this: 1. Use ft_preprocessing to read all your data as one long trial relative to your first trigger. For this you will need to enter a .trl field that has a single row with start, end, and offset in samplenr. You can get the sample number of your trigger (as well as the (relative) beginning and end sample numbers) using ft_read_events. The output of ft_preprocessing will give you a single trial defined in time around your trigger. 2. You can then use ft_redefinetrial to segment the data into short (non-overlapping) segments. Check it's help for details. But realize you will now define segments in terms of time, not samples. The benefit of this order of things is that in the first preprocessing step you can do things like filtering on the whole dataset, if you can spare the RAM. Hope this helps, Stephen Virus-free. www.avast.com <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On 5 December 2017 at 10:55, Boukje Habets wrote: > Dear Fieldtrippers, > > Im new to Fieldtrip and have a question about segmentation. I want to do a > freqanalysis on EEG data (Brainvision Recorder). > I have one file per condition (so only containing one trigger code, and a > start code at the beginning of the file) that i want to segment into 2sec > pieces. Ive been trying to find a way to add a trigger with Fieldtrip, so > that I can segment around a new trigger. Using a pre- and poststim > timewindow around the trigger code is not a solution, as this gives me > overlapping segments, which i do not want. > This doesnt seem possible? > > After reading about cfg.trialfun, I saw that i can segment a continuous > file into segments that i can define in terms of length (sec/samples). I > guess this is the easiest way for me to segment my file. However, i want to > be able to define the start and end point of segmentation, as my file > contains a part in the beginning without codes (EEG was being recorded, but > experiment was running yet). I have been playing around with the commands > begsample and endsample, but that didnt change the window of segmentation > (meaning it always segments my whole file, giving me 'empty' segments). > > Does anybody know how to solve this? > > Thanks for your time, > > Boukje Habets > > -- > > Dr. Boukje Habets > Biopsychology & Cognitive Neuroscience (AE14) > Faculty of Psychology and Sports Science | Bielefeld University > PO-Box 100131 | D-33501 Bielefeld, Germany > Phone: (49) 521 - 106 67 533 | Fax: (49) 521 - 106 15 67 530 > Office: UHG T3-250 > ---------------------------------------------------------------- > _______________________________________________ > 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 Dec 5 11:57:33 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 5 Dec 2017 10:57:33 +0000 Subject: [FieldTrip] Question about segmentation In-Reply-To: <71c0e7f647c8c.5a267b20@uni-bielefeld.de> References: <71c0e7f647c8c.5a267b20@uni-bielefeld.de> Message-ID: <851A8ED2-B8C9-4889-A997-F34090596BE5@donders.ru.nl> Dear Boukje, I don’t think that ‘adding a trigger’ is necessary. Instead, I think you should be able to do something like this: start_idx = X*fsample; end_idx = Y*fsample; (X and Y are the intended start and end points of the data, in seconds relative to the onset of the data recording, fsample is the sampling frequency in Hz) cfg = []; cfg.datafile = ‘the-name-of-your-datafile’; cfg.trl = [start_idx end_idx 0]; cfg = … (some other optional parameters to be defined here) data =ft_preprocessing(cfg); cfg = []; cfg.length = 2; data_segmented = ft_redefinetrial(cfg, data); best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > On 5 Dec 2017, at 10:55, Boukje Habets wrote: > > Dear Fieldtrippers, > > Im new to Fieldtrip and have a question about segmentation. I want to do a freqanalysis on EEG data (Brainvision Recorder). > I have one file per condition (so only containing one trigger code, and a start code at the beginning of the file) that i want to segment into 2sec pieces. Ive been trying to find a way to add a trigger with Fieldtrip, so that I can segment around a new trigger. Using a pre- and poststim timewindow around the trigger code is not a solution, as this gives me overlapping segments, which i do not want. > This doesnt seem possible? > > After reading about cfg.trialfun, I saw that i can segment a continuous file into segments that i can define in terms of length (sec/samples). I guess this is the easiest way for me to segment my file. However, i want to be able to define the start and end point of segmentation, as my file contains a part in the beginning without codes (EEG was being recorded, but experiment was running yet). I have been playing around with the commands begsample and endsample, but that didnt change the window of segmentation (meaning it always segments my whole file, giving me 'empty' segments). > > Does anybody know how to solve this? > > Thanks for your time, > > Boukje Habets > > -- > > Dr. Boukje Habets > Biopsychology & Cognitive Neuroscience (AE14) > Faculty of Psychology and Sports Science | Bielefeld University > PO-Box 100131 | D-33501 Bielefeld, Germany > Phone: (49) 521 - 106 67 533 | Fax: (49) 521 - 106 15 67 530 > Office: UHG T3-250 > ---------------------------------------------------------------- _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From boukje.habets at uni-bielefeld.de Thu Dec 7 10:09:56 2017 From: boukje.habets at uni-bielefeld.de (Boukje Habets) Date: Thu, 07 Dec 2017 10:09:56 +0100 Subject: [FieldTrip] Question about segmentation In-Reply-To: References: Message-ID: <7170d1644abcb.5a291374@uni-bielefeld.de> Hi Stephen and Jan-Mathijs, Thanks for your replies! I indeed did not need to add a trigger, i just didnt define the timewindow (with respect to the first trigger code) correctly before. Now its working just fine Thanks for your help, Boukje Am 05.12.17 12:12 schrieb fieldtrip-request at science.ru.nl: > > 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. Question about segmentation (Boukje Habets) > 2. Re: Question about segmentation (Stephen Whitmarsh) > 3. Re: Question about segmentation (Schoffelen, J.M. (Jan Mathijs)) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 05 Dec 2017 10:55:28 +0100 > From: Boukje Habets > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Question about segmentation > Message-ID: <71c0e7f647c8c.5a267b20 at uni-bielefeld.de> > Content-Type: text/plain; charset="us-ascii" > > Dear Fieldtrippers, > > Im new to Fieldtrip and have a question about segmentation. I want to do a freqanalysis on EEG data (Brainvision Recorder). > I have one file per condition (so only containing one trigger code, and a start code at the beginning of the file) that i want to segment into 2sec pieces. Ive been trying to find a way to add a trigger with Fieldtrip, so that I can segment around a new trigger. Using a pre- and poststim timewindow around the trigger code is not a solution, as this gives me overlapping segments, which i do not want. > This doesnt seem possible? > > After reading about cfg.trialfun, I saw that i can segment a continuous file into segments that i can define in terms of length (sec/samples). I guess this is the easiest way for me to segment my file. However, i want to be able to define the start and end point of segmentation, as my file contains a part in the beginning without codes (EEG was being recorded, but experiment was running yet). I have been playing around with the commands begsample and endsample, but that didnt change the window of segmentation (meaning it always segments my whole file, giving me 'empty' segments). > > Does anybody know how to solve this? > > Thanks for your time, > > Boukje Habets > > -- > > Dr. Boukje Habets > Biopsychology & Cognitive Neuroscience (AE14) > Faculty of Psychology and Sports Science | Bielefeld University > PO-Box 100131 | D-33501 Bielefeld, Germany > Phone: (49) 521 - 106 67 533 | Fax: (49) 521 - 106 15 67 530 > Office: UHG T3-250 > ---------------------------------------------------------------- > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 2 > Date: Tue, 5 Dec 2017 11:52:16 +0100 > From: Stephen Whitmarsh > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Question about segmentation > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi Boukje, > > Your question is not totally clear to me, so apologies if this is not what > you mean. I gather that you want to segment your data into non-overlapping > 2-sec intervals, starting at a single trigger in your data? > > In any case, everything is possible, it just relies on understanding of the > trl structure (always defined in samplenumbers) and the use of > ft_preprocessing (in your case to read data and replace samples into a > time-axis) and ft_redefinetrial (can be done afterwards) > > It you only want to segment your data into non-overlapping 2-sec intervals > you could do something like this: > > 1. Use ft_preprocessing to read all your data as one long trial relative > to your first trigger. For this you will need to enter a .trl field that > has a single row with start, end, and offset in samplenr. You can get the > sample number of your trigger (as well as the (relative) beginning and end > sample numbers) using ft_read_events. The output of ft_preprocessing will > give you a single trial defined in time around your trigger. > 2. You can then use ft_redefinetrial to segment the data into short > (non-overlapping) segments. Check it's help for details. But realize you > will now define segments in terms of time, not samples. > > The benefit of this order of things is that in the first preprocessing step > you can do things like filtering on the whole dataset, if you can spare the > RAM. > > Hope this helps, > Stephen > > > > > > > Virus-free. > www.avast.com > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > On 5 December 2017 at 10:55, Boukje Habets > wrote: > > > Dear Fieldtrippers, > > > > Im new to Fieldtrip and have a question about segmentation. I want to do a > > freqanalysis on EEG data (Brainvision Recorder). > > I have one file per condition (so only containing one trigger code, and a > > start code at the beginning of the file) that i want to segment into 2sec > > pieces. Ive been trying to find a way to add a trigger with Fieldtrip, so > > that I can segment around a new trigger. Using a pre- and poststim > > timewindow around the trigger code is not a solution, as this gives me > > overlapping segments, which i do not want. > > This doesnt seem possible? > > > > After reading about cfg.trialfun, I saw that i can segment a continuous > > file into segments that i can define in terms of length (sec/samples). I > > guess this is the easiest way for me to segment my file. However, i want to > > be able to define the start and end point of segmentation, as my file > > contains a part in the beginning without codes (EEG was being recorded, but > > experiment was running yet). I have been playing around with the commands > > begsample and endsample, but that didnt change the window of segmentation > > (meaning it always segments my whole file, giving me 'empty' segments). > > > > Does anybody know how to solve this? > > > > Thanks for your time, > > > > Boukje Habets > > > > -- > > > > Dr. Boukje Habets > > Biopsychology & Cognitive Neuroscience (AE14) > > Faculty of Psychology and Sports Science | Bielefeld University > > PO-Box 100131 | D-33501 Bielefeld, Germany > > Phone: (49) 521 - 106 67 533 | Fax: (49) 521 - 106 15 67 530 > > Office: UHG T3-250 > > ---------------------------------------------------------------- > > _______________________________________________ > > 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: 3 > Date: Tue, 5 Dec 2017 10:57:33 +0000 > From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Question about segmentation > Message-ID: <851A8ED2-B8C9-4889-A997-F34090596BE5 at donders.ru.nl> > Content-Type: text/plain; charset="utf-8" > > Dear Boukje, > > I don?t think that ?adding a trigger? is necessary. > > Instead, I think you should be able to do something like this: > > start_idx = X*fsample; > end_idx = Y*fsample; > > (X and Y are the intended start and end points of the data, in seconds relative to the onset of the data recording, fsample is the sampling frequency in Hz) > > cfg = []; > cfg.datafile = ?the-name-of-your-datafile?; > cfg.trl = [start_idx end_idx 0]; > cfg = ? (some other optional parameters to be defined here) > data =ft_preprocessing(cfg); > > cfg = []; > cfg.length = 2; > data_segmented = ft_redefinetrial(cfg, data); > > best wishes, > Jan-Mathijs > > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > > > > > > On 5 Dec 2017, at 10:55, Boukje Habets wrote: > > > > Dear Fieldtrippers, > > > > Im new to Fieldtrip and have a question about segmentation. I want to do a freqanalysis on EEG data (Brainvision Recorder). > > I have one file per condition (so only containing one trigger code, and a start code at the beginning of the file) that i want to segment into 2sec pieces. Ive been trying to find a way to add a trigger with Fieldtrip, so that I can segment around a new trigger. Using a pre- and poststim timewindow around the trigger code is not a solution, as this gives me overlapping segments, which i do not want. > > This doesnt seem possible? > > > > After reading about cfg.trialfun, I saw that i can segment a continuous file into segments that i can define in terms of length (sec/samples). I guess this is the easiest way for me to segment my file. However, i want to be able to define the start and end point of segmentation, as my file contains a part in the beginning without codes (EEG was being recorded, but experiment was running yet). I have been playing around with the commands begsample and endsample, but that didnt change the window of segmentation (meaning it always segments my whole file, giving me 'empty' segments). > > > > Does anybody know how to solve this? > > > > Thanks for your time, > > > > Boukje Habets > > > > -- > > > > Dr. Boukje Habets > > Biopsychology & Cognitive Neuroscience (AE14) > > Faculty of Psychology and Sports Science | Bielefeld University > > PO-Box 100131 | D-33501 Bielefeld, Germany > > Phone: (49) 521 - 106 67 533 | Fax: (49) 521 - 106 15 67 530 > > Office: UHG T3-250 > > ---------------------------------------------------------------- _______________________________________________ > > 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 > > End of fieldtrip Digest, Vol 85, Issue 3 > **************************************** > -- Dr. Boukje Habets Biopsychology & Cognitive Neuroscience (AE14) Faculty of Psychology and Sports Science | Bielefeld University PO-Box 100131 | D-33501 Bielefeld, Germany Phone: (49) 521 - 106 67 533 | Fax: (49) 521 - 106 15 67 530 Office: UHG T3-250 ---------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From akoles01 at mail.bbk.ac.uk Thu Dec 7 16:02:44 2017 From: akoles01 at mail.bbk.ac.uk (Anna Kolesnik) Date: Thu, 7 Dec 2017 15:02:44 +0000 Subject: [FieldTrip] Fwd: Netstation >> Fieldtrip conversion References: Message-ID: <3EDA86DB-659F-4ACA-AEA7-7F601A56AECD@mail.bbk.ac.uk> Dear members of the discussion list, I am looking for advice on how best to export pre-processed data from Netstation (version 5+) to Fieldtrip. We have data that is already filtered, segmented, and cleaned for artefacts that needs to be imported into Fieldtrip to run the time-frequency analysis. I know that it is possible to export the processed file to EEGLAB (although I know of some bugs), but has anyone successfully attempted to export to Fieldtrip? If so, what processing stage was it at and what was the format most suitable for this operation? Thank you in advance! Anna Kolesnik PhD student at the Centre for Brain and Cognitive Development Birkbeck College, University of London The BMA House, Tavistock Square WC1H 9JP From dariashn at ugr.es Thu Dec 7 20:24:30 2017 From: dariashn at ugr.es (=?utf-8?Q?Dar=C3=ADas_Manuel_Holgado_Nu=C3=B1ez?=) Date: Thu, 7 Dec 2017 20:24:30 +0100 Subject: [FieldTrip] Dependant samples F multivariate Message-ID: <9F7CADE9-5655-4686-B5E2-672D2CF82B08@ugr.es> Dear list My name is Darias Holgado and I am working in the Mind, Brain and Behaviour Research Centre in Granada on tDCS, EEG and Sport performance. I am analysing data of a project, where we recorded EEG under three tDCS’ stimulation. I have carried out a tDCS’s study in a within-subjects fashion. I have 3 conditions (anodal, cathodal and sham) x one measure (3x1). I am performing permutation test with the montecarlo approach and the ft_statfun_dsamplesFmultivariate. After having specified the design and running the script, it seems that it is ok, but in the output the total number of variables appears as 2, when it is supposed it should say 3. is it that correct? The design I specified it seems correct and it is working but this data is confusing. The cfg and design I use are as follows: %Within-Subject design 3 condition x 1 measure cfg.design(1,1:3*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub) 3*ones(1,Nsub)]; cfg.design(2,1:3*Nsub) = [1:Nsub 1:Nsub 1:Nsub]; cfg.ivar = 1; cfg.uvar = 2; cfg.channel = chanlocs; cfg.method = 'montecarlo'; cfg.statistic = 'ft_statfun_depsamplesFmultivariate'; cfg.correctm = 'cluster'; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.numrandomization = 5000; cfg.tail = 1; % cfg.clustertail = 1; cfg.alpha = 0.025; %cfg.frequency = freqrange; %cfg.avgoverfreq = 'yes'; cfg.neighbours = neighbours; Thank you for your time Best regards, --------------------------------------------------------------------------------- Darías Holgado Nuñez Mind, Brain and Behaviour Research Centre. University of Granada (Spain) https://www.researchgate.net/profile/Darias_Holgado -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at me.com Fri Dec 8 07:46:48 2017 From: nathanweisz at me.com (Nathan Weisz) Date: Fri, 08 Dec 2017 07:46:48 +0100 Subject: [FieldTrip] Postdoc Position @Blechert-lab Message-ID: FYI. Post-doc and PhD position focusing on the cognitive neuroscience of eating behavior at the center for cognitive neuroscience, Salzburg University, advertized on www.eat.sbg.ac.at -------------- next part -------------- An HTML attachment was scrubbed... URL: From i.charest at bham.ac.uk Fri Dec 8 13:58:00 2017 From: i.charest at bham.ac.uk (Ian Charest (School of Psychology)) Date: Fri, 8 Dec 2017 12:58:00 +0000 Subject: [FieldTrip] PhD position on the neurocognitive mechanisms of conscious access Message-ID: <97F95B166F2157409BE1EC68292F25AC4360AA19@EX13.adf.bham.ac.uk> Dear Fieldtrip discussion list, see below for details of a fully funded PhD position in Birmingham, UK. Best wishes, Ian Charest Lecturer, School of Psychology, University of Birmingham, UK iancharest.com _________________________ Advert: The School of Psychology at the University of Birmingham is looking for a bright and motivated PhD student to join the Charest Laboratory (iancharest.com). The PhD position to be filled is part of a project recently funded by a European Research Council Starting Grant entitled: "Spatio-Temporal Attention and Representation Tracking: the precise neural architecture of conscious object perception" (START). The Project: START is an ambitious programme of work that will make use of cutting-edge multivariate pattern analyses (MVPA) techniques to reveal the brain mechanisms that are critical for consciously perceiving visual objects in tasks that manipulate conscious access to visual information. The ability to consciously recognise faces, objects, or sounds is crucial for adaptive behaviour and survival. Yet, how our conscious experience of the world emerges in our brain remains unknown. The overall aim of the START programme is to fill an important gap in our understanding of consciousness by elucidating the neural underpinnings of conscious access. How does the brain select relevant information among distractors, and keep this information in mind? Why does our ability to consciously recognise salient objects sometimes fail under pressure and exhibit variability across days and individuals? START will try to address these important questions by precisely tracking where in the brain and when in time the representations critical for conscious access are established, by using novel approaches of Representational Similarity Analyses which combines the strengths of EEG, fMRI, and Deep Convolutional Neuronal Networks. This project will provide new insights on the precise spatio-temporal dynamics of conscious access, the mechanisms governing it, and the idiosyncratic subtleties behind the meanderings of consciousness. The candidate: The successful candidate will have (or be in the process of obtaining) a Masters degree in cognitive neuroscience or a related field. Previous experience with psychophysical tasks that manipulate conscious access in vision is desirable. Given the nature of the project, good understanding of and experience with fMRI, EEG/MEG and data analysis is desirable. Experience in using matlab or python (and Psychtoolbox or PsychoPy) is a requirement. The successful applicant will have experience with multivariate pattern analyses (Representational Similarity Analysis, Fisher linear discriminants, etc) of neuroimaging data. This post will require designing experiments, collecting and analysing data associated with the project, preparing manuscripts for publication, presenting results at national and international conferences and the possible supervision of research assistants and students. The School: The School of Psychology at the University of Birmingham (http://www.birmingham.ac.uk/schools/psychology/index.aspx) is one of the largest and most successful in the UK, currently ranked in the top 5 Schools in the country (REF 2014). The School is soon to move to new accommodation in the form of a fully refurbished, purpose-designed space and a new-build Centre for Human Brain Health that will house our new MRI, MEG, EEG, NIRS, sleep lab, and the recently appointed Chair in Translational Neuroscience. The University of Birmingham is an equal opportunities employer. The School of Psychology has a Bronze Athena SWAN award and strives to maintain a flexible and supportive environment that enables its staff to flourish. For informal enquiries about the project please contact Dr. Ian Charest (i.charest at bham.ac.uk). Formal applications must be made via the postgraduate admissions system in the School of Psychology. Applicants are encouraged to attach to their application a short and original project proposal (500 words). http://www.birmingham.ac.uk/students/courses/postgraduate/research/psych/psychology.aspx#CourseDetailsTab Full advert of the position on find a phd: https://www.findaphd.com/search/projectdetails.aspx?PJID=92145 -------------- next part -------------- An HTML attachment was scrubbed... URL: From omerxsharon at gmail.com Sat Dec 9 13:12:48 2017 From: omerxsharon at gmail.com (Omer Sharon) Date: Sat, 9 Dec 2017 14:12:48 +0200 Subject: [FieldTrip] Netstation >> Fieldtrip conversion Message-ID: Hi Anna Fieltrip could read the MFF file directly using ft_preprocessing(), use the folder like it was a file. In NS5 there is an issue with the triggers' files and the spaces should be replaces with underscores (fix it if you get an error). I move to field-trip in a very early stage, but you can export to fieldtrip in any stage you like. Good luck Omer Sharon PhD student at NirLab Department of physiology and pharmacology Sackler Faculty of Medicine Tel Aviv University, Israel On Fri, Dec 8, 2017 at 1:00 PM, wrote: > 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. Fwd: Netstation >> Fieldtrip conversion (Anna Kolesnik) > 2. Dependant samples F multivariate (Dar?as Manuel Holgado Nu?ez) > 3. Postdoc Position @Blechert-lab (Nathan Weisz) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 7 Dec 2017 15:02:44 +0000 > From: Anna Kolesnik > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Fwd: Netstation >> Fieldtrip conversion > Message-ID: <3EDA86DB-659F-4ACA-AEA7-7F601A56AECD at mail.bbk.ac.uk> > Content-Type: text/plain; charset=us-ascii > > Dear members of the discussion list, > > I am looking for advice on how best to export pre-processed data from > Netstation (version 5+) to Fieldtrip. We have data that is already > filtered, segmented, and cleaned for artefacts that needs to be imported > into Fieldtrip to run the time-frequency analysis. > I know that it is possible to export the processed file to EEGLAB > (although I know of some bugs), but has anyone successfully attempted to > export to Fieldtrip? If so, what processing stage was it at and what was > the format most suitable for this operation? > > > Thank you in advance! > > > Anna Kolesnik > PhD student at the Centre for Brain and Cognitive Development > Birkbeck College, University of London > The BMA House, Tavistock Square > WC1H 9JP > > > ------------------------------ > > Message: 2 > Date: Thu, 7 Dec 2017 20:24:30 +0100 > From: Dar?as Manuel Holgado Nu?ez > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Dependant samples F multivariate > Message-ID: <9F7CADE9-5655-4686-B5E2-672D2CF82B08 at ugr.es> > Content-Type: text/plain; charset="utf-8" > > Dear list > > My name is Darias Holgado and I am working in the Mind, Brain and > Behaviour Research Centre in Granada on tDCS, EEG and Sport performance. I > am analysing data of a project, where we recorded EEG under three tDCS? > stimulation. > > I have carried out a tDCS?s study in a within-subjects fashion. I have 3 > conditions (anodal, cathodal and sham) x one measure (3x1). I am performing > permutation test with the montecarlo approach and the ft_statfun_ > dsamplesFmultivariate. > After having specified the design and running the script, it seems that it > is ok, but in the output the total number of variables appears as 2, when > it is supposed it should say 3. is it that correct? The design I specified > it seems correct and it is working but this data is confusing. > > The cfg and design I use are as follows: > > %Within-Subject design 3 condition x 1 measure > cfg.design(1,1:3*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub) 3*ones(1,Nsub)]; > cfg.design(2,1:3*Nsub) = [1:Nsub 1:Nsub 1:Nsub]; > cfg.ivar = 1; > cfg.uvar = 2; > > cfg.channel = chanlocs; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_depsamplesFmultivariate'; > cfg.correctm = 'cluster'; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.numrandomization = 5000; > cfg.tail = 1; > % cfg.clustertail = 1; > cfg.alpha = 0.025; > %cfg.frequency = freqrange; > %cfg.avgoverfreq = 'yes'; > cfg.neighbours = neighbours; > > > Thank you for your time > > > Best regards, > ------------------------------------------------------------ > --------------------- > Dar?as Holgado Nu?ez > Mind, Brain and Behaviour Research Centre. > University of Granada (Spain) > https://www.researchgate.net/profile/Darias_Holgado > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20171207/96780d19/attachment-0001.html> > > ------------------------------ > > Message: 3 > Date: Fri, 08 Dec 2017 07:46:48 +0100 > From: Nathan Weisz > To: FieldTrip discussion list > Subject: [FieldTrip] Postdoc Position @Blechert-lab > Message-ID: > Content-Type: text/plain; charset="us-ascii" > > FYI. > > Post-doc and PhD position focusing on the cognitive neuroscience of > eating behavior at the center for cognitive neuroscience, Salzburg > University, advertized on > www.eat.sbg.ac.at > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20171208/0634be20/attachment-0001.html> > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 85, Issue 5 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From xiew1202 at gmail.com Sat Dec 9 13:23:48 2017 From: xiew1202 at gmail.com (Xie Wanze) Date: Sat, 09 Dec 2017 12:23:48 +0000 Subject: [FieldTrip] Netstation >> Fieldtrip conversion In-Reply-To: References: Message-ID: Anna, You may also read in the segmented data into Eeglab, and then use eeglab2fieldtrip function to export them into field trip format. Wanze Omer Sharon 于2017年12月9日 周六上午7:13写道: > Hi Anna > > Fieltrip could read the MFF file directly using ft_preprocessing(), use > the folder like it was a file. In NS5 there is an issue with the triggers' > files and the spaces should be replaces with underscores (fix it if you get > an error). > > I move to field-trip in a very early stage, but you can export to > fieldtrip in any stage you like. > > Good luck > > Omer Sharon > PhD student at NirLab > Department of physiology and pharmacology > Sackler Faculty of Medicine > Tel Aviv University, Israel > > > On Fri, Dec 8, 2017 at 1:00 PM, wrote: > >> 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. Fwd: Netstation >> Fieldtrip conversion (Anna Kolesnik) >> 2. Dependant samples F multivariate (Dar?as Manuel Holgado Nu?ez) >> 3. Postdoc Position @Blechert-lab (Nathan Weisz) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Thu, 7 Dec 2017 15:02:44 +0000 >> From: Anna Kolesnik >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] Fwd: Netstation >> Fieldtrip conversion >> Message-ID: <3EDA86DB-659F-4ACA-AEA7-7F601A56AECD at mail.bbk.ac.uk> >> Content-Type: text/plain; charset=us-ascii > > >> >> Dear members of the discussion list, >> >> I am looking for advice on how best to export pre-processed data from >> Netstation (version 5+) to Fieldtrip. We have data that is already >> filtered, segmented, and cleaned for artefacts that needs to be imported >> into Fieldtrip to run the time-frequency analysis. >> I know that it is possible to export the processed file to EEGLAB >> (although I know of some bugs), but has anyone successfully attempted to >> export to Fieldtrip? If so, what processing stage was it at and what was >> the format most suitable for this operation? >> >> >> Thank you in advance! >> >> >> Anna Kolesnik >> PhD student at the Centre for Brain and Cognitive Development >> Birkbeck College, University of London >> The BMA House, Tavistock Square >> WC1H 9JP >> >> >> ------------------------------ >> >> Message: 2 >> Date: Thu, 7 Dec 2017 20:24:30 +0100 >> From: Dar?as Manuel Holgado Nu?ez >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] Dependant samples F multivariate >> Message-ID: <9F7CADE9-5655-4686-B5E2-672D2CF82B08 at ugr.es> >> Content-Type: text/plain; charset="utf-8" >> >> Dear list >> >> My name is Darias Holgado and I am working in the Mind, Brain and >> Behaviour Research Centre in Granada on tDCS, EEG and Sport performance. I >> am analysing data of a project, where we recorded EEG under three tDCS? >> stimulation. >> >> I have carried out a tDCS?s study in a within-subjects fashion. I have 3 >> conditions (anodal, cathodal and sham) x one measure (3x1). I am performing >> permutation test with the montecarlo approach and the >> ft_statfun_dsamplesFmultivariate. >> After having specified the design and running the script, it seems that >> it is ok, but in the output the total number of variables appears as 2, >> when it is supposed it should say 3. is it that correct? The design I >> specified it seems correct and it is working but this data is confusing. >> >> The cfg and design I use are as follows: >> >> %Within-Subject design 3 condition x 1 measure >> cfg.design(1,1:3*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub) 3*ones(1,Nsub)]; >> cfg.design(2,1:3*Nsub) = [1:Nsub 1:Nsub 1:Nsub]; >> cfg.ivar = 1; >> cfg.uvar = 2; >> >> cfg.channel = chanlocs; >> cfg.method = 'montecarlo'; >> cfg.statistic = 'ft_statfun_depsamplesFmultivariate'; >> cfg.correctm = 'cluster'; >> cfg.clusterstatistic = 'maxsum'; >> cfg.minnbchan = 2; >> cfg.numrandomization = 5000; >> cfg.tail = 1; >> % cfg.clustertail = 1; >> cfg.alpha = 0.025; >> %cfg.frequency = freqrange; >> %cfg.avgoverfreq = 'yes'; >> cfg.neighbours = neighbours; >> >> >> Thank you for your time >> >> >> Best regards, >> >> --------------------------------------------------------------------------------- >> Dar?as Holgado Nu?ez >> Mind, Brain and Behaviour Research Centre. >> University of Granada (Spain) >> https://www.researchgate.net/profile/Darias_Holgado >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20171207/96780d19/attachment-0001.html >> > >> >> ------------------------------ >> >> Message: 3 >> Date: Fri, 08 Dec 2017 07:46:48 +0100 >> From: Nathan Weisz >> To: FieldTrip discussion list >> Subject: [FieldTrip] Postdoc Position @Blechert-lab >> Message-ID: >> Content-Type: text/plain; charset="us-ascii" >> >> FYI. >> >> Post-doc and PhD position focusing on the cognitive neuroscience of >> eating behavior at the center for cognitive neuroscience, Salzburg >> University, advertized on >> www.eat.sbg.ac.at >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20171208/0634be20/attachment-0001.html >> > >> >> ------------------------------ > > >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> End of fieldtrip Digest, Vol 85, Issue 5 >> **************************************** >> > > _______________________________________________ > 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 mikexcohen at gmail.com Sat Dec 9 22:14:41 2017 From: mikexcohen at gmail.com (Mike X Cohen) Date: Sat, 9 Dec 2017 22:14:41 +0100 Subject: [FieldTrip] Neuroscience data analysis summer-school announcements Message-ID: Dear colleagues, I am happy to announce *two week-long neuroscience data analysis courses* at the Radboud University in Netherlands in August 2018: One about time-frequency/synchronization/statistics, and one about linear algebra and source-separation. Below are the direct links to the course pages with application information. You can also find more information, including syllabi, on mikexcohen.com (scroll down to "In-vivo teaching"). *Please pass these links around to your colleagues/students who might be interested in one or both of these courses!* Analyzing neural time series data (6-10 August). Fourier transform, convolution, time-frequency analysis, synchronization, nonparametric statistics, simulating time series data. Linear algebra for neuroscientists (13-17 August). Matrix algebra, least-squares model fitting, eigendecomposition, multivariate source separation, state-space analyses, simulating multicomponent and multichannal time series data. Please note that applications, if approved, are selected on a first-come-first-serve basis, and that the number of participants for each course is limited. If you have questions about the courses, please feel free to contact me. Mike -- Mike X Cohen, PhD New online courses: mikexcohen.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From urieduardo at gmail.com Tue Dec 12 14:38:42 2017 From: urieduardo at gmail.com (=?UTF-8?Q?Uri_Eduardo_Ram=C3=ADrez_Pasos?=) Date: Tue, 12 Dec 2017 14:38:42 +0100 Subject: [FieldTrip] ft_sourcestatistics Message-ID: Dear fieldtrippers, I have a couple questions regarding source reconstruction that I hope you can help me with. 1. What is the best way to 'normalize' the position values in each forward model across my subjects so that I can run ft_sourcestatistics with cfg.statistic = 'ft_statfun_depsamplesT' ? 2. For one of my subjects, their leadfield keeps containing only NaNs. What could be the source (no pun intended) of the problem? 3. If my experiment's design has three 'levels' (say A1, A2, A3) for one 'factor', is it valid to subtract source values (obtained using method 'dics') for a comparison (e.g. A1-A3 vs A2-A3)? 4. What could have gone wrong when i get the warning “matrix is singular, close to singular or badly scaled. Results may be inaccurate.” How does one go about solving this? Best regards, Eduardo Ramírez, PhD candidate University of Würzburg -------------- next part -------------- An HTML attachment was scrubbed... URL: From mi_mayer at gmx.de Tue Dec 12 17:24:36 2017 From: mi_mayer at gmx.de (Irene Sophia Mayer) Date: Tue, 12 Dec 2017 17:24:36 +0100 Subject: [FieldTrip] Forward model EEG no MRI Message-ID: An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Tue Dec 12 17:37:51 2017 From: julian.keil at gmail.com (Julian Keil) Date: Tue, 12 Dec 2017 17:37:51 +0100 Subject: [FieldTrip] Forward model EEG no MRI In-Reply-To: References: Message-ID: <6EA73EED-F0B6-4676-99A0-FE1723A6578A@gmail.com> Dear Sophia, Fieldtrip comes with a number of precomputed Headmodels as well as standard MRIs which you can use (take a look into the „forward“-folder in the FT directory). You just have to make sure, your electrodes fit to the headmodels, but you would have to do this with a „real“ MRI as well. Good luck, Julian > Am 12.12.2017 um 17:24 schrieb Irene Sophia Mayer : > > Dear Fieldtrippers, > > I am attempting to do source reconstruction with Fieldtrip for the first time. I have EEG data but no MRI, just measurements of the electrode positions (with Zebris). However, I got already stuck at creating the forward model. > > Do I need to prepare my own sourcemodel with ft_prepare_sourcemodel or can I use the default options in ft_prepare_leadfield? > > All tutorials for creating a headmodel use an MRI, how can I do it without MRI images of my subjects? > > I have tried to use ft_prepare_headmodel with > headmodel = ft_prepare_headmodel(cfg, elec) with the output of FT_READ_SENS headmo > elec = > chanpos: [62x3 double] > elecpos: [62x3 double] > label: {62x1 cell} > type: 'eeg1005' > unit: 'mm' > > Unfortunately, it first told me: Either a segmentated MRI or data with closed triangulated mesh is required as data > input for the bemcp, dipoli or openmeeg method, and when I tried other methods, I got: The data input might already be a sensor description. Reference to non-existent field 'outputfile' > > I would be thankful for tips on how to do this! > > Best, > Sophia > _______________________________________________ > 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 julian.keil at gmail.com Tue Dec 12 17:49:01 2017 From: julian.keil at gmail.com (Julian Keil) Date: Tue, 12 Dec 2017 17:49:01 +0100 Subject: [FieldTrip] ft_sourcestatistics In-Reply-To: References: Message-ID: <6E37C718-06F7-439B-87B1-329FEFFACFF8@gmail.com> Dear Eduardo, @1: Do you mean normalize across the group? What you could do is interpolate the source-level data to an MRI and then use ft_volumenormalise to normalize all images to a common standard MRI. Check the FT site here: http://www.fieldtriptoolbox.org/tutorial/sourcemodel?s[]=warp Alternatively, you could take care that a common source grid is warped to the individual headmodel prior to the source analysis. In this case, you don’t need to normalize, as all subjects have the same number of sources. Check the tutorials on the FT-website for hints (e.g. http://www.fieldtriptoolbox.org/tutorial/salzburg?s[]=warp or http://www.fieldtriptoolbox.org/tutorial/beamformingextended?s[]=warp ) @2: Did you build your own headmodel? It might be that the elements of the headmodel intersect. I would go back and double check all steps leading up to the leadfield computation for errors. @3: I have no idea. @4: When does this happen? Good luck, Julian > Am 12.12.2017 um 14:38 schrieb Uri Eduardo Ramírez Pasos : > > Dear fieldtrippers, > > I have a couple questions regarding source reconstruction that I hope you can help me with. > > 1. What is the best way to 'normalize' the position values in each forward model across my subjects so that I can run ft_sourcestatistics with cfg.statistic = 'ft_statfun_depsamplesT' ? > > 2. For one of my subjects, their leadfield keeps containing only NaNs. What could be the source (no pun intended) of the problem? > > 3. If my experiment's design has three 'levels' (say A1, A2, A3) for one 'factor', is it valid to subtract source values (obtained using method 'dics') for a comparison (e.g. A1-A3 vs A2-A3)? > > 4. What could have gone wrong when i get the warning “matrix is singular, close to singular or badly scaled. Results may be inaccurate.” How does one go about solving this? > > Best regards, > Eduardo Ramírez, PhD candidate > University of Würzburg > _______________________________________________ > 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 cmista at bioingenieria.edu.ar Wed Dec 13 14:16:17 2017 From: cmista at bioingenieria.edu.ar (Christian Mista) Date: Wed, 13 Dec 2017 10:16:17 -0300 Subject: [FieldTrip] About connectivity and ft_topoplotCC Message-ID: Hi all, I'm starting with EEG analysis and Fiedltrip, and I'll would like to plot topographical maps of the connectivity (using imaginary part of coherence). I tried ft_topoplotCC to make a connection line/arrow graph, but I think I'm doing something wrong because the graph at 10 hz seems to be the same at 50 hz (attached some images). In addition, I was wondering if there is any way to set a threshold, so only fewer lines are plotted in the connection map. Below the code I'm using in matlab. %CODE %calculate coherence cfg = []; cfg.method = 'mtmfft'; cfg.taper = 'hanning'; %connectivity analysis needs power and phase -> 'pownadcsd' cfg.output = 'powandcsd'; % windows of frequency of interest foilim cfg.foilim = [1 60]; freq1 = ft_freqanalysis(cfg, data); %calculating the imaginary part of the coherence cfg = []; cfg.method = 'coh'; cfg.complex = 'absimag'; conn1 = ft_connectivityanalysis(cfg, freq1); %The conectome %figure;imagesc(conn1.cohspctrm); cfg = []; %my layout cfg.layout = layout; cfg.foi = 10; ft_topoplotCC(cfg, conn1) cfg = []; cfg.layout = layout; cfg.foi = 50; ft_topoplotCC(cfg, conn1) Best regards / Cordiales saludos Christian -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: connections10Hz.jpg Type: image/jpeg Size: 35441 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: connections50Hz.jpg Type: image/jpeg Size: 37955 bytes Desc: not available URL: From urieduardo at gmail.com Thu Dec 14 15:09:36 2017 From: urieduardo at gmail.com (=?UTF-8?Q?Uri_Eduardo_Ram=C3=ADrez_Pasos?=) Date: Thu, 14 Dec 2017 15:09:36 +0100 Subject: [FieldTrip] ft_sourcestatistics In-Reply-To: <6E37C718-06F7-439B-87B1-329FEFFACFF8@gmail.com> References: <6E37C718-06F7-439B-87B1-329FEFFACFF8@gmail.com> Message-ID: Dear Julian, Thanks a lot for your advice! Some follow-up questions and clarifications. 1a. I've looked at both approaches suggested in http://www.fieldtriptoolbox.org/tutorial/sourcemodel?s%5B%5D=warp. For the first approach (interpolate then normalize volumes), I used the following code (for EEG data), where I compute source values from two conditions, ON and OFF: cfg = []; cfg.method = 'dics'; cfg.frequency = 18; cfg.grid = grid; cfg.headmodel = headmodel; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.keepfilter = 'yes'; cfg.dics.realfilter = 'yes'; sourceAllneg_pos = ft_sourceanalysis(cfg, freqAll); cfg.grid.filter = sourceAllneg_pos.avg.filter; sourceOFF_con = ft_sourceanalysis(cfg, freqOFF); sourceON_con = ft_sourceanalysis(cfg, freqON); atlas = ft_read_atlas( '~/Documents/MATLAB/fieldtrip-20170618/template/atlas/aal/ROI_MNI_V4.nii'); cfg=[]; cfg.parameter='pow'; cont_sources{pat,1,1}=ft_sourceinterpolate(cfg, sourceOFF_con, atlas); cont_sources{pat,1,2}=ft_sourceinterpolate(cfg, sourceON_con, atlas); cfg=[]; cfg.parameter='pow'; [mri] = ft_volumenormalise(cfg, mri) Using ft_sourceinterpolate normalized the .pos values across my subjects, however I'm not sure what to do with the MRI variable created with ft_volumenormalize, but I'm guessing it should be integrated somewhere for results to be valid. 1b. I also tried the second method in the tutorial (Subject-specific grids), but the standard_sourcemodel3dxmm.mat files are based on the single shell method, and hence only relevant for MEG. When inputting cfg.grid.template= 'cortex_xxxx.surf.gii' (the other templates, which I hope are for EEG), I get the error using load: 'Number of columns on line 2 of ASCII file cortex_xxxx.surf.gii must be the same as previous lines. 2. Yes, I just used %get mri mri = ft_read_mri('0001.dcm'); %segment mri cfg=[]; cfg.output={'brain','skull','scalp'}; segmentedmri=ft_volumesegment(cfg,mri); % Y % r % a % s % n cfg=[]; cfg.tissue={'brain','skull','scalp'}; cfg.numvertices=[3000 2000 1000]; cfg.method='projectmesh';% or 'iso2mesh', 'isosurface', bnd=ft_prepare_mesh(cfg,segmentedmri); cfg=[]; cfg.method='bemcp';%or dipoli on a mac, or openmeeg headmodel = ft_prepare_headmodel(cfg,bnd); I'm using a mac, though I can't get dipoli to work. I've used this for the other subjects without every problem. I have no fiducials, not sure if this has any influence. 3. I've thought about this further, it doesn't make much sense to do this at the source level. 4. The warning occurs after running cfg=[]; cfg.method='bemcp';%or dipoli on a mac, or openmeeg headmodel = ft_prepare_headmodel(cfg,bnd); , though I also get this when running sample data from fieldtrip tutorials. Again, thank you immensely for your pointers! Uri 2017-12-12 17:49 GMT+01:00 Julian Keil : > Dear Eduardo, > > @1: Do you mean normalize across the group? What you could do is > interpolate the source-level data to an MRI and then use ft_volumenormalise > to normalize all images to a common standard MRI. Check the FT site here: > http://www.fieldtriptoolbox.org/tutorial/sourcemodel?s[]=warp > Alternatively, you could take care that a common source grid is warped to > the individual headmodel prior to the source analysis. In this case, you > don’t need to normalize, as all subjects have the same number of sources. > Check the tutorials on the FT-website for hints (e.g. http://www. > fieldtriptoolbox.org/tutorial/salzburg?s[]=warp or http:// > www.fieldtriptoolbox.org/tutorial/beamformingextended?s[]=warp) > > @2: Did you build your own headmodel? It might be that the elements of the > headmodel intersect. I would go back and double check all steps leading up > to the leadfield computation for errors. > > @3: I have no idea. > > @4: When does this happen? > > Good luck, > > Julian > > Am 12.12.2017 um 14:38 schrieb Uri Eduardo Ramírez Pasos < > urieduardo at gmail.com>: > > Dear fieldtrippers, > > I have a couple questions regarding source reconstruction that I hope you > can help me with. > > 1. What is the best way to 'normalize' the position values in each forward > model across my subjects so that I can run ft_sourcestatistics with > cfg.statistic = 'ft_statfun_depsamplesT' ? > > 2. For one of my subjects, their leadfield keeps containing only NaNs. > What could be the source (no pun intended) of the problem? > > 3. If my experiment's design has three 'levels' (say A1, A2, A3) for one > 'factor', is it valid to subtract source values (obtained using method > 'dics') for a comparison (e.g. A1-A3 vs A2-A3)? > > 4. What could have gone wrong when i get the warning “matrix is singular, > close to singular or badly scaled. Results may be inaccurate.” How does one > go about solving this? > > Best regards, > Eduardo Ramírez, PhD candidate > University of Würzburg > _______________________________________________ > 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 caschera at dis.uniroma1.it Fri Dec 15 10:51:20 2017 From: caschera at dis.uniroma1.it (Stefano Caschera) Date: Fri, 15 Dec 2017 10:51:20 +0100 Subject: [FieldTrip] Including brain lesion - OpenMeeg Message-ID: Hi, I would like to include a brain lesion to obtain a leadfield through openmeeg. I have already computed the meshes. Is it possible to use ft_prepare_headmodel and openmeeg_dsm ? And how? I tried but I've got strange results. As I know openmeeg can handle four layers but probably the brain has to be the inner one. If it is not possible using openmeeg, can you suggest me another method? Thank you, Stefano -- Stefano Caschera, PhD Student *Neuroelectrical Imaging and BCI lab* Fondazione Santa Lucia, IRCCS Via Ardeatina, 306 I-00179, Rome, Italy *Department of Computer, Control, andManagement Engineering "Antonio Ruberti"* Sapienza, University of Rome V. Ariosto, 25 00185, Rome, Italy Tel +39 06 5150 1165 Email: stefano.caschera at uniroma1.it caschera at dis.uniroma1.it s.caschera at hsantalucia.it ___________________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.homolle at donders.ru.nl Fri Dec 15 11:12:49 2017 From: s.homolle at donders.ru.nl (Simon Homolle) Date: Fri, 15 Dec 2017 11:12:49 +0100 Subject: [FieldTrip] Including brain lesion - OpenMeeg In-Reply-To: References: Message-ID: <92ED8BAC-B04F-4AF0-B989-46E94B2CD8F9@donders.ru.nl> Dear Stefano, What do you mean by strange results? Some figures describing the results would help to give you further help. You talked about 4 layers so i presume you used Skin, Skull, Brain and Lesion? Are these nested compartments? Could you show some visualisation of the meshes/segmentations you used? seg_i = ft_datatype_segmentation(segmentedmri,'segmentationstyle','indexed'); cfg = []; cfg.funparameter = 'seg'; cfg.funcolormap = lines(6); % distinct color per tissue cfg.location = 'center'; cfg.atlas = seg_i; % the segmentation can also be used as atlas ft_sourceplot(cfg, seg_i); Best regards, Simon Homölle PhD Candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Phone: +31-(0)24-36-65059 > On 15 Dec 2017, at 10:51, Stefano Caschera wrote: > > Hi, > I would like to include a brain lesion to obtain a leadfield through openmeeg. > > I have already computed the meshes. > > Is it possible to use ft_prepare_headmodel and openmeeg_dsm ? > And how? I tried but I've got strange results. As I know openmeeg can handle four layers but probably the brain has to be the inner one. > > If it is not possible using openmeeg, can you suggest me another method? > > Thank you, > Stefano > > -- > Stefano Caschera, PhD Student > > Neuroelectrical Imaging and BCI lab > Fondazione Santa Lucia, IRCCS > Via Ardeatina, 306 > I-00179, Rome, Italy > > Department of Computer, Control, and > Management Engineering "Antonio Ruberti" > Sapienza, University of Rome > V. Ariosto, 25 > 00185, Rome, Italy > > Tel +39 06 5150 1165 > Email: stefano.caschera at uniroma1.it > caschera at dis.uniroma1.it > s.caschera at hsantalucia.it > ___________________________________________________ > _______________________________________________ > 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 sarang at cfin.au.dk Fri Dec 15 23:11:17 2017 From: sarang at cfin.au.dk (Sarang S. Dalal) Date: Fri, 15 Dec 2017 22:11:17 +0000 Subject: [FieldTrip] Including brain lesion - OpenMeeg In-Reply-To: <92ED8BAC-B04F-4AF0-B989-46E94B2CD8F9@donders.ru.nl> References: <92ED8BAC-B04F-4AF0-B989-46E94B2CD8F9@donders.ru.nl> Message-ID: <1513375868.2120.25.camel@cfin.au.dk> Dear Stefano, OpenMEEG can do what you need. We wrote the function in FieldTrip that sets up the OpenMEEG parameters (fieldtrip/forward/private/leadfield_openmeeg.m) with the assumption that there would be either 3 layers (scalp, skull, brain) or 4 layers (scalp, skull, csf, brain). These layers are assumed to be nested from outside to inside, with no surfaces crossing or touching. As Simon suggested, you probably have lesion nested within brain. So, if you don't have a CSF layer, you could use the 4-layer functionality that is already there, with the order [scalp skull brain lesion]. You will have to configure cfg.conductivity appropriately with the same order. You may also take a look at the examples from my group where we script MRI segmentations and set up OpenMEEG computations in practice (for 3- and 4-layer nested geometries): https://github.com/meeg-cfin/nemolab/blob/master/basics/nemo_mriproc.m https://github.com/meeg-cfin/nemolab/blob/master/basics/nemo_makeleadfield.m OpenMEEG will also support non-nested configurations, but you will have to adapt leadfield_openmeeg.m to get it to work with FieldTrip. You can have a look at the documentation on the OpenMEEG website for a description of how to write the parameter files for that situation. Cheers, Sarang On Fri, 2017-12-15 at 11:12 +0100, Simon Homolle wrote: Dear Stefano, What do you mean by strange results? Some figures describing the results would help to give you further help. You talked about 4 layers so i presume you used Skin, Skull, Brain and Lesion? Are these nested compartments? Could you show some visualisation of the meshes/segmentations you used? seg_i = ft_datatype_segmentation(segmentedmri,'segmentationstyle','indexed'); cfg = []; cfg.funparameter = 'seg'; cfg.funcolormap = lines(6); % distinct color per tissue cfg.location = 'center'; cfg.atlas = seg_i; % the segmentation can also be used as atlas ft_sourceplot(cfg, seg_i); Best regards, Simon Homölle PhD Candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Phone: +31-(0)24-36-65059 On 15 Dec 2017, at 10:51, Stefano Caschera > wrote: Hi, I would like to include a brain lesion to obtain a leadfield through openmeeg. I have already computed the meshes. Is it possible to use ft_prepare_headmodel and openmeeg_dsm ? And how? I tried but I've got strange results. As I know openmeeg can handle four layers but probably the brain has to be the inner one. If it is not possible using openmeeg, can you suggest me another method? Thank you, Stefano -- Stefano Caschera, PhD Student Neuroelectrical Imaging and BCI lab Fondazione Santa Lucia, IRCCS Via Ardeatina, 306 I-00179, Rome, Italy Department of Computer, Control, and Management Engineering "Antonio Ruberti" Sapienza, University of Rome V. Ariosto, 25 00185, Rome, Italy Tel +39 06 5150 1165 Email: stefano.caschera at uniroma1.it caschera at dis.uniroma1.it s.caschera at hsantalucia.it ___________________________________________________ _______________________________________________ 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 pascualm at key.uzh.ch Tue Dec 19 16:32:49 2017 From: pascualm at key.uzh.ch (pascualm at key.uzh.ch) Date: Wed, 20 Dec 2017 00:32:49 +0900 Subject: [FieldTrip] Measures of time series coupling based on generalized weighted multiple regression Message-ID: Dear Colleagues, The pre-print at: https://doi.org/10.1101/235721 entitled "Measures of time series coupling based on generalized weighted multiple regression" might be of interest to those working in the field of brain connectivity based on signals of electric neuronal activity. The abstract can be found below, under the signature. Cordially, Roberto ... Roberto D. Pascual-Marqui, PhD, PD The KEY Institute for Brain-Mind Research, University of Zurich Visiting Professor at Neuropsychiatry, Kansai Medical University, Osaka [www.keyinst.uzh.ch/loreta] [scholar.google.com/citations?user=pascualmarqui] /////////////// Abstract: The sharing and the transmission of information between cortical brain regions is carried out by mechanisms that are still not fully understood. A deeper understanding should shed light on how consciousness and cognition are implemented in the brain. Research activity in this field has recently been focusing on the discovery of non-conventional coupling mechanisms, such as all forms of cross-frequency couplings between diverse combinations of amplitudes and phases, applied to measured or estimated cortical signals of electric neuronal activity. However, all coupling measures that involve phase computation have poor statistical properties. In this work, the conventional estimators for the well-known phase-phase (phase synchronization or locking), phase-amplitude, and phase-amplitude-amplitude couplings are generalized by means of the weighted multiple regression model. The choice of appropriate weights produces estimators that bypass the need for computing the complex-valued phase. In addition, a new coupling, denoted as the inhibitory coupling (InhCo), is introduced and defined as the dependence of one complex-valued variable on the inverse and on the conjugate inverse of another complex-valued variable. A weighted version denoted as wInhCo is also introduced, bypassing the need for computing the inverse of a complex variable, which has very poor statistical properties. The importance of this form of inhibitory coupling is that it may capture well-known processes, such as the observed inverse alpha/gamma relation within the same cortical region, or the inverse alpha/alpha relation between distant cortical regions. /////////////// From a.stolk8 at gmail.com Thu Dec 21 04:40:38 2017 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Wed, 20 Dec 2017 19:40:38 -0800 Subject: [FieldTrip] iEEG analysis protocol Message-ID: For those of you who work with human intracranial data (iEEG), see here for a preprint of our analysis protocol (directly integrated with FieldTrip): https://www.biorxiv.org/content/early/2017/12/08/230912 *Integrated analysis of anatomical and electrophysiological human intracranial data* The exquisite spatiotemporal precision of human intracranial EEG recordings (iEEG) permits characterizing neural processing with a level of detail that is inaccessible to scalp-EEG, MEG, or fMRI. However, the same qualities that make iEEG an exceptionally powerful tool also present unique challenges. Until now, the fusion of anatomical data (MRI and CT images) with the electrophysiological data and its subsequent analysis has relied on technologically and conceptually challenging combinations of software. Here, we describe a comprehensive protocol that addresses the complexities associated with human iEEG, providing complete transparency and flexibility in the evolution of raw data into illustrative representations. The protocol is directly integrated with an open source toolbox for electrophysiological data analysis (FieldTrip). This allows iEEG researchers to build on a continuously growing body of scriptable and reproducible analysis methods that, over the past decade, have been developed and employed by a large research community. We demonstrate the protocol for an example complex iEEG data set to provide an intuitive and rapid approach to dealing with both neuroanatomical information and large electrophysiological data sets. We explain how the protocol can be largely automated, taking under an hour to complete, and readily adjusted to iEEG data sets with other characteristics. -------------- next part -------------- An HTML attachment was scrubbed... URL: From prabodh.sontakke at gmail.com Thu Dec 21 06:41:02 2017 From: prabodh.sontakke at gmail.com (prabodh sontakke) Date: Thu, 21 Dec 2017 11:11:02 +0530 Subject: [FieldTrip] help Message-ID: Dear Sir/Madam, I am doing a MTech project on "Study of complex network on EEG time series", doing so I need to calculate the connectivity measures .In the fieldtrip I don't know what value of Input and varagin to take and I am using the 23 electrodes location of Alzheimer patient with 400 sampling frequency and 124000 instances of each electrode location. Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From christoph.kayser at uni-bielefeld.de Fri Dec 22 21:48:33 2017 From: christoph.kayser at uni-bielefeld.de (Christoph Kayser) Date: Fri, 22 Dec 2017 21:48:33 +0100 Subject: [FieldTrip] PhD / Postdoc position Bielefeld, Germany Message-ID: <7130e2be26f92.5a3d7db1@uni-bielefeld.de> The Department of Cognitive Neuroscience at Bielefeld University, Germany, is advertising a 3-year Postdoctoral position, and a 3-year PhD position in auditory and multisensory neuroimaging studies. We are looking to fill two 3-year positions to complement our research on auditory or multisensory perception based on a combination of behavioural, neuroimaging (EEG) and statistical modelling techniques. The Department for Cognitive Neuroscience is dedicated to understanding the integration of sensory information in the brain. The planned studies use state of the art EEG imaging, combined with eyetracking, psychophysical paradigms, and substantive quantitative data analysis to better understand when and how the brain transforms sensory information into a conscious percept. Further details about our research can be found on our website http://www.uni-bielefeld.de/biologie/cns/ The positions involve all aspects of study design, implementation, data collection, data analysis and the write up of results. Contributions to the supervision of student projects or the preparation of practical courses are expected. Applicants should have a background in neuroscience, cognitive science, psychology, mathematics, or a relevant discipline. Applicants for the post-doc position should have a doctoral degree or equivalent title in a relevant discipline. We are especially interested in devotion to advanced quantitative data analysis including the capabilities to program or modify analysis code. The ideal applicant will have a strong analytical background and direct experience using MATLAB software. Applicants should have enthusiasm, and a clear, demonstrable capacity for acquiring expertise in these techniques. The positions are funded for 3 years starting ideally in April 2018, at Germany salary grades TV-L E13 (100% for post-doc, 65% for PhD student). The official adverts with all relevant details (in German) can be found here, under references ‘wiss17359’ and ‘wiss17356’: https://www.uni-bielefeld.de/Universitaet/Aktuelles/Stellenausschreibungen/auswiss_2013.html Questions and applications (cover letter, CV) should be directed until 31st of January 2018 to the PI: Christoph.Kayser at uni-bielefeld.de. -- ------------------------------------------------------------------------- Prof. Christoph Kayser Research Group Cognitive Neuroscience, Faculty of Biology UHG W3-110, Bielefeld University Universitätsstr. 25 33615 Bielefeld, Germany Tel. +49 (521) 106-5700 -------------- next part -------------- An HTML attachment was scrubbed... URL: From bick35 at gmail.com Fri Dec 29 17:24:01 2017 From: bick35 at gmail.com (steph) Date: Fri, 29 Dec 2017 11:24:01 -0500 Subject: [FieldTrip] Research Assistant Positions in ECoG Lab in New York Message-ID: Dear all, The ECoG Laboratory for Human Brain Mapping at the Feinstein Institute for Medical Research – Hofstra Northwell School of Medicine is looking for two research assistants. The successful candidates will help with the lab’s research into (1) improving the identification of functional and pathological brain regions in individuals suffering from epilepsy, (2) the neural mechanisms of cognition, and (3) characterization of macroscale human brain networks. The lab works exclusively with patients being evaluated for epilepsy surgery using methods such as electrocorticography (ECoG), MRI, fMRI, DTI, and direct electrical brain stimulation. The start date is as soon as possible. The responsibilities of both research assistants include assisting with the collection and analysis of the aforementioned data, managing lab equipment, and helping to present lab findings at conferences and in journals. One position will further focus on project management and administration, working with a research coordinator on IRB matters, and assistance with preparing progress reports and grant applications. The second position is more computationally focused and will require more in-depth analysis of neural and behavioral data, database management, and the development of analysis scripts (depending on proficiency with coding and signal processing). Both RAs will have their own scientific projects with dedicated time to work on them. Past research assistants in the lab have presented their work at clinical and basic research conferences, co-authored publications, and are working on first author publications. They have gone on to medical schools or PhD programs after spending 1-3 years in the lab. These unique positions will expose the successful applicant to basic and clinical neuroscience as well as neurosurgery, neurology, and neuropsychology. The location of the institute allows living either in the suburban neighborhoods of Long Island, or in vibrant Brooklyn or Queens. Some employees also commute from Manhattan. It is a great opportunity for recent post-bacs interested in medical school or graduate school in neuroscience/biomedical engineering. ------------- Qualifications ------------- Minimum: -B.A./B.S./B.E. in an appropriate discipline (e.g., neuroscience, psychology, biomedical engineering, computer science, physics) -For the second RA position: Experience with at least one programming language (MATLAB, R, or Python) and statistical analyses -1 year commitment Desirable: -Prior experience working with neuroimaging, EEG/MEG, or brain stimulation data -Previous experience working with patients -Previous work in a research laboratory that shows evidence of independent scholarship, problem solving, and motivation -2 year commitment preferred For more information about the position please send your CV along with your questions to Drs. Stephan Bickel (sbickel at northwell.edu ) and Ashesh Mehta (amehta.northwell.edu ). We are looking forward to hearing from you! -------------- next part -------------- An HTML attachment was scrubbed... URL: From michak at is.umk.pl Fri Dec 1 15:57:57 2017 From: michak at is.umk.pl (=?UTF-8?Q?Micha=C5=82_Komorowski?=) Date: Fri, 1 Dec 2017 23:57:57 +0900 Subject: [FieldTrip] non-existent mat in BEM headmodel Message-ID: When I had a problem with dipoli I have done this: If there is a problem with not finding file dipoli.glnx86 even if it exist in proper location, just install gcc-multilib package. refer to: - https://bbs.archlinux.org/viewtopic.php?id=131156 (about problem) - https://stackoverflow.com/questions/23970684/how-to-install-32-bit-glibc-on-64-bit-ubuntu (installing) So maybe try to install it and run again. Michał Komorowski -------------- next part -------------- An HTML attachment was scrubbed... URL: From boukje.habets at uni-bielefeld.de Tue Dec 5 10:55:28 2017 From: boukje.habets at uni-bielefeld.de (Boukje Habets) Date: Tue, 05 Dec 2017 10:55:28 +0100 Subject: [FieldTrip] Question about segmentation Message-ID: <71c0e7f647c8c.5a267b20@uni-bielefeld.de> Dear Fieldtrippers, Im new to Fieldtrip and have a question about segmentation. I want to do a freqanalysis on EEG data (Brainvision Recorder). I have one file per condition (so only containing one trigger code, and a start code at the beginning of the file) that i want to segment into 2sec pieces. Ive been trying to find a way to add a trigger with Fieldtrip, so that I can segment around a new trigger. Using a pre- and poststim timewindow around the trigger code is not a solution, as this gives me overlapping segments, which i do not want. This doesnt seem possible? After reading about cfg.trialfun, I saw that i can segment a continuous file into segments that i can define in terms of length (sec/samples). I guess this is the easiest way for me to segment my file. However, i want to be able to define the start and end point of segmentation, as my file contains a part in the beginning without codes (EEG was being recorded, but experiment was running yet). I have been playing around with the commands begsample and endsample, but that didnt change the window of segmentation (meaning it always segments my whole file, giving me 'empty' segments). Does anybody know how to solve this? Thanks for your time, Boukje Habets -- Dr. Boukje Habets Biopsychology & Cognitive Neuroscience (AE14) Faculty of Psychology and Sports Science | Bielefeld University PO-Box 100131 | D-33501 Bielefeld, Germany Phone: (49) 521 - 106 67 533 | Fax: (49) 521 - 106 15 67 530 Office: UHG T3-250 ---------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Tue Dec 5 11:52:16 2017 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Tue, 5 Dec 2017 11:52:16 +0100 Subject: [FieldTrip] Question about segmentation In-Reply-To: <71c0e7f647c8c.5a267b20@uni-bielefeld.de> References: <71c0e7f647c8c.5a267b20@uni-bielefeld.de> Message-ID: Hi Boukje, Your question is not totally clear to me, so apologies if this is not what you mean. I gather that you want to segment your data into non-overlapping 2-sec intervals, starting at a single trigger in your data? In any case, everything is possible, it just relies on understanding of the trl structure (always defined in samplenumbers) and the use of ft_preprocessing (in your case to read data and replace samples into a time-axis) and ft_redefinetrial (can be done afterwards) It you only want to segment your data into non-overlapping 2-sec intervals you could do something like this: 1. Use ft_preprocessing to read all your data as one long trial relative to your first trigger. For this you will need to enter a .trl field that has a single row with start, end, and offset in samplenr. You can get the sample number of your trigger (as well as the (relative) beginning and end sample numbers) using ft_read_events. The output of ft_preprocessing will give you a single trial defined in time around your trigger. 2. You can then use ft_redefinetrial to segment the data into short (non-overlapping) segments. Check it's help for details. But realize you will now define segments in terms of time, not samples. The benefit of this order of things is that in the first preprocessing step you can do things like filtering on the whole dataset, if you can spare the RAM. Hope this helps, Stephen Virus-free. www.avast.com <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On 5 December 2017 at 10:55, Boukje Habets wrote: > Dear Fieldtrippers, > > Im new to Fieldtrip and have a question about segmentation. I want to do a > freqanalysis on EEG data (Brainvision Recorder). > I have one file per condition (so only containing one trigger code, and a > start code at the beginning of the file) that i want to segment into 2sec > pieces. Ive been trying to find a way to add a trigger with Fieldtrip, so > that I can segment around a new trigger. Using a pre- and poststim > timewindow around the trigger code is not a solution, as this gives me > overlapping segments, which i do not want. > This doesnt seem possible? > > After reading about cfg.trialfun, I saw that i can segment a continuous > file into segments that i can define in terms of length (sec/samples). I > guess this is the easiest way for me to segment my file. However, i want to > be able to define the start and end point of segmentation, as my file > contains a part in the beginning without codes (EEG was being recorded, but > experiment was running yet). I have been playing around with the commands > begsample and endsample, but that didnt change the window of segmentation > (meaning it always segments my whole file, giving me 'empty' segments). > > Does anybody know how to solve this? > > Thanks for your time, > > Boukje Habets > > -- > > Dr. Boukje Habets > Biopsychology & Cognitive Neuroscience (AE14) > Faculty of Psychology and Sports Science | Bielefeld University > PO-Box 100131 | D-33501 Bielefeld, Germany > Phone: (49) 521 - 106 67 533 | Fax: (49) 521 - 106 15 67 530 > Office: UHG T3-250 > ---------------------------------------------------------------- > _______________________________________________ > 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 Dec 5 11:57:33 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 5 Dec 2017 10:57:33 +0000 Subject: [FieldTrip] Question about segmentation In-Reply-To: <71c0e7f647c8c.5a267b20@uni-bielefeld.de> References: <71c0e7f647c8c.5a267b20@uni-bielefeld.de> Message-ID: <851A8ED2-B8C9-4889-A997-F34090596BE5@donders.ru.nl> Dear Boukje, I don’t think that ‘adding a trigger’ is necessary. Instead, I think you should be able to do something like this: start_idx = X*fsample; end_idx = Y*fsample; (X and Y are the intended start and end points of the data, in seconds relative to the onset of the data recording, fsample is the sampling frequency in Hz) cfg = []; cfg.datafile = ‘the-name-of-your-datafile’; cfg.trl = [start_idx end_idx 0]; cfg = … (some other optional parameters to be defined here) data =ft_preprocessing(cfg); cfg = []; cfg.length = 2; data_segmented = ft_redefinetrial(cfg, data); best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > On 5 Dec 2017, at 10:55, Boukje Habets wrote: > > Dear Fieldtrippers, > > Im new to Fieldtrip and have a question about segmentation. I want to do a freqanalysis on EEG data (Brainvision Recorder). > I have one file per condition (so only containing one trigger code, and a start code at the beginning of the file) that i want to segment into 2sec pieces. Ive been trying to find a way to add a trigger with Fieldtrip, so that I can segment around a new trigger. Using a pre- and poststim timewindow around the trigger code is not a solution, as this gives me overlapping segments, which i do not want. > This doesnt seem possible? > > After reading about cfg.trialfun, I saw that i can segment a continuous file into segments that i can define in terms of length (sec/samples). I guess this is the easiest way for me to segment my file. However, i want to be able to define the start and end point of segmentation, as my file contains a part in the beginning without codes (EEG was being recorded, but experiment was running yet). I have been playing around with the commands begsample and endsample, but that didnt change the window of segmentation (meaning it always segments my whole file, giving me 'empty' segments). > > Does anybody know how to solve this? > > Thanks for your time, > > Boukje Habets > > -- > > Dr. Boukje Habets > Biopsychology & Cognitive Neuroscience (AE14) > Faculty of Psychology and Sports Science | Bielefeld University > PO-Box 100131 | D-33501 Bielefeld, Germany > Phone: (49) 521 - 106 67 533 | Fax: (49) 521 - 106 15 67 530 > Office: UHG T3-250 > ---------------------------------------------------------------- _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From boukje.habets at uni-bielefeld.de Thu Dec 7 10:09:56 2017 From: boukje.habets at uni-bielefeld.de (Boukje Habets) Date: Thu, 07 Dec 2017 10:09:56 +0100 Subject: [FieldTrip] Question about segmentation In-Reply-To: References: Message-ID: <7170d1644abcb.5a291374@uni-bielefeld.de> Hi Stephen and Jan-Mathijs, Thanks for your replies! I indeed did not need to add a trigger, i just didnt define the timewindow (with respect to the first trigger code) correctly before. Now its working just fine Thanks for your help, Boukje Am 05.12.17 12:12 schrieb fieldtrip-request at science.ru.nl: > > 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. Question about segmentation (Boukje Habets) > 2. Re: Question about segmentation (Stephen Whitmarsh) > 3. Re: Question about segmentation (Schoffelen, J.M. (Jan Mathijs)) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 05 Dec 2017 10:55:28 +0100 > From: Boukje Habets > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Question about segmentation > Message-ID: <71c0e7f647c8c.5a267b20 at uni-bielefeld.de> > Content-Type: text/plain; charset="us-ascii" > > Dear Fieldtrippers, > > Im new to Fieldtrip and have a question about segmentation. I want to do a freqanalysis on EEG data (Brainvision Recorder). > I have one file per condition (so only containing one trigger code, and a start code at the beginning of the file) that i want to segment into 2sec pieces. Ive been trying to find a way to add a trigger with Fieldtrip, so that I can segment around a new trigger. Using a pre- and poststim timewindow around the trigger code is not a solution, as this gives me overlapping segments, which i do not want. > This doesnt seem possible? > > After reading about cfg.trialfun, I saw that i can segment a continuous file into segments that i can define in terms of length (sec/samples). I guess this is the easiest way for me to segment my file. However, i want to be able to define the start and end point of segmentation, as my file contains a part in the beginning without codes (EEG was being recorded, but experiment was running yet). I have been playing around with the commands begsample and endsample, but that didnt change the window of segmentation (meaning it always segments my whole file, giving me 'empty' segments). > > Does anybody know how to solve this? > > Thanks for your time, > > Boukje Habets > > -- > > Dr. Boukje Habets > Biopsychology & Cognitive Neuroscience (AE14) > Faculty of Psychology and Sports Science | Bielefeld University > PO-Box 100131 | D-33501 Bielefeld, Germany > Phone: (49) 521 - 106 67 533 | Fax: (49) 521 - 106 15 67 530 > Office: UHG T3-250 > ---------------------------------------------------------------- > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 2 > Date: Tue, 5 Dec 2017 11:52:16 +0100 > From: Stephen Whitmarsh > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Question about segmentation > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi Boukje, > > Your question is not totally clear to me, so apologies if this is not what > you mean. I gather that you want to segment your data into non-overlapping > 2-sec intervals, starting at a single trigger in your data? > > In any case, everything is possible, it just relies on understanding of the > trl structure (always defined in samplenumbers) and the use of > ft_preprocessing (in your case to read data and replace samples into a > time-axis) and ft_redefinetrial (can be done afterwards) > > It you only want to segment your data into non-overlapping 2-sec intervals > you could do something like this: > > 1. Use ft_preprocessing to read all your data as one long trial relative > to your first trigger. For this you will need to enter a .trl field that > has a single row with start, end, and offset in samplenr. You can get the > sample number of your trigger (as well as the (relative) beginning and end > sample numbers) using ft_read_events. The output of ft_preprocessing will > give you a single trial defined in time around your trigger. > 2. You can then use ft_redefinetrial to segment the data into short > (non-overlapping) segments. Check it's help for details. But realize you > will now define segments in terms of time, not samples. > > The benefit of this order of things is that in the first preprocessing step > you can do things like filtering on the whole dataset, if you can spare the > RAM. > > Hope this helps, > Stephen > > > > > > > Virus-free. > www.avast.com > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > On 5 December 2017 at 10:55, Boukje Habets > wrote: > > > Dear Fieldtrippers, > > > > Im new to Fieldtrip and have a question about segmentation. I want to do a > > freqanalysis on EEG data (Brainvision Recorder). > > I have one file per condition (so only containing one trigger code, and a > > start code at the beginning of the file) that i want to segment into 2sec > > pieces. Ive been trying to find a way to add a trigger with Fieldtrip, so > > that I can segment around a new trigger. Using a pre- and poststim > > timewindow around the trigger code is not a solution, as this gives me > > overlapping segments, which i do not want. > > This doesnt seem possible? > > > > After reading about cfg.trialfun, I saw that i can segment a continuous > > file into segments that i can define in terms of length (sec/samples). I > > guess this is the easiest way for me to segment my file. However, i want to > > be able to define the start and end point of segmentation, as my file > > contains a part in the beginning without codes (EEG was being recorded, but > > experiment was running yet). I have been playing around with the commands > > begsample and endsample, but that didnt change the window of segmentation > > (meaning it always segments my whole file, giving me 'empty' segments). > > > > Does anybody know how to solve this? > > > > Thanks for your time, > > > > Boukje Habets > > > > -- > > > > Dr. Boukje Habets > > Biopsychology & Cognitive Neuroscience (AE14) > > Faculty of Psychology and Sports Science | Bielefeld University > > PO-Box 100131 | D-33501 Bielefeld, Germany > > Phone: (49) 521 - 106 67 533 | Fax: (49) 521 - 106 15 67 530 > > Office: UHG T3-250 > > ---------------------------------------------------------------- > > _______________________________________________ > > 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: 3 > Date: Tue, 5 Dec 2017 10:57:33 +0000 > From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Question about segmentation > Message-ID: <851A8ED2-B8C9-4889-A997-F34090596BE5 at donders.ru.nl> > Content-Type: text/plain; charset="utf-8" > > Dear Boukje, > > I don?t think that ?adding a trigger? is necessary. > > Instead, I think you should be able to do something like this: > > start_idx = X*fsample; > end_idx = Y*fsample; > > (X and Y are the intended start and end points of the data, in seconds relative to the onset of the data recording, fsample is the sampling frequency in Hz) > > cfg = []; > cfg.datafile = ?the-name-of-your-datafile?; > cfg.trl = [start_idx end_idx 0]; > cfg = ? (some other optional parameters to be defined here) > data =ft_preprocessing(cfg); > > cfg = []; > cfg.length = 2; > data_segmented = ft_redefinetrial(cfg, data); > > best wishes, > Jan-Mathijs > > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > > > > > > On 5 Dec 2017, at 10:55, Boukje Habets wrote: > > > > Dear Fieldtrippers, > > > > Im new to Fieldtrip and have a question about segmentation. I want to do a freqanalysis on EEG data (Brainvision Recorder). > > I have one file per condition (so only containing one trigger code, and a start code at the beginning of the file) that i want to segment into 2sec pieces. Ive been trying to find a way to add a trigger with Fieldtrip, so that I can segment around a new trigger. Using a pre- and poststim timewindow around the trigger code is not a solution, as this gives me overlapping segments, which i do not want. > > This doesnt seem possible? > > > > After reading about cfg.trialfun, I saw that i can segment a continuous file into segments that i can define in terms of length (sec/samples). I guess this is the easiest way for me to segment my file. However, i want to be able to define the start and end point of segmentation, as my file contains a part in the beginning without codes (EEG was being recorded, but experiment was running yet). I have been playing around with the commands begsample and endsample, but that didnt change the window of segmentation (meaning it always segments my whole file, giving me 'empty' segments). > > > > Does anybody know how to solve this? > > > > Thanks for your time, > > > > Boukje Habets > > > > -- > > > > Dr. Boukje Habets > > Biopsychology & Cognitive Neuroscience (AE14) > > Faculty of Psychology and Sports Science | Bielefeld University > > PO-Box 100131 | D-33501 Bielefeld, Germany > > Phone: (49) 521 - 106 67 533 | Fax: (49) 521 - 106 15 67 530 > > Office: UHG T3-250 > > ---------------------------------------------------------------- _______________________________________________ > > 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 > > End of fieldtrip Digest, Vol 85, Issue 3 > **************************************** > -- Dr. Boukje Habets Biopsychology & Cognitive Neuroscience (AE14) Faculty of Psychology and Sports Science | Bielefeld University PO-Box 100131 | D-33501 Bielefeld, Germany Phone: (49) 521 - 106 67 533 | Fax: (49) 521 - 106 15 67 530 Office: UHG T3-250 ---------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From akoles01 at mail.bbk.ac.uk Thu Dec 7 16:02:44 2017 From: akoles01 at mail.bbk.ac.uk (Anna Kolesnik) Date: Thu, 7 Dec 2017 15:02:44 +0000 Subject: [FieldTrip] Fwd: Netstation >> Fieldtrip conversion References: Message-ID: <3EDA86DB-659F-4ACA-AEA7-7F601A56AECD@mail.bbk.ac.uk> Dear members of the discussion list, I am looking for advice on how best to export pre-processed data from Netstation (version 5+) to Fieldtrip. We have data that is already filtered, segmented, and cleaned for artefacts that needs to be imported into Fieldtrip to run the time-frequency analysis. I know that it is possible to export the processed file to EEGLAB (although I know of some bugs), but has anyone successfully attempted to export to Fieldtrip? If so, what processing stage was it at and what was the format most suitable for this operation? Thank you in advance! Anna Kolesnik PhD student at the Centre for Brain and Cognitive Development Birkbeck College, University of London The BMA House, Tavistock Square WC1H 9JP From dariashn at ugr.es Thu Dec 7 20:24:30 2017 From: dariashn at ugr.es (=?utf-8?Q?Dar=C3=ADas_Manuel_Holgado_Nu=C3=B1ez?=) Date: Thu, 7 Dec 2017 20:24:30 +0100 Subject: [FieldTrip] Dependant samples F multivariate Message-ID: <9F7CADE9-5655-4686-B5E2-672D2CF82B08@ugr.es> Dear list My name is Darias Holgado and I am working in the Mind, Brain and Behaviour Research Centre in Granada on tDCS, EEG and Sport performance. I am analysing data of a project, where we recorded EEG under three tDCS’ stimulation. I have carried out a tDCS’s study in a within-subjects fashion. I have 3 conditions (anodal, cathodal and sham) x one measure (3x1). I am performing permutation test with the montecarlo approach and the ft_statfun_dsamplesFmultivariate. After having specified the design and running the script, it seems that it is ok, but in the output the total number of variables appears as 2, when it is supposed it should say 3. is it that correct? The design I specified it seems correct and it is working but this data is confusing. The cfg and design I use are as follows: %Within-Subject design 3 condition x 1 measure cfg.design(1,1:3*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub) 3*ones(1,Nsub)]; cfg.design(2,1:3*Nsub) = [1:Nsub 1:Nsub 1:Nsub]; cfg.ivar = 1; cfg.uvar = 2; cfg.channel = chanlocs; cfg.method = 'montecarlo'; cfg.statistic = 'ft_statfun_depsamplesFmultivariate'; cfg.correctm = 'cluster'; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.numrandomization = 5000; cfg.tail = 1; % cfg.clustertail = 1; cfg.alpha = 0.025; %cfg.frequency = freqrange; %cfg.avgoverfreq = 'yes'; cfg.neighbours = neighbours; Thank you for your time Best regards, --------------------------------------------------------------------------------- Darías Holgado Nuñez Mind, Brain and Behaviour Research Centre. University of Granada (Spain) https://www.researchgate.net/profile/Darias_Holgado -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at me.com Fri Dec 8 07:46:48 2017 From: nathanweisz at me.com (Nathan Weisz) Date: Fri, 08 Dec 2017 07:46:48 +0100 Subject: [FieldTrip] Postdoc Position @Blechert-lab Message-ID: FYI. Post-doc and PhD position focusing on the cognitive neuroscience of eating behavior at the center for cognitive neuroscience, Salzburg University, advertized on www.eat.sbg.ac.at -------------- next part -------------- An HTML attachment was scrubbed... URL: From i.charest at bham.ac.uk Fri Dec 8 13:58:00 2017 From: i.charest at bham.ac.uk (Ian Charest (School of Psychology)) Date: Fri, 8 Dec 2017 12:58:00 +0000 Subject: [FieldTrip] PhD position on the neurocognitive mechanisms of conscious access Message-ID: <97F95B166F2157409BE1EC68292F25AC4360AA19@EX13.adf.bham.ac.uk> Dear Fieldtrip discussion list, see below for details of a fully funded PhD position in Birmingham, UK. Best wishes, Ian Charest Lecturer, School of Psychology, University of Birmingham, UK iancharest.com _________________________ Advert: The School of Psychology at the University of Birmingham is looking for a bright and motivated PhD student to join the Charest Laboratory (iancharest.com). The PhD position to be filled is part of a project recently funded by a European Research Council Starting Grant entitled: "Spatio-Temporal Attention and Representation Tracking: the precise neural architecture of conscious object perception" (START). The Project: START is an ambitious programme of work that will make use of cutting-edge multivariate pattern analyses (MVPA) techniques to reveal the brain mechanisms that are critical for consciously perceiving visual objects in tasks that manipulate conscious access to visual information. The ability to consciously recognise faces, objects, or sounds is crucial for adaptive behaviour and survival. Yet, how our conscious experience of the world emerges in our brain remains unknown. The overall aim of the START programme is to fill an important gap in our understanding of consciousness by elucidating the neural underpinnings of conscious access. How does the brain select relevant information among distractors, and keep this information in mind? Why does our ability to consciously recognise salient objects sometimes fail under pressure and exhibit variability across days and individuals? START will try to address these important questions by precisely tracking where in the brain and when in time the representations critical for conscious access are established, by using novel approaches of Representational Similarity Analyses which combines the strengths of EEG, fMRI, and Deep Convolutional Neuronal Networks. This project will provide new insights on the precise spatio-temporal dynamics of conscious access, the mechanisms governing it, and the idiosyncratic subtleties behind the meanderings of consciousness. The candidate: The successful candidate will have (or be in the process of obtaining) a Masters degree in cognitive neuroscience or a related field. Previous experience with psychophysical tasks that manipulate conscious access in vision is desirable. Given the nature of the project, good understanding of and experience with fMRI, EEG/MEG and data analysis is desirable. Experience in using matlab or python (and Psychtoolbox or PsychoPy) is a requirement. The successful applicant will have experience with multivariate pattern analyses (Representational Similarity Analysis, Fisher linear discriminants, etc) of neuroimaging data. This post will require designing experiments, collecting and analysing data associated with the project, preparing manuscripts for publication, presenting results at national and international conferences and the possible supervision of research assistants and students. The School: The School of Psychology at the University of Birmingham (http://www.birmingham.ac.uk/schools/psychology/index.aspx) is one of the largest and most successful in the UK, currently ranked in the top 5 Schools in the country (REF 2014). The School is soon to move to new accommodation in the form of a fully refurbished, purpose-designed space and a new-build Centre for Human Brain Health that will house our new MRI, MEG, EEG, NIRS, sleep lab, and the recently appointed Chair in Translational Neuroscience. The University of Birmingham is an equal opportunities employer. The School of Psychology has a Bronze Athena SWAN award and strives to maintain a flexible and supportive environment that enables its staff to flourish. For informal enquiries about the project please contact Dr. Ian Charest (i.charest at bham.ac.uk). Formal applications must be made via the postgraduate admissions system in the School of Psychology. Applicants are encouraged to attach to their application a short and original project proposal (500 words). http://www.birmingham.ac.uk/students/courses/postgraduate/research/psych/psychology.aspx#CourseDetailsTab Full advert of the position on find a phd: https://www.findaphd.com/search/projectdetails.aspx?PJID=92145 -------------- next part -------------- An HTML attachment was scrubbed... URL: From omerxsharon at gmail.com Sat Dec 9 13:12:48 2017 From: omerxsharon at gmail.com (Omer Sharon) Date: Sat, 9 Dec 2017 14:12:48 +0200 Subject: [FieldTrip] Netstation >> Fieldtrip conversion Message-ID: Hi Anna Fieltrip could read the MFF file directly using ft_preprocessing(), use the folder like it was a file. In NS5 there is an issue with the triggers' files and the spaces should be replaces with underscores (fix it if you get an error). I move to field-trip in a very early stage, but you can export to fieldtrip in any stage you like. Good luck Omer Sharon PhD student at NirLab Department of physiology and pharmacology Sackler Faculty of Medicine Tel Aviv University, Israel On Fri, Dec 8, 2017 at 1:00 PM, wrote: > 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. Fwd: Netstation >> Fieldtrip conversion (Anna Kolesnik) > 2. Dependant samples F multivariate (Dar?as Manuel Holgado Nu?ez) > 3. Postdoc Position @Blechert-lab (Nathan Weisz) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 7 Dec 2017 15:02:44 +0000 > From: Anna Kolesnik > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Fwd: Netstation >> Fieldtrip conversion > Message-ID: <3EDA86DB-659F-4ACA-AEA7-7F601A56AECD at mail.bbk.ac.uk> > Content-Type: text/plain; charset=us-ascii > > Dear members of the discussion list, > > I am looking for advice on how best to export pre-processed data from > Netstation (version 5+) to Fieldtrip. We have data that is already > filtered, segmented, and cleaned for artefacts that needs to be imported > into Fieldtrip to run the time-frequency analysis. > I know that it is possible to export the processed file to EEGLAB > (although I know of some bugs), but has anyone successfully attempted to > export to Fieldtrip? If so, what processing stage was it at and what was > the format most suitable for this operation? > > > Thank you in advance! > > > Anna Kolesnik > PhD student at the Centre for Brain and Cognitive Development > Birkbeck College, University of London > The BMA House, Tavistock Square > WC1H 9JP > > > ------------------------------ > > Message: 2 > Date: Thu, 7 Dec 2017 20:24:30 +0100 > From: Dar?as Manuel Holgado Nu?ez > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Dependant samples F multivariate > Message-ID: <9F7CADE9-5655-4686-B5E2-672D2CF82B08 at ugr.es> > Content-Type: text/plain; charset="utf-8" > > Dear list > > My name is Darias Holgado and I am working in the Mind, Brain and > Behaviour Research Centre in Granada on tDCS, EEG and Sport performance. I > am analysing data of a project, where we recorded EEG under three tDCS? > stimulation. > > I have carried out a tDCS?s study in a within-subjects fashion. I have 3 > conditions (anodal, cathodal and sham) x one measure (3x1). I am performing > permutation test with the montecarlo approach and the ft_statfun_ > dsamplesFmultivariate. > After having specified the design and running the script, it seems that it > is ok, but in the output the total number of variables appears as 2, when > it is supposed it should say 3. is it that correct? The design I specified > it seems correct and it is working but this data is confusing. > > The cfg and design I use are as follows: > > %Within-Subject design 3 condition x 1 measure > cfg.design(1,1:3*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub) 3*ones(1,Nsub)]; > cfg.design(2,1:3*Nsub) = [1:Nsub 1:Nsub 1:Nsub]; > cfg.ivar = 1; > cfg.uvar = 2; > > cfg.channel = chanlocs; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_depsamplesFmultivariate'; > cfg.correctm = 'cluster'; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.numrandomization = 5000; > cfg.tail = 1; > % cfg.clustertail = 1; > cfg.alpha = 0.025; > %cfg.frequency = freqrange; > %cfg.avgoverfreq = 'yes'; > cfg.neighbours = neighbours; > > > Thank you for your time > > > Best regards, > ------------------------------------------------------------ > --------------------- > Dar?as Holgado Nu?ez > Mind, Brain and Behaviour Research Centre. > University of Granada (Spain) > https://www.researchgate.net/profile/Darias_Holgado > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20171207/96780d19/attachment-0001.html> > > ------------------------------ > > Message: 3 > Date: Fri, 08 Dec 2017 07:46:48 +0100 > From: Nathan Weisz > To: FieldTrip discussion list > Subject: [FieldTrip] Postdoc Position @Blechert-lab > Message-ID: > Content-Type: text/plain; charset="us-ascii" > > FYI. > > Post-doc and PhD position focusing on the cognitive neuroscience of > eating behavior at the center for cognitive neuroscience, Salzburg > University, advertized on > www.eat.sbg.ac.at > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20171208/0634be20/attachment-0001.html> > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 85, Issue 5 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From xiew1202 at gmail.com Sat Dec 9 13:23:48 2017 From: xiew1202 at gmail.com (Xie Wanze) Date: Sat, 09 Dec 2017 12:23:48 +0000 Subject: [FieldTrip] Netstation >> Fieldtrip conversion In-Reply-To: References: Message-ID: Anna, You may also read in the segmented data into Eeglab, and then use eeglab2fieldtrip function to export them into field trip format. Wanze Omer Sharon 于2017年12月9日 周六上午7:13写道: > Hi Anna > > Fieltrip could read the MFF file directly using ft_preprocessing(), use > the folder like it was a file. In NS5 there is an issue with the triggers' > files and the spaces should be replaces with underscores (fix it if you get > an error). > > I move to field-trip in a very early stage, but you can export to > fieldtrip in any stage you like. > > Good luck > > Omer Sharon > PhD student at NirLab > Department of physiology and pharmacology > Sackler Faculty of Medicine > Tel Aviv University, Israel > > > On Fri, Dec 8, 2017 at 1:00 PM, wrote: > >> 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. Fwd: Netstation >> Fieldtrip conversion (Anna Kolesnik) >> 2. Dependant samples F multivariate (Dar?as Manuel Holgado Nu?ez) >> 3. Postdoc Position @Blechert-lab (Nathan Weisz) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Thu, 7 Dec 2017 15:02:44 +0000 >> From: Anna Kolesnik >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] Fwd: Netstation >> Fieldtrip conversion >> Message-ID: <3EDA86DB-659F-4ACA-AEA7-7F601A56AECD at mail.bbk.ac.uk> >> Content-Type: text/plain; charset=us-ascii > > >> >> Dear members of the discussion list, >> >> I am looking for advice on how best to export pre-processed data from >> Netstation (version 5+) to Fieldtrip. We have data that is already >> filtered, segmented, and cleaned for artefacts that needs to be imported >> into Fieldtrip to run the time-frequency analysis. >> I know that it is possible to export the processed file to EEGLAB >> (although I know of some bugs), but has anyone successfully attempted to >> export to Fieldtrip? If so, what processing stage was it at and what was >> the format most suitable for this operation? >> >> >> Thank you in advance! >> >> >> Anna Kolesnik >> PhD student at the Centre for Brain and Cognitive Development >> Birkbeck College, University of London >> The BMA House, Tavistock Square >> WC1H 9JP >> >> >> ------------------------------ >> >> Message: 2 >> Date: Thu, 7 Dec 2017 20:24:30 +0100 >> From: Dar?as Manuel Holgado Nu?ez >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] Dependant samples F multivariate >> Message-ID: <9F7CADE9-5655-4686-B5E2-672D2CF82B08 at ugr.es> >> Content-Type: text/plain; charset="utf-8" >> >> Dear list >> >> My name is Darias Holgado and I am working in the Mind, Brain and >> Behaviour Research Centre in Granada on tDCS, EEG and Sport performance. I >> am analysing data of a project, where we recorded EEG under three tDCS? >> stimulation. >> >> I have carried out a tDCS?s study in a within-subjects fashion. I have 3 >> conditions (anodal, cathodal and sham) x one measure (3x1). I am performing >> permutation test with the montecarlo approach and the >> ft_statfun_dsamplesFmultivariate. >> After having specified the design and running the script, it seems that >> it is ok, but in the output the total number of variables appears as 2, >> when it is supposed it should say 3. is it that correct? The design I >> specified it seems correct and it is working but this data is confusing. >> >> The cfg and design I use are as follows: >> >> %Within-Subject design 3 condition x 1 measure >> cfg.design(1,1:3*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub) 3*ones(1,Nsub)]; >> cfg.design(2,1:3*Nsub) = [1:Nsub 1:Nsub 1:Nsub]; >> cfg.ivar = 1; >> cfg.uvar = 2; >> >> cfg.channel = chanlocs; >> cfg.method = 'montecarlo'; >> cfg.statistic = 'ft_statfun_depsamplesFmultivariate'; >> cfg.correctm = 'cluster'; >> cfg.clusterstatistic = 'maxsum'; >> cfg.minnbchan = 2; >> cfg.numrandomization = 5000; >> cfg.tail = 1; >> % cfg.clustertail = 1; >> cfg.alpha = 0.025; >> %cfg.frequency = freqrange; >> %cfg.avgoverfreq = 'yes'; >> cfg.neighbours = neighbours; >> >> >> Thank you for your time >> >> >> Best regards, >> >> --------------------------------------------------------------------------------- >> Dar?as Holgado Nu?ez >> Mind, Brain and Behaviour Research Centre. >> University of Granada (Spain) >> https://www.researchgate.net/profile/Darias_Holgado >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20171207/96780d19/attachment-0001.html >> > >> >> ------------------------------ >> >> Message: 3 >> Date: Fri, 08 Dec 2017 07:46:48 +0100 >> From: Nathan Weisz >> To: FieldTrip discussion list >> Subject: [FieldTrip] Postdoc Position @Blechert-lab >> Message-ID: >> Content-Type: text/plain; charset="us-ascii" >> >> FYI. >> >> Post-doc and PhD position focusing on the cognitive neuroscience of >> eating behavior at the center for cognitive neuroscience, Salzburg >> University, advertized on >> www.eat.sbg.ac.at >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20171208/0634be20/attachment-0001.html >> > >> >> ------------------------------ > > >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> End of fieldtrip Digest, Vol 85, Issue 5 >> **************************************** >> > > _______________________________________________ > 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 mikexcohen at gmail.com Sat Dec 9 22:14:41 2017 From: mikexcohen at gmail.com (Mike X Cohen) Date: Sat, 9 Dec 2017 22:14:41 +0100 Subject: [FieldTrip] Neuroscience data analysis summer-school announcements Message-ID: Dear colleagues, I am happy to announce *two week-long neuroscience data analysis courses* at the Radboud University in Netherlands in August 2018: One about time-frequency/synchronization/statistics, and one about linear algebra and source-separation. Below are the direct links to the course pages with application information. You can also find more information, including syllabi, on mikexcohen.com (scroll down to "In-vivo teaching"). *Please pass these links around to your colleagues/students who might be interested in one or both of these courses!* Analyzing neural time series data (6-10 August). Fourier transform, convolution, time-frequency analysis, synchronization, nonparametric statistics, simulating time series data. Linear algebra for neuroscientists (13-17 August). Matrix algebra, least-squares model fitting, eigendecomposition, multivariate source separation, state-space analyses, simulating multicomponent and multichannal time series data. Please note that applications, if approved, are selected on a first-come-first-serve basis, and that the number of participants for each course is limited. If you have questions about the courses, please feel free to contact me. Mike -- Mike X Cohen, PhD New online courses: mikexcohen.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From urieduardo at gmail.com Tue Dec 12 14:38:42 2017 From: urieduardo at gmail.com (=?UTF-8?Q?Uri_Eduardo_Ram=C3=ADrez_Pasos?=) Date: Tue, 12 Dec 2017 14:38:42 +0100 Subject: [FieldTrip] ft_sourcestatistics Message-ID: Dear fieldtrippers, I have a couple questions regarding source reconstruction that I hope you can help me with. 1. What is the best way to 'normalize' the position values in each forward model across my subjects so that I can run ft_sourcestatistics with cfg.statistic = 'ft_statfun_depsamplesT' ? 2. For one of my subjects, their leadfield keeps containing only NaNs. What could be the source (no pun intended) of the problem? 3. If my experiment's design has three 'levels' (say A1, A2, A3) for one 'factor', is it valid to subtract source values (obtained using method 'dics') for a comparison (e.g. A1-A3 vs A2-A3)? 4. What could have gone wrong when i get the warning “matrix is singular, close to singular or badly scaled. Results may be inaccurate.” How does one go about solving this? Best regards, Eduardo Ramírez, PhD candidate University of Würzburg -------------- next part -------------- An HTML attachment was scrubbed... URL: From mi_mayer at gmx.de Tue Dec 12 17:24:36 2017 From: mi_mayer at gmx.de (Irene Sophia Mayer) Date: Tue, 12 Dec 2017 17:24:36 +0100 Subject: [FieldTrip] Forward model EEG no MRI Message-ID: An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Tue Dec 12 17:37:51 2017 From: julian.keil at gmail.com (Julian Keil) Date: Tue, 12 Dec 2017 17:37:51 +0100 Subject: [FieldTrip] Forward model EEG no MRI In-Reply-To: References: Message-ID: <6EA73EED-F0B6-4676-99A0-FE1723A6578A@gmail.com> Dear Sophia, Fieldtrip comes with a number of precomputed Headmodels as well as standard MRIs which you can use (take a look into the „forward“-folder in the FT directory). You just have to make sure, your electrodes fit to the headmodels, but you would have to do this with a „real“ MRI as well. Good luck, Julian > Am 12.12.2017 um 17:24 schrieb Irene Sophia Mayer : > > Dear Fieldtrippers, > > I am attempting to do source reconstruction with Fieldtrip for the first time. I have EEG data but no MRI, just measurements of the electrode positions (with Zebris). However, I got already stuck at creating the forward model. > > Do I need to prepare my own sourcemodel with ft_prepare_sourcemodel or can I use the default options in ft_prepare_leadfield? > > All tutorials for creating a headmodel use an MRI, how can I do it without MRI images of my subjects? > > I have tried to use ft_prepare_headmodel with > headmodel = ft_prepare_headmodel(cfg, elec) with the output of FT_READ_SENS headmo > elec = > chanpos: [62x3 double] > elecpos: [62x3 double] > label: {62x1 cell} > type: 'eeg1005' > unit: 'mm' > > Unfortunately, it first told me: Either a segmentated MRI or data with closed triangulated mesh is required as data > input for the bemcp, dipoli or openmeeg method, and when I tried other methods, I got: The data input might already be a sensor description. Reference to non-existent field 'outputfile' > > I would be thankful for tips on how to do this! > > Best, > Sophia > _______________________________________________ > 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 julian.keil at gmail.com Tue Dec 12 17:49:01 2017 From: julian.keil at gmail.com (Julian Keil) Date: Tue, 12 Dec 2017 17:49:01 +0100 Subject: [FieldTrip] ft_sourcestatistics In-Reply-To: References: Message-ID: <6E37C718-06F7-439B-87B1-329FEFFACFF8@gmail.com> Dear Eduardo, @1: Do you mean normalize across the group? What you could do is interpolate the source-level data to an MRI and then use ft_volumenormalise to normalize all images to a common standard MRI. Check the FT site here: http://www.fieldtriptoolbox.org/tutorial/sourcemodel?s[]=warp Alternatively, you could take care that a common source grid is warped to the individual headmodel prior to the source analysis. In this case, you don’t need to normalize, as all subjects have the same number of sources. Check the tutorials on the FT-website for hints (e.g. http://www.fieldtriptoolbox.org/tutorial/salzburg?s[]=warp or http://www.fieldtriptoolbox.org/tutorial/beamformingextended?s[]=warp ) @2: Did you build your own headmodel? It might be that the elements of the headmodel intersect. I would go back and double check all steps leading up to the leadfield computation for errors. @3: I have no idea. @4: When does this happen? Good luck, Julian > Am 12.12.2017 um 14:38 schrieb Uri Eduardo Ramírez Pasos : > > Dear fieldtrippers, > > I have a couple questions regarding source reconstruction that I hope you can help me with. > > 1. What is the best way to 'normalize' the position values in each forward model across my subjects so that I can run ft_sourcestatistics with cfg.statistic = 'ft_statfun_depsamplesT' ? > > 2. For one of my subjects, their leadfield keeps containing only NaNs. What could be the source (no pun intended) of the problem? > > 3. If my experiment's design has three 'levels' (say A1, A2, A3) for one 'factor', is it valid to subtract source values (obtained using method 'dics') for a comparison (e.g. A1-A3 vs A2-A3)? > > 4. What could have gone wrong when i get the warning “matrix is singular, close to singular or badly scaled. Results may be inaccurate.” How does one go about solving this? > > Best regards, > Eduardo Ramírez, PhD candidate > University of Würzburg > _______________________________________________ > 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 cmista at bioingenieria.edu.ar Wed Dec 13 14:16:17 2017 From: cmista at bioingenieria.edu.ar (Christian Mista) Date: Wed, 13 Dec 2017 10:16:17 -0300 Subject: [FieldTrip] About connectivity and ft_topoplotCC Message-ID: Hi all, I'm starting with EEG analysis and Fiedltrip, and I'll would like to plot topographical maps of the connectivity (using imaginary part of coherence). I tried ft_topoplotCC to make a connection line/arrow graph, but I think I'm doing something wrong because the graph at 10 hz seems to be the same at 50 hz (attached some images). In addition, I was wondering if there is any way to set a threshold, so only fewer lines are plotted in the connection map. Below the code I'm using in matlab. %CODE %calculate coherence cfg = []; cfg.method = 'mtmfft'; cfg.taper = 'hanning'; %connectivity analysis needs power and phase -> 'pownadcsd' cfg.output = 'powandcsd'; % windows of frequency of interest foilim cfg.foilim = [1 60]; freq1 = ft_freqanalysis(cfg, data); %calculating the imaginary part of the coherence cfg = []; cfg.method = 'coh'; cfg.complex = 'absimag'; conn1 = ft_connectivityanalysis(cfg, freq1); %The conectome %figure;imagesc(conn1.cohspctrm); cfg = []; %my layout cfg.layout = layout; cfg.foi = 10; ft_topoplotCC(cfg, conn1) cfg = []; cfg.layout = layout; cfg.foi = 50; ft_topoplotCC(cfg, conn1) Best regards / Cordiales saludos Christian -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: connections10Hz.jpg Type: image/jpeg Size: 35441 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: connections50Hz.jpg Type: image/jpeg Size: 37955 bytes Desc: not available URL: From urieduardo at gmail.com Thu Dec 14 15:09:36 2017 From: urieduardo at gmail.com (=?UTF-8?Q?Uri_Eduardo_Ram=C3=ADrez_Pasos?=) Date: Thu, 14 Dec 2017 15:09:36 +0100 Subject: [FieldTrip] ft_sourcestatistics In-Reply-To: <6E37C718-06F7-439B-87B1-329FEFFACFF8@gmail.com> References: <6E37C718-06F7-439B-87B1-329FEFFACFF8@gmail.com> Message-ID: Dear Julian, Thanks a lot for your advice! Some follow-up questions and clarifications. 1a. I've looked at both approaches suggested in http://www.fieldtriptoolbox.org/tutorial/sourcemodel?s%5B%5D=warp. For the first approach (interpolate then normalize volumes), I used the following code (for EEG data), where I compute source values from two conditions, ON and OFF: cfg = []; cfg.method = 'dics'; cfg.frequency = 18; cfg.grid = grid; cfg.headmodel = headmodel; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.keepfilter = 'yes'; cfg.dics.realfilter = 'yes'; sourceAllneg_pos = ft_sourceanalysis(cfg, freqAll); cfg.grid.filter = sourceAllneg_pos.avg.filter; sourceOFF_con = ft_sourceanalysis(cfg, freqOFF); sourceON_con = ft_sourceanalysis(cfg, freqON); atlas = ft_read_atlas( '~/Documents/MATLAB/fieldtrip-20170618/template/atlas/aal/ROI_MNI_V4.nii'); cfg=[]; cfg.parameter='pow'; cont_sources{pat,1,1}=ft_sourceinterpolate(cfg, sourceOFF_con, atlas); cont_sources{pat,1,2}=ft_sourceinterpolate(cfg, sourceON_con, atlas); cfg=[]; cfg.parameter='pow'; [mri] = ft_volumenormalise(cfg, mri) Using ft_sourceinterpolate normalized the .pos values across my subjects, however I'm not sure what to do with the MRI variable created with ft_volumenormalize, but I'm guessing it should be integrated somewhere for results to be valid. 1b. I also tried the second method in the tutorial (Subject-specific grids), but the standard_sourcemodel3dxmm.mat files are based on the single shell method, and hence only relevant for MEG. When inputting cfg.grid.template= 'cortex_xxxx.surf.gii' (the other templates, which I hope are for EEG), I get the error using load: 'Number of columns on line 2 of ASCII file cortex_xxxx.surf.gii must be the same as previous lines. 2. Yes, I just used %get mri mri = ft_read_mri('0001.dcm'); %segment mri cfg=[]; cfg.output={'brain','skull','scalp'}; segmentedmri=ft_volumesegment(cfg,mri); % Y % r % a % s % n cfg=[]; cfg.tissue={'brain','skull','scalp'}; cfg.numvertices=[3000 2000 1000]; cfg.method='projectmesh';% or 'iso2mesh', 'isosurface', bnd=ft_prepare_mesh(cfg,segmentedmri); cfg=[]; cfg.method='bemcp';%or dipoli on a mac, or openmeeg headmodel = ft_prepare_headmodel(cfg,bnd); I'm using a mac, though I can't get dipoli to work. I've used this for the other subjects without every problem. I have no fiducials, not sure if this has any influence. 3. I've thought about this further, it doesn't make much sense to do this at the source level. 4. The warning occurs after running cfg=[]; cfg.method='bemcp';%or dipoli on a mac, or openmeeg headmodel = ft_prepare_headmodel(cfg,bnd); , though I also get this when running sample data from fieldtrip tutorials. Again, thank you immensely for your pointers! Uri 2017-12-12 17:49 GMT+01:00 Julian Keil : > Dear Eduardo, > > @1: Do you mean normalize across the group? What you could do is > interpolate the source-level data to an MRI and then use ft_volumenormalise > to normalize all images to a common standard MRI. Check the FT site here: > http://www.fieldtriptoolbox.org/tutorial/sourcemodel?s[]=warp > Alternatively, you could take care that a common source grid is warped to > the individual headmodel prior to the source analysis. In this case, you > don’t need to normalize, as all subjects have the same number of sources. > Check the tutorials on the FT-website for hints (e.g. http://www. > fieldtriptoolbox.org/tutorial/salzburg?s[]=warp or http:// > www.fieldtriptoolbox.org/tutorial/beamformingextended?s[]=warp) > > @2: Did you build your own headmodel? It might be that the elements of the > headmodel intersect. I would go back and double check all steps leading up > to the leadfield computation for errors. > > @3: I have no idea. > > @4: When does this happen? > > Good luck, > > Julian > > Am 12.12.2017 um 14:38 schrieb Uri Eduardo Ramírez Pasos < > urieduardo at gmail.com>: > > Dear fieldtrippers, > > I have a couple questions regarding source reconstruction that I hope you > can help me with. > > 1. What is the best way to 'normalize' the position values in each forward > model across my subjects so that I can run ft_sourcestatistics with > cfg.statistic = 'ft_statfun_depsamplesT' ? > > 2. For one of my subjects, their leadfield keeps containing only NaNs. > What could be the source (no pun intended) of the problem? > > 3. If my experiment's design has three 'levels' (say A1, A2, A3) for one > 'factor', is it valid to subtract source values (obtained using method > 'dics') for a comparison (e.g. A1-A3 vs A2-A3)? > > 4. What could have gone wrong when i get the warning “matrix is singular, > close to singular or badly scaled. Results may be inaccurate.” How does one > go about solving this? > > Best regards, > Eduardo Ramírez, PhD candidate > University of Würzburg > _______________________________________________ > 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 caschera at dis.uniroma1.it Fri Dec 15 10:51:20 2017 From: caschera at dis.uniroma1.it (Stefano Caschera) Date: Fri, 15 Dec 2017 10:51:20 +0100 Subject: [FieldTrip] Including brain lesion - OpenMeeg Message-ID: Hi, I would like to include a brain lesion to obtain a leadfield through openmeeg. I have already computed the meshes. Is it possible to use ft_prepare_headmodel and openmeeg_dsm ? And how? I tried but I've got strange results. As I know openmeeg can handle four layers but probably the brain has to be the inner one. If it is not possible using openmeeg, can you suggest me another method? Thank you, Stefano -- Stefano Caschera, PhD Student *Neuroelectrical Imaging and BCI lab* Fondazione Santa Lucia, IRCCS Via Ardeatina, 306 I-00179, Rome, Italy *Department of Computer, Control, andManagement Engineering "Antonio Ruberti"* Sapienza, University of Rome V. Ariosto, 25 00185, Rome, Italy Tel +39 06 5150 1165 Email: stefano.caschera at uniroma1.it caschera at dis.uniroma1.it s.caschera at hsantalucia.it ___________________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.homolle at donders.ru.nl Fri Dec 15 11:12:49 2017 From: s.homolle at donders.ru.nl (Simon Homolle) Date: Fri, 15 Dec 2017 11:12:49 +0100 Subject: [FieldTrip] Including brain lesion - OpenMeeg In-Reply-To: References: Message-ID: <92ED8BAC-B04F-4AF0-B989-46E94B2CD8F9@donders.ru.nl> Dear Stefano, What do you mean by strange results? Some figures describing the results would help to give you further help. You talked about 4 layers so i presume you used Skin, Skull, Brain and Lesion? Are these nested compartments? Could you show some visualisation of the meshes/segmentations you used? seg_i = ft_datatype_segmentation(segmentedmri,'segmentationstyle','indexed'); cfg = []; cfg.funparameter = 'seg'; cfg.funcolormap = lines(6); % distinct color per tissue cfg.location = 'center'; cfg.atlas = seg_i; % the segmentation can also be used as atlas ft_sourceplot(cfg, seg_i); Best regards, Simon Homölle PhD Candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Phone: +31-(0)24-36-65059 > On 15 Dec 2017, at 10:51, Stefano Caschera wrote: > > Hi, > I would like to include a brain lesion to obtain a leadfield through openmeeg. > > I have already computed the meshes. > > Is it possible to use ft_prepare_headmodel and openmeeg_dsm ? > And how? I tried but I've got strange results. As I know openmeeg can handle four layers but probably the brain has to be the inner one. > > If it is not possible using openmeeg, can you suggest me another method? > > Thank you, > Stefano > > -- > Stefano Caschera, PhD Student > > Neuroelectrical Imaging and BCI lab > Fondazione Santa Lucia, IRCCS > Via Ardeatina, 306 > I-00179, Rome, Italy > > Department of Computer, Control, and > Management Engineering "Antonio Ruberti" > Sapienza, University of Rome > V. Ariosto, 25 > 00185, Rome, Italy > > Tel +39 06 5150 1165 > Email: stefano.caschera at uniroma1.it > caschera at dis.uniroma1.it > s.caschera at hsantalucia.it > ___________________________________________________ > _______________________________________________ > 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 sarang at cfin.au.dk Fri Dec 15 23:11:17 2017 From: sarang at cfin.au.dk (Sarang S. Dalal) Date: Fri, 15 Dec 2017 22:11:17 +0000 Subject: [FieldTrip] Including brain lesion - OpenMeeg In-Reply-To: <92ED8BAC-B04F-4AF0-B989-46E94B2CD8F9@donders.ru.nl> References: <92ED8BAC-B04F-4AF0-B989-46E94B2CD8F9@donders.ru.nl> Message-ID: <1513375868.2120.25.camel@cfin.au.dk> Dear Stefano, OpenMEEG can do what you need. We wrote the function in FieldTrip that sets up the OpenMEEG parameters (fieldtrip/forward/private/leadfield_openmeeg.m) with the assumption that there would be either 3 layers (scalp, skull, brain) or 4 layers (scalp, skull, csf, brain). These layers are assumed to be nested from outside to inside, with no surfaces crossing or touching. As Simon suggested, you probably have lesion nested within brain. So, if you don't have a CSF layer, you could use the 4-layer functionality that is already there, with the order [scalp skull brain lesion]. You will have to configure cfg.conductivity appropriately with the same order. You may also take a look at the examples from my group where we script MRI segmentations and set up OpenMEEG computations in practice (for 3- and 4-layer nested geometries): https://github.com/meeg-cfin/nemolab/blob/master/basics/nemo_mriproc.m https://github.com/meeg-cfin/nemolab/blob/master/basics/nemo_makeleadfield.m OpenMEEG will also support non-nested configurations, but you will have to adapt leadfield_openmeeg.m to get it to work with FieldTrip. You can have a look at the documentation on the OpenMEEG website for a description of how to write the parameter files for that situation. Cheers, Sarang On Fri, 2017-12-15 at 11:12 +0100, Simon Homolle wrote: Dear Stefano, What do you mean by strange results? Some figures describing the results would help to give you further help. You talked about 4 layers so i presume you used Skin, Skull, Brain and Lesion? Are these nested compartments? Could you show some visualisation of the meshes/segmentations you used? seg_i = ft_datatype_segmentation(segmentedmri,'segmentationstyle','indexed'); cfg = []; cfg.funparameter = 'seg'; cfg.funcolormap = lines(6); % distinct color per tissue cfg.location = 'center'; cfg.atlas = seg_i; % the segmentation can also be used as atlas ft_sourceplot(cfg, seg_i); Best regards, Simon Homölle PhD Candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Phone: +31-(0)24-36-65059 On 15 Dec 2017, at 10:51, Stefano Caschera > wrote: Hi, I would like to include a brain lesion to obtain a leadfield through openmeeg. I have already computed the meshes. Is it possible to use ft_prepare_headmodel and openmeeg_dsm ? And how? I tried but I've got strange results. As I know openmeeg can handle four layers but probably the brain has to be the inner one. If it is not possible using openmeeg, can you suggest me another method? Thank you, Stefano -- Stefano Caschera, PhD Student Neuroelectrical Imaging and BCI lab Fondazione Santa Lucia, IRCCS Via Ardeatina, 306 I-00179, Rome, Italy Department of Computer, Control, and Management Engineering "Antonio Ruberti" Sapienza, University of Rome V. Ariosto, 25 00185, Rome, Italy Tel +39 06 5150 1165 Email: stefano.caschera at uniroma1.it caschera at dis.uniroma1.it s.caschera at hsantalucia.it ___________________________________________________ _______________________________________________ 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 pascualm at key.uzh.ch Tue Dec 19 16:32:49 2017 From: pascualm at key.uzh.ch (pascualm at key.uzh.ch) Date: Wed, 20 Dec 2017 00:32:49 +0900 Subject: [FieldTrip] Measures of time series coupling based on generalized weighted multiple regression Message-ID: Dear Colleagues, The pre-print at: https://doi.org/10.1101/235721 entitled "Measures of time series coupling based on generalized weighted multiple regression" might be of interest to those working in the field of brain connectivity based on signals of electric neuronal activity. The abstract can be found below, under the signature. Cordially, Roberto ... Roberto D. Pascual-Marqui, PhD, PD The KEY Institute for Brain-Mind Research, University of Zurich Visiting Professor at Neuropsychiatry, Kansai Medical University, Osaka [www.keyinst.uzh.ch/loreta] [scholar.google.com/citations?user=pascualmarqui] /////////////// Abstract: The sharing and the transmission of information between cortical brain regions is carried out by mechanisms that are still not fully understood. A deeper understanding should shed light on how consciousness and cognition are implemented in the brain. Research activity in this field has recently been focusing on the discovery of non-conventional coupling mechanisms, such as all forms of cross-frequency couplings between diverse combinations of amplitudes and phases, applied to measured or estimated cortical signals of electric neuronal activity. However, all coupling measures that involve phase computation have poor statistical properties. In this work, the conventional estimators for the well-known phase-phase (phase synchronization or locking), phase-amplitude, and phase-amplitude-amplitude couplings are generalized by means of the weighted multiple regression model. The choice of appropriate weights produces estimators that bypass the need for computing the complex-valued phase. In addition, a new coupling, denoted as the inhibitory coupling (InhCo), is introduced and defined as the dependence of one complex-valued variable on the inverse and on the conjugate inverse of another complex-valued variable. A weighted version denoted as wInhCo is also introduced, bypassing the need for computing the inverse of a complex variable, which has very poor statistical properties. The importance of this form of inhibitory coupling is that it may capture well-known processes, such as the observed inverse alpha/gamma relation within the same cortical region, or the inverse alpha/alpha relation between distant cortical regions. /////////////// From a.stolk8 at gmail.com Thu Dec 21 04:40:38 2017 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Wed, 20 Dec 2017 19:40:38 -0800 Subject: [FieldTrip] iEEG analysis protocol Message-ID: For those of you who work with human intracranial data (iEEG), see here for a preprint of our analysis protocol (directly integrated with FieldTrip): https://www.biorxiv.org/content/early/2017/12/08/230912 *Integrated analysis of anatomical and electrophysiological human intracranial data* The exquisite spatiotemporal precision of human intracranial EEG recordings (iEEG) permits characterizing neural processing with a level of detail that is inaccessible to scalp-EEG, MEG, or fMRI. However, the same qualities that make iEEG an exceptionally powerful tool also present unique challenges. Until now, the fusion of anatomical data (MRI and CT images) with the electrophysiological data and its subsequent analysis has relied on technologically and conceptually challenging combinations of software. Here, we describe a comprehensive protocol that addresses the complexities associated with human iEEG, providing complete transparency and flexibility in the evolution of raw data into illustrative representations. The protocol is directly integrated with an open source toolbox for electrophysiological data analysis (FieldTrip). This allows iEEG researchers to build on a continuously growing body of scriptable and reproducible analysis methods that, over the past decade, have been developed and employed by a large research community. We demonstrate the protocol for an example complex iEEG data set to provide an intuitive and rapid approach to dealing with both neuroanatomical information and large electrophysiological data sets. We explain how the protocol can be largely automated, taking under an hour to complete, and readily adjusted to iEEG data sets with other characteristics. -------------- next part -------------- An HTML attachment was scrubbed... URL: From prabodh.sontakke at gmail.com Thu Dec 21 06:41:02 2017 From: prabodh.sontakke at gmail.com (prabodh sontakke) Date: Thu, 21 Dec 2017 11:11:02 +0530 Subject: [FieldTrip] help Message-ID: Dear Sir/Madam, I am doing a MTech project on "Study of complex network on EEG time series", doing so I need to calculate the connectivity measures .In the fieldtrip I don't know what value of Input and varagin to take and I am using the 23 electrodes location of Alzheimer patient with 400 sampling frequency and 124000 instances of each electrode location. Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From christoph.kayser at uni-bielefeld.de Fri Dec 22 21:48:33 2017 From: christoph.kayser at uni-bielefeld.de (Christoph Kayser) Date: Fri, 22 Dec 2017 21:48:33 +0100 Subject: [FieldTrip] PhD / Postdoc position Bielefeld, Germany Message-ID: <7130e2be26f92.5a3d7db1@uni-bielefeld.de> The Department of Cognitive Neuroscience at Bielefeld University, Germany, is advertising a 3-year Postdoctoral position, and a 3-year PhD position in auditory and multisensory neuroimaging studies. We are looking to fill two 3-year positions to complement our research on auditory or multisensory perception based on a combination of behavioural, neuroimaging (EEG) and statistical modelling techniques. The Department for Cognitive Neuroscience is dedicated to understanding the integration of sensory information in the brain. The planned studies use state of the art EEG imaging, combined with eyetracking, psychophysical paradigms, and substantive quantitative data analysis to better understand when and how the brain transforms sensory information into a conscious percept. Further details about our research can be found on our website http://www.uni-bielefeld.de/biologie/cns/ The positions involve all aspects of study design, implementation, data collection, data analysis and the write up of results. Contributions to the supervision of student projects or the preparation of practical courses are expected. Applicants should have a background in neuroscience, cognitive science, psychology, mathematics, or a relevant discipline. Applicants for the post-doc position should have a doctoral degree or equivalent title in a relevant discipline. We are especially interested in devotion to advanced quantitative data analysis including the capabilities to program or modify analysis code. The ideal applicant will have a strong analytical background and direct experience using MATLAB software. Applicants should have enthusiasm, and a clear, demonstrable capacity for acquiring expertise in these techniques. The positions are funded for 3 years starting ideally in April 2018, at Germany salary grades TV-L E13 (100% for post-doc, 65% for PhD student). The official adverts with all relevant details (in German) can be found here, under references ‘wiss17359’ and ‘wiss17356’: https://www.uni-bielefeld.de/Universitaet/Aktuelles/Stellenausschreibungen/auswiss_2013.html Questions and applications (cover letter, CV) should be directed until 31st of January 2018 to the PI: Christoph.Kayser at uni-bielefeld.de. -- ------------------------------------------------------------------------- Prof. Christoph Kayser Research Group Cognitive Neuroscience, Faculty of Biology UHG W3-110, Bielefeld University Universitätsstr. 25 33615 Bielefeld, Germany Tel. +49 (521) 106-5700 -------------- next part -------------- An HTML attachment was scrubbed... URL: From bick35 at gmail.com Fri Dec 29 17:24:01 2017 From: bick35 at gmail.com (steph) Date: Fri, 29 Dec 2017 11:24:01 -0500 Subject: [FieldTrip] Research Assistant Positions in ECoG Lab in New York Message-ID: Dear all, The ECoG Laboratory for Human Brain Mapping at the Feinstein Institute for Medical Research – Hofstra Northwell School of Medicine is looking for two research assistants. The successful candidates will help with the lab’s research into (1) improving the identification of functional and pathological brain regions in individuals suffering from epilepsy, (2) the neural mechanisms of cognition, and (3) characterization of macroscale human brain networks. The lab works exclusively with patients being evaluated for epilepsy surgery using methods such as electrocorticography (ECoG), MRI, fMRI, DTI, and direct electrical brain stimulation. The start date is as soon as possible. The responsibilities of both research assistants include assisting with the collection and analysis of the aforementioned data, managing lab equipment, and helping to present lab findings at conferences and in journals. One position will further focus on project management and administration, working with a research coordinator on IRB matters, and assistance with preparing progress reports and grant applications. The second position is more computationally focused and will require more in-depth analysis of neural and behavioral data, database management, and the development of analysis scripts (depending on proficiency with coding and signal processing). Both RAs will have their own scientific projects with dedicated time to work on them. Past research assistants in the lab have presented their work at clinical and basic research conferences, co-authored publications, and are working on first author publications. They have gone on to medical schools or PhD programs after spending 1-3 years in the lab. These unique positions will expose the successful applicant to basic and clinical neuroscience as well as neurosurgery, neurology, and neuropsychology. The location of the institute allows living either in the suburban neighborhoods of Long Island, or in vibrant Brooklyn or Queens. Some employees also commute from Manhattan. It is a great opportunity for recent post-bacs interested in medical school or graduate school in neuroscience/biomedical engineering. ------------- Qualifications ------------- Minimum: -B.A./B.S./B.E. in an appropriate discipline (e.g., neuroscience, psychology, biomedical engineering, computer science, physics) -For the second RA position: Experience with at least one programming language (MATLAB, R, or Python) and statistical analyses -1 year commitment Desirable: -Prior experience working with neuroimaging, EEG/MEG, or brain stimulation data -Previous experience working with patients -Previous work in a research laboratory that shows evidence of independent scholarship, problem solving, and motivation -2 year commitment preferred For more information about the position please send your CV along with your questions to Drs. Stephan Bickel (sbickel at northwell.edu ) and Ashesh Mehta (amehta.northwell.edu ). We are looking forward to hearing from you! -------------- next part -------------- An HTML attachment was scrubbed... URL: