From joscha.schmiedt at esi-frankfurt.de Wed Apr 1 14:03:27 2015 From: joscha.schmiedt at esi-frankfurt.de (Schmiedt, Joscha) Date: Wed, 1 Apr 2015 12:03:27 +0000 Subject: [FieldTrip] A Fieldtrip data format? In-Reply-To: References: <5548CAB3-F9A2-4C6B-B958-3CF27CF2C27F@esi-frankfurt.de> Message-ID: Hi Gio, Thanks for the info. The fcdc_matbin approach indeed would be suitable data for raw data. However, I’m looking for a fast solution for data that is already processed and cut into trials, in particular with varying trial length. Joscha > On Mar 31, 2015, at 22:39, Gio Piantoni wrote: > > Hi Joscha, > > FieldTrip already has its own simple uncompressed file format. > fcdc_matbin "It is not an official file format, but was invented here > at the FCDC. It consists of two files: a *.mat matlab file that > contains the header (and optionally the events) and a *.bin binary > file that contains the data." > http://www.fieldtriptoolbox.org/faq/reading_is_slow_can_i_write_my_raw_data_to_a_more_efficient_file_format > > If you want to look at the code: > https://github.com/fieldtrip/fieldtrip/blob/master/fileio/ft_write_data.m#L275 > > You should be able to read it as usual with ft_preprocessing. You can > convert your files to the fcdc_matbin using ft_preprocessing as well: > https://github.com/fieldtrip/fieldtrip/blob/master/ft_preprocessing.m#L581 > Be careful about not losing precision though. > > The only catch is that, as far as I know, you cannot export your > preprocessed data through ft_preprocessing at the moment, because > ft_write_data is now inside this if-part: > https://github.com/fieldtrip/fieldtrip/blob/master/ft_preprocessing.m#L252 > but it's only a matter of adapting that to your needs. > > Would this work for you? > > -g > > On Tue, Mar 31, 2015 at 9:09 AM, Schmiedt, Joscha > wrote: >> Hi, >> >> When working with Fieldtrip it is very convenient to store the data and >> analyses using MATLAB’s save and load functions. However, for large and/or >> complex data with many channels (>2GB) MATLAB enforces compression, which is >> pretty useless for electrophysiology data and slows down the load and save >> performance by a factor of up to 8 (see e.g. >> http://undocumentedmatlab.com/blog/improving-save-performance). The MATLAB >> file format is based on HDF5, which is generally an open and future-proof >> data format, but unfortunately MATLAB doesn’t allow you to disable the >> compression. >> >> An option to overcome this could be to develop a simple data format for >> Fieldtrip data that is also based on HDF5. Is or has there been any >> development going into that direction? Would there be any interest? Of >> course, creating yet another data format is almost never a good idea >> (https://xkcd.com/927/), but since HDF5 is well-documented and readable with >> almost any software, it might be worth thinking about it. >> >> I’d be happy to hear your thoughts. >> >> Joscha >> >> --------------------------------- >> Joscha Schmiedt >> PhD Student >> >> Ernst Strüngmann Institute (ESI) for Neuroscience >> in Cooperation with Max Planck Society >> Deutschordenstraße 46 >> 60528 Frankfurt am Main >> Germany >> >> Tel.: +49 (0)69 96769 241 >> >> Sitz der Gesellschaft: Frankfurt am Main >> Registergericht: Amtsgericht Frankfurt - HRB 84266 >> Geschäftsführer: Prof. Dr. Pascal Fries >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From orionblue8 at gmail.com Wed Apr 1 19:41:36 2015 From: orionblue8 at gmail.com (Orion) Date: Wed, 1 Apr 2015 12:41:36 -0500 Subject: [FieldTrip] how gamma power is calculated Message-ID: Does anyone in the Fieldtrip community calculate the "running gamma power"? This is what I call the parameter after doing a power analysis on each trial, and then to simplify the data by one dimension, averaging the bins within the 35-45 Hz or 30-94 Hz band. Coincidentally a plot of the running gamma power resembles a plot of the EEG first derivative (absolute value of). Can anyone explain why? Orion -------------- next part -------------- An HTML attachment was scrubbed... URL: From federica.ma at gmail.com Wed Apr 1 19:43:30 2015 From: federica.ma at gmail.com (Federica Mauro) Date: Wed, 1 Apr 2015 19:43:30 +0200 Subject: [FieldTrip] Spectral coherence Message-ID: Hi, I was starting to perform the tutorial on spectral coherence (the one is here: http://www.fieldtriptoolbox.org/tutorial/coherence?s[]=spectral&s[]=coherence), but, as I start with the first step I receive an error for the ft_freqanalysis function. The error is: freq = ft_freqanalysis(cfg, data); *??? Undefined function or variable 'abort'.* *Error in ==> ft_freqanalysis at 198* *if abort* what can I do? Thanks in advance! Federica -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.rotonda at gmail.com Thu Apr 2 02:33:52 2015 From: marco.rotonda at gmail.com (Marco Rotonda) Date: Thu, 2 Apr 2015 02:33:52 +0200 Subject: [FieldTrip] how gamma power is calculated In-Reply-To: References: Message-ID: Hi Orion, maybe you can have a look at: http://www.fieldtriptoolbox.org/example/ft_realtime_hilbert I did that code some years ago, so it's a bit outdated, but I think you can have an idea of what you're looking for. Marco On 1 April 2015 at 19:41, Orion wrote: > Does anyone in the Fieldtrip community calculate the "running gamma > power"? This is what I call the parameter after doing a power analysis on > each trial, and then to simplify the data by one dimension, averaging the > bins within the 35-45 Hz or 30-94 Hz band. > > Coincidentally a plot of the running gamma power resembles a plot of the > EEG first derivative (absolute value of). Can anyone explain why? > > Orion > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.sandeep29 at gmail.com Thu Apr 2 08:10:06 2015 From: b.sandeep29 at gmail.com (sandeep b) Date: Thu, 2 Apr 2015 11:40:06 +0530 Subject: [FieldTrip] Unable to download fieldtrip toolbox from the download link Message-ID: Dear Administrator, I am unable to download fieldtrip toolbox from the given link ( http://www.fieldtriptoolbox.org/download). Is there any other other way to get the toolbox. Kindly please suggest me to get the toolbox Thank you Sandeep -------------- next part -------------- An HTML attachment was scrubbed... URL: From dorothee-brigitte.hoppe at student.uni-tuebingen.de Thu Apr 2 15:44:05 2015 From: dorothee-brigitte.hoppe at student.uni-tuebingen.de (Dorothee Hoppe) Date: Thu, 02 Apr 2015 15:44:05 +0200 Subject: [FieldTrip] ICA on each trial or collapsing over all trials Message-ID: <20150402154405.14144i9yubvrxw2t@webmail.uni-tuebingen.de> Dear Discussion Group members, we want to use ICA for artifact correction, and now got stuck at the point of deciding whether to compute the ICs on the trial level or on the whole dataset for a subject. Using the whole dataset, the advantage is probably a higher power of the ICA because of the larger data input, so for example a blink component gets probably more distinctive. On the other hand, we observed, that artifacts that occur only in a small set of trials, like strong muscle artifacts cannot be detected that way, or even lead to a distortion of the components for that special trial. Would you recommend an ICA on each trial or collapsing over all trials (both options within each subject)? Are there other arguments to favor or reject these options? Best regards, Dorothée From mahjoory86 at gmail.com Thu Apr 2 15:51:23 2015 From: mahjoory86 at gmail.com (Keyvan Mahjoory) Date: Thu, 2 Apr 2015 15:51:23 +0200 Subject: [FieldTrip] Fwd: Power Maps on Surface In-Reply-To: References: Message-ID: Dear Fieldtrip Users, I used the surface file "cortex_5124.surf.gii" to restrict sources on cortex. I wonder how I can plot powermaps on surface? cfg.surffile=ft_read_headshape('cortex_5124.surf.gii'); even I save it's output in a new .mat file: "sourcemodel.mat" and tried cgf.surffile = 'sourcemodel.mat'; in either case the function "ft_sourceplot" gives error. cfg = []; cfg.method = 'surface'; cfg.funparameter = 'avg.pow'; cfg.funcolormap = 'jet'; cfg.surffile='sourcemodel.mat'; ft_sourceplot(cfg, src) In my code I have defined surface vertices and triangles, as well as power per vertex, I wonder What is wrong in my code? Many Thanks in advance, Best, Keyvan -------------- next part -------------- An HTML attachment was scrubbed... URL: From ayobimpe2004 at gmail.com Thu Apr 2 17:36:57 2015 From: ayobimpe2004 at gmail.com (Azeez Adebimpe) Date: Thu, 2 Apr 2015 17:36:57 +0200 Subject: [FieldTrip] Fwd: Power Maps on Surface In-Reply-To: References: Message-ID: Hello, Your code is right I also encouter the same problem but you can project on the surface with ft_plot_mesh ft_plot_mesh(bnd, 'vertexcolor', m); bnd is the your source modle and m is avg.pow value Azeez On Thu, Apr 2, 2015 at 3:51 PM, Keyvan Mahjoory wrote: > Dear Fieldtrip Users, > > > I used the surface file "cortex_5124.surf.gii" to restrict sources on > cortex. I wonder how I can plot powermaps on surface? > > cfg.surffile=ft_read_headshape('cortex_5124.surf.gii'); > > even I save it's output in a new .mat file: "sourcemodel.mat" and tried > cgf.surffile = 'sourcemodel.mat'; > > in either case the function "ft_sourceplot" gives error. > > cfg = []; > cfg.method = 'surface'; > cfg.funparameter = 'avg.pow'; > cfg.funcolormap = 'jet'; > cfg.surffile='sourcemodel.mat'; > ft_sourceplot(cfg, src) > > In my code I have defined surface vertices and triangles, as well as power > per vertex, I wonder What is wrong in my code? > > Many Thanks in advance, > Best, > Keyvan > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jorn at artinis.com Fri Apr 3 09:23:24 2015 From: jorn at artinis.com (=?utf-8?Q?J=C3=B6rn_M._Horschig?=) Date: Fri, 3 Apr 2015 09:23:24 +0200 Subject: [FieldTrip] Fwd: Power Maps on Surface In-Reply-To: References: Message-ID: <001b01d06ddf$12a60870$37f21950$@artinis.com> Hey. You should specify cfg.surffile really as the path to the file, and not read in the content apriori. This section here might help (the ‘exercise’ part of the tutorial lists a cfg-example for surface plotting). http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_sources_of_oscillatory_gamma-band_activity Best, Jörn -- Jörn M. Horschig, Software Engineer Artinis Medical Systems | +31 481 350 980 From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Azeez Adebimpe Sent: Thursday, April 2, 2015 5:37 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] Fwd: Power Maps on Surface Hello, Your code is right I also encouter the same problem but you can project on the surface with ft_plot_mesh ft_plot_mesh(bnd, 'vertexcolor', m); bnd is the your source modle and m is avg.pow value Azeez On Thu, Apr 2, 2015 at 3:51 PM, Keyvan Mahjoory > wrote: Dear Fieldtrip Users, I used the surface file "cortex_5124.surf.gii" to restrict sources on cortex. I wonder how I can plot powermaps on surface? cfg.surffile=ft_read_headshape('cortex_5124.surf.gii'); even I save it's output in a new .mat file: "sourcemodel.mat" and tried cgf.surffile = 'sourcemodel.mat'; in either case the function "ft_sourceplot" gives error. cfg = []; cfg.method = 'surface'; cfg.funparameter = 'avg.pow'; cfg.funcolormap = 'jet'; cfg.surffile='sourcemodel.mat'; ft_sourceplot(cfg, src) In my code I have defined surface vertices and triangles, as well as power per vertex, I wonder What is wrong in my code? Many Thanks in advance, Best, Keyvan _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From abarnyeu at hotmail.com Sun Apr 5 05:03:02 2015 From: abarnyeu at hotmail.com (Charles West) Date: Sat, 4 Apr 2015 20:03:02 -0700 Subject: [FieldTrip] cfg structure for plotting topographical maps Message-ID: Hi everyone, I am new to FieldTrip and am confused about the cfg structure that is required for running Field Trip functions. I would like to plot the topographical maps of a frequency range (e.g. 5 to 10 Hz) using Field Trip. I used the besa2fieldtrip function to create data. I receive the following error message when running ft_topoplotER. Please let me know why the following error appears. Many thanks! Charles West >>cfg.layout = 'layout.lay'; >>cfg.parameter = 'avg' >>ft_topoplotER(cfg, data); reading layout from file layout.lay the call to "ft_prepare_layout" took 0 seconds Attempt to reference field of non-structure array. Error in ft_datatype_sens (line 136) nchan = length(sens.label); Error in ft_datatype_timelock (line 99) timelock.elec = ft_datatype_sens(timelock.elec); Error in ft_checkdata (line 227) data = ft_datatype_timelock(data); Error in topoplot_common (line 74) data = ft_checkdata(data, 'datatype', {'comp', 'timelock', 'freq'}); Error in ft_topoplotER (line 192) cfg = topoplot_common(cfg, varargin{:}); -------------- next part -------------- An HTML attachment was scrubbed... URL: From rikkert.hindriks at upf.edu Wed Apr 8 09:32:37 2015 From: rikkert.hindriks at upf.edu (HINDRIKS, RIKKERT) Date: Wed, 8 Apr 2015 09:32:37 +0200 Subject: [FieldTrip] Unit of simulated EEG using openMEEG Message-ID: Dear all, Could anyone tell me what are the units of the entries in BEM leadfield matrices generated using openMEEG? For example, if I multiply the matrix with a vector of dipole moments in Am, do I get microVolts? (after taking the average reference) Thanks a lot, Rikkert -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at telecom-paristech.fr Wed Apr 8 10:08:02 2015 From: alexandre.gramfort at telecom-paristech.fr (Alexandre Gramfort) Date: Wed, 8 Apr 2015 10:08:02 +0200 Subject: [FieldTrip] Unit of simulated EEG using openMEEG In-Reply-To: References: Message-ID: hi, if your meshes are in meters then moments in Am produce volts. hope this helps Alex On Wed, Apr 8, 2015 at 9:32 AM, HINDRIKS, RIKKERT wrote: > > Dear all, > > Could anyone tell me what are the units of the entries in BEM leadfield > matrices generated using openMEEG? > > For example, if I multiply the matrix with a vector of dipole moments in Am, > do I get microVolts? (after taking the > average reference) > > Thanks a lot, > Rikkert > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From munsif.jatoi at gmail.com Wed Apr 8 10:08:28 2015 From: munsif.jatoi at gmail.com (Munsif Jatoi) Date: Wed, 8 Apr 2015 16:08:28 +0800 Subject: [FieldTrip] Unit of simulated EEG using openMEEG In-Reply-To: References: Message-ID: Dear Hindriks, The leadfield matrix has got orientation and moments of dipoles. When it is multiplied by dipole numbers say 1 or 2 at certain location, it will be generating the voltage matrix. Put it in a more simple way, V= KJ +e where, V= potential (volts), K= leadfield and J= current density (A/m2). So the generated data has units of microvolts or the units of voltage. I hope you got the point. Thanks, Munsif. On Wed, Apr 8, 2015 at 3:32 PM, HINDRIKS, RIKKERT wrote: > > Dear all, > > Could anyone tell me what are the units of the entries in BEM leadfield > matrices generated using openMEEG? > > For example, if I multiply the matrix with a vector of dipole moments in > Am, do I get microVolts? (after taking the > average reference) > > Thanks a lot, > Rikkert > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Munsif Ali H.Jatoi, Ph D Scholar, Centre for Intelligent Signals and Imaging Research, Universiti Teknologi PETRONAS, Malaysia. http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at telecom-paristech.fr Wed Apr 8 10:21:24 2015 From: alexandre.gramfort at telecom-paristech.fr (Alexandre Gramfort) Date: Wed, 8 Apr 2015 10:21:24 +0200 Subject: [FieldTrip] Unit of simulated EEG using openMEEG In-Reply-To: References: Message-ID: hi, OpenMEEG as used by default in Fieldtrip uses dipoles moments (not current density) so it's expressed in Am. Current density is also possible but not the default method exposed. Alex On Wed, Apr 8, 2015 at 10:08 AM, Munsif Jatoi wrote: > Dear Hindriks, > > The leadfield matrix has got orientation and moments of dipoles. When it is > multiplied by dipole numbers say 1 or 2 at certain location, it will be > generating the voltage matrix. Put it in a more simple way, V= KJ +e where, > V= potential (volts), K= leadfield and J= current density (A/m2). So the > generated data has units of microvolts or the units of voltage. I hope you > got the point. > > > Thanks, > > Munsif. > > > On Wed, Apr 8, 2015 at 3:32 PM, HINDRIKS, RIKKERT > wrote: >> >> >> Dear all, >> >> Could anyone tell me what are the units of the entries in BEM leadfield >> matrices generated using openMEEG? >> >> For example, if I multiply the matrix with a vector of dipole moments in >> Am, do I get microVolts? (after taking the >> average reference) >> >> Thanks a lot, >> Rikkert >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Munsif Ali H.Jatoi, > > Ph D Scholar, > Centre for Intelligent Signals and Imaging Research, > Universiti Teknologi PETRONAS, > Malaysia. > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > From rikkert.hindriks at upf.edu Wed Apr 8 11:20:46 2015 From: rikkert.hindriks at upf.edu (HINDRIKS, RIKKERT) Date: Wed, 8 Apr 2015 11:20:46 +0200 Subject: [FieldTrip] Unit of simulated EEG using openMEEG In-Reply-To: References: Message-ID: Hi Alex, I see, thanks. I have specified the meshes in mm's so a unit dipole moment is expressed in Amm right? Thus a homogeneous dipole field with moment x Amm leads to scalp potentials of 10^(-2)*L*x (where L is the computed leadfield matrix). The thing is that if I place a single dipole with moment Q = 10 nAm = 10^(-6) Amm (which is about the required value to pick up a measurable MEG signal), this gives scalp voltages LQ in the order of picoV (at most something of the order 10^(-11) for appropriately placed dipoles) while you would expect it to be in the order of microV no? Could it be that in the specification of the headmodel, I should use S/mm instead of S/m for the conductivities? (I use the "standard" values of 0.33 S/m , 0.0041 S/m, and 0.33 S/m for brain, skull, and scalp, resp.) Kind regards and thanks, Rikkert On Wed, Apr 8, 2015 at 10:08 AM, Alexandre Gramfort < alexandre.gramfort at telecom-paristech.fr> wrote: > hi, > > if your meshes are in meters then moments in Am produce volts. > > hope this helps > Alex > > On Wed, Apr 8, 2015 at 9:32 AM, HINDRIKS, RIKKERT > wrote: > > > > Dear all, > > > > Could anyone tell me what are the units of the entries in BEM leadfield > > matrices generated using openMEEG? > > > > For example, if I multiply the matrix with a vector of dipole moments in > Am, > > do I get microVolts? (after taking the > > average reference) > > > > Thanks a lot, > > Rikkert > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at telecom-paristech.fr Wed Apr 8 11:29:48 2015 From: alexandre.gramfort at telecom-paristech.fr (Alexandre Gramfort) Date: Wed, 8 Apr 2015 11:29:48 +0200 Subject: [FieldTrip] Unit of simulated EEG using openMEEG In-Reply-To: References: Message-ID: hi Rikkert, the unit of conductivities have no impact as it's only their ratio that is used in computation. For the rest run simple simulations to get more intuition. HTH Alex On Wed, Apr 8, 2015 at 11:20 AM, HINDRIKS, RIKKERT wrote: > Hi Alex, > > I see, thanks. I have specified the meshes in mm's so a unit dipole moment > is expressed in Amm right? > Thus a homogeneous dipole field with moment x Amm leads to scalp potentials > of 10^(-2)*L*x (where L > is the computed leadfield matrix). > > The thing is that if I place a single dipole with moment Q = 10 nAm = > 10^(-6) Amm (which is about the > required value to pick up a measurable MEG signal), this gives scalp > voltages LQ in the order of picoV > (at most something of the order 10^(-11) for appropriately placed dipoles) > while you would expect it to > be in the order of microV no? > > Could it be that in the specification of the headmodel, I should use S/mm > instead of S/m for the conductivities? > (I use the "standard" values of 0.33 S/m , 0.0041 S/m, and 0.33 S/m for > brain, skull, and scalp, resp.) > > > Kind regards and thanks, > Rikkert > > > On Wed, Apr 8, 2015 at 10:08 AM, Alexandre Gramfort > wrote: >> >> hi, >> >> if your meshes are in meters then moments in Am produce volts. >> >> hope this helps >> Alex >> >> On Wed, Apr 8, 2015 at 9:32 AM, HINDRIKS, RIKKERT >> wrote: >> > >> > Dear all, >> > >> > Could anyone tell me what are the units of the entries in BEM leadfield >> > matrices generated using openMEEG? >> > >> > For example, if I multiply the matrix with a vector of dipole moments in >> > Am, >> > do I get microVolts? (after taking the >> > average reference) >> > >> > Thanks a lot, >> > Rikkert >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From rikkert.hindriks at upf.edu Wed Apr 8 12:32:41 2015 From: rikkert.hindriks at upf.edu (HINDRIKS, RIKKERT) Date: Wed, 8 Apr 2015 12:32:41 +0200 Subject: [FieldTrip] Unit of simulated EEG using openMEEG In-Reply-To: References: Message-ID: Hi Alex, Ok, clear, thanks. But in any case, when using a typical dipole moment of 10 nAm, you would like to end up with voltages in the experimental range, that is, in the order of microVolts (after taking the average reference) I would appreciate it very much if someone could elucidate this for me. Kind regards, Rikkert On Wed, Apr 8, 2015 at 11:29 AM, Alexandre Gramfort < alexandre.gramfort at telecom-paristech.fr> wrote: > hi Rikkert, > > the unit of conductivities have no impact as it's only their ratio > that is used in computation. > > For the rest run simple simulations to get more intuition. > > HTH > Alex > > > On Wed, Apr 8, 2015 at 11:20 AM, HINDRIKS, RIKKERT > wrote: > > Hi Alex, > > > > I see, thanks. I have specified the meshes in mm's so a unit dipole > moment > > is expressed in Amm right? > > Thus a homogeneous dipole field with moment x Amm leads to scalp > potentials > > of 10^(-2)*L*x (where L > > is the computed leadfield matrix). > > > > The thing is that if I place a single dipole with moment Q = 10 nAm = > > 10^(-6) Amm (which is about the > > required value to pick up a measurable MEG signal), this gives scalp > > voltages LQ in the order of picoV > > (at most something of the order 10^(-11) for appropriately placed > dipoles) > > while you would expect it to > > be in the order of microV no? > > > > Could it be that in the specification of the headmodel, I should use S/mm > > instead of S/m for the conductivities? > > (I use the "standard" values of 0.33 S/m , 0.0041 S/m, and 0.33 S/m for > > brain, skull, and scalp, resp.) > > > > > > Kind regards and thanks, > > Rikkert > > > > > > On Wed, Apr 8, 2015 at 10:08 AM, Alexandre Gramfort > > wrote: > >> > >> hi, > >> > >> if your meshes are in meters then moments in Am produce volts. > >> > >> hope this helps > >> Alex > >> > >> On Wed, Apr 8, 2015 at 9:32 AM, HINDRIKS, RIKKERT > >> wrote: > >> > > >> > Dear all, > >> > > >> > Could anyone tell me what are the units of the entries in BEM > leadfield > >> > matrices generated using openMEEG? > >> > > >> > For example, if I multiply the matrix with a vector of dipole moments > in > >> > Am, > >> > do I get microVolts? (after taking the > >> > average reference) > >> > > >> > Thanks a lot, > >> > Rikkert > >> > > >> > _______________________________________________ > >> > fieldtrip mailing list > >> > fieldtrip at donders.ru.nl > >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at telecom-paristech.fr Wed Apr 8 16:32:57 2015 From: alexandre.gramfort at telecom-paristech.fr (Alexandre Gramfort) Date: Wed, 8 Apr 2015 16:32:57 +0200 Subject: [FieldTrip] Unit of simulated EEG using openMEEG In-Reply-To: References: Message-ID: hi, > But in any case, when using a typical dipole moment of 10 nAm, you would > like to end up with voltages in the experimental range, that is, in the > order > of microVolts (after taking the average reference) yes this should be the case if you use meshes in meters. A From Alexander.Hunold at tu-ilmenau.de Wed Apr 8 17:05:27 2015 From: Alexander.Hunold at tu-ilmenau.de (Hunold Alexander TU Ilmenau) Date: Wed, 8 Apr 2015 15:05:27 +0000 Subject: [FieldTrip] =?windows-1252?q?7th_International_Summer_School_in_B?= =?windows-1252?q?iomedical_Engineering_=84New_Instrumentation_for_brain_m?= =?windows-1252?q?easurements_and_stimulation=93=2C_17th_-_29th_August_201?= =?windows-1252?q?5_in_Lutherstadt_Wittenberg=2C_Germany?= Message-ID: <5B8562898ECA5A4594C9879007B90670395D7F5C@MB1.x.chg> Dear colleagues, we are pleased to announce the 7th International Summer School in Biomedical Engineering on "New Instrumentation for brain measurements and stimulation" August, 17-29, 2015 in Lutherstadt Wittenberg, Germany. This event stands in the tradition of a series of successful summer schools on hot themes in biomedical engineering, dedicated to intense learning in the fruitful atmosphere of tight interaction between students and world-leading specialists. This year’s summer school is devoted to new hardware technologies for measuring and stimulating the brain, such as dry electroencephalography (EEG) electrodes, optically pumped magnetic field sensors, neuronal current imaging based on low-field magnetic resonance and multichannel transcranial current stimulation. In particular, the 7th International Summer School on Biomedical Engineering will focus on ways how these new technical advances may help to overcome current limitations in human neurosciences and medicine. It will cover both theoretical foundations and practical applications. We aim at a thorough understanding of the underlying mechanisms. Thus, we will develop a critical view on current applications and possible future developments. The second important aim of the summer school consists in providing contact with both leading experts in the field and other students with similar interests, thereby facilitating the exchange of ideas on latest developments in the field. Target Group: - PhD students - Advanced Master students - Researchers entering the field of brain measurement and stimulation techniques Further Information about the 7th International Summer School in Biomedical Engineering: www.iss2015.org We would be happy to receive your application. Please pass this announcement to your colleagues who might be interested. Sincerely, Jens Haueisen and Thomas Knösche -------------- next part -------------- An HTML attachment was scrubbed... URL: From vanwijk.bernadette at gmail.com Wed Apr 8 17:07:42 2015 From: vanwijk.bernadette at gmail.com (Bernadette van Wijk) Date: Wed, 8 Apr 2015 16:07:42 +0100 Subject: [FieldTrip] SPM course for MEG/EEG in London: May 11-13 Message-ID: Dear all, We are pleased to announce that our annual *SPM course for MEG/EEG* will take place this year from *Monday May 11* to *Wednesday May 13 2015*. Hosted by University College London, the course will be held at Queen Square, a very central location in London (UK). The course will present instruction on the analysis of MEG and EEG data. The first two days will combine theoretical presentations with practical demonstrations of the different data analysis methods implemented in SPM. On the last day participants will have the opportunity to work on SPM tutorial data sets under the supervision of the course faculty. We also invite students to bring their own data for analysis. The course is suitable for both beginners and more advanced users. The topics that will be covered range from pre-processing and statistical analysis to source localization and dynamic causal modelling. The program is listed below. Registration is now open. We offer a reduced rate when attending both the MEG/EEG course and the fMRI course during the second half of the week. For full details of both courses see 'Statistical Parametric Mapping short courses' at http://www.ucl.ac.uk/ion/courses-viewer where you can also register. Available places are limited so please register as early as possible if you would like to attend! *Monday May 11th* 9.00 - 9.30 Registration 9.30 - 9.45 SPM introduction and resources *Guillaume Flandin* 9.45 - 10.30 What are we measuring with M/EEG? *Stefan Kiebel* 10.30 - 11.15 Data pre-processing *Holly Rossiter* *Coffee* 11.45 - 12.30 Data pre-processing - demo *Deborah Talmi, Megumi Fukuda* 12.30 - 13.15 General linear model and classical inference *Christophe Phillips* *Lunch* 14.15 - 15.00 Multiple comparisons problem and solutions *Gareth Barnes* 15.00 - 15.45 Bayesian inference *Chris Mathys* *Coffee* 16.15 - 18.00 Tutorial on group M/EEG dataset analysis *Vladimir Litvak, Jason Taylor* *Tuesday May 12th* 9.30 - 10.15 M/EEG source analysis *Saskia Helbling* 10.15 - 11.15 M/EEG source analysis - demo *Jose Lopez, Jason Taylor, Sofie Meyer* *Coffee* 11.45 - 12.30 The principles of DCM *Ryszard Auksztulewicz* 12.30 - 13.15 DCM for evoked responses *Harriet Brown* *Lunch* 14.15 - 15.00 DCM for steady state responses *Rosalyn Moran* 15.00 - 15.45 DCM for time-frequency responses *Bernadette van Wijk* 15.45 - 16.30 DCM - demo *Andre Marreiros, Martin Dietz * *Coffee* 17.00 - 17.45 Bayesian model selection and averaging *Will Penny* 17.45 - 18.45 Clinic - Questions & Answers session *Karl Friston* 19.00 onwards - Social Event *Wednesday May 13th* 9.30 – 17.00 Practical hands-on session in UCL computer class rooms. Participants can either work on SPM tutorial datasets or on their own data with the help of the faculty. There will also be an opportunity to ask questions in small tutorial groups for further discussions on the topics of the lectures. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Apr 9 09:04:11 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 9 Apr 2015 09:04:11 +0200 Subject: [FieldTrip] Call for applications for 15 early stage researchers Message-ID: Dear all Positions for 15 early stage researchers (doctoral students) are offered in a project aiming to develop and apply new brain research methods to study normal and atypical cognitive development of children. Applicants from all relevant academic disciplines are encouraged to apply, including cognitive neuroscience, computer science, educational sciences, engineering, medicine, mathematics, psychology, physics, statistics, and related disciplines. The selected doctoral students will enroll in the graduate school of the host institution and work towards their PhD. The multidisciplinary ChildBrain (Advancing brain research in children’s developmental neurocognitive disorders) project is funded by the Horizon 2020 Marie Skłodowska-Curie action of the European Union. It is part of the Innovative Training Network (ITN) actions. The positions are open at five top ranked academic institutions and three innovative companies in PhD projects under three broader themes of neurocognitive disorders, brain development and brain research methods (see project descriptions at www.childbrain.eu). The academic and private sector partners will offer the students project-specific research, scientific collaboration, secondments, workshops and courses on scientific and entrepreneurial skills, as well as excellent supervision. Salaries are competitive (please see details under specific ESR projects). Successful applicants should have a degree that allows a direct entry into doctoral studies and less than 4 years of experience in research; and not have lived more than 12 months during the last 3 years in the country where doctoral studies are started; this is due to emphasis on mobility in the ITN projects. Women and men from all countries are encouraged to apply. Please see details on the projects and how to apply at www.childbrain.eu. Deadline for the first round of applications is April 30th 2015 (June 30th 2015 for ESR projects 2, 5, 9 and 11). best regards, Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ChildBrain_call_for_applications.pdf Type: application/pdf Size: 204906 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Apr 9 13:50:31 2015 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 9 Apr 2015 13:50:31 +0200 Subject: [FieldTrip] Be careful with nonlinear warping of your individual grids to MNI Message-ID: Dear FieldTrip community, I have encountered a little problem inverse-MNI-warping the grids of my individual subjects for the purpose of averaging my beamformer results, in line with: http://www.fieldtriptoolbox.org/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space?s[]=grid When I visually checked the resultant individual grids, I found that 6 out of 25 subjects had severely distorted grids. See attached examples. A bit of distortion could be expected, but IMHO this is too much. It is the result of nonlinear warping (done in the example script mentioned above) and solved by using cfg.grid.nonlinear = 'no, in the following part of the script: cfg = []; cfg.grid.warpmni = 'yes'; cfg.grid.template = template_scm; cfg.grid.nonlinear = 'no'; cfg.mri = mri_segmented; grid = ft_prepare_sourcemodel(cfg); Ofcourse this is not a Fieldtrip bug in any way, but just something to be aware of, and a warning I wanted to share. And it really shows that it is important to check all of the warped individual grids! I will redo only these subjects with linear instead of nonlinear warping. That is, unless anyone has a better solution? All the best, Stephen Whitmarsh -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... 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Name: pp_20_headmodel_grid_a.png Type: image/png Size: 151143 bytes Desc: not available URL: From thismoment at 163.com Sun Apr 12 17:32:05 2015 From: thismoment at 163.com (thismoment) Date: Sun, 12 Apr 2015 23:32:05 +0800 Subject: [FieldTrip] error when I convert .mri data into mgz or other format Message-ID: <552A8FF2.2000705@163.com> Hi Experts, I got a set of MEG. The anatomical MRI was stored in .mri format (CTF device) and MEG was stored in a folder named by xxx.ds. I do not know how to do segmentation of .mri into scalp,skull and cortex. So I try to convert .mri into .mgz or other format so that it can be used in freesurfer for reconstruction. I used the following command. x=ft_read_mri('MEG619.mri','dataformat','ctf_mri4'); y=ft_write_mri('ddd',x,'dataformat','mgz', 'transform',x.transform) the error was >> y=ft_write_mri('ddd',x,'dataformat','mgz', 'transform',x.transform) Error using fwrite Cannot write value: unsupported class struct Error in save_mgh (line 107) fwrite(fid,vol,'float32'); Error in ft_write_mri (line 79) save_mgh(dat, filename, transform); I failed to do it. 1. Anyone know what happens ? 2. Freesurfer can use .mri directly to reconstruct ? 3. Are there other methods to convert .mri into .mgz or .dicom format? Best wishes, J. Zhang 2015-04-12 thismoment -------------- next part -------------- An HTML attachment was scrubbed... URL: From wanyu at gazzaleylab.ucsf.edu Tue Apr 14 00:48:45 2015 From: wanyu at gazzaleylab.ucsf.edu (WanYu Hsu) Date: Mon, 13 Apr 2015 15:48:45 -0700 Subject: [FieldTrip] questions about topoplot and notch filter Message-ID: Hi community, Recently I am analyzing EEG dataset with only 20 channels and I am focusing on coherence between frontal and posterior electrodes in frequency domain. I got two questions here: 1. I wanted to topoplot the coherence between each pair of electrodes that we're interested in, and I tried the following script: cfg = []; cfg.colorparam = 'plvspctrm'; cfg.layout = 'biosemi64.lay'; cfg.foi =[4]; ft_topoplotCC(cfg, plv_avg_stim); The electrode layout and coherence we wanted to see were in the plot, but the plot did not show coherence related to FP1, FP2, and FPz. Am I doing something wrong? 2. I would like to apply notch filter to remove 6 Hz and first I tried cfg.dftfilter ='yes'; cfg.dftfreq = [6] but the 6Hz signal was still there. Then I also tried cfg.bsfilter ='yes'; cfg.bsfreq =[5 7]; This worked well to remove 6Hz signal, but it also affected 5Hz and 7Hz. Is there any way to remove 6 Hz specificlly? Any help would be appreciated. Best, Wanyu Hsu -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue Apr 14 09:47:31 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 14 Apr 2015 09:47:31 +0200 Subject: [FieldTrip] error when I convert .mri data into mgz or other format In-Reply-To: <552A8FF2.2000705@163.com> References: <552A8FF2.2000705@163.com> Message-ID: <31465C27-5C1C-4076-929C-358CC7BD7AE6@donders.ru.nl> Hi Zhang, You should specify the anatomical data as a 3D array, not as a structure. So rather than ft_write_mri('ddd',x,'dataformat','mgz', 'transform',x.transform) you should do ft_write_mri('ddd’,x.anatomy,'dataformat','mgz', 'transform',x.transform) Note also that you should not expect an output from ft_write_mri. best regards, Robert On 12 Apr 2015, at 17:32, thismoment wrote: > Hi Experts, > > I got a set of MEG. The anatomical MRI was stored in .mri format (CTF device) and MEG was stored in a folder named by xxx.ds. > I do not know how to do segmentation of .mri into scalp,skull and cortex. So I try to convert .mri into .mgz or other format so > that it can be used in freesurfer for reconstruction. > I used the following command. > > x=ft_read_mri('MEG619.mri','dataformat','ctf_mri4'); > y=ft_write_mri('ddd',x,'dataformat','mgz', 'transform',x.transform) > > the error was > > >> y=ft_write_mri('ddd',x,'dataformat','mgz', 'transform',x.transform) > Error using fwrite > Cannot write value: unsupported class struct > > Error in save_mgh (line 107) > fwrite(fid,vol,'float32'); > > Error in ft_write_mri (line 79) > save_mgh(dat, filename, transform); > > I failed to do it. > 1. Anyone know what happens ? > 2. Freesurfer can use .mri directly to reconstruct ? > 3. Are there other methods to convert .mri into .mgz or .dicom format? > > Best wishes, > J. Zhang > > > 2015-04-12 > thismoment > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue Apr 14 09:52:31 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 14 Apr 2015 09:52:31 +0200 Subject: [FieldTrip] questions about topoplot and notch filter In-Reply-To: References: Message-ID: <62310C2D-1246-4BF3-83C7-AD2F23FDF98E@donders.ru.nl> Dear WanYu Regarding your first question: I am not sure what you expected to see in the figure, and what you actually did see. Perhaps you should be using ft_connectivityplot instead. Note that the high-level plotting functions (the ones that take a cfg as first input) are only there to help you to get started with the figures, you can always plot the actual data yourself using low-level matlab functions and using the helper functions in the fieldtrip/plotting directory. Regarding the second question, perhaps these address your question http://www.fieldtriptoolbox.org/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter http://www.fieldtriptoolbox.org/tag/filter?do=showtag&tag=filter best regards, Robert On 14 Apr 2015, at 00:48, WanYu Hsu wrote: > Hi community, > Recently I am analyzing EEG dataset with only 20 channels and I am focusing on coherence between frontal and posterior electrodes in frequency domain. > > I got two questions here: > > 1. I wanted to topoplot the coherence between each pair of electrodes that we're interested in, and I tried the following script: > > cfg = []; > cfg.colorparam = 'plvspctrm'; > cfg.layout = 'biosemi64.lay'; > cfg.foi =[4]; > ft_topoplotCC(cfg, plv_avg_stim); > > The electrode layout and coherence we wanted to see were in the plot, but the plot did not show coherence related to FP1, FP2, and FPz. Am I doing something wrong? > > > > 2. I would like to apply notch filter to remove 6 Hz and first I tried > > cfg.dftfilter ='yes'; > cfg.dftfreq = [6] > but the 6Hz signal was still there. > Then I also tried > > cfg.bsfilter ='yes'; > cfg.bsfreq =[5 7]; > > This worked well to remove 6Hz signal, but it also affected 5Hz and 7Hz. > > Is there any way to remove 6 Hz specificlly? > > Any help would be appreciated. > > > > Best, > > Wanyu Hsu > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue Apr 14 09:55:29 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 14 Apr 2015 09:55:29 +0200 Subject: [FieldTrip] MEG postdoctoral position at Karolinska Institutet Message-ID: <1348BCC9-DB8E-4DEF-8178-B2CB53476D8E@donders.ru.nl> Postdoctoral studies in Magnetoencephalography (scholarship) Karolinska Institutet, The Department of Neuroscience, Ehrsson Research groups at the Department of Neuroscience study different aspects of the function of the normal nervous system, as well as disturbances, injuries and diseases affecting the nervous system. Projects include a broad range of studies at the molecular and cellular levels, the network level and at the level of the overall organization of the nervous system. The department also conducts undergraduate education in neuroscience, anatomy and histology in a number of programs at Karolinska Institutet. To read more about our department, please visit our webpage; www.ki.se/en/neuro/startpage Duties We are seeking a highly talented and enthusiastic researcher with a PhD in neuroimaging awarded within the past three years to work on projects in which magnetoencephalography (MEG) is applied to the problem of how we come to experience limbs as part of our own body. The research will be conducted at the Brain, Body and Self Laboratory at the Department of Neuroscience (www.ehrssonlab.se). This center has widespread expertise in fMRI and human behavioural experiments. The MEG experiments will be conducted at the recently established the “National Facility Magnetoencephalography (www.natmeg.se) that is equipped with a state-of-the-art MEG system (Electa Neuromag TRIUX), complementary physiological recording devices (MEG compatible 128–channel EEG, plethysmography, EMG, ECG, eyetracking), and sophisticated stimulus delivery platforms (visual, auditory, olfactory, pain, somatosensory; including a robot system for tactile stimulation of the hands). The ideal candidate will have expertise in the acquisition and analysis of MEG data, (preferably on an Elekta Triux or Vectorview system), expertise in analysis of MEG data (preferably on FieldTrip and/or MNE), as well as excellent programming skills (preferably including MatLab and Neurobs Presentation). Expertise in analysis of EEG data would be an advantage. The candidate is expected to work on projects in which MEG methods are applied to questions relating to how multisensory signals from the body are integrated at the levels of cortical structures to give rise to dynamic changes in the feeling of ownership of limbs. Good social skills are important as the candidate is expected to actively collaborate with other members of the laboratory, in addition to running his or her own project. Applicants should be able to demonstrate a consistently good academic record, including publications in international journals. Entry requirements Scholarships to pursue postdoctoral studies may be awarded to individuals who come from other countries with the intention of remaining in Sweden only while obtaining all or part of their education. The head of the department determines whether their previous training and scholarly qualifications correspond to a Swedish PhD or higher. Having received a salary or other remuneration from Karolinska Institutet during the past two years may be disqualifying. One requirement for receiving a scholarship for postdoctoral studies is central registration as a postdoc. Type of scholarship Karolinska Institutet awards scholarships to pursue postdoctoral studies. This educational scholarship, which is paid for a maximum of two years within four years after the receipt of a PhD or the equivalent, is tax-exempt. The amount is set for twelve months at a time and is paid out on a monthly basis. In exceptional cases, shorter periods may be acceptable. Application process An application must contain the following documents in English: Curriculum vitae and qualifications, presented in accordance with Karolinska Institutet’s qualifications portfolio (http://ki.se/meritportfolj ) A complete list of publications A summary of current research (no more than one page) Verifications for crediting of illness, military service, work for labour unions or student organisations, parental leave or similar circumstances Verification from the thesis defence committee or the equivalent (only if the thesis defence is scheduled within three months after the application deadline) Contact details for two reference persons The application is to be submitted through the MyNetwork recruitment system. Karolinska Institutet is one of the world´s leading medical universities. Its mission is to contribute to the improvement of human health through research and education. Karolinska Institutet accounts for over 40 per cent of the medical academic research conducted in Sweden and offers the country´s broadest range of education in medicine and health sciences. Since 1901 the Nobel Assembly at Karolinska Institutet has selected the Nobel laureates in Physiology or Medicine. Pursuant to the regulations of the Swedish National Archives, applications are kept on file for two years after the appointment has gained legal force. The regulations do not apply to attachments that have been printed or otherwise published. Karolinska Institutet strives to provide a workplace that has approximately the same number of women and men, is free of discrimination and offers equal opportunity to everyone. For temp agencies and recruiters, and to salespersons: We politely, yet firmly, decline direct contact with temp agencies and recruiters, as well as those selling additional job announcements. Type of employment: Postdoctoral studies. Working hours: Full time First day of employment: As soon as possible Reference number: 2-1291/2015 Contact: Henrik Ehrsson, professor, henrik.ehrsson at ki.se Union representative: Peter Århem, SACO, 46-8 524 869 03 Anne Edgren, OFR, 08-616 16 29 Gunnar Stenberg, SEKO, 08-524 880 75 Published: 27.Mar.2015 Last application date: 07.May.2015 Contact Henrik Ehrsson, professor, henrik.ehrsson at ki.se Link to ad: http://ki.mynetworkglobal.com/what:job/jobID:61655/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: cid:134.gif Type: image/gif Size: 8101 bytes Desc: not available URL: From f.roux at bcbl.eu Tue Apr 14 18:12:26 2015 From: f.roux at bcbl.eu (=?utf-8?B?RnLDqWTDqXJpYw==?= Roux) Date: Tue, 14 Apr 2015 18:12:26 +0200 (CEST) Subject: [FieldTrip] missing samples after donwsampling In-Reply-To: <1130111699.32607.1429027894577.JavaMail.root@bcbl.eu> Message-ID: <1165544691.32620.1429027946414.JavaMail.root@bcbl.eu> Dear all, i've noticed that after invoking ft_resampledata not all trials have the same number of samples. For instance: cfg = []; cfg.resamplefs = 400; [meg_data] = ft_resamplefs(cfg,meg_data); will return length(meg_data.trial{1}) = 2601 whereas length(meg_data.trial{2}) = 2600 This is causing a conflict upstream in my analysis pipeline and I wanted to ask if there was a way to fix this? I am using fieldtrip-20150115. Any thoughts or help would be highly appreciated. Best, Fred -- Frédéric Roux Postdoctoral Scientist BCBL. Basque Center on Cognition, Brain % Language. f.roux at bcbl.eu Tel: +34 943 309 300 Ext 211 Fax: +34 943 309 052 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer --------------------------------------------------------------------------- From pgoodin at swin.edu.au Wed Apr 15 02:06:33 2015 From: pgoodin at swin.edu.au (Peter Goodin) Date: Wed, 15 Apr 2015 00:06:33 +0000 Subject: [FieldTrip] Why the general use of parametric test as observed test statistic for permutation cluster tests? Message-ID: Hi Fieldtrip list, I'm just wondering if someone can explain if there is a reasoning behind the general use of a parametric test to calculate the initial step in the permutation cluster test and not a non-parametric test (e.g t-test over Mann Whitey U)? Is it just due to the assumption of a Gaussian distribution or is there something deeper going on? Thanks, Peter _______________________ Peter Goodin, BSc (Hons), Ph.D Candidate (submitted). Brain and Psychological Sciences Research Centre (BPsych) Swinburne University, Hawthorn, Vic, 3122 http://www.swinburne.edu.au/swinburneresearchers/index.php?fuseaction=profile&pid=4149 Monash Alfred Psychiatry Research Centre (MAPrc) Level 4, 607 St Kilda Road, Melbourne 3004 From tamaonvaliaikainenmaili at gmail.com Wed Apr 15 10:32:32 2015 From: tamaonvaliaikainenmaili at gmail.com (hm ham) Date: Wed, 15 Apr 2015 11:32:32 +0300 Subject: [FieldTrip] EEG MNE with standard_bem and statistics sanity Message-ID: Hello fellow fieldtrippers, I sent these questions a few weeks back, but I think they got buried in the weekend emails, so I'm asking the same things again. Sorry for the spam. I'm using fieldtrip to do a MNE for EEG data with no subject MRIs and I have a few questions to which I can't get a straight answer from tutorials or from mailing list history. I guess this is sort of a sanity check. First, I'm wondering about the correct sourcemodel, as loading the standard_bem and setting the third mesh as the source points in ft_prepare_leadfield gives an error: Warning: dipole lies on boundary of volume model. Code: % Electrodes, vol, sourcemodel all set in same scale with ft_convert_units vol = load('standard_bem'); cfg = []; cfg.elec = elec_aligned; % electrodes aligned to skin surface cfg.grid.pos = vol.bnd(3).pnt; % source points cfg.grid.inside = 1:size(vol.bnd(3).pnt,1); cfg.vol = vol; cfg.reducerank = 3; leadfield = ft_prepare_leadfield(cfg); Using the code below works: vol = load('standard_bem'); sourcemodel = ft_read_headshape('cortex_8196.surf.gii'); cfg = []; cfg.elec = elec_aligned; % electrodes aligned to skin surface cfg.grid.pos = sourcemodel; % source points cfg.grid.inside = 1:size(sourcemodel,1); cfg.vol = vol; cfg.reducerank = 3; leadfield = ft_prepare_leadfield(cfg); But as the http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg seems to suggest the third mesh in vol should be the brain? Or is the third compartment there just for conduction calculations? As using the sourcemodel 'cortex_8196.surf.gii' at least gave an output I went forward with those for now, to see what other problems I'd encounter. Running the MNE: cfg = []; cfg.elec = elec_aligned; cfg.method = 'mne'; cfg.grid = leadfield; cfg.vol = vol; cfg.mne.prewhiten = 'yes'; cfg.mne.lambda = 60; %Hmmm? cfg.mne.scalesourcecov = 'yes'; cfg.mne.normalize = 'yes'; cfg.channel = 'all'; cond_12_source{subject_id} = ft_sourceanalysis(cfg,cond_12{subject_id}); So secondly, I'm concerned with the lambda value, as different tutorials give very different advice ranging from 3 to 1e8. Running the MNE with 3 seems to give very unstable results when comparing the results between subjects or conditions. The data is somewhat contaminated with leftover eye-movement artefacts (removed with ICA). And that 3 is from the tutorial where the data is from MEG. So a bigger lambda is in order, but how big? Or just let the minimumnormestimate.m calculate it from the data? I have to point out that the eye-movements are somewhat spread around the trial durations and not present in the calculation window of the .cov field from ft_timelockanalysis. Should I maybe calculate the .cov field from the whole trial? Third, there has been talk of MNE statistics in the mailing list, and it seems that the ft_timelockstatistics will do the job if a neighbours structure is provided. I build the neighbours structure from the sourcemodel mesh like this: sourcemodel = ft_read_headshape('cortex_8196.surf.gii'); nsources = length(sourcemodel.pnt); neighbours=struct; for i=1:nsources neighbours(i).label = num2str(i); neighb_nodes = sourcemodel.tri((sourcemodel.tri(:,1)==i | sourcemodel.tri(:,2)==i | sourcemodel.tri(:,3)==i),:); neighb_nodes = unique(neighb_nodes)'; idx = (neighb_nodes ~= i); neighb_nodes = neighb_nodes(idx); for k=1:length(neighb_nodes) neighbours(i).neighblabel{k} = num2str(neighb_nodes(k)); end end This seemed to give reasonable neighbours and just going by distance gave some sources that were on the other side of a gyrus. Although now with the above method the distances between the sources are not uniform. I also had to tweak the data structures a little bit, labels and such. Then I ran the tests with: cfg=[]; cfg.parameter = 'avg.pow'; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT'; cfg.parameter = 'avg'; cfg.correctm = 'cluster'; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.numrandomization = 1000; cfg.tail = 1; cfg.correcttail ='alpha'; cfg.alpha = 0.05; cfg.latency = [0.4 0.5]; cfg.avgovertime = 'yes'; cfg.neighbours = neighbours; cfg.design = [1:15 1:15;ones(1,15), ones(1,15)*2]; cfg.uvar = 1; cfg.ivar = 2; cond1_stat = ft_timelockstatistics(cfg, cond_11_source{:}, cond_12_source{:}); Looking at the resulting clusters from ft_timelockstatistics there were clusters that when plotted showed disconnected sources. For example, plotted like this for the first cluster: paint = ones(8196,3); indx = find(cond1_stat.posclusterslabelmat == 1); paint(indx,2) = 0; ft_plot_mesh(sourcemodel,'vertexcolor',paint); Gave the output in the attachment, in that case the third source is atleast close, but still not a neighbour to the two next to it. Is there maybe something I'm missing with using the ft_timelockstatistics like this? I hope someone can clarify some of these issues. Thank you already in advance! Tatu -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: disconnected_cluster.png Type: image/png Size: 83016 bytes Desc: not available URL: From noahertz6 at gmail.com Wed Apr 15 14:21:46 2015 From: noahertz6 at gmail.com (Noa Hertz) Date: Wed, 15 Apr 2015 15:21:46 +0300 Subject: [FieldTrip] Beamforming analysis in frequency band Message-ID: Hi all, I'm doing source analysis in the frequency domain of a resting-state data. when doing the source analysis, I want to use several frequency bands of interest, such as beta (13-30 Hz) and gamma (30-48 Hz). My problem is about the cfg.frequency parameter, which must be a scalar (whereas i'm interested in a frequency band). Arbitrarily choosing a frequency in the middle of the range doesn't seem right. What is the common practice when doing source analysis using this function? Does the cfg.tapsmofrq parameter is supposed to enable choosing frequency band instead of a single peak frequency? Any suggestions will be very much helpful! Thanks, Noa *This is the script I’m using: cfg = []; cfg.method ='mtmfft'; cfg.output ='fourier'; cfg.keeptapers = 'yes'; cfg.foilim = [30 48]; cfg.tapsmofrq = 2; freqClosed=ft_freqanalysis(cfg,eyesClosed); * cfg = []; cfg.method='pcc'; cfg.frequency = 39; % must be a scalar cfg.lambda = 0; cfg.vol = vol; cfg.grid = grid; cfg.feedback = 'textbar'; cfg.keepfilter='yes'; source1 = ft_sourceanalysis(cfg, freqClosed); -- My signature: http://www.documentarywire.com/earthlings/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Wed Apr 15 16:25:59 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 15 Apr 2015 16:25:59 +0200 Subject: [FieldTrip] next week: live broadcast of MEG/EEG toolkit lectures Message-ID: <827C8444-E803-4DA3-A475-78E0696A6C5C@donders.ru.nl> Dear FieldTrip users, Next Monday the 4-day MEG/EEG toolkit course will start at the Donders in Nijmegen. To maximize the impact of the course, we will be live broadcasting the lectures! The computer hands-on sessions are not suited for recording and live broadcasting, but following the corresponding lecture you might want to do some tutorials on your own. The program for the live broadcasts is (starting next Monday 20 April) Monday 09:45-10:45 Introduction to EEG/MEG and introduction to the FieldTrip toolbox Monday 15:15-16:30 Fundamentals of neuronal oscillations and synchrony Tuesday 11:00-12:15 Forward and inverse modeling Tuesday 13:00-14:00 Source reconstruction using beamformers Wednesday 09:00-10:00 Statistics using non-parametric randomization techniques Wednesday 13:00-14:00 Connectivity analysis in MEG and EEG data All indicated times are Central European Time (CET), i.e. the local time here in Nijmegen. You can watch the live lectures at our YouTube channel on https://www.youtube.com/user/FieldTripToolboxTV. If you go there now, you will already see that the live events have been scheduled. The full course program is on http://www.fieldtriptoolbox.org/workshop/toolkit2015, where it will be further updated during the next days. If at any moment in doubt during next week, please go to the toolkit2015 page to get the latest updates. I’ll also post the links to the youtube live streams there. best regards, Robert (on behalf of the FieldTrip team) PS this is the very first time for us to do a live broadcast. Of course we hope it will all work as planned, but we might run into some technical difficulties. As we cannot communicate all details to each of you individually, please keep an eye on http://www.fieldtriptoolbox.org/workshop/toolkit2015 for the latest news. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Wed Apr 15 16:41:41 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 15 Apr 2015 16:41:41 +0200 Subject: [FieldTrip] next week: live broadcast of MEG/EEG toolkit lectures Message-ID: <1299A68A-2F15-462A-9D13-6C4C5DE3AD1F@donders.ru.nl> Dear FieldTrip users, Next Monday the 4-day MEG/EEG toolkit course will start at the Donders in Nijmegen. To maximize the impact of the course, we will be live broadcasting the lectures! The computer hands-on sessions are not suited for recording and live broadcasting, but following the corresponding lecture you might want to do some tutorials on your own. The program for the live broadcasts is (starting next Monday 20 April) Monday 09:45-10:45 Introduction to EEG/MEG and introduction to the FieldTrip toolbox Monday 15:15-16:30 Fundamentals of neuronal oscillations and synchrony Tuesday 11:00-12:15 Forward and inverse modeling Tuesday 13:00-14:00 Source reconstruction using beamformers Wednesday 09:00-10:00 Statistics using non-parametric randomization techniques Wednesday 13:00-14:00 Connectivity analysis in MEG and EEG data All indicated times are Central European Time (CET), i.e. the local time here in Nijmegen. You can watch the live lectures at our YouTube channel on https://www.youtube.com/user/FieldTripToolboxTV. If you go there now, you will already see that the live events have been scheduled. The full course program is on http://www.fieldtriptoolbox.org/workshop/toolkit2015, where it will be further updated during the next days. If at any moment in doubt during next week, please go to the toolkit2015 page to get the latest updates. I’ll also post the links to the youtube live streams there. best regards, Robert (on behalf of the FieldTrip team) PS this is the very first time for us to do a live broadcast. Of course we hope it will all work as planned, but we might run into some technical difficulties. As we cannot communicate all details to each of you individually, please keep an eye on http://www.fieldtriptoolbox.org/workshop/toolkit2015 for the latest news. -------------- next part -------------- An HTML attachment was scrubbed... URL: From spa268 at nyu.edu Wed Apr 15 18:17:41 2015 From: spa268 at nyu.edu (Stephen Politzer-Ahles) Date: Wed, 15 Apr 2015 18:17:41 +0200 Subject: [FieldTrip] Why the general use of parametric test as observed test statistic for permutation cluster tests? Message-ID: Hi Peter, As far as I know this is just a default coded in fieldtrip, but can easily be replaced (by using your own statfun rather than e.g. depsamplesF, depsamplesT, etc.). According to Maris & Oostenveld (2007), the observed statistic used to calculate clusters can be anything, if I recall correctly. Best, Steve > Message: 2 > Date: Wed, 15 Apr 2015 00:06:33 +0000 > From: Peter Goodin > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] Why the general use of parametric test as > observed test statistic for permutation cluster tests? > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > Hi Fieldtrip list, > > I'm just wondering if someone can explain if there is a reasoning behind the > general use of a parametric test to calculate the initial step in the > permutation cluster test and not a non-parametric test (e.g t-test over Mann > Whitey U)? Is it just due to the assumption of a Gaussian distribution or is > there something deeper going on? > > Thanks, > > Peter > > _______________________ > Peter Goodin, > BSc (Hons), Ph.D Candidate (submitted). > > Brain and Psychological Sciences Research Centre (BPsych) > Swinburne University, > Hawthorn, Vic, 3122 > http://www.swinburne.edu.au/swinburneresearchers/index.php?fuseaction=profile&pid=4149 > > Monash Alfred Psychiatry Research Centre (MAPrc) > Level 4, 607 St Kilda Road, > Melbourne 3004 > Stephen Politzer-Ahles New York University, Abu Dhabi Neuroscience of Language Lab http://www.nyu.edu/projects/politzer-ahles/ From pgoodin at swin.edu.au Thu Apr 16 00:23:25 2015 From: pgoodin at swin.edu.au (Peter Goodin) Date: Wed, 15 Apr 2015 22:23:25 +0000 Subject: [FieldTrip] Why the general use of parametric test as observed test statistic for permutation cluster tests? In-Reply-To: References: Message-ID: Hi Steve, You recall correctly indeed! It was actually that statement that got me thinking about the default use of t-test rather than checking the initial distribution! Peter __________________________ Peter Goodin, BSc (Hons), Ph.D Candidate (submitted). Brain and Psychological Sciences Research Centre (BPsych) Swinburne University, Hawthorn, Vic, 3122 http://www.swinburne.edu.au/swinburneresearchers/index.php?fuseaction=profile&pid=4149 Monash Alfred Psychiatry Research Centre (MAPrc) Level 4, 607 St Kilda Road, Melbourne 3004 ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Stephen Politzer-Ahles [spa268 at nyu.edu] Sent: Thursday, 16 April 2015 2:17 AM To: fieldtrip at science.ru.nl Subject: Re: [FieldTrip] Why the general use of parametric test as observed test statistic for permutation cluster tests? Hi Peter, As far as I know this is just a default coded in fieldtrip, but can easily be replaced (by using your own statfun rather than e.g. depsamplesF, depsamplesT, etc.). According to Maris & Oostenveld (2007), the observed statistic used to calculate clusters can be anything, if I recall correctly. Best, Steve > Message: 2 > Date: Wed, 15 Apr 2015 00:06:33 +0000 > From: Peter Goodin > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] Why the general use of parametric test as > observed test statistic for permutation cluster tests? > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > Hi Fieldtrip list, > > I'm just wondering if someone can explain if there is a reasoning behind the > general use of a parametric test to calculate the initial step in the > permutation cluster test and not a non-parametric test (e.g t-test over Mann > Whitey U)? Is it just due to the assumption of a Gaussian distribution or is > there something deeper going on? > > Thanks, > > Peter > > _______________________ > Peter Goodin, > BSc (Hons), Ph.D Candidate (submitted). > > Brain and Psychological Sciences Research Centre (BPsych) > Swinburne University, > Hawthorn, Vic, 3122 > http://www.swinburne.edu.au/swinburneresearchers/index.php?fuseaction=profile&pid=4149 > > Monash Alfred Psychiatry Research Centre (MAPrc) > Level 4, 607 St Kilda Road, > Melbourne 3004 > Stephen Politzer-Ahles New York University, Abu Dhabi Neuroscience of Language Lab http://www.nyu.edu/projects/politzer-ahles/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From federica.ma at gmail.com Thu Apr 16 11:41:17 2015 From: federica.ma at gmail.com (Federica Mauro) Date: Thu, 16 Apr 2015 09:41:17 +0000 Subject: [FieldTrip] Problems with ft_freqanalysis Message-ID: <5cead4654ee14611ae745be82f0fcc49@EXPRD02.hosting.ru.nl> Hi everybody, I'm trying to compute coherence analyses following the coherence tutorial at http://www.fieldtriptoolbox.org/tutorial/coherence. Since a couple of days, I have this error message in computing ft_freqanalysis: Error using load Unable to read file precompute_dpss: No such file or directory. Error in dpss (line 9) load precompute_dpss Error in ft_specest_mtmfft>double_dpss (line 335) tap = dpss(double(a), double(b), varargin{:}); Error in ft_specest_mtmfft (line 151) tap = double_dpss(ndatsample,ndatsample*(tapsmofrq./fsample))'; Error in ft_freqanalysis (line 494) [spectrum,ntaper,foi] = ft_specest_mtmfft(dat, time, 'taper', cfg.taper, options{:}, 'feedback', fbopt); Is that a bug? Here is the code I'm using: cfg = []; cfg.output = 'powandcsd'; cfg.method = 'mtmfft'; cfg.foilim = [5 40]; cfg.tapsmofrq = 5; cfg.keeptrials = 'yes'; freq = ft_freqanalysis(cfg, eeg); Thank you in advance, Federica -------------- next part -------------- An HTML attachment was scrubbed... URL: From f.roux at bcbl.eu Thu Apr 16 11:50:06 2015 From: f.roux at bcbl.eu (=?utf-8?B?RnLDqWTDqXJpYw==?= Roux) Date: Thu, 16 Apr 2015 11:50:06 +0200 (CEST) Subject: [FieldTrip] [SPAM] Problems with ft_freqanalysis In-Reply-To: <5cead4654ee14611ae745be82f0fcc49@EXPRD02.hosting.ru.nl> Message-ID: <1216046341.56584.1429177806762.JavaMail.root@bcbl.eu> Hi Fredrica, this is most likely do to a path problem. Try adding this at the beginning of your script/function: restorde_defaultpath; addpath('/path2fieldtrip/fieldtrip-2015xxxx/'); ft_defaults; HTH -- Frédéric Roux Postdoctoral Scientist BCBL. Basque Center on Cognition, Brain % Language. f.roux at bcbl.eu Tel: +34 943 309 300 Ext 211 Fax: +34 943 309 052 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer --------------------------------------------------------------------------- ----- Original Message ----- From: "Federica Mauro" To: "donders fieldtrip" Sent: Thursday, April 16, 2015 11:41:17 AM Subject: [SPAM] [FieldTrip] Problems with ft_freqanalysis Hi everybody, I'm trying to compute coherence analyses following the coherence tutorial at http://www.fieldtriptoolbox.org/tutorial/coherence . Since a couple of days, I have this error message in computing ft_freqanalysis: Error using load Unable to read file precompute_dpss: No such file or directory. Error in dpss (line 9) load precompute_dpss Error in ft_specest_mtmfft>double_dpss (line 335) tap = dpss(double(a), double(b), varargin{:}); Error in ft_specest_mtmfft (line 151) tap = double_dpss(ndatsample,ndatsample*(tapsmofrq./fsample))'; Error in ft_freqanalysis (line 494) [spectrum,ntaper,foi] = ft_specest_mtmfft(dat, time, 'taper', cfg.taper, options{:}, 'feedback', fbopt); Is that a bug? Here is the code I'm using: cfg = []; cfg.output = 'powandcsd'; cfg.method = 'mtmfft'; cfg.foilim = [5 40]; cfg.tapsmofrq = 5; cfg.keeptrials = 'yes'; freq = ft_freqanalysis(cfg, eeg); Thank you in advance, Federica _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From r.oostenveld at donders.ru.nl Thu Apr 16 12:06:42 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 16 Apr 2015 12:06:42 +0200 Subject: [FieldTrip] Problems with ft_freqanalysis In-Reply-To: <5cead4654ee14611ae745be82f0fcc49@EXPRD02.hosting.ru.nl> References: <5cead4654ee14611ae745be82f0fcc49@EXPRD02.hosting.ru.nl> Message-ID: Hi Federica, The error message you run into relates to the presence (or absence) of the Mathworks signal processing toolbox. FieldTrip relies on a number of MATLAB toolboxes (see http://www.fieldtriptoolbox.org/faq/requirements). Where possible, we try to avoid extra commercial toolboxes. Therefore we have some drop-in replacement functions in fieldtrip/external/signal (which were obtained from the Octave project). For the DPSS function (used for multitapering) however we don’t have a fully satisfactory solution. The error message you get suggests that you are using the "fieldtrip/external/signal/dpss_hack” directory. That is one that should not be on your path, unless you explicitly add it. You should only add in case you don’t have the signal processing toolbox and know what you are doing (i.e. after having read the README in that directory). I suspect you have used add path(genpath(…)) or the GUI equivalent of it. Please see http://www.fieldtriptoolbox.org/faq/should_i_add_fieldtrip_with_all_subdirectories_to_my_matlab_path and remove the dpss_hack directory from your path. best Robert PS for the low frequency range you are interested in I suspect that multitapering won’t be the most optimal anyway. Better add cfg.taper=‘hanning’ to your analysis, and see Nietzsche explain it next Monday on https://www.youtube.com/watch?v=vwPpSglPJTE On 16 Apr 2015, at 11:41, Federica Mauro wrote: > Hi everybody, > > I'm trying to compute coherence analyses following the coherence tutorial at http://www.fieldtriptoolbox.org/tutorial/coherence. > Since a couple of days, I have this error message in computing ft_freqanalysis: > > Error using load > Unable to read file precompute_dpss: No such file or directory. > > Error in dpss (line 9) > load precompute_dpss > > Error in ft_specest_mtmfft>double_dpss (line 335) > tap = dpss(double(a), double(b), varargin{:}); > > Error in ft_specest_mtmfft (line 151) > tap = > double_dpss(ndatsample,ndatsample*(tapsmofrq./fsample))'; > > Error in ft_freqanalysis (line 494) > [spectrum,ntaper,foi] = ft_specest_mtmfft(dat, time, 'taper', > cfg.taper, options{:}, 'feedback', fbopt); > > Is that a bug? > > > Here is the code I'm using: > cfg = []; > cfg.output = 'powandcsd'; > cfg.method = 'mtmfft'; > cfg.foilim = [5 40]; > cfg.tapsmofrq = 5; > cfg.keeptrials = 'yes'; > > freq = ft_freqanalysis(cfg, eeg); > > > Thank you in advance, > Federica > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Thu Apr 16 13:53:41 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Thu, 16 Apr 2015 13:53:41 +0200 Subject: [FieldTrip] Beamforming analysis in frequency band In-Reply-To: References: Message-ID: <9BC70F24-9E97-4247-B0C0-365CCC154C70@uni-konstanz.de> Dear Noa, you should use frequency smoothening to achieve this. For example, a configuration of cfg.foilim = [20 20] ; and cfg.tapsmofrq = 10; will allow you to estimate sources in the 10 to 30 Hz band. > Hi all, > > I'm doing source analysis in the frequency domain of a resting-state data. > when doing the source analysis, I want to use several frequency bands of interest, such as beta (13-30 Hz) and gamma (30-48 Hz). > My problem is about the cfg.frequency parameter, which must be a scalar (whereas i'm interested in a frequency band). Arbitrarily choosing a frequency in the middle of the range doesn't seem right. > > What is the common practice when doing source analysis using this function? You could evaluate this tutorial: http://www.fieldtriptoolbox.org/tutorial/beamformer > Does the cfg.tapsmofrq parameter is supposed to enable choosing frequency band instead of a single peak frequency? and some detailed explanation in a pictorial form here: https://www.youtube.com/watch?v=7eS11DtbIPw best tzvetan > > Any suggestions will be very much helpful! > > Thanks, > Noa > > > This is the script I’m using: > > cfg = []; > cfg.method ='mtmfft'; > cfg.output ='fourier'; > cfg.keeptapers = 'yes'; > cfg.foilim = [30 48]; > cfg.tapsmofrq = 2; > freqClosed=ft_freqanalysis(cfg,eyesClosed); > > > > cfg = []; > cfg.method='pcc'; > cfg.frequency = 39; % must be a scalar > cfg.lambda = 0; > cfg.vol = vol; > cfg.grid = grid; > cfg.feedback = 'textbar'; > cfg.keepfilter='yes'; > source1 = ft_sourceanalysis(cfg, freqClosed); > > > -- > My signature: > > http://www.documentarywire.com/earthlings/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From federica.ma at gmail.com Thu Apr 16 16:44:18 2015 From: federica.ma at gmail.com (Federica Mauro) Date: Thu, 16 Apr 2015 16:44:18 +0200 Subject: [FieldTrip] [SPAM] Problems with ft_freqanalysis In-Reply-To: <1216046341.56584.1429177806762.JavaMail.root@bcbl.eu> References: <5cead4654ee14611ae745be82f0fcc49@EXPRD02.hosting.ru.nl> <1216046341.56584.1429177806762.JavaMail.root@bcbl.eu> Message-ID: Thanks, you've been really helpful. Thanks also for the tip on the taper cfg, Looking forward to the seminar! Federica 2015-04-16 11:50 GMT+02:00 Frédéric Roux : > Hi Fredrica, > > this is most likely do to a path problem. > > Try adding this at the beginning of your script/function: > > restorde_defaultpath; > addpath('/path2fieldtrip/fieldtrip-2015xxxx/'); > ft_defaults; > > HTH > > -- > Frédéric Roux > Postdoctoral Scientist > BCBL. Basque Center on Cognition, Brain % Language. > > f.roux at bcbl.eu > Tel: +34 943 309 300 Ext 211 > Fax: +34 943 309 052 > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > --------------------------------------------------------------------------- > > > ----- Original Message ----- > From: "Federica Mauro" > To: "donders fieldtrip" > Sent: Thursday, April 16, 2015 11:41:17 AM > Subject: [SPAM] [FieldTrip] Problems with ft_freqanalysis > > > > > > > > > > Hi everybody, > > I'm trying to compute coherence analyses following the coherence tutorial > at http://www.fieldtriptoolbox.org/tutorial/coherence . > Since a couple of days, I have this error message in computing > ft_freqanalysis: > > Error using load > Unable to read file precompute_dpss: No such file or directory. > > Error in dpss (line 9) > load precompute_dpss > > Error in ft_specest_mtmfft>double_dpss (line 335) > tap = dpss(double(a), double(b), varargin{:}); > > Error in ft_specest_mtmfft (line 151) > tap = > double_dpss(ndatsample,ndatsample*(tapsmofrq./fsample))'; > > Error in ft_freqanalysis (line 494) > [spectrum,ntaper,foi] = ft_specest_mtmfft(dat, time, 'taper', > cfg.taper, options{:}, 'feedback', fbopt); > > Is that a bug? > > > Here is the code I'm using: > cfg = []; > cfg.output = 'powandcsd'; > cfg.method = 'mtmfft'; > cfg.foilim = [5 40]; > cfg.tapsmofrq = 5; > cfg.keeptrials = 'yes'; > > freq = ft_freqanalysis(cfg, eeg); > > > Thank you in advance, > Federica > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From n.lam at donders.ru.nl Thu Apr 16 17:26:17 2015 From: n.lam at donders.ru.nl (Lam, N.H.L. (Nietzsche)) Date: Thu, 16 Apr 2015 15:26:17 +0000 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? Message-ID: Dear FieldTrip users, Next week we will provide a live broadcast of the lectures from the 4-day MEG/EEG toolkit course at the Donders in Nijmegen, on our YouTube channel https://www.youtube.com/user/FieldTripToolboxTV Please check whether the videos are available in your country (click on one of the scheduled live stream videos - you should see a clock that counts down to the lecture). If you get the message "Live streaming is not available in your country due to right issues" please reply to this email and state your country so that we can find a solution prior to the toolkit next week. We appreciate your help to make this a smooth broadcast. Best, Nietzsche (on behalf of the FieldTrip team) P.S. Full course program of the workshop http://www.fieldtriptoolbox.org/workshop/toolkit2015, Best, Nietzsche (on behalf of the FieldTrip team) -------------- next part -------------- An HTML attachment was scrubbed... URL: From tomh at kurage.nimh.nih.gov Thu Apr 16 17:39:50 2015 From: tomh at kurage.nimh.nih.gov (Tom Holroyd) Date: Thu, 16 Apr 2015 11:39:50 -0400 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: References: Message-ID: <20150416113950.253a352c@kurage.nimh.nih.gov> https://youtu.be/-RpQklxbCsg?list=PLbVcEw60xnKNuNKwBSWgzdZCXxNDMh3Gr I just watched that, no problems, and I get the countdowns for the newer links. Looking forward to it! I was almost surprised I didn't need to install a new Flash player or something. Thanks! On Thu, 16 Apr 2015 15:26:17 +0000 "Lam, N.H.L. (Nietzsche)" wrote: > Dear FieldTrip users, > > Next week we will provide a live broadcast of the lectures from the > 4-day MEG/EEG toolkit course at the Donders in Nijmegen, on our > YouTube channel https://www.youtube.com/user/FieldTripToolboxTV > > Please check whether the videos are available in your country (click > on one of the scheduled live stream videos - you should see a clock > that counts down to the lecture). If you get the message "Live > streaming is not available in your country due to right issues" > please reply to this email and state your country so that we can find > a solution prior to the toolkit next week. We appreciate your help > to make this a smooth broadcast. > > Best, > Nietzsche (on behalf of the FieldTrip team) > > P.S. Full course program of the workshop > http://www.fieldtriptoolbox.org/workshop/toolkit2015, > > > > > > > > > Best, > Nietzsche (on behalf of the FieldTrip team) -- Dr. Tom -- "There are not more than five musical notes, yet the combinations of these five give rise to more melodies than can ever be heard." -- Sun Tzu From Holger.Krause at med.uni-duesseldorf.de Thu Apr 16 17:45:03 2015 From: Holger.Krause at med.uni-duesseldorf.de (Holger Krause) Date: Thu, 16 Apr 2015 17:45:03 +0200 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: References: Message-ID: <201504161745.05273.Holger.Krause@med.uni-duesseldorf.de> Am Donnerstag, 16. April 2015 schrieb Lam, N.H.L. (Nietzsche): > Please check whether the videos are available in your country (click on one > of the scheduled live stream videos - you should see a clock that counts > down to the lecture). If you get the message "Live streaming is not > available in your country due to right issues" please reply to this email > and state your country so that we can find a solution prior to the toolkit > next week. We appreciate your help to make this a smooth broadcast. https://www.youtube.com/watch?v=ZBwh0Vm4fh4 Germany :-( "Live Streaming ist wegen Rechteproblemen in Deutschland leider nicht möglich." Best, Holger From kgm at tf.uni-kiel.de Thu Apr 16 17:52:39 2015 From: kgm at tf.uni-kiel.de (kgm) Date: Thu, 16 Apr 2015 17:52:39 +0200 Subject: [FieldTrip] =?utf-8?q?Can_you_view_the_Livestream_lectures_=28MEG?= =?utf-8?q?/EEG_toolkit=29=3F?= In-Reply-To: References: Message-ID: <8b25592765751ea3e1c8afa0e3936788@tf.uni-kiel.de> Dear all, I am a user from Germany and I get the message "Live streaming is not available in your country due to rights issues" when I click one of the scheduled videos. Looking forward for the solution. Thanks in advance! Best regards, Kidist G.Mideksa On 2015-04-16 17:26, Lam, N.H.L. (Nietzsche) wrote: > Dear FieldTrip users, > > Next week we will provide a live broadcast of the lectures from the > 4-day MEG/EEG toolkit course at the Donders in Nijmegen, on our > YouTube channel https://www.youtube.com/user/FieldTripToolboxTV > > Please CHECK WHETHER THE VIDEOS ARE AVAILABLE IN YOUR COUNTRY (click > on one of the scheduled live stream videos - you should see a clock > that counts down to the lecture). If you get the message "Live > streaming is not available in your country due to right issues" please > reply to this email and state your country so that we can find a > solution prior to the toolkit next week. We appreciate your help to > make this a smooth broadcast. > > Best, > Nietzsche (on behalf of the FieldTrip team) > > P.S. Full course program of the workshop > http://www.fieldtriptoolbox.org/workshop/toolkit2015 [1], > > Best, > Nietzsche (on behalf of the FieldTrip team) > > Links: > ------ > [1] http://www.fieldtriptoolbox.org/workshop/toolkit2015 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From david.schubring at uni-konstanz.de Thu Apr 16 18:07:43 2015 From: david.schubring at uni-konstanz.de (David Schubring) Date: Thu, 16 Apr 2015 18:07:43 +0200 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: <201504161745.05273.Holger.Krause@med.uni-duesseldorf.de> References: <201504161745.05273.Holger.Krause@med.uni-duesseldorf.de> Message-ID: <552FDE4F.3060501@uni-konstanz.de> Hello FieldTrip users, I don't know about the exact legal situation here, but since you probably won't stream copyrighted material a proxy plugin should be fine? At least it works for me (in germany) - which means, at the moment I can see the countdown. There is a ton of browser plugins for unblocking youtube, the one I use for Mozilla Firefox is called "ProxTube" (there should be one for Chrome as well): https://addons.mozilla.org/de/firefox/addon/proxtube/ Cheers, David Am 16.04.15 um 17:45 schrieb Holger Krause: > Am Donnerstag, 16. April 2015 schrieb Lam, N.H.L. (Nietzsche): >> Please check whether the videos are available in your country (click on one >> of the scheduled live stream videos - you should see a clock that counts >> down to the lecture). If you get the message "Live streaming is not >> available in your country due to right issues" please reply to this email >> and state your country so that we can find a solution prior to the toolkit >> next week. We appreciate your help to make this a smooth broadcast. > > https://www.youtube.com/watch?v=ZBwh0Vm4fh4 > > Germany :-( > > "Live Streaming ist wegen Rechteproblemen in Deutschland leider nicht > möglich." > > Best, > > Holger > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Dipl.-Psych. David Schubring Clinical Psychology University of Konstanz P.O. Box 905 78457 Konstanz Phone: +49-(0)7531-88-4889 From ingrid.sor at neuro.uu.se Fri Apr 17 09:43:44 2015 From: ingrid.sor at neuro.uu.se (=?windows-1252?Q?Ingrid_S=F6r?=) Date: Fri, 17 Apr 2015 09:43:44 +0200 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: References: Message-ID: <5530B9B0.9030104@neuro.uu.se> Hi, Works fine in Sweden! Looks like some interesting material. Best, Ingrid On 2015-04-16 17:26, Lam, N.H.L. (Nietzsche) wrote: > Dear FieldTrip users, > > Next week we will provide a live broadcast of the lectures from the > 4-day MEG/EEG toolkit course at the Donders in Nijmegen, on our > YouTube channel https://www.youtube.com/user/FieldTripToolboxTV > > Please*check whether the videos are available in your country* (click > on one of the scheduled live stream videos - you should see a clock > that counts down to the lecture). If you get the message "Live > streaming is not available in your country due to right issues" please > reply to this email and state your country so that we can find a > solution prior to the toolkit next week. We appreciate your help to > make this a smooth broadcast. > > Best, > Nietzsche (on behalf of the FieldTrip team) > > P.S. Full course program of the workshop > http://www.fieldtriptoolbox.org/workshop/toolkit2015, > > > > > > > > > Best, > Nietzsche (on behalf of the FieldTrip team) > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From mariya.kharaman at uni-konstanz.de Fri Apr 17 09:45:25 2015 From: mariya.kharaman at uni-konstanz.de (Mariya Kharaman) Date: Fri, 17 Apr 2015 09:45:25 +0200 Subject: [FieldTrip] =?utf-8?q?Can_you_view_the_Livestream_lectures_=28MEG?= =?utf-8?q?/EEG_toolkit=29=3F?= In-Reply-To: Message-ID: Dear all, I am in Germany and as it seems, I will not be able to watch the videos ("Live Streaming ist wegen Rechteproblemen in Deutschland leider nicht möglich." = "Live streaming is not available in your country due to right issues". I really hope the solution will be found! Thank you very much! Best wishes, Mariya Am Donnerstag, 16. April 2015 17:26 CEST, "Lam, N.H.L. (Nietzsche)" schrieb: > Dear FieldTrip users, > > Next week we will provide a live broadcast of the lectures from the 4-day MEG/EEG toolkit course at the Donders in Nijmegen, on our YouTube channel https://www.youtube.com/user/FieldTripToolboxTV > > Please check whether the videos are available in your country (click on one of the scheduled live stream videos - you should see a clock that counts down to the lecture). If you get the message "Live streaming is not available in your country due to right issues" please reply to this email and state your country so that we can find a solution prior to the toolkit next week. We appreciate your help to make this a smooth broadcast. > > Best, > Nietzsche (on behalf of the FieldTrip team) > > P.S. Full course program of the workshop http://www.fieldtriptoolbox.org/workshop/toolkit2015, > > > > > > > > > Best, > Nietzsche (on behalf of the FieldTrip team) From smoratti at psi.ucm.es Fri Apr 17 11:09:28 2015 From: smoratti at psi.ucm.es (smoratti at psi.ucm.es) Date: Fri, 17 Apr 2015 11:09:28 +0200 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: <201504161745.05273.Holger.Krause@med.uni-duesseldorf.de> References: <201504161745.05273.Holger.Krause@med.uni-duesseldorf.de> Message-ID: <04EC09B5-FE5B-491A-965A-5BACFC4C29EE@psi.ucm.es> in Spain it seems to work… best, Stephan ________________________________________________________ Stephan Moratti, PhD see: Stephan's research profile Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas Despacho (Office) 1326-0 28223 Pozuelo de Alarcón (Madrid) Spain and Center for Biomedical Technology Laboratory for Cognitive and Computational Neuroscience Parque Científico y Tecnológico de la Universidad Politecnica de Madrid Campus Montegancedo 28223 Pozuelo de Alarcón (Madrid) Spain email: smoratti at psi.ucm.es Tel.: +34 679219982 El 16/04/2015, a las 17:45, Holger Krause escribió: > Am Donnerstag, 16. April 2015 schrieb Lam, N.H.L. (Nietzsche): >> Please check whether the videos are available in your country (click on one >> of the scheduled live stream videos - you should see a clock that counts >> down to the lecture). If you get the message "Live streaming is not >> available in your country due to right issues" please reply to this email >> and state your country so that we can find a solution prior to the toolkit >> next week. We appreciate your help to make this a smooth broadcast. > > https://www.youtube.com/watch?v=ZBwh0Vm4fh4 > > Germany :-( > > "Live Streaming ist wegen Rechteproblemen in Deutschland leider nicht > möglich." > > Best, > > Holger > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From n.lam at donders.ru.nl Fri Apr 17 12:11:13 2015 From: n.lam at donders.ru.nl (Lam, N.H.L. (Nietzsche)) Date: Fri, 17 Apr 2015 10:11:13 +0000 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: <8b25592765751ea3e1c8afa0e3936788@tf.uni-kiel.de> References: , <8b25592765751ea3e1c8afa0e3936788@tf.uni-kiel.de> Message-ID: Dear FieldTrip Users, It seems that the viewing problem is only limited to Germany (we have checked in other countries as well). We suggest that you use a proxy plugin to circumvent the issue of not being able to view the video. A fellow FT user has suggested the following for Firefox https://addons.mozilla.org/de/firefox/addon/proxtube/ Similar proxy plugins exist for other web browsers (note that these were found on google, and have not be personally tested by the FieldTrip team): https://chrome.google.com/webstore/detail/proxxy/clkkaggocmafajhbcbknhcgnbmagjohi?hl=en http://www.chip.de/downloads/FoxyProxy-fuer-Chrome_53036930.html We suggest you determine a suitable proxy well in advance of the lecture(s), as it may be more than a 5 minute fix for some of you. Best, Nietzsche (on behalf of the FieldTrip team) ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of kgm [kgm at tf.uni-kiel.de] Sent: 16 April 2015 17:52 To: FieldTrip discussion list Subject: Re: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? Dear all, I am a user from Germany and I get the message "Live streaming is not available in your country due to rights issues" when I click one of the scheduled videos. Looking forward for the solution. Thanks in advance! Best regards, Kidist G.Mideksa On 2015-04-16 17:26, Lam, N.H.L. (Nietzsche) wrote: > Dear FieldTrip users, > > Next week we will provide a live broadcast of the lectures from the > 4-day MEG/EEG toolkit course at the Donders in Nijmegen, on our > YouTube channel https://www.youtube.com/user/FieldTripToolboxTV > > Please CHECK WHETHER THE VIDEOS ARE AVAILABLE IN YOUR COUNTRY (click > on one of the scheduled live stream videos - you should see a clock > that counts down to the lecture). If you get the message "Live > streaming is not available in your country due to right issues" please > reply to this email and state your country so that we can find a > solution prior to the toolkit next week. We appreciate your help to > make this a smooth broadcast. > > Best, > Nietzsche (on behalf of the FieldTrip team) > > P.S. Full course program of the workshop > http://www.fieldtriptoolbox.org/workshop/toolkit2015 [1], > > Best, > Nietzsche (on behalf of the FieldTrip team) > > Links: > ------ > [1] http://www.fieldtriptoolbox.org/workshop/toolkit2015 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From eva.patai at psych.ox.ac.uk Fri Apr 17 13:35:46 2015 From: eva.patai at psych.ox.ac.uk (Zita Eva Patai) Date: Fri, 17 Apr 2015 12:35:46 +0100 Subject: [FieldTrip] interpolation of bad channels matlab error Message-ID: Dear FTers I have been trying to fix some bad channels in my data through interpolation. It seems to not be working. My code is below. Please note my data object is converted from SPM (in case that matters). Thanks very much in advance, zita data = fsample: 250 label: {324x1 cell} trial: {1x505 cell} time: {1x505 cell} grad: [1x1 struct] triallist: {1x505 cell} >> cfg2 cfg2 = badchannel: {2x1 cell} method: 'nearest' neighbours: [1x306 struct] >> [interp]=ft_channelrepair(cfg2,data) the input is raw data with 324 channels and 505 trials using gradiometers specified in the data repairing channel MEG1132 using neighbour repairing channel MEG1421 using neighbour repairing bad channels for 505 trials .Error using * MTIMES is not supported for one sparse input and one single input. Error in ft_channelrepair (line 172) interp.trial{i} = repair * data.trial{i}; -- Eva Zita Patai, DPhil Postdoctoral Researcher Oxford Centre for Human Brain Activity University of Oxford -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri Apr 17 13:53:54 2015 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 17 Apr 2015 11:53:54 +0000 Subject: [FieldTrip] interpolation of bad channels matlab error In-Reply-To: References: Message-ID: <876E7EA3-688A-49EB-9B5A-2241570DD41D@fcdonders.ru.nl> Hi Eva, The MATLAB error suggests that your data is represented as single precision floating point numbers, and matrix multiplication is apparently not supported when you want to multiply with a sparse matrix. You could try and convert your data to double precision: data=ft_struct2double(data); and then call ft_channelrepair. Best, Jan-Mathijs On Apr 17, 2015, at 1:35 PM, Zita Eva Patai > wrote: Dear FTers I have been trying to fix some bad channels in my data through interpolation. It seems to not be working. My code is below. Please note my data object is converted from SPM (in case that matters). Thanks very much in advance, zita data = fsample: 250 label: {324x1 cell} trial: {1x505 cell} time: {1x505 cell} grad: [1x1 struct] triallist: {1x505 cell} >> cfg2 cfg2 = badchannel: {2x1 cell} method: 'nearest' neighbours: [1x306 struct] >> [interp]=ft_channelrepair(cfg2,data) the input is raw data with 324 channels and 505 trials using gradiometers specified in the data repairing channel MEG1132 using neighbour repairing channel MEG1421 using neighbour repairing bad channels for 505 trials .Error using * MTIMES is not supported for one sparse input and one single input. Error in ft_channelrepair (line 172) interp.trial{i} = repair * data.trial{i}; -- Eva Zita Patai, DPhil Postdoctoral Researcher Oxford Centre for Human Brain Activity University of Oxford _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jdien07 at mac.com Fri Apr 17 19:09:37 2015 From: jdien07 at mac.com (Joseph Dien) Date: Fri, 17 Apr 2015 13:09:37 -0400 Subject: [FieldTrip] Johns Hopkins Research Assistant Position Message-ID: General Description: Research of the Division is focused on improving aspects of cognition in humans, particularly those related to speech, communication, and cognitive control, in both normally developing individuals and in individuals with developmental and acquired disorders, such as autism, Lesch-Nyhan syndrome, and stroke. Studies use a mix of techniques from experimental psychology, transcranial Direct Current Stimulation (tDCS), structural imaging, fMRI, psychophysiological measures, and especially EEG. RA will be directly responsible for 1-2 projects themselves, and will assist with several other projects in the Division. Involvement will be in any and all aspects: library research; writing up research plans; subject recruitment; scheduling; testing (including psychological and experimental tasks); collecting data; cleaning data; maintaining files; initial analyses; draft and final write-ups. Interacts, as needed, with Institutional Review Board. Participates in regular laboratory research meetings. Maintains, monitors, and orders research supplies. Helps with statistical analyses, using software such as MATLAB, NetStation, SPM8, MRIcron, and SPSS. Reports directly to the Director of the Division, with delegated reporting to other faculty in the Division, faculty associated with the Division, and senior staff. Qualifications: Bachelor's degree in related discipline required. Some related experience required. Additional education may substitute for required experience and additional related experience may substitute for required education, to the extent permitted by the JHU equivalency formula. Must have ability to use a personal computer. Prefer experience with analytic tools, and with writing academic manuscripts and grants. Must be well-organized, efficient, accurate, responsible, and enthusiastic. Must be able to interact effectively with faculty, staff, and subjects. Experience administering and scoring cognitive and behavioral measures preferred. Experience with MS Word, Excel, SPSS, MATLAB, SPM8, and NetStation software preferred. Preferred Qualifications: Bachelor’s or Master’s Degree in Experimental Psychology, Cognitive Science, Neuroscience, or a related field preferred. Posting at: https://hrnt.jhu.edu/jhujobs/job_view.cfm?view_req_id=65838&view=sch Contact Joseph Dien (jdien1 at jhmi.edu ) for more information. Joe -------------------------------------------------------------------------------- Joseph Dien, PhD Research Associate Cognitive Neurology/Neuropsychology The Johns Hopkins University School of Medicine Lab E-mail: jdien1 at jhmi.edu Private E-mail: jdien07 at mac.com Office Phone: 410-614-3115 Cell Phone: 202-297-8117 Fax: 410-955-0188 http://joedien.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From vahidgerami.mse at gmail.com Sun Apr 19 08:28:14 2015 From: vahidgerami.mse at gmail.com (vahid gerami) Date: Sun, 19 Apr 2015 10:58:14 +0430 Subject: [FieldTrip] EEG from brain sensory motor area Message-ID: dear eeglab community i've recorded some eeg signals from sensory motor area. the signals are recorded while the right hand was moving regularly. now i want to detect the ERP changes on the signal caused by the hand movement. does any one have the same experience? how can i do the job? please help me about the procedure. regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From noahertz6 at gmail.com Sun Apr 19 12:57:46 2015 From: noahertz6 at gmail.com (Noa Hertz) Date: Sun, 19 Apr 2015 13:57:46 +0300 Subject: [FieldTrip] Beamforming analysis in frequency band In-Reply-To: <9BC70F24-9E97-4247-B0C0-365CCC154C70@uni-konstanz.de> References: <9BC70F24-9E97-4247-B0C0-365CCC154C70@uni-konstanz.de> Message-ID: Thank you Tzvetan! This raised two more question regarding the source analysis: 1. What is the difference between defining the frequency range under cfg.foi (such as cfg.foi=[30 48]) and defining if under the cfg.tapsmofrq (such as cfg.foi=[39 39] cfg.tapsmofrq=9)? 2. the cfg.tapsmofrq option only exist in the ft_freqanalysis function, and not in the ft_sourceanalysis function. in ft_sourceanalysis the only option is cfg.frequency which, as I mention, has to be a scalar. My question is whether defining the cfg.tapsmofrq in the ft_freqanalysis is also causing the source analysis to use the range of frequencies and not the single frequency. *Thanks a lot,* *Noa* 2015-04-16 14:53 GMT+03:00 Tzvetan Popov : > > Dear Noa, > > you should use frequency smoothening to achieve this. For example, a > configuration of cfg.foilim = [20 20] ; and cfg.tapsmofrq = 10; will allow > you to estimate sources in the 10 to 30 Hz band. > > Hi all, > > I'm doing source analysis in the frequency domain of a resting-state data. > when doing the source analysis, I want to use several frequency bands of > interest, such as beta (13-30 Hz) and gamma (30-48 Hz). > My problem is about the cfg.frequency parameter, which must be a scalar > (whereas i'm interested in a frequency band). Arbitrarily choosing a > frequency in the middle of the range doesn't seem right. > > What is the common practice when doing source analysis using this function? > > You could evaluate this tutorial: > http://www.fieldtriptoolbox.org/tutorial/beamformer > > Does the cfg.tapsmofrq parameter is supposed to enable choosing frequency > band instead of a single peak frequency? > > and some detailed explanation in a pictorial form here: > https://www.youtube.com/watch?v=7eS11DtbIPw > > best > tzvetan > > > Any suggestions will be very much helpful! > > Thanks, > Noa > > > > > > > > > > > > > > *This is the script I’m using: cfg = []; cfg.method ='mtmfft'; > cfg.output ='fourier'; cfg.keeptapers = 'yes'; cfg.foilim = [30 > 48]; cfg.tapsmofrq = 2; > freqClosed=ft_freqanalysis(cfg,eyesClosed); * > > cfg = []; > cfg.method='pcc'; > cfg.frequency = 39; % must be a scalar > cfg.lambda = 0; > cfg.vol = vol; > cfg.grid = grid; > cfg.feedback = 'textbar'; > cfg.keepfilter='yes'; > source1 = ft_sourceanalysis(cfg, freqClosed); > > > -- > My signature: > > http://www.documentarywire.com/earthlings/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- מעכשיו זאת החתימה שלי.. חובה לראות http://www.documentarywire.com/earthlings/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From stidimitriadis at gmail.com Sun Apr 19 19:03:09 2015 From: stidimitriadis at gmail.com (Stavros Dimitriadis) Date: Sun, 19 Apr 2015 10:03:09 -0700 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: <04EC09B5-FE5B-491A-965A-5BACFC4C29EE@psi.ucm.es> References: <201504161745.05273.Holger.Krause@med.uni-duesseldorf.de> <04EC09B5-FE5B-491A-965A-5BACFC4C29EE@psi.ucm.es> Message-ID: Dear All In Greece it works fine ! Best wishes Dimitriadis Stavros, PhD Research Fellow Aristotle University of Thessaloniki, Greece Department of Informatics http://users.auth.gr/~stdimitr/index.html 1)Artificial Intelligence Information Analysis lab Department of Informatics *Aristotle University of Thessaloniki * 2)NeuroInformatics.GRoup , AUTH, Greece 2015-04-17 2:09 GMT-07:00 smoratti at psi.ucm.es : > > in Spain it seems to work… > > best, > > Stephan > > ________________________________________________________ > Stephan Moratti, PhD > > see: Stephan's research profile > > > Universidad Complutense de Madrid > Facultad de Psicología > Departamento de Psicología Básica I > Campus de Somosaguas > Despacho (Office) 1326-0 > 28223 Pozuelo de Alarcón (Madrid) > Spain > > and > > Center for Biomedical Technology > Laboratory for Cognitive and Computational Neuroscience > Parque Científico y Tecnológico de la Universidad Politecnica de Madrid > Campus Montegancedo > 28223 Pozuelo de Alarcón (Madrid) > Spain > > > email: smoratti at psi.ucm.es > Tel.: +34 679219982 > > El 16/04/2015, a las 17:45, Holger Krause escribió: > > Am Donnerstag, 16. April 2015 schrieb Lam, N.H.L. (Nietzsche): > > Please check whether the videos are available in your country (click on one > > of the scheduled live stream videos - you should see a clock that counts > > down to the lecture). If you get the message "Live streaming is not > > available in your country due to right issues" please reply to this email > > and state your country so that we can find a solution prior to the toolkit > > next week. We appreciate your help to make this a smooth broadcast. > > > https://www.youtube.com/watch?v=ZBwh0Vm4fh4 > > Germany :-( > > "Live Streaming ist wegen Rechteproblemen in Deutschland leider nicht > möglich." > > Best, > > Holger > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From laura.marzetti at gmail.com Sun Apr 19 19:35:58 2015 From: laura.marzetti at gmail.com (Laura Marzetti) Date: Sun, 19 Apr 2015 19:35:58 +0200 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: References: <201504161745.05273.Holger.Krause@med.uni-duesseldorf.de> <04EC09B5-FE5B-491A-965A-5BACFC4C29EE@psi.ucm.es> Message-ID: In Italy as well :-) Best, Laura Inviato da iPhone > Il giorno 19/apr/2015, alle ore 07:03 PM, Stavros Dimitriadis ha scritto: > > Dear All > In Greece it works fine ! > > Best wishes > Dimitriadis Stavros, PhD > > Research Fellow > Aristotle University of Thessaloniki, Greece > Department of Informatics > http://users.auth.gr/~stdimitr/index.html > > 1)Artificial Intelligence Information Analysis lab Department of Informatics > Aristotle University of Thessaloniki > 2)NeuroInformatics.GRoup , AUTH, Greece > > > 2015-04-17 2:09 GMT-07:00 smoratti at psi.ucm.es : >> >> in Spain it seems to work… >> >> best, >> >> Stephan >> >> ________________________________________________________ >> Stephan Moratti, PhD >> >> see: Stephan's research profile >> >> Universidad Complutense de Madrid >> Facultad de Psicología >> Departamento de Psicología Básica I >> Campus de Somosaguas >> Despacho (Office) 1326-0 >> 28223 Pozuelo de Alarcón (Madrid) >> Spain >> >> and >> >> Center for Biomedical Technology >> Laboratory for Cognitive and Computational Neuroscience >> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid >> Campus Montegancedo >> 28223 Pozuelo de Alarcón (Madrid) >> Spain >> >> >> email: smoratti at psi.ucm.es >> Tel.: +34 679219982 >> >>> El 16/04/2015, a las 17:45, Holger Krause escribió: >>> >>> Am Donnerstag, 16. April 2015 schrieb Lam, N.H.L. (Nietzsche): >>>> Please check whether the videos are available in your country (click on one >>>> of the scheduled live stream videos - you should see a clock that counts >>>> down to the lecture). If you get the message "Live streaming is not >>>> available in your country due to right issues" please reply to this email >>>> and state your country so that we can find a solution prior to the toolkit >>>> next week. We appreciate your help to make this a smooth broadcast. >>> >>> https://www.youtube.com/watch?v=ZBwh0Vm4fh4 >>> >>> Germany :-( >>> >>> "Live Streaming ist wegen Rechteproblemen in Deutschland leider nicht >>> möglich." >>> >>> Best, >>> >>> Holger >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Sun Apr 19 19:49:20 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Sun, 19 Apr 2015 19:49:20 +0200 Subject: [FieldTrip] Beamforming analysis in frequency band In-Reply-To: References: <9BC70F24-9E97-4247-B0C0-365CCC154C70@uni-konstanz.de> Message-ID: <5F97C157-EB31-41B1-8F19-6DFB1D3E6E1C@uni-konstanz.de> Dear Noa, > Thank you Tzvetan! > > This raised two more question regarding the source analysis: > > 1. What is the difference between defining the frequency range under cfg.foi (such as cfg.foi=[30 48]) and defining if under the cfg.tapsmofrq (such as cfg.foi=[39 39] cfg.tapsmofrq=9)? The difference is that in the resulting output of ft_freqanalysis (lets name it freq) will contain a freq.freq field containing of 19 freq bins presuming frequency resolution of 1 Hz. Each of these is computed with smofrq of plus minus 9 Hz. In the second case freq.freq is one frequency bin namely 39 Hz. > 2. the cfg.tapsmofrq option only exist in the ft_freqanalysis function, and not in the ft_sourceanalysis function. in ft_sourceanalysis the only option is cfg.frequency which, as I mention, has to be a scalar. My question is whether defining the cfg.tapsmofrq in the ft_freqanalysis is also causing the source analysis to use the range of frequencies and not the single frequency. Yes. best tzvetan > > Thanks a lot, > Noa > > 2015-04-16 14:53 GMT+03:00 Tzvetan Popov : > > Dear Noa, > > you should use frequency smoothening to achieve this. For example, a configuration of cfg.foilim = [20 20] ; and cfg.tapsmofrq = 10; will allow you to estimate sources in the 10 to 30 Hz band. > >> Hi all, >> >> I'm doing source analysis in the frequency domain of a resting-state data. >> when doing the source analysis, I want to use several frequency bands of interest, such as beta (13-30 Hz) and gamma (30-48 Hz). >> My problem is about the cfg.frequency parameter, which must be a scalar (whereas i'm interested in a frequency band). Arbitrarily choosing a frequency in the middle of the range doesn't seem right. >> >> What is the common practice when doing source analysis using this function? > You could evaluate this tutorial: > http://www.fieldtriptoolbox.org/tutorial/beamformer > >> Does the cfg.tapsmofrq parameter is supposed to enable choosing frequency band instead of a single peak frequency? > and some detailed explanation in a pictorial form here: > https://www.youtube.com/watch?v=7eS11DtbIPw > > best > tzvetan > >> >> Any suggestions will be very much helpful! >> >> Thanks, >> Noa >> >> >> This is the script I’m using: >> >> cfg = []; >> cfg.method ='mtmfft'; >> cfg.output ='fourier'; >> cfg.keeptapers = 'yes'; >> cfg.foilim = [30 48]; >> cfg.tapsmofrq = 2; >> freqClosed=ft_freqanalysis(cfg,eyesClosed); >> >> >> >> cfg = []; >> cfg.method='pcc'; >> cfg.frequency = 39; % must be a scalar >> cfg.lambda = 0; >> cfg.vol = vol; >> cfg.grid = grid; >> cfg.feedback = 'textbar'; >> cfg.keepfilter='yes'; >> source1 = ft_sourceanalysis(cfg, freqClosed); >> >> >> -- >> My signature: >> >> http://www.documentarywire.com/earthlings/ >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > מעכשיו זאת החתימה שלי.. חובה לראות > > http://www.documentarywire.com/earthlings/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.maris at donders.ru.nl Tue Apr 21 07:38:52 2015 From: e.maris at donders.ru.nl (Maris, E.G.G. (Eric)) Date: Tue, 21 Apr 2015 05:38:52 +0000 Subject: [FieldTrip] coherence and group analyses In-Reply-To: References: Message-ID: <5B808383-6841-4F99-AEE9-73D64A807C47@donders.ru.nl> Dear Jean-Marc Lina, I’m sorry for this very late reply. Your post (which I requested) had slipped my attention. Involved in source analyses from MEG/EEG data, I am going through your papers related to statistical testing (Nonparametric stat testing of coherence differences, 2007 and stat testing in electrophys studies, 2012). Mostly concerned with coherence and coherency (either topography or tomography), I have some questions related to nonparametric statistical testing in the case where we have 2 groups (one group per condition, N subjects in each group) of individuals (n trials for each subjects). I will greatly appreciated some information that could help clarifying the followings: - how do we design the null distribution? permutations are among all subjects? How do we handle fixed/random effects? When you have multiple subjects, you should go for a random effects analysis. This implies that the ingredients for your statistical analysis are coherence values for every subject within every condition. What you do next depends on whether you have a within-groups or a between-groups design. In a within-groups design, every subject has participated in the multiple experimental conditions that you want to compare, and in a between-groups design, every subject has participated in only a single condition and you want to compare these conditions (e.g., patients versus controls, high-versus-low performers). In a within-groups design, the permutation distribution is obtained by randomly permuting the conditions within every subject. In a between-groups design, the permutation distribution is obtained by randomly permuting the subjects between the conditions. - Can we reproduce stricto sensu the Monte-Carlo approach described in the 2007 publication at the level of subjects (each subject being a UO) ? For an analysis that involves all subjects, the permutation distribution is obtained in a different way as described in the 2007 paper. In that paper, we had between-trials design, which is formally equivalent to a between-subjects designs (involving random permutations of trials between conditions). In a random effects analysis of the data of all subjects, one has to randomly permute the subject-level coherences between the conditions within every subject. - Can we use the stat defined as the difference of the imaginary part of the coherence ? (averaged over the subjects in a group?) Yes, you can use every statistic you expect to be sensitive for the phenomenon that you are investigating. Best, Eric With my anticipated thanks, Best JM Lina From: Robert Oostenveld > Cc: > To: FieldTrip discussion list > Date: 3 Mar 2015 21:54:55 CET Reply-To: FieldTrip discussion list > Subject: Re: [FieldTrip] Magnetic dipole fit vs Equiv. Current dipole fit Hi Jim You can do an inverse solution with any method (including dipole fitting) by specifying cfg.vol=[] in the corresponding high-level function (e.g. ft_prepare_leadfield, ft_dipolefitting or ft_sourceanalysis). This causes the forward model to be computed with a magnetic dipole. If you want to track this down to the lower lever code, have a look at these lines in the code “forward/ft_voltype.m" line 115 of 138 --83%-- col 11 “forward/ft_compute_leadfield.m" line 280 of 611 --45%-- col 12 My appologies for this not being documented better. I have been using this myself to check on the localization of the headcoils in the CTF “hz.ds” datasets, which worked fine. I hope you can get it to work for the Sandia Labs system. For the CTF system it is not needed to do these computations in MATLAB, since the CTF electronics does this in (alomst) real-time and the positions are streamed along with the MEG channel data. That makes this this http://fieldtrip.fcdonders.nl/getting_started/realtime_headlocalizer easy for the system we have in Nijmegen. Arjen and I have also been working on making it work for the Elekta system where the fitting has to be done in MATLAB, but have not been able sofar to get it to work robustly. You can find the experiences and (still open) report at http://bugzilla.fcdonders.nl/show_bug.cgi?id=1792. best regards Robert On 25 Feb 2015, at 22:40, Jim McKay > wrote: Hello Fieldtrippers, I am consulting with the Sandia Labs on development of an atomic magnetometer based MEG system prototype. One of the areas I am working on is head localization, so I was looking at the code for the realtime head localization in Fieldtrip. I was surprised to see that although the comments talk about using a magnetic dipole forward solution, it actually used the FT dipolefit code which is based on an equivalent current dipole, as far as I can tell. There should be a significant difference in the forward solutions between MD and ECD, so how does this work? Or am I just missing something? Cheers, Jim -- Jim McKay Candoo Systems Inc. - Magnetic field sensors, systems, and site surveys Tel. 778-840-0361 jim.mckay at candoosys.com www.candoosys.com _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From: Robert Oostenveld > To: FieldTrip discussion list > Date: 3 Mar 2015 22:14:42 CET Reply-To: FieldTrip discussion list > Subject: Re: [FieldTrip] inconsistent chanunit for Neuromag data Hi Steve The grad.chanunit pertains to the units that would be computed as the forward solution. The hdr.chanunit pertains to the units of the channel-level data. Using the ft_convert_units helper function you could convert the units of the gradiometer definition from cm to mm or m. This changes the baseline of the planar gradiometers with a factor of 10 or 100. However, the planar gradient chanel data is not updated simultaneously and remains in the same units (fieldstrength per distance). So it can happen that grad.chanunit and hdr.chanunit are inconsistent. The consequence (which many people on the list will have noticed, but might not have understood) is that the forward solution - and therefore the inverse solution - for the Elekta planar gradiometer channels can easily be incorrect: due to the data being in T/m and the forward solution in T/cm (or some other units, I don’t know the typical units from the top of my head). As long as you always use the same pipeline on hte planar gradiometers, you will most likely not notice since you will be interpreting the sourc estimates in “arbitrary units” anyway. But if you were to combine the planar channels with the magnetometers, the planar channels (fieldstrength per distance) would be affected differently than the manetometer channels (fieldstrength) by your choise of geometrical units. Using the ft_datatype_sens helper function you can ensure that the scaling of the grad structure (which affects the “coilpos" field but also the rows of the “tra" field that correspond to the planar channels) is consistent with your channel level data. If you specify all your data in SI units (T, m, V, etc.) the units of the forward computations will be correct and hence the units of the inverse estimates will also be consistent in SI units (e.g. dipole moment in A/m). The thing is that the different fieldtrip import functions (which come from various origins) return data in non-SI units more often than not :-( If you work with channel level data, SI units are often not nice. ERFs in Tesla are very small (10^-12). ERPs are usually expressed in uV. Also for anatomcial MRIs it is not convenient to express data in SI units (m) and mm is common. The CTF system by default expresses geometrical distance in cm. Etc… So all systems by themselves made their own “convenient” choices. But if all the data comes together with the physical model, it becomes a mess. The logical choice to solve the inconsistencies is to express it in SI units. I hope this helps in clarifying the situation. best regards, Robert PS if you search on bugzilla, you can see some (still open) bugs that pertain to this On 27 Feb 2015, at 03:53, Steve Patterson > wrote: Hello, I noticed that fieldtrip produces inconsistent channel units when I read in Neuromag (vectorview) data. For example: %%%%%%%%%%%%%%%%%%%%%%%% cfg = []; cfg.dataset = 'example.fif'; cfg.trialfun = 'ft_trialfun_general'; cfg.trialdef.eventtype = 'STI101'; cfg.trialdef.eventvalue = [17 18 20]; cfg.trialdef.prestim = 0.500; cfg.trialdef.poststim = 1.000; cfg = ft_definetrial(cfg); data = ft_preprocessing(cfg); disp(data.hdr.chanunit(1:6)); 'T/m' 'T/m' 'T' 'T/m' 'T/m' 'T' disp(data.grad.chanunit(1:6)); 'T' 'T' 'T' 'T' 'T' 'T' %%%%%%%%%%%%%%%%%%%%%%%% data.hdr.chanunit is correct and data.grad.chanunit is wrong. data.grad.chanunit must take precedence in further analysis, because I've noticed this causes problems downstream. For example, when using ft_dipolesimulation, the simulated data on the gradiometer channels is too small in amplitude by a factor of 1/(16.8E-3) (the distance between the gradiometer coil pair in meters). This is reflected in the grad.tra matrix, whose non-zero values are all 1's and -1's, whereas they should be 1's (magnetometers), and +/- 1/16.8E-3 (gradiometers). If you could fix this, it would be much appreciated! thanks, Steve _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From: Robert Oostenveld > To: FieldTrip discussion list > Date: 3 Mar 2015 22:18:34 CET Reply-To: FieldTrip discussion list > Subject: Re: [FieldTrip] eeglab2fieldtrip - Fieldtrip vs EEGLAB version Hi Omar, The eeglab2fieldtrip.m function lives on the boudary between the two projects. We (i.e. Arno and me) have decided to maintain it on the EEGLAB side and copy it to FieldTrip whenever needed. That is why it is in fieldtrip/external/eeglab. If you go to https://code.google.com/p/fieldtrip/source/list?path=/trunk/external/eeglab/eeglab2fieldtrip.m&start=10122 you can see the history. See also http://bugzilla.fcdonders.nl/show_bug.cgi?id=2770 In general for (almost) all code in fieldtrip/external it is being maintained externally, and often by people that are not directly related to the fieldtrip project. best Robert On 16 Feb 2015, at 16:38, Mian, Omar > wrote: Hello, There seem to be differences between the eeglab2fieldtrip.m when the Fieldtrip and EEGLAB versions are compared. Is this an oversight? Which one is “better” ? data.cfg.version.id contains a later date in the Fieldtrip version, but the file properties modified date is later in the EEGLAB version. The versions I am comparing are: \fieldtrip-20150109\external\eeglab\eeglab2fieldtrip.m \eeglab13_4_4b\plugins\dipfit2.3\eeglab2fieldtrip.m Thanks Omar --------------------------- Omar Mian, Phd Research Fellow School of Applied Sciences London South Bank University 103 Borough Road London SE1 0AA Copyright in this email and in any attachments belongs to London South Bank University. This email, and its attachments if any, may be confidential or legally privileged and is intended to be seen only by the person to whom it is addressed. If you are not the intended recipient, please note the following: (1) You should take immediate action to notify the sender and delete the original email and all copies from your computer systems; (2) You should not read copy or use the contents of the email nor disclose it or its existence to anyone else. The views expressed herein are those of the author(s) and should not be taken as those of London South Bank University, unless this is specifically stated. London South Bank University is a company limited by guarantee registered in England and Wales. The following details apply to London South Bank University: Company number - 00986761; Registered office and trading address - 103 Borough Road London SE1 0AA; VAT number - 778 1116 17 Email address - LSBUinfo at lsbu.ac.uk _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From: Tolga Ozkurt > To: > Date: 4 Mar 2015 09:54:53 CET Reply-To: FieldTrip discussion list > Subject: [FieldTrip] Visualization of Channels for Human Connectome Project MEG data Dear Fieldtrip list, I was seeing the MEG files uploaded by “Human Connectome Project”, which seem to be pre-processed by Fieldtrip. The resting data were collected in supine position with 4D Neuromag 248 channels. When I use the standard command for layout cfg.layout = '4D248.lay'; the channel locations do not seem to fit. (Please see the attached figure). I do not quite know the channel distribution of the system; but it seems some channels are out of the head. Could you give me an idea to project the channel layout properly? Thank you. Tolga -- Tolga Esat Özkurt, PhD Department of Health Informatics Middle East Technical University http://www.metu.edu.tr/~ozkurt/ From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Date: 4 Mar 2015 11:34:27 CET Reply-To: FieldTrip discussion list > Subject: Re: [FieldTrip] Visualization of Channels for Human Connectome Project MEG data Hi Tolga, There’s a layout that ‘better fits’ the projected channel locations, and which you can obtain from the megconnectome software that accompanies the HCP MEG data. The software can be obtained from here: humanconnectome.org/documentation/MEG1/meg-pipeline.html If you download one of the packages and unzip it, you’ll find a ‘template’ directory. Inside, there’s a 4D248.mat file (note that you need the ‘4D248.mat’ in cfg.layout in that case), which you can use as a layout for visualization. Best wishes, Jan-Mathijs On Mar 4, 2015, at 9:54 AM, Tolga Ozkurt > wrote: Dear Fieldtrip list, I was seeing the MEG files uploaded by “Human Connectome Project”, which seem to be pre-processed by Fieldtrip. The resting data were collected in supine position with 4D Neuromag 248 channels. When I use the standard command for layout cfg.layout = '4D248.lay'; the channel locations do not seem to fit. (Please see the attached figure). I do not quite know the channel distribution of the system; but it seems some channels are out of the head. Could you give me an idea to project the channel layout properly? Thank you. Tolga -- Tolga Esat Özkurt, PhD Department of Health Informatics Middle East Technical University http://www.metu.edu.tr/~ozkurt/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From joscha.schmiedt at esi-frankfurt.de Tue Apr 21 10:52:36 2015 From: joscha.schmiedt at esi-frankfurt.de (Schmiedt, Joscha) Date: Tue, 21 Apr 2015 08:52:36 +0000 Subject: [FieldTrip] A Fieldtrip data format? In-Reply-To: References: <5548CAB3-F9A2-4C6B-B958-3CF27CF2C27F@esi-frankfurt.de> , Message-ID: <17F994D43E9ADA418DE0040CC6F4A96B7FD2964A@UM-EXCDAG-A01.um.gwdg.de> Hey, For your information: there is a concerted effort by many big labs to create a standard data format for electrophysiology: https://crcns.org/NWB/Overview It will actually be based on HDF5. Joscha ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Schmiedt, Joscha [joscha.schmiedt at esi-frankfurt.de] Sent: Wednesday, April 01, 2015 2:03 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] A Fieldtrip data format? Hi Gio, Thanks for the info. The fcdc_matbin approach indeed would be suitable data for raw data. However, I’m looking for a fast solution for data that is already processed and cut into trials, in particular with varying trial length. Joscha > On Mar 31, 2015, at 22:39, Gio Piantoni wrote: > > Hi Joscha, > > FieldTrip already has its own simple uncompressed file format. > fcdc_matbin "It is not an official file format, but was invented here > at the FCDC. It consists of two files: a *.mat matlab file that > contains the header (and optionally the events) and a *.bin binary > file that contains the data." > http://www.fieldtriptoolbox.org/faq/reading_is_slow_can_i_write_my_raw_data_to_a_more_efficient_file_format > > If you want to look at the code: > https://github.com/fieldtrip/fieldtrip/blob/master/fileio/ft_write_data.m#L275 > > You should be able to read it as usual with ft_preprocessing. You can > convert your files to the fcdc_matbin using ft_preprocessing as well: > https://github.com/fieldtrip/fieldtrip/blob/master/ft_preprocessing.m#L581 > Be careful about not losing precision though. > > The only catch is that, as far as I know, you cannot export your > preprocessed data through ft_preprocessing at the moment, because > ft_write_data is now inside this if-part: > https://github.com/fieldtrip/fieldtrip/blob/master/ft_preprocessing.m#L252 > but it's only a matter of adapting that to your needs. > > Would this work for you? > > -g > > On Tue, Mar 31, 2015 at 9:09 AM, Schmiedt, Joscha > wrote: >> Hi, >> >> When working with Fieldtrip it is very convenient to store the data and >> analyses using MATLAB’s save and load functions. However, for large and/or >> complex data with many channels (>2GB) MATLAB enforces compression, which is >> pretty useless for electrophysiology data and slows down the load and save >> performance by a factor of up to 8 (see e.g. >> http://undocumentedmatlab.com/blog/improving-save-performance). The MATLAB >> file format is based on HDF5, which is generally an open and future-proof >> data format, but unfortunately MATLAB doesn’t allow you to disable the >> compression. >> >> An option to overcome this could be to develop a simple data format for >> Fieldtrip data that is also based on HDF5. Is or has there been any >> development going into that direction? Would there be any interest? Of >> course, creating yet another data format is almost never a good idea >> (https://xkcd.com/927/), but since HDF5 is well-documented and readable with >> almost any software, it might be worth thinking about it. >> >> I’d be happy to hear your thoughts. >> >> Joscha >> >> --------------------------------- >> Joscha Schmiedt >> PhD Student >> >> Ernst Strüngmann Institute (ESI) for Neuroscience >> in Cooperation with Max Planck Society >> Deutschordenstraße 46 >> 60528 Frankfurt am Main >> Germany >> >> Tel.: +49 (0)69 96769 241 >> >> Sitz der Gesellschaft: Frankfurt am Main >> Registergericht: Amtsgericht Frankfurt - HRB 84266 >> Geschäftsführer: Prof. Dr. Pascal Fries >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From anne.keller at sickkids.ca Tue Apr 21 18:59:07 2015 From: anne.keller at sickkids.ca (Anne Keller) Date: Tue, 21 Apr 2015 16:59:07 +0000 Subject: [FieldTrip] ICA before beamformer In-Reply-To: <69B46D4F7B3C33449A56153DF85867882EA7A0@SKMBXX02.sickkids.ca> References: <69B46D4F7B3C33449A56153DF85867882EA7A0@SKMBXX02.sickkids.ca> Message-ID: <69B46D4F7B3C33449A56153DF85867882EA7C8@SKMBXX02.sickkids.ca> Hi Fieldtrip-ers, I'm working with MEG data collected from children, and I am hoping to do source localization via beamformer. Our kids have lots of eye movement and blinks, so I was hoping to perform ICA prior to beamformer. How can I address the matrix regularization aspect after I remove components? Is there a fieldtrip function that corrects this? Due to lab requirements, I will be using SPM's beamformer (but Fieldtrip's ICA and reject components functions). Thanks so much in advance! Best, Anne ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. From drivolta81 at gmail.com Wed Apr 22 11:56:06 2015 From: drivolta81 at gmail.com (Davide Rivolta) Date: Wed, 22 Apr 2015 09:56:06 +0000 Subject: [FieldTrip] 20 PhD excellence scholarships at UEL Message-ID: Dear all, I just wish to let you know that 20 fully-funded UEL Excellence Studentships will be made available to PhD applicants, starting September 2015 (www.uel.ac.uk/studentships). For more information please do not hesitate to contact Ben Whitham in the Graduate School (B.Whitham at uel.ac.uk). Bests, Davide -- Davide Rivolta, PhD -------------- next part -------------- An HTML attachment was scrubbed... URL: From singhharsimrat at gmail.com Wed Apr 22 14:13:50 2015 From: singhharsimrat at gmail.com (Harsimrat Singh) Date: Wed, 22 Apr 2015 13:13:50 +0100 Subject: [FieldTrip] Compatibility of ft_layoutplot with MATLAB 2014b Message-ID: Hi Fieldtrippers I think I might have found a problem in ft_layoutplot compatibility with the newer versions of MATLAB. Now MATLAB doesn't let you add numeric values to an array of graphics objects - hence it throws an error Error using sprintf Function is not defined for 'matlab.ui.Figure' inputs. Best regards Harsimrat -------------------------------------------- *Dr Harsimrat Singh* *Department of Cancer and Surgery* *St. Marys Hospital Campus* *Imperial College London* *Praed Street, London W2 1NY* *harsimrat.singh at imperial.ac.uk * -------------- next part -------------- An HTML attachment was scrubbed... URL: From luke.bloy at gmail.com Wed Apr 22 22:55:14 2015 From: luke.bloy at gmail.com (Luke Bloy) Date: Wed, 22 Apr 2015 16:55:14 -0400 Subject: [FieldTrip] Source localizing resting state data Message-ID: Hi everyone, Following up on two recent email threads ( http://mailman.science.ru.nl/pipermail/fieldtrip/2015-April/009120.html and http://mailman.science.ru.nl/pipermail/fieldtrip/2015-January/008796.html) I'd like to ask the fieldtrip community what they feel is the best source localization methods for resting state data? Note that at this point i'm only thinking about simple things like localizing resting alpha and beta rhythms. -Thanks Luke -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Thu Apr 23 08:47:21 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Thu, 23 Apr 2015 08:47:21 +0200 Subject: [FieldTrip] Compatibility of ft_layoutplot with MATLAB 2014b In-Reply-To: References: Message-ID: <98A59F44-6729-41F0-AA81-D26E523B7584@uni-konstanz.de> Dear Harsimrat, Please update your FT version. This should solve the issue. Best Tzvetan > Am 22.04.2015 um 14:13 schrieb Harsimrat Singh : > > Hi Fieldtrippers > > I think I might have found a problem in ft_layoutplot compatibility with the newer versions of MATLAB. Now MATLAB doesn't let you add numeric values to an array of graphics objects - hence it throws an error > > Error using sprintf > Function is not defined for 'matlab.ui.Figure' inputs. > > Best regards > Harsimrat > > -------------------------------------------- > Dr Harsimrat Singh > Department of Cancer and Surgery > St. Marys Hospital Campus > Imperial College London > Praed Street, London W2 1NY > harsimrat.singh at imperial.ac.uk > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From ofcastaneda at outlook.com Thu Apr 23 15:58:27 2015 From: ofcastaneda at outlook.com (=?utf-8?B?T3NjYXIgRmVybmFuZG8gQ2FzdGHDsWVkYSBGZXJuw6FuZGV6?=) Date: Thu, 23 Apr 2015 13:58:27 +0000 Subject: [FieldTrip] =?utf-8?q?Using_Fieldtrip_with_BCI2000?= Message-ID: Dear community, My name is Oscar Castañeda and I’ve been using the Fieldtrip Buffer to extract samples from BCI2000; the samples were obtained using an Emotiv Headset. However, I have a problem with data adquisition: When I use the instruction ft_read_data(filename, ‘header’,hdr,‘begsample’,begsample,’endsample’,endsample,’chanindx’,chanindx) [where chanindx is a list going from number 1 to 14] and I compare the obtained data with the one stored in the corresponding BCI2000 .dat file, I find that the samples are equal for the first Emotiv cannel (AF3), just as we would expect. But for the rest of channels, the data returned by ft_read_data is not equal to the one from the .dat file, and varies in a non-constant proportion of 90% to 110% of the .dat sample. Why could this be happening? I would appreciate very much any kind of help. Thank you very much, Oscar -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.herring at donders.ru.nl Thu Apr 23 22:33:53 2015 From: j.herring at donders.ru.nl (Herring, J.D. (Jim)) Date: Thu, 23 Apr 2015 20:33:53 +0000 Subject: [FieldTrip] ICA before beamformer In-Reply-To: <69B46D4F7B3C33449A56153DF85867882EA7C8@SKMBXX02.sickkids.ca> References: <69B46D4F7B3C33449A56153DF85867882EA7A0@SKMBXX02.sickkids.ca> <69B46D4F7B3C33449A56153DF85867882EA7C8@SKMBXX02.sickkids.ca> Message-ID: <2E61E12F-DC21-4FB9-B91F-8FDD4843B311@donders.ru.nl> Dear Anne, If I am not mistaken SPM actually uses Fieldtrip’s DICS beamformer implementation. In any case, after doing ICA the grad field in your data structure should be corrected so you should be safe in using SPM's beamformer given that you use the grad contained in the data structure produced after cleaning with ICA in Fieldtrip. Best, Jim > On 21 Apr 2015, at 18:59, Anne Keller wrote: > > Hi Fieldtrip-ers, > > I'm working with MEG data collected from children, and I am hoping to do source localization via beamformer. Our kids have lots of eye movement and blinks, so I was hoping to perform ICA prior to beamformer. How can I address the matrix regularization aspect after I remove components? Is there a fieldtrip function that corrects this? Due to lab requirements, I will be using SPM's beamformer (but Fieldtrip's ICA and reject components functions). > > Thanks so much in advance! > > Best, > Anne > > ________________________________ > > This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From ronny.ibrahim at mq.edu.au Fri Apr 24 06:49:11 2015 From: ronny.ibrahim at mq.edu.au (Ronny Ibrahim) Date: Fri, 24 Apr 2015 14:49:11 +1000 Subject: [FieldTrip] MEG160 KIT layout file template Message-ID: Hi Community, I was wondering whether there is any fieldtrip '.lay' layout file for the MEG160 KIT system that I am currently using : This is a paper on the MEG system http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=783918 I have tried reading the coordinates using ft_read_header from the '*.con' file and trying to use this information to construct my own '.lay' file based on the Yokogawa's yokogawa440pg.lay planar gradiometer layout file ( while removing several sensors which weren't there in the MEG160 KIT system) but after plotting a few eye-blink responses, the topo_plot output does not seem to look right. Therefore, I would like to thank you for your kind help and inputs in resolving my simple issue here. Any help will be much appreciate it. Kind Regards, Ronny -------------- next part -------------- An HTML attachment was scrubbed... URL: From annika.notbohm at uni-oldenburg.de Fri Apr 24 11:51:37 2015 From: annika.notbohm at uni-oldenburg.de (Annika Notbohm) Date: Fri, 24 Apr 2015 11:51:37 +0200 Subject: [FieldTrip] PhD-Conference: Entrainment of Brain Oscillations (EBO) in Oldenburg, Germany Message-ID: <553A1229.3070500@uni-oldenburg.de> Dear (PhD-) students of brain oscillations and entrainment, we want to call your attention to our PhD conference: * **Entrainment of Brain Oscillations (EBO) * at 17th-18th September 2015 at the Hanse Wissenschaftskolleg (Delmenhorst, Germany). The conference is organized by four PhD students from the University of Oldenburg, together with Prof. Dr. Christoph Herrmann. Confirmed keynote speakers are /Prof. Dr. Ole Jensen (Donders Institute)/ and /Prof. Dr. Joachim Gross (University of Glasgow)/ who will also hold a one day workshop on "Analytical methods for studies of brain oscillations" as a pre-meeting to the conference. If you are interested in participating at our conference, please submit a poster abstract following the guidelines on our website (http://www.uni-oldenburg.de/ebo/abstract-submission). As we intend to realize a fair selection of poster abstracts, we kindly ask you to use the abstract template for blinded submission, as can be found on the link given above. POSTER DEADLINE: JUNE 20th 2015 Three symposia will be held during the conference which deal with entrainment of brain oscillations by using auditory, visual or electrical methods. The main focus in all three sessions will lie on basic research on the mechanism of entrainment as well as on causality of modified oscillations and behavior. We intend to create a platform that allows intensive exchange and potential collaborations between the participants. Therefore, the conference will be kept rather small (50 participants) and specific regarding the topic. More detailed information and a (preliminary) program can be found on the website www.uni-oldenburg.de/EBO. For further questions don't hesitate to contact us via EBO at uni-oldenburg.de. Please feel free to forward this e-mail to others who could be interested in our conference. Best regards, Alina Baltus, Anna-Katharina Bauer, Annika Notbohm and Johannes Vosskuhl -- Annika Notbohm, M.Sc. Experimental Psychology Lab Department of Psychology European Medical School Carl von Ossietzky Universität Ammerländer Heerstr. 114-118 26129 Oldenburg, Germany Tel: +49 441 798 2628 Mobile: +49 176 22716261 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mehmetakifozcoban at gmail.com Fri Apr 24 15:22:49 2015 From: mehmetakifozcoban at gmail.com (=?UTF-8?B?TWVobWV0IEFraWYgw5Z6w6dvYmFu?=) Date: Fri, 24 Apr 2015 16:22:49 +0300 Subject: [FieldTrip] =?utf-8?b?SMSx?= Message-ID: -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Fri Apr 24 17:02:49 2015 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Fri, 24 Apr 2015 17:02:49 +0200 Subject: [FieldTrip] =?utf-8?b?SMSx?= In-Reply-To: References: Message-ID: Hi! On 24 April 2015 at 15:22, Mehmet Akif Özçoban wrote: > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From haiteng.jiang at gmail.com Sun Apr 26 16:38:48 2015 From: haiteng.jiang at gmail.com (Haiteng Jiang) Date: Sun, 26 Apr 2015 16:38:48 +0200 Subject: [FieldTrip] Source localizing resting state data (Luke Bloy) Message-ID: Hi Luke, In my experience, the best way to deal with central bias issue is leadfield normalization on resting state . This is much more robust compared to neural activity index (NAI) across subjects. You can specify cfg.normalize = 'yes' when you compute leadfied using ft_prepare_leadfield function . This strategy gave me satisfactory results in the end. Hope this helps, Haiteng > > Message: 2 > Date: Wed, 22 Apr 2015 16:55:14 -0400 > From: Luke Bloy > To: FieldTrip list serve > Subject: [FieldTrip] Source localizing resting state data > Message-ID: > < > CAG5Ru-pJKH91o9EHD+kc53TQXc8F3X4Ogsa0UOC5wiJmLPvEvA at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi everyone, > > Following up on two recent email threads ( > http://mailman.science.ru.nl/pipermail/fieldtrip/2015-April/009120.html > and > http://mailman.science.ru.nl/pipermail/fieldtrip/2015-January/008796.html > ) > > I'd like to ask the fieldtrip community what they feel is the best source > localization methods for resting state data? Note that at this point i'm > only thinking about simple things like localizing resting alpha and beta > rhythms. > > -Thanks > Luke > > -- Haiteng Jiang PhD candidate Donders Institute for Brain, Cognition and Behaviour Neuronal Oscillations Group Computational Cognitive Neuroscience Lab https://sites.google.com/site/haitengjiang/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From Olaf.Hauk at mrc-cbu.cam.ac.uk Tue Apr 28 17:41:54 2015 From: Olaf.Hauk at mrc-cbu.cam.ac.uk (Olaf Hauk) Date: Tue, 28 Apr 2015 15:41:54 +0000 Subject: [FieldTrip] Methods Skills Survey Message-ID: Hello - I would be very grateful if you could participate in this methods skills survey, which will help the development of future methods training events. It is anonymous and should take about 10-15 minutes. Please participate only once. Please visit this link to go to the survey: https://www.surveymonkey.com/s/3JL2CZX Are you an undergraduate student, PhD student, or post-doc who is working or planning to work in the cognitive sciences? If so, then we would like to invite you to participate in an online survey that will help us develop more efficient methods training programmes for cognitive scientists and neuroscientists. Cognitive science and neuroscience are highly interdisciplinary, and it is important for us to know the skills of researchers who are moving into these fields. The survey should take you 10-15 minutes, and you will be asked some questions related to data analysis as well as about yourself (but you will remain anonymous). You will not receive any remuneration for your participation - but your information may benefit a large number of future students in the cognitive sciences. This is not an exam. Depending on your background, you may not be able to answer some or even many of these questions at all - but this information is also very useful to us. Please only participate in this survey once, and please do not consult the internet, books or friends to answer the questions. This survey is run by Dr. Olaf Hauk from the MRC Cognition and Brain Sciences Unit, Cambridge, UK. The data from this survey may be used in future presentations and publications. Olaf Hauk, PhD MRC Cognition and Brain Sciences Unit Phone: +44(0)1223 273702 Fax: +44(0)1223 359062 Web: http://www.mrc-cbu.cam.ac.uk/people/olaf.hauk/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From joseluisblues at gmail.com Wed Apr 29 09:35:47 2015 From: joseluisblues at gmail.com (Jose) Date: Wed, 29 Apr 2015 09:35:47 +0200 Subject: [FieldTrip] fast & coarse artifact rejection Message-ID: Dear fellows, My name is José Luis, I’m working with Micromed data in the Clinic Research Unit in Ville-Evrard in France. I succeed at importing and reading my data with Fieldtrip. I would like to do a superficial and fast ERP analysis (just for checking purposes), and I was wondering if there any way to tell Fieldtrip to remove trials that exceed a threshold (like -+80 uV). Meaning that I don’t want to go through ICA or any other method like this (for the moment). Is that possible?, Any hint would be appreciated. best, José Luis -- José Luis ULLOA FULGERI 33 (0)6.29.50.64.93 -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.herring at donders.ru.nl Wed Apr 29 09:54:49 2015 From: j.herring at donders.ru.nl (Herring, J.D. (Jim)) Date: Wed, 29 Apr 2015 07:54:49 +0000 Subject: [FieldTrip] fast & coarse artifact rejection In-Reply-To: References: Message-ID: <8D64FA7B-D59E-41F0-AC21-3A09289C4A84@donders.ru.nl> Hi Jose, Yes, using ft_artifact_zvalue you can z-transform your data and mark trials for rejection that exceed a certain threshold. Marked trials can be rejected with ft_rejectartifact. See http://www.fieldtriptoolbox.org/tutorial/automatic_artifact_rejection for a walkthrough and examples. Best, Jim On 29 Apr 2015, at 09:35, Jose > wrote: Dear fellows, My name is José Luis, I’m working with Micromed data in the Clinic Research Unit in Ville-Evrard in France. I succeed at importing and reading my data with Fieldtrip. I would like to do a superficial and fast ERP analysis (just for checking purposes), and I was wondering if there any way to tell Fieldtrip to remove trials that exceed a threshold (like -+80 uV). Meaning that I don’t want to go through ICA or any other method like this (for the moment). Is that possible?, Any hint would be appreciated. best, José Luis -- José Luis ULLOA FULGERI 33 (0)6.29.50.64.93 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From barbara.schorr at uni-ulm.de Wed Apr 29 11:01:30 2015 From: barbara.schorr at uni-ulm.de (Barbara Schorr) Date: Wed, 29 Apr 2015 11:01:30 +0200 Subject: [FieldTrip] Renormalized PDC In-Reply-To: References: Message-ID: <55409DEA.70404@uni-ulm.de> Dear Fieldtrippers, I am working on a connectivity analysis (partial directed coherence) in EEG data. I found this paper by Schelter, B.; Timmer, J.; Eichler, M. (2009). "Assesssing the strength of directed influences among neural signals using renormalized partial directed coherence"./J. Neurosci Methods/*179*(1): who suggest to rather use a renormalized PDC. Has anybody here used this before and could tell me how to calculate this rPDC in Fieldtrip? All the best, Barbara Am 27.04.2015 um 12:00 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 > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Re: Source localizing resting state data (Luke Bloy) > (Haiteng Jiang) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 26 Apr 2015 16:38:48 +0200 > From: Haiteng Jiang > To: fieldtrip at science.ru.nl > Subject: Re: [FieldTrip] Source localizing resting state data (Luke > Bloy) > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi Luke, > In my experience, the best way to deal with central bias issue is > leadfield normalization on resting state . This is much more robust > compared to neural activity index (NAI) across subjects. You can specify > cfg.normalize = 'yes' when you compute leadfied > using ft_prepare_leadfield function . This strategy gave me satisfactory > results in the end. > > Hope this helps, > Haiteng > > >> Message: 2 >> Date: Wed, 22 Apr 2015 16:55:14 -0400 >> From: Luke Bloy >> To: FieldTrip list serve >> Subject: [FieldTrip] Source localizing resting state data >> Message-ID: >> < >> CAG5Ru-pJKH91o9EHD+kc53TQXc8F3X4Ogsa0UOC5wiJmLPvEvA at mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi everyone, >> >> Following up on two recent email threads ( >> http://mailman.science.ru.nl/pipermail/fieldtrip/2015-April/009120.html >> and >> http://mailman.science.ru.nl/pipermail/fieldtrip/2015-January/008796.html >> ) >> >> I'd like to ask the fieldtrip community what they feel is the best source >> localization methods for resting state data? Note that at this point i'm >> only thinking about simple things like localizing resting alpha and beta >> rhythms. >> >> -Thanks >> Luke >> >> > -- Barbara Schorr, MSc Clinical and Biological Psychology University of Ulm Albert-Einstein-Allee 47 89069 Ulm Therapiezentrum Burgau Kapuzinerstraße 34 89331 Burgau -------------- next part -------------- An HTML attachment was scrubbed... URL: From guiraudh at gmail.com Wed Apr 29 14:45:56 2015 From: guiraudh at gmail.com (=?UTF-8?B?SMOpbMOobmUgR3VpcmF1ZA==?=) Date: Wed, 29 Apr 2015 14:45:56 +0200 Subject: [FieldTrip] Search for a template children. Message-ID: Dear community, My name is Hélène Guiraud and i'm working in DDL lab in Lyon (France) on speech perception in children using MEG. The children involved in the study don't pass MRI. We want to achieve source reconstruction from a template. However I can't find a template corresponding to the anatomy of a child (8-12 years). Can someone tell me if there are template children and where I can find them? Best, Hélène Guiraud -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.schneider at uke.uni-hamburg.de Wed Apr 29 15:53:13 2015 From: t.schneider at uke.uni-hamburg.de (Till Schneider) Date: Wed, 29 Apr 2015 15:53:13 +0200 Subject: [FieldTrip] Search for a template children. In-Reply-To: References: Message-ID: <5540E249.3000200@uke.uni-hamburg.de> Dear Helene, McGill University provides MNI brains for different age groups between 4.5y to 18y. http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1 You will probably find the template brain you are searching for in this database. Best regards, Till -- Till Schneider, PhD Cognitive and Clinical Neurophysiology Group Dept. of Neurophysiology and Pathophysiology University Medical Center Hamburg-Eppendorf Martinistr. 52 20246 Hamburg Germany phone +49-40-7410-53188 fax +49-40-7410-57126 www.uke.de/neurophysiologie Am 29.04.15 um 14:45 schrieb Hélène Guiraud: > Dear community, > > My name is Hélène Guiraud and i'm working in DDL lab in Lyon (France) > on speech perception in children using MEG. > The children involved in the study don't pass MRI. We want to achieve > source reconstruction from a template. However I can't find a template > corresponding to the anatomy of a child (8-12 years). > Can someone tell me if there are template children and where I can > find them? > > Best, > > Hélène Guiraud > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahjoory86 at gmail.com Wed Apr 29 16:25:35 2015 From: mahjoory86 at gmail.com (Keyvan Mahjoory) Date: Wed, 29 Apr 2015 16:25:35 +0200 Subject: [FieldTrip] ICBM 152 templates in FT Message-ID: Dear Fieldtrip Users, I perform source analysis in Fieldtrip with a template head model ( standard_bem ) and a template source model (cortex_5124.surf.gii ) to constarin estimated sources on cortex. These templates are based on Colin27, But I prefere to use the template ICBM152 instead. Does FT include ICBM template? I mean templates for both head model and cortical surfe. Many Thanks in advance, Keyvan -------------- next part -------------- An HTML attachment was scrubbed... URL: From RICHARDS at mailbox.sc.edu Thu Apr 30 14:12:22 2015 From: RICHARDS at mailbox.sc.edu (RICHARDS, JOHN) Date: Thu, 30 Apr 2015 12:12:22 +0000 Subject: [FieldTrip] re template for children Message-ID: We have a template for children‹actually have for infants from 2 weeks through adults at 89 years. We also have average electrode positions for EGI sensor nets (GSN128, HGSN128) and the 10-10 system; and segmented priors, stereotaxic atlases, and segmented heads (BEM, FEM). I also have been using this recently with FT for infants and child/adolescent/adult ages. WWW site: http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ Fro www site: This is a database of average MRIs and associated MRI volumes for developmental MRI work. It consists of average MRI templates, segmented partial volume estimate volumes for GM, WM, T2W-derived CSF (Description ). The database is separated into head-based and brain-based averages. The data are separated by ages in months, years, 6-month, or 5-year intervals (Ages and Templates ). The templates are grouped into first year (2 weeks through 12 months), early childhood (15 months through 4 years), childhood (4 years through 10 years), adolescence (10.5 years through 17.5 years) and adults (18 years through 89 years). Tools for cortical source analysis of EEG and ERP are provided. These tools are based on the average MRI templates, segmenting, and atlases. Also see my www site, jerlab.psych.sc.edu for publications describing this. We have a recent chapter that has a good description of the issues behind the database (with Wanze Xie). We have a paper accepted at Neuroimage for their upcoming ³Data Sharing² issue (with Carmen Sanchez, Michelle Phillips-Meek, and Wanze Xie). John *********************************************** John E. Richards Carolina Distinguished Professor Department of Psychology University of South Carolina Columbia, SC 29208 Dept Phone: 803 777 2079 Fax: 803 777 9558 Email: richards-john at sc.edu HTTP: jerlab.psych.sc.edu *********************************************** On 4/30/15, 6:00 AM, "fieldtrip-request at science.ru.nl" wrote: >Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > >To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > >You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of fieldtrip digest..." > > >Today's Topics: > > 1. Search for a template children. (H?l?ne Guiraud) > 2. Re: Search for a template children. (Till Schneider) > 3. ICBM 152 templates in FT (Keyvan Mahjoory) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Wed, 29 Apr 2015 14:45:56 +0200 >From: H?l?ne Guiraud >To: fieldtrip at science.ru.nl >Subject: [FieldTrip] Search for a template children. >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Dear community, > >My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) on >speech perception in children using MEG. >The children involved in the study don't pass MRI. We want to achieve >source reconstruction from a template. However I can't find a template >corresponding to the anatomy of a child (8-12 years). >Can someone tell me if there are template children and where I can find >them? > >Best, > >H?l?ne Guiraud >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >9b53e/attachment-0001.html> > >------------------------------ > >Message: 2 >Date: Wed, 29 Apr 2015 15:53:13 +0200 >From: Till Schneider >To: FieldTrip discussion list >Subject: Re: [FieldTrip] Search for a template children. >Message-ID: <5540E249.3000200 at uke.uni-hamburg.de> >Content-Type: text/plain; charset="windows-1252"; Format="flowed" > >Dear Helene, > >McGill University provides MNI brains for different age groups between >4.5y to 18y. >http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1 >You will probably find the template brain you are searching for in this >database. > >Best regards, >Till > >-- > >Till Schneider, PhD > >Cognitive and Clinical Neurophysiology Group >Dept. of Neurophysiology and Pathophysiology >University Medical Center Hamburg-Eppendorf >Martinistr. 52 >20246 Hamburg >Germany > >phone +49-40-7410-53188 >fax +49-40-7410-57126 >www.uke.de/neurophysiologie > > > >Am 29.04.15 um 14:45 schrieb H?l?ne Guiraud: >> Dear community, >> >> My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) >> on speech perception in children using MEG. >> The children involved in the study don't pass MRI. We want to achieve >> source reconstruction from a template. However I can't find a template >> corresponding to the anatomy of a child (8-12 years). >> Can someone tell me if there are template children and where I can >> find them? >> >> Best, >> >> H?l?ne Guiraud >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > >-- > >_____________________________________________________________________ > >Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen >Rechts; Gerichtsstand: Hamburg | www.uke.de >Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Prof. Dr. >Dr. Uwe Koch-Gromus, Joachim Pr?l?, Rainer Schoppik >_____________________________________________________________________ > >SAVE PAPER - THINK BEFORE PRINTING >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >44937/attachment-0001.html> > >------------------------------ > >Message: 3 >Date: Wed, 29 Apr 2015 16:25:35 +0200 >From: Keyvan Mahjoory >To: FieldTrip discussion list >Subject: [FieldTrip] ICBM 152 templates in FT >Message-ID: > >Content-Type: text/plain; charset="iso-8859-1" > >Dear Fieldtrip Users, > >I perform source analysis in Fieldtrip with a template head model ( >standard_bem ) and a >template source model (cortex_5124.surf.gii >) to constarin >estimated sources on cortex. These templates are based on Colin27, But I >prefere to use the template ICBM152 instead. >Does FT include ICBM template? I mean templates for both head model and >cortical surfe. > >Many Thanks in advance, >Keyvan >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >9daf3/attachment-0001.html> > >------------------------------ > >_______________________________________________ >fieldtrip mailing list >fieldtrip at donders.ru.nl >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >End of fieldtrip Digest, Vol 53, Issue 23 >***************************************** From frsantos at fpce.up.pt Thu Apr 30 17:34:23 2015 From: frsantos at fpce.up.pt (Fernando Ferreira-Santos) Date: Thu, 30 Apr 2015 15:34:23 +0000 Subject: [FieldTrip] Porto IV CAN: 4th Cognitive and Affective Neurophysiology Summer School Message-ID: <2BAB036A9BAEA44984A131DFCE4461080109B9E53D@SRVMBX02.fpceup.psi.up.pt> Dear colleagues, The Laboratory of Neuropsychopsysiology of the University of Porto (http://www.fpce.up.pt/labpsi/) is pleased to announce the 4th edition of the International Cognitive and Affective Neurophysiology Summer School: Acquisition, processing, and analysis of EEG signal. This summer school is focused on the application of Electroencephalography (EEG) and Event Related Potential (ERP) techniques to the study of cognitive and affective processes. The course will be fully taught in English and is aimed at an introductory level, so no previous experience with EEG or ERP is required. This event will take place from 7-12 of September 2015 in the lovely city of Porto. In last year’s edition the course was fully booked and, as such, we recommend early registration (course places are attributed by order of registration). For additional details and instructions on how to register, please consult our website (http://www.fpce.up.pt/labpsi/summerschool/). Please feel free to pass this information along to students or researchers that may be potentially interested. Thanks you and best wishes, -- Fernando Ferreira-Santos, PhD Lecturer Laboratory of Neuropsychophysiology Faculty of Psychology and Education Sciences University of Porto Rua Alfredo Allen, 4200-135 Porto (Portugal) Tel.: +351 226079700 (ext. 409) E-mail: frsantos at fpce.up.pt http://www.fpce.up.pt/labpsi/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From joscha.schmiedt at esi-frankfurt.de Wed Apr 1 14:03:27 2015 From: joscha.schmiedt at esi-frankfurt.de (Schmiedt, Joscha) Date: Wed, 1 Apr 2015 12:03:27 +0000 Subject: [FieldTrip] A Fieldtrip data format? In-Reply-To: References: <5548CAB3-F9A2-4C6B-B958-3CF27CF2C27F@esi-frankfurt.de> Message-ID: Hi Gio, Thanks for the info. The fcdc_matbin approach indeed would be suitable data for raw data. However, I’m looking for a fast solution for data that is already processed and cut into trials, in particular with varying trial length. Joscha > On Mar 31, 2015, at 22:39, Gio Piantoni wrote: > > Hi Joscha, > > FieldTrip already has its own simple uncompressed file format. > fcdc_matbin "It is not an official file format, but was invented here > at the FCDC. It consists of two files: a *.mat matlab file that > contains the header (and optionally the events) and a *.bin binary > file that contains the data." > http://www.fieldtriptoolbox.org/faq/reading_is_slow_can_i_write_my_raw_data_to_a_more_efficient_file_format > > If you want to look at the code: > https://github.com/fieldtrip/fieldtrip/blob/master/fileio/ft_write_data.m#L275 > > You should be able to read it as usual with ft_preprocessing. You can > convert your files to the fcdc_matbin using ft_preprocessing as well: > https://github.com/fieldtrip/fieldtrip/blob/master/ft_preprocessing.m#L581 > Be careful about not losing precision though. > > The only catch is that, as far as I know, you cannot export your > preprocessed data through ft_preprocessing at the moment, because > ft_write_data is now inside this if-part: > https://github.com/fieldtrip/fieldtrip/blob/master/ft_preprocessing.m#L252 > but it's only a matter of adapting that to your needs. > > Would this work for you? > > -g > > On Tue, Mar 31, 2015 at 9:09 AM, Schmiedt, Joscha > wrote: >> Hi, >> >> When working with Fieldtrip it is very convenient to store the data and >> analyses using MATLAB’s save and load functions. However, for large and/or >> complex data with many channels (>2GB) MATLAB enforces compression, which is >> pretty useless for electrophysiology data and slows down the load and save >> performance by a factor of up to 8 (see e.g. >> http://undocumentedmatlab.com/blog/improving-save-performance). The MATLAB >> file format is based on HDF5, which is generally an open and future-proof >> data format, but unfortunately MATLAB doesn’t allow you to disable the >> compression. >> >> An option to overcome this could be to develop a simple data format for >> Fieldtrip data that is also based on HDF5. Is or has there been any >> development going into that direction? Would there be any interest? Of >> course, creating yet another data format is almost never a good idea >> (https://xkcd.com/927/), but since HDF5 is well-documented and readable with >> almost any software, it might be worth thinking about it. >> >> I’d be happy to hear your thoughts. >> >> Joscha >> >> --------------------------------- >> Joscha Schmiedt >> PhD Student >> >> Ernst Strüngmann Institute (ESI) for Neuroscience >> in Cooperation with Max Planck Society >> Deutschordenstraße 46 >> 60528 Frankfurt am Main >> Germany >> >> Tel.: +49 (0)69 96769 241 >> >> Sitz der Gesellschaft: Frankfurt am Main >> Registergericht: Amtsgericht Frankfurt - HRB 84266 >> Geschäftsführer: Prof. Dr. Pascal Fries >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From orionblue8 at gmail.com Wed Apr 1 19:41:36 2015 From: orionblue8 at gmail.com (Orion) Date: Wed, 1 Apr 2015 12:41:36 -0500 Subject: [FieldTrip] how gamma power is calculated Message-ID: Does anyone in the Fieldtrip community calculate the "running gamma power"? This is what I call the parameter after doing a power analysis on each trial, and then to simplify the data by one dimension, averaging the bins within the 35-45 Hz or 30-94 Hz band. Coincidentally a plot of the running gamma power resembles a plot of the EEG first derivative (absolute value of). Can anyone explain why? Orion -------------- next part -------------- An HTML attachment was scrubbed... URL: From federica.ma at gmail.com Wed Apr 1 19:43:30 2015 From: federica.ma at gmail.com (Federica Mauro) Date: Wed, 1 Apr 2015 19:43:30 +0200 Subject: [FieldTrip] Spectral coherence Message-ID: Hi, I was starting to perform the tutorial on spectral coherence (the one is here: http://www.fieldtriptoolbox.org/tutorial/coherence?s[]=spectral&s[]=coherence), but, as I start with the first step I receive an error for the ft_freqanalysis function. The error is: freq = ft_freqanalysis(cfg, data); *??? Undefined function or variable 'abort'.* *Error in ==> ft_freqanalysis at 198* *if abort* what can I do? Thanks in advance! Federica -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.rotonda at gmail.com Thu Apr 2 02:33:52 2015 From: marco.rotonda at gmail.com (Marco Rotonda) Date: Thu, 2 Apr 2015 02:33:52 +0200 Subject: [FieldTrip] how gamma power is calculated In-Reply-To: References: Message-ID: Hi Orion, maybe you can have a look at: http://www.fieldtriptoolbox.org/example/ft_realtime_hilbert I did that code some years ago, so it's a bit outdated, but I think you can have an idea of what you're looking for. Marco On 1 April 2015 at 19:41, Orion wrote: > Does anyone in the Fieldtrip community calculate the "running gamma > power"? This is what I call the parameter after doing a power analysis on > each trial, and then to simplify the data by one dimension, averaging the > bins within the 35-45 Hz or 30-94 Hz band. > > Coincidentally a plot of the running gamma power resembles a plot of the > EEG first derivative (absolute value of). Can anyone explain why? > > Orion > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.sandeep29 at gmail.com Thu Apr 2 08:10:06 2015 From: b.sandeep29 at gmail.com (sandeep b) Date: Thu, 2 Apr 2015 11:40:06 +0530 Subject: [FieldTrip] Unable to download fieldtrip toolbox from the download link Message-ID: Dear Administrator, I am unable to download fieldtrip toolbox from the given link ( http://www.fieldtriptoolbox.org/download). Is there any other other way to get the toolbox. Kindly please suggest me to get the toolbox Thank you Sandeep -------------- next part -------------- An HTML attachment was scrubbed... URL: From dorothee-brigitte.hoppe at student.uni-tuebingen.de Thu Apr 2 15:44:05 2015 From: dorothee-brigitte.hoppe at student.uni-tuebingen.de (Dorothee Hoppe) Date: Thu, 02 Apr 2015 15:44:05 +0200 Subject: [FieldTrip] ICA on each trial or collapsing over all trials Message-ID: <20150402154405.14144i9yubvrxw2t@webmail.uni-tuebingen.de> Dear Discussion Group members, we want to use ICA for artifact correction, and now got stuck at the point of deciding whether to compute the ICs on the trial level or on the whole dataset for a subject. Using the whole dataset, the advantage is probably a higher power of the ICA because of the larger data input, so for example a blink component gets probably more distinctive. On the other hand, we observed, that artifacts that occur only in a small set of trials, like strong muscle artifacts cannot be detected that way, or even lead to a distortion of the components for that special trial. Would you recommend an ICA on each trial or collapsing over all trials (both options within each subject)? Are there other arguments to favor or reject these options? Best regards, Dorothée From mahjoory86 at gmail.com Thu Apr 2 15:51:23 2015 From: mahjoory86 at gmail.com (Keyvan Mahjoory) Date: Thu, 2 Apr 2015 15:51:23 +0200 Subject: [FieldTrip] Fwd: Power Maps on Surface In-Reply-To: References: Message-ID: Dear Fieldtrip Users, I used the surface file "cortex_5124.surf.gii" to restrict sources on cortex. I wonder how I can plot powermaps on surface? cfg.surffile=ft_read_headshape('cortex_5124.surf.gii'); even I save it's output in a new .mat file: "sourcemodel.mat" and tried cgf.surffile = 'sourcemodel.mat'; in either case the function "ft_sourceplot" gives error. cfg = []; cfg.method = 'surface'; cfg.funparameter = 'avg.pow'; cfg.funcolormap = 'jet'; cfg.surffile='sourcemodel.mat'; ft_sourceplot(cfg, src) In my code I have defined surface vertices and triangles, as well as power per vertex, I wonder What is wrong in my code? Many Thanks in advance, Best, Keyvan -------------- next part -------------- An HTML attachment was scrubbed... URL: From ayobimpe2004 at gmail.com Thu Apr 2 17:36:57 2015 From: ayobimpe2004 at gmail.com (Azeez Adebimpe) Date: Thu, 2 Apr 2015 17:36:57 +0200 Subject: [FieldTrip] Fwd: Power Maps on Surface In-Reply-To: References: Message-ID: Hello, Your code is right I also encouter the same problem but you can project on the surface with ft_plot_mesh ft_plot_mesh(bnd, 'vertexcolor', m); bnd is the your source modle and m is avg.pow value Azeez On Thu, Apr 2, 2015 at 3:51 PM, Keyvan Mahjoory wrote: > Dear Fieldtrip Users, > > > I used the surface file "cortex_5124.surf.gii" to restrict sources on > cortex. I wonder how I can plot powermaps on surface? > > cfg.surffile=ft_read_headshape('cortex_5124.surf.gii'); > > even I save it's output in a new .mat file: "sourcemodel.mat" and tried > cgf.surffile = 'sourcemodel.mat'; > > in either case the function "ft_sourceplot" gives error. > > cfg = []; > cfg.method = 'surface'; > cfg.funparameter = 'avg.pow'; > cfg.funcolormap = 'jet'; > cfg.surffile='sourcemodel.mat'; > ft_sourceplot(cfg, src) > > In my code I have defined surface vertices and triangles, as well as power > per vertex, I wonder What is wrong in my code? > > Many Thanks in advance, > Best, > Keyvan > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jorn at artinis.com Fri Apr 3 09:23:24 2015 From: jorn at artinis.com (=?utf-8?Q?J=C3=B6rn_M._Horschig?=) Date: Fri, 3 Apr 2015 09:23:24 +0200 Subject: [FieldTrip] Fwd: Power Maps on Surface In-Reply-To: References: Message-ID: <001b01d06ddf$12a60870$37f21950$@artinis.com> Hey. You should specify cfg.surffile really as the path to the file, and not read in the content apriori. This section here might help (the ‘exercise’ part of the tutorial lists a cfg-example for surface plotting). http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_sources_of_oscillatory_gamma-band_activity Best, Jörn -- Jörn M. Horschig, Software Engineer Artinis Medical Systems | +31 481 350 980 From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Azeez Adebimpe Sent: Thursday, April 2, 2015 5:37 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] Fwd: Power Maps on Surface Hello, Your code is right I also encouter the same problem but you can project on the surface with ft_plot_mesh ft_plot_mesh(bnd, 'vertexcolor', m); bnd is the your source modle and m is avg.pow value Azeez On Thu, Apr 2, 2015 at 3:51 PM, Keyvan Mahjoory > wrote: Dear Fieldtrip Users, I used the surface file "cortex_5124.surf.gii" to restrict sources on cortex. I wonder how I can plot powermaps on surface? cfg.surffile=ft_read_headshape('cortex_5124.surf.gii'); even I save it's output in a new .mat file: "sourcemodel.mat" and tried cgf.surffile = 'sourcemodel.mat'; in either case the function "ft_sourceplot" gives error. cfg = []; cfg.method = 'surface'; cfg.funparameter = 'avg.pow'; cfg.funcolormap = 'jet'; cfg.surffile='sourcemodel.mat'; ft_sourceplot(cfg, src) In my code I have defined surface vertices and triangles, as well as power per vertex, I wonder What is wrong in my code? Many Thanks in advance, Best, Keyvan _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From abarnyeu at hotmail.com Sun Apr 5 05:03:02 2015 From: abarnyeu at hotmail.com (Charles West) Date: Sat, 4 Apr 2015 20:03:02 -0700 Subject: [FieldTrip] cfg structure for plotting topographical maps Message-ID: Hi everyone, I am new to FieldTrip and am confused about the cfg structure that is required for running Field Trip functions. I would like to plot the topographical maps of a frequency range (e.g. 5 to 10 Hz) using Field Trip. I used the besa2fieldtrip function to create data. I receive the following error message when running ft_topoplotER. Please let me know why the following error appears. Many thanks! Charles West >>cfg.layout = 'layout.lay'; >>cfg.parameter = 'avg' >>ft_topoplotER(cfg, data); reading layout from file layout.lay the call to "ft_prepare_layout" took 0 seconds Attempt to reference field of non-structure array. Error in ft_datatype_sens (line 136) nchan = length(sens.label); Error in ft_datatype_timelock (line 99) timelock.elec = ft_datatype_sens(timelock.elec); Error in ft_checkdata (line 227) data = ft_datatype_timelock(data); Error in topoplot_common (line 74) data = ft_checkdata(data, 'datatype', {'comp', 'timelock', 'freq'}); Error in ft_topoplotER (line 192) cfg = topoplot_common(cfg, varargin{:}); -------------- next part -------------- An HTML attachment was scrubbed... URL: From rikkert.hindriks at upf.edu Wed Apr 8 09:32:37 2015 From: rikkert.hindriks at upf.edu (HINDRIKS, RIKKERT) Date: Wed, 8 Apr 2015 09:32:37 +0200 Subject: [FieldTrip] Unit of simulated EEG using openMEEG Message-ID: Dear all, Could anyone tell me what are the units of the entries in BEM leadfield matrices generated using openMEEG? For example, if I multiply the matrix with a vector of dipole moments in Am, do I get microVolts? (after taking the average reference) Thanks a lot, Rikkert -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at telecom-paristech.fr Wed Apr 8 10:08:02 2015 From: alexandre.gramfort at telecom-paristech.fr (Alexandre Gramfort) Date: Wed, 8 Apr 2015 10:08:02 +0200 Subject: [FieldTrip] Unit of simulated EEG using openMEEG In-Reply-To: References: Message-ID: hi, if your meshes are in meters then moments in Am produce volts. hope this helps Alex On Wed, Apr 8, 2015 at 9:32 AM, HINDRIKS, RIKKERT wrote: > > Dear all, > > Could anyone tell me what are the units of the entries in BEM leadfield > matrices generated using openMEEG? > > For example, if I multiply the matrix with a vector of dipole moments in Am, > do I get microVolts? (after taking the > average reference) > > Thanks a lot, > Rikkert > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From munsif.jatoi at gmail.com Wed Apr 8 10:08:28 2015 From: munsif.jatoi at gmail.com (Munsif Jatoi) Date: Wed, 8 Apr 2015 16:08:28 +0800 Subject: [FieldTrip] Unit of simulated EEG using openMEEG In-Reply-To: References: Message-ID: Dear Hindriks, The leadfield matrix has got orientation and moments of dipoles. When it is multiplied by dipole numbers say 1 or 2 at certain location, it will be generating the voltage matrix. Put it in a more simple way, V= KJ +e where, V= potential (volts), K= leadfield and J= current density (A/m2). So the generated data has units of microvolts or the units of voltage. I hope you got the point. Thanks, Munsif. On Wed, Apr 8, 2015 at 3:32 PM, HINDRIKS, RIKKERT wrote: > > Dear all, > > Could anyone tell me what are the units of the entries in BEM leadfield > matrices generated using openMEEG? > > For example, if I multiply the matrix with a vector of dipole moments in > Am, do I get microVolts? (after taking the > average reference) > > Thanks a lot, > Rikkert > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Munsif Ali H.Jatoi, Ph D Scholar, Centre for Intelligent Signals and Imaging Research, Universiti Teknologi PETRONAS, Malaysia. http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at telecom-paristech.fr Wed Apr 8 10:21:24 2015 From: alexandre.gramfort at telecom-paristech.fr (Alexandre Gramfort) Date: Wed, 8 Apr 2015 10:21:24 +0200 Subject: [FieldTrip] Unit of simulated EEG using openMEEG In-Reply-To: References: Message-ID: hi, OpenMEEG as used by default in Fieldtrip uses dipoles moments (not current density) so it's expressed in Am. Current density is also possible but not the default method exposed. Alex On Wed, Apr 8, 2015 at 10:08 AM, Munsif Jatoi wrote: > Dear Hindriks, > > The leadfield matrix has got orientation and moments of dipoles. When it is > multiplied by dipole numbers say 1 or 2 at certain location, it will be > generating the voltage matrix. Put it in a more simple way, V= KJ +e where, > V= potential (volts), K= leadfield and J= current density (A/m2). So the > generated data has units of microvolts or the units of voltage. I hope you > got the point. > > > Thanks, > > Munsif. > > > On Wed, Apr 8, 2015 at 3:32 PM, HINDRIKS, RIKKERT > wrote: >> >> >> Dear all, >> >> Could anyone tell me what are the units of the entries in BEM leadfield >> matrices generated using openMEEG? >> >> For example, if I multiply the matrix with a vector of dipole moments in >> Am, do I get microVolts? (after taking the >> average reference) >> >> Thanks a lot, >> Rikkert >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Munsif Ali H.Jatoi, > > Ph D Scholar, > Centre for Intelligent Signals and Imaging Research, > Universiti Teknologi PETRONAS, > Malaysia. > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > From rikkert.hindriks at upf.edu Wed Apr 8 11:20:46 2015 From: rikkert.hindriks at upf.edu (HINDRIKS, RIKKERT) Date: Wed, 8 Apr 2015 11:20:46 +0200 Subject: [FieldTrip] Unit of simulated EEG using openMEEG In-Reply-To: References: Message-ID: Hi Alex, I see, thanks. I have specified the meshes in mm's so a unit dipole moment is expressed in Amm right? Thus a homogeneous dipole field with moment x Amm leads to scalp potentials of 10^(-2)*L*x (where L is the computed leadfield matrix). The thing is that if I place a single dipole with moment Q = 10 nAm = 10^(-6) Amm (which is about the required value to pick up a measurable MEG signal), this gives scalp voltages LQ in the order of picoV (at most something of the order 10^(-11) for appropriately placed dipoles) while you would expect it to be in the order of microV no? Could it be that in the specification of the headmodel, I should use S/mm instead of S/m for the conductivities? (I use the "standard" values of 0.33 S/m , 0.0041 S/m, and 0.33 S/m for brain, skull, and scalp, resp.) Kind regards and thanks, Rikkert On Wed, Apr 8, 2015 at 10:08 AM, Alexandre Gramfort < alexandre.gramfort at telecom-paristech.fr> wrote: > hi, > > if your meshes are in meters then moments in Am produce volts. > > hope this helps > Alex > > On Wed, Apr 8, 2015 at 9:32 AM, HINDRIKS, RIKKERT > wrote: > > > > Dear all, > > > > Could anyone tell me what are the units of the entries in BEM leadfield > > matrices generated using openMEEG? > > > > For example, if I multiply the matrix with a vector of dipole moments in > Am, > > do I get microVolts? (after taking the > > average reference) > > > > Thanks a lot, > > Rikkert > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at telecom-paristech.fr Wed Apr 8 11:29:48 2015 From: alexandre.gramfort at telecom-paristech.fr (Alexandre Gramfort) Date: Wed, 8 Apr 2015 11:29:48 +0200 Subject: [FieldTrip] Unit of simulated EEG using openMEEG In-Reply-To: References: Message-ID: hi Rikkert, the unit of conductivities have no impact as it's only their ratio that is used in computation. For the rest run simple simulations to get more intuition. HTH Alex On Wed, Apr 8, 2015 at 11:20 AM, HINDRIKS, RIKKERT wrote: > Hi Alex, > > I see, thanks. I have specified the meshes in mm's so a unit dipole moment > is expressed in Amm right? > Thus a homogeneous dipole field with moment x Amm leads to scalp potentials > of 10^(-2)*L*x (where L > is the computed leadfield matrix). > > The thing is that if I place a single dipole with moment Q = 10 nAm = > 10^(-6) Amm (which is about the > required value to pick up a measurable MEG signal), this gives scalp > voltages LQ in the order of picoV > (at most something of the order 10^(-11) for appropriately placed dipoles) > while you would expect it to > be in the order of microV no? > > Could it be that in the specification of the headmodel, I should use S/mm > instead of S/m for the conductivities? > (I use the "standard" values of 0.33 S/m , 0.0041 S/m, and 0.33 S/m for > brain, skull, and scalp, resp.) > > > Kind regards and thanks, > Rikkert > > > On Wed, Apr 8, 2015 at 10:08 AM, Alexandre Gramfort > wrote: >> >> hi, >> >> if your meshes are in meters then moments in Am produce volts. >> >> hope this helps >> Alex >> >> On Wed, Apr 8, 2015 at 9:32 AM, HINDRIKS, RIKKERT >> wrote: >> > >> > Dear all, >> > >> > Could anyone tell me what are the units of the entries in BEM leadfield >> > matrices generated using openMEEG? >> > >> > For example, if I multiply the matrix with a vector of dipole moments in >> > Am, >> > do I get microVolts? (after taking the >> > average reference) >> > >> > Thanks a lot, >> > Rikkert >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From rikkert.hindriks at upf.edu Wed Apr 8 12:32:41 2015 From: rikkert.hindriks at upf.edu (HINDRIKS, RIKKERT) Date: Wed, 8 Apr 2015 12:32:41 +0200 Subject: [FieldTrip] Unit of simulated EEG using openMEEG In-Reply-To: References: Message-ID: Hi Alex, Ok, clear, thanks. But in any case, when using a typical dipole moment of 10 nAm, you would like to end up with voltages in the experimental range, that is, in the order of microVolts (after taking the average reference) I would appreciate it very much if someone could elucidate this for me. Kind regards, Rikkert On Wed, Apr 8, 2015 at 11:29 AM, Alexandre Gramfort < alexandre.gramfort at telecom-paristech.fr> wrote: > hi Rikkert, > > the unit of conductivities have no impact as it's only their ratio > that is used in computation. > > For the rest run simple simulations to get more intuition. > > HTH > Alex > > > On Wed, Apr 8, 2015 at 11:20 AM, HINDRIKS, RIKKERT > wrote: > > Hi Alex, > > > > I see, thanks. I have specified the meshes in mm's so a unit dipole > moment > > is expressed in Amm right? > > Thus a homogeneous dipole field with moment x Amm leads to scalp > potentials > > of 10^(-2)*L*x (where L > > is the computed leadfield matrix). > > > > The thing is that if I place a single dipole with moment Q = 10 nAm = > > 10^(-6) Amm (which is about the > > required value to pick up a measurable MEG signal), this gives scalp > > voltages LQ in the order of picoV > > (at most something of the order 10^(-11) for appropriately placed > dipoles) > > while you would expect it to > > be in the order of microV no? > > > > Could it be that in the specification of the headmodel, I should use S/mm > > instead of S/m for the conductivities? > > (I use the "standard" values of 0.33 S/m , 0.0041 S/m, and 0.33 S/m for > > brain, skull, and scalp, resp.) > > > > > > Kind regards and thanks, > > Rikkert > > > > > > On Wed, Apr 8, 2015 at 10:08 AM, Alexandre Gramfort > > wrote: > >> > >> hi, > >> > >> if your meshes are in meters then moments in Am produce volts. > >> > >> hope this helps > >> Alex > >> > >> On Wed, Apr 8, 2015 at 9:32 AM, HINDRIKS, RIKKERT > >> wrote: > >> > > >> > Dear all, > >> > > >> > Could anyone tell me what are the units of the entries in BEM > leadfield > >> > matrices generated using openMEEG? > >> > > >> > For example, if I multiply the matrix with a vector of dipole moments > in > >> > Am, > >> > do I get microVolts? (after taking the > >> > average reference) > >> > > >> > Thanks a lot, > >> > Rikkert > >> > > >> > _______________________________________________ > >> > fieldtrip mailing list > >> > fieldtrip at donders.ru.nl > >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at telecom-paristech.fr Wed Apr 8 16:32:57 2015 From: alexandre.gramfort at telecom-paristech.fr (Alexandre Gramfort) Date: Wed, 8 Apr 2015 16:32:57 +0200 Subject: [FieldTrip] Unit of simulated EEG using openMEEG In-Reply-To: References: Message-ID: hi, > But in any case, when using a typical dipole moment of 10 nAm, you would > like to end up with voltages in the experimental range, that is, in the > order > of microVolts (after taking the average reference) yes this should be the case if you use meshes in meters. A From Alexander.Hunold at tu-ilmenau.de Wed Apr 8 17:05:27 2015 From: Alexander.Hunold at tu-ilmenau.de (Hunold Alexander TU Ilmenau) Date: Wed, 8 Apr 2015 15:05:27 +0000 Subject: [FieldTrip] =?windows-1252?q?7th_International_Summer_School_in_B?= =?windows-1252?q?iomedical_Engineering_=84New_Instrumentation_for_brain_m?= =?windows-1252?q?easurements_and_stimulation=93=2C_17th_-_29th_August_201?= =?windows-1252?q?5_in_Lutherstadt_Wittenberg=2C_Germany?= Message-ID: <5B8562898ECA5A4594C9879007B90670395D7F5C@MB1.x.chg> Dear colleagues, we are pleased to announce the 7th International Summer School in Biomedical Engineering on "New Instrumentation for brain measurements and stimulation" August, 17-29, 2015 in Lutherstadt Wittenberg, Germany. This event stands in the tradition of a series of successful summer schools on hot themes in biomedical engineering, dedicated to intense learning in the fruitful atmosphere of tight interaction between students and world-leading specialists. This year’s summer school is devoted to new hardware technologies for measuring and stimulating the brain, such as dry electroencephalography (EEG) electrodes, optically pumped magnetic field sensors, neuronal current imaging based on low-field magnetic resonance and multichannel transcranial current stimulation. In particular, the 7th International Summer School on Biomedical Engineering will focus on ways how these new technical advances may help to overcome current limitations in human neurosciences and medicine. It will cover both theoretical foundations and practical applications. We aim at a thorough understanding of the underlying mechanisms. Thus, we will develop a critical view on current applications and possible future developments. The second important aim of the summer school consists in providing contact with both leading experts in the field and other students with similar interests, thereby facilitating the exchange of ideas on latest developments in the field. Target Group: - PhD students - Advanced Master students - Researchers entering the field of brain measurement and stimulation techniques Further Information about the 7th International Summer School in Biomedical Engineering: www.iss2015.org We would be happy to receive your application. Please pass this announcement to your colleagues who might be interested. Sincerely, Jens Haueisen and Thomas Knösche -------------- next part -------------- An HTML attachment was scrubbed... URL: From vanwijk.bernadette at gmail.com Wed Apr 8 17:07:42 2015 From: vanwijk.bernadette at gmail.com (Bernadette van Wijk) Date: Wed, 8 Apr 2015 16:07:42 +0100 Subject: [FieldTrip] SPM course for MEG/EEG in London: May 11-13 Message-ID: Dear all, We are pleased to announce that our annual *SPM course for MEG/EEG* will take place this year from *Monday May 11* to *Wednesday May 13 2015*. Hosted by University College London, the course will be held at Queen Square, a very central location in London (UK). The course will present instruction on the analysis of MEG and EEG data. The first two days will combine theoretical presentations with practical demonstrations of the different data analysis methods implemented in SPM. On the last day participants will have the opportunity to work on SPM tutorial data sets under the supervision of the course faculty. We also invite students to bring their own data for analysis. The course is suitable for both beginners and more advanced users. The topics that will be covered range from pre-processing and statistical analysis to source localization and dynamic causal modelling. The program is listed below. Registration is now open. We offer a reduced rate when attending both the MEG/EEG course and the fMRI course during the second half of the week. For full details of both courses see 'Statistical Parametric Mapping short courses' at http://www.ucl.ac.uk/ion/courses-viewer where you can also register. Available places are limited so please register as early as possible if you would like to attend! *Monday May 11th* 9.00 - 9.30 Registration 9.30 - 9.45 SPM introduction and resources *Guillaume Flandin* 9.45 - 10.30 What are we measuring with M/EEG? *Stefan Kiebel* 10.30 - 11.15 Data pre-processing *Holly Rossiter* *Coffee* 11.45 - 12.30 Data pre-processing - demo *Deborah Talmi, Megumi Fukuda* 12.30 - 13.15 General linear model and classical inference *Christophe Phillips* *Lunch* 14.15 - 15.00 Multiple comparisons problem and solutions *Gareth Barnes* 15.00 - 15.45 Bayesian inference *Chris Mathys* *Coffee* 16.15 - 18.00 Tutorial on group M/EEG dataset analysis *Vladimir Litvak, Jason Taylor* *Tuesday May 12th* 9.30 - 10.15 M/EEG source analysis *Saskia Helbling* 10.15 - 11.15 M/EEG source analysis - demo *Jose Lopez, Jason Taylor, Sofie Meyer* *Coffee* 11.45 - 12.30 The principles of DCM *Ryszard Auksztulewicz* 12.30 - 13.15 DCM for evoked responses *Harriet Brown* *Lunch* 14.15 - 15.00 DCM for steady state responses *Rosalyn Moran* 15.00 - 15.45 DCM for time-frequency responses *Bernadette van Wijk* 15.45 - 16.30 DCM - demo *Andre Marreiros, Martin Dietz * *Coffee* 17.00 - 17.45 Bayesian model selection and averaging *Will Penny* 17.45 - 18.45 Clinic - Questions & Answers session *Karl Friston* 19.00 onwards - Social Event *Wednesday May 13th* 9.30 – 17.00 Practical hands-on session in UCL computer class rooms. Participants can either work on SPM tutorial datasets or on their own data with the help of the faculty. There will also be an opportunity to ask questions in small tutorial groups for further discussions on the topics of the lectures. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Apr 9 09:04:11 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 9 Apr 2015 09:04:11 +0200 Subject: [FieldTrip] Call for applications for 15 early stage researchers Message-ID: Dear all Positions for 15 early stage researchers (doctoral students) are offered in a project aiming to develop and apply new brain research methods to study normal and atypical cognitive development of children. Applicants from all relevant academic disciplines are encouraged to apply, including cognitive neuroscience, computer science, educational sciences, engineering, medicine, mathematics, psychology, physics, statistics, and related disciplines. The selected doctoral students will enroll in the graduate school of the host institution and work towards their PhD. The multidisciplinary ChildBrain (Advancing brain research in children’s developmental neurocognitive disorders) project is funded by the Horizon 2020 Marie Skłodowska-Curie action of the European Union. It is part of the Innovative Training Network (ITN) actions. The positions are open at five top ranked academic institutions and three innovative companies in PhD projects under three broader themes of neurocognitive disorders, brain development and brain research methods (see project descriptions at www.childbrain.eu). The academic and private sector partners will offer the students project-specific research, scientific collaboration, secondments, workshops and courses on scientific and entrepreneurial skills, as well as excellent supervision. Salaries are competitive (please see details under specific ESR projects). Successful applicants should have a degree that allows a direct entry into doctoral studies and less than 4 years of experience in research; and not have lived more than 12 months during the last 3 years in the country where doctoral studies are started; this is due to emphasis on mobility in the ITN projects. Women and men from all countries are encouraged to apply. Please see details on the projects and how to apply at www.childbrain.eu. Deadline for the first round of applications is April 30th 2015 (June 30th 2015 for ESR projects 2, 5, 9 and 11). best regards, Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ChildBrain_call_for_applications.pdf Type: application/pdf Size: 204906 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Apr 9 13:50:31 2015 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 9 Apr 2015 13:50:31 +0200 Subject: [FieldTrip] Be careful with nonlinear warping of your individual grids to MNI Message-ID: Dear FieldTrip community, I have encountered a little problem inverse-MNI-warping the grids of my individual subjects for the purpose of averaging my beamformer results, in line with: http://www.fieldtriptoolbox.org/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space?s[]=grid When I visually checked the resultant individual grids, I found that 6 out of 25 subjects had severely distorted grids. See attached examples. A bit of distortion could be expected, but IMHO this is too much. It is the result of nonlinear warping (done in the example script mentioned above) and solved by using cfg.grid.nonlinear = 'no, in the following part of the script: cfg = []; cfg.grid.warpmni = 'yes'; cfg.grid.template = template_scm; cfg.grid.nonlinear = 'no'; cfg.mri = mri_segmented; grid = ft_prepare_sourcemodel(cfg); Ofcourse this is not a Fieldtrip bug in any way, but just something to be aware of, and a warning I wanted to share. And it really shows that it is important to check all of the warped individual grids! I will redo only these subjects with linear instead of nonlinear warping. That is, unless anyone has a better solution? All the best, Stephen Whitmarsh -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... 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Name: pp_20_headmodel_grid_a.png Type: image/png Size: 151143 bytes Desc: not available URL: From thismoment at 163.com Sun Apr 12 17:32:05 2015 From: thismoment at 163.com (thismoment) Date: Sun, 12 Apr 2015 23:32:05 +0800 Subject: [FieldTrip] error when I convert .mri data into mgz or other format Message-ID: <552A8FF2.2000705@163.com> Hi Experts, I got a set of MEG. The anatomical MRI was stored in .mri format (CTF device) and MEG was stored in a folder named by xxx.ds. I do not know how to do segmentation of .mri into scalp,skull and cortex. So I try to convert .mri into .mgz or other format so that it can be used in freesurfer for reconstruction. I used the following command. x=ft_read_mri('MEG619.mri','dataformat','ctf_mri4'); y=ft_write_mri('ddd',x,'dataformat','mgz', 'transform',x.transform) the error was >> y=ft_write_mri('ddd',x,'dataformat','mgz', 'transform',x.transform) Error using fwrite Cannot write value: unsupported class struct Error in save_mgh (line 107) fwrite(fid,vol,'float32'); Error in ft_write_mri (line 79) save_mgh(dat, filename, transform); I failed to do it. 1. Anyone know what happens ? 2. Freesurfer can use .mri directly to reconstruct ? 3. Are there other methods to convert .mri into .mgz or .dicom format? Best wishes, J. Zhang 2015-04-12 thismoment -------------- next part -------------- An HTML attachment was scrubbed... URL: From wanyu at gazzaleylab.ucsf.edu Tue Apr 14 00:48:45 2015 From: wanyu at gazzaleylab.ucsf.edu (WanYu Hsu) Date: Mon, 13 Apr 2015 15:48:45 -0700 Subject: [FieldTrip] questions about topoplot and notch filter Message-ID: Hi community, Recently I am analyzing EEG dataset with only 20 channels and I am focusing on coherence between frontal and posterior electrodes in frequency domain. I got two questions here: 1. I wanted to topoplot the coherence between each pair of electrodes that we're interested in, and I tried the following script: cfg = []; cfg.colorparam = 'plvspctrm'; cfg.layout = 'biosemi64.lay'; cfg.foi =[4]; ft_topoplotCC(cfg, plv_avg_stim); The electrode layout and coherence we wanted to see were in the plot, but the plot did not show coherence related to FP1, FP2, and FPz. Am I doing something wrong? 2. I would like to apply notch filter to remove 6 Hz and first I tried cfg.dftfilter ='yes'; cfg.dftfreq = [6] but the 6Hz signal was still there. Then I also tried cfg.bsfilter ='yes'; cfg.bsfreq =[5 7]; This worked well to remove 6Hz signal, but it also affected 5Hz and 7Hz. Is there any way to remove 6 Hz specificlly? Any help would be appreciated. Best, Wanyu Hsu -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue Apr 14 09:47:31 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 14 Apr 2015 09:47:31 +0200 Subject: [FieldTrip] error when I convert .mri data into mgz or other format In-Reply-To: <552A8FF2.2000705@163.com> References: <552A8FF2.2000705@163.com> Message-ID: <31465C27-5C1C-4076-929C-358CC7BD7AE6@donders.ru.nl> Hi Zhang, You should specify the anatomical data as a 3D array, not as a structure. So rather than ft_write_mri('ddd',x,'dataformat','mgz', 'transform',x.transform) you should do ft_write_mri('ddd’,x.anatomy,'dataformat','mgz', 'transform',x.transform) Note also that you should not expect an output from ft_write_mri. best regards, Robert On 12 Apr 2015, at 17:32, thismoment wrote: > Hi Experts, > > I got a set of MEG. The anatomical MRI was stored in .mri format (CTF device) and MEG was stored in a folder named by xxx.ds. > I do not know how to do segmentation of .mri into scalp,skull and cortex. So I try to convert .mri into .mgz or other format so > that it can be used in freesurfer for reconstruction. > I used the following command. > > x=ft_read_mri('MEG619.mri','dataformat','ctf_mri4'); > y=ft_write_mri('ddd',x,'dataformat','mgz', 'transform',x.transform) > > the error was > > >> y=ft_write_mri('ddd',x,'dataformat','mgz', 'transform',x.transform) > Error using fwrite > Cannot write value: unsupported class struct > > Error in save_mgh (line 107) > fwrite(fid,vol,'float32'); > > Error in ft_write_mri (line 79) > save_mgh(dat, filename, transform); > > I failed to do it. > 1. Anyone know what happens ? > 2. Freesurfer can use .mri directly to reconstruct ? > 3. Are there other methods to convert .mri into .mgz or .dicom format? > > Best wishes, > J. Zhang > > > 2015-04-12 > thismoment > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue Apr 14 09:52:31 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 14 Apr 2015 09:52:31 +0200 Subject: [FieldTrip] questions about topoplot and notch filter In-Reply-To: References: Message-ID: <62310C2D-1246-4BF3-83C7-AD2F23FDF98E@donders.ru.nl> Dear WanYu Regarding your first question: I am not sure what you expected to see in the figure, and what you actually did see. Perhaps you should be using ft_connectivityplot instead. Note that the high-level plotting functions (the ones that take a cfg as first input) are only there to help you to get started with the figures, you can always plot the actual data yourself using low-level matlab functions and using the helper functions in the fieldtrip/plotting directory. Regarding the second question, perhaps these address your question http://www.fieldtriptoolbox.org/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter http://www.fieldtriptoolbox.org/tag/filter?do=showtag&tag=filter best regards, Robert On 14 Apr 2015, at 00:48, WanYu Hsu wrote: > Hi community, > Recently I am analyzing EEG dataset with only 20 channels and I am focusing on coherence between frontal and posterior electrodes in frequency domain. > > I got two questions here: > > 1. I wanted to topoplot the coherence between each pair of electrodes that we're interested in, and I tried the following script: > > cfg = []; > cfg.colorparam = 'plvspctrm'; > cfg.layout = 'biosemi64.lay'; > cfg.foi =[4]; > ft_topoplotCC(cfg, plv_avg_stim); > > The electrode layout and coherence we wanted to see were in the plot, but the plot did not show coherence related to FP1, FP2, and FPz. Am I doing something wrong? > > > > 2. I would like to apply notch filter to remove 6 Hz and first I tried > > cfg.dftfilter ='yes'; > cfg.dftfreq = [6] > but the 6Hz signal was still there. > Then I also tried > > cfg.bsfilter ='yes'; > cfg.bsfreq =[5 7]; > > This worked well to remove 6Hz signal, but it also affected 5Hz and 7Hz. > > Is there any way to remove 6 Hz specificlly? > > Any help would be appreciated. > > > > Best, > > Wanyu Hsu > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue Apr 14 09:55:29 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 14 Apr 2015 09:55:29 +0200 Subject: [FieldTrip] MEG postdoctoral position at Karolinska Institutet Message-ID: <1348BCC9-DB8E-4DEF-8178-B2CB53476D8E@donders.ru.nl> Postdoctoral studies in Magnetoencephalography (scholarship) Karolinska Institutet, The Department of Neuroscience, Ehrsson Research groups at the Department of Neuroscience study different aspects of the function of the normal nervous system, as well as disturbances, injuries and diseases affecting the nervous system. Projects include a broad range of studies at the molecular and cellular levels, the network level and at the level of the overall organization of the nervous system. The department also conducts undergraduate education in neuroscience, anatomy and histology in a number of programs at Karolinska Institutet. To read more about our department, please visit our webpage; www.ki.se/en/neuro/startpage Duties We are seeking a highly talented and enthusiastic researcher with a PhD in neuroimaging awarded within the past three years to work on projects in which magnetoencephalography (MEG) is applied to the problem of how we come to experience limbs as part of our own body. The research will be conducted at the Brain, Body and Self Laboratory at the Department of Neuroscience (www.ehrssonlab.se). This center has widespread expertise in fMRI and human behavioural experiments. The MEG experiments will be conducted at the recently established the “National Facility Magnetoencephalography (www.natmeg.se) that is equipped with a state-of-the-art MEG system (Electa Neuromag TRIUX), complementary physiological recording devices (MEG compatible 128–channel EEG, plethysmography, EMG, ECG, eyetracking), and sophisticated stimulus delivery platforms (visual, auditory, olfactory, pain, somatosensory; including a robot system for tactile stimulation of the hands). The ideal candidate will have expertise in the acquisition and analysis of MEG data, (preferably on an Elekta Triux or Vectorview system), expertise in analysis of MEG data (preferably on FieldTrip and/or MNE), as well as excellent programming skills (preferably including MatLab and Neurobs Presentation). Expertise in analysis of EEG data would be an advantage. The candidate is expected to work on projects in which MEG methods are applied to questions relating to how multisensory signals from the body are integrated at the levels of cortical structures to give rise to dynamic changes in the feeling of ownership of limbs. Good social skills are important as the candidate is expected to actively collaborate with other members of the laboratory, in addition to running his or her own project. Applicants should be able to demonstrate a consistently good academic record, including publications in international journals. Entry requirements Scholarships to pursue postdoctoral studies may be awarded to individuals who come from other countries with the intention of remaining in Sweden only while obtaining all or part of their education. The head of the department determines whether their previous training and scholarly qualifications correspond to a Swedish PhD or higher. Having received a salary or other remuneration from Karolinska Institutet during the past two years may be disqualifying. One requirement for receiving a scholarship for postdoctoral studies is central registration as a postdoc. Type of scholarship Karolinska Institutet awards scholarships to pursue postdoctoral studies. This educational scholarship, which is paid for a maximum of two years within four years after the receipt of a PhD or the equivalent, is tax-exempt. The amount is set for twelve months at a time and is paid out on a monthly basis. In exceptional cases, shorter periods may be acceptable. Application process An application must contain the following documents in English: Curriculum vitae and qualifications, presented in accordance with Karolinska Institutet’s qualifications portfolio (http://ki.se/meritportfolj ) A complete list of publications A summary of current research (no more than one page) Verifications for crediting of illness, military service, work for labour unions or student organisations, parental leave or similar circumstances Verification from the thesis defence committee or the equivalent (only if the thesis defence is scheduled within three months after the application deadline) Contact details for two reference persons The application is to be submitted through the MyNetwork recruitment system. Karolinska Institutet is one of the world´s leading medical universities. Its mission is to contribute to the improvement of human health through research and education. Karolinska Institutet accounts for over 40 per cent of the medical academic research conducted in Sweden and offers the country´s broadest range of education in medicine and health sciences. Since 1901 the Nobel Assembly at Karolinska Institutet has selected the Nobel laureates in Physiology or Medicine. Pursuant to the regulations of the Swedish National Archives, applications are kept on file for two years after the appointment has gained legal force. The regulations do not apply to attachments that have been printed or otherwise published. Karolinska Institutet strives to provide a workplace that has approximately the same number of women and men, is free of discrimination and offers equal opportunity to everyone. For temp agencies and recruiters, and to salespersons: We politely, yet firmly, decline direct contact with temp agencies and recruiters, as well as those selling additional job announcements. Type of employment: Postdoctoral studies. Working hours: Full time First day of employment: As soon as possible Reference number: 2-1291/2015 Contact: Henrik Ehrsson, professor, henrik.ehrsson at ki.se Union representative: Peter Århem, SACO, 46-8 524 869 03 Anne Edgren, OFR, 08-616 16 29 Gunnar Stenberg, SEKO, 08-524 880 75 Published: 27.Mar.2015 Last application date: 07.May.2015 Contact Henrik Ehrsson, professor, henrik.ehrsson at ki.se Link to ad: http://ki.mynetworkglobal.com/what:job/jobID:61655/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: cid:134.gif Type: image/gif Size: 8101 bytes Desc: not available URL: From f.roux at bcbl.eu Tue Apr 14 18:12:26 2015 From: f.roux at bcbl.eu (=?utf-8?B?RnLDqWTDqXJpYw==?= Roux) Date: Tue, 14 Apr 2015 18:12:26 +0200 (CEST) Subject: [FieldTrip] missing samples after donwsampling In-Reply-To: <1130111699.32607.1429027894577.JavaMail.root@bcbl.eu> Message-ID: <1165544691.32620.1429027946414.JavaMail.root@bcbl.eu> Dear all, i've noticed that after invoking ft_resampledata not all trials have the same number of samples. For instance: cfg = []; cfg.resamplefs = 400; [meg_data] = ft_resamplefs(cfg,meg_data); will return length(meg_data.trial{1}) = 2601 whereas length(meg_data.trial{2}) = 2600 This is causing a conflict upstream in my analysis pipeline and I wanted to ask if there was a way to fix this? I am using fieldtrip-20150115. Any thoughts or help would be highly appreciated. Best, Fred -- Frédéric Roux Postdoctoral Scientist BCBL. Basque Center on Cognition, Brain % Language. f.roux at bcbl.eu Tel: +34 943 309 300 Ext 211 Fax: +34 943 309 052 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer --------------------------------------------------------------------------- From pgoodin at swin.edu.au Wed Apr 15 02:06:33 2015 From: pgoodin at swin.edu.au (Peter Goodin) Date: Wed, 15 Apr 2015 00:06:33 +0000 Subject: [FieldTrip] Why the general use of parametric test as observed test statistic for permutation cluster tests? Message-ID: Hi Fieldtrip list, I'm just wondering if someone can explain if there is a reasoning behind the general use of a parametric test to calculate the initial step in the permutation cluster test and not a non-parametric test (e.g t-test over Mann Whitey U)? Is it just due to the assumption of a Gaussian distribution or is there something deeper going on? Thanks, Peter _______________________ Peter Goodin, BSc (Hons), Ph.D Candidate (submitted). Brain and Psychological Sciences Research Centre (BPsych) Swinburne University, Hawthorn, Vic, 3122 http://www.swinburne.edu.au/swinburneresearchers/index.php?fuseaction=profile&pid=4149 Monash Alfred Psychiatry Research Centre (MAPrc) Level 4, 607 St Kilda Road, Melbourne 3004 From tamaonvaliaikainenmaili at gmail.com Wed Apr 15 10:32:32 2015 From: tamaonvaliaikainenmaili at gmail.com (hm ham) Date: Wed, 15 Apr 2015 11:32:32 +0300 Subject: [FieldTrip] EEG MNE with standard_bem and statistics sanity Message-ID: Hello fellow fieldtrippers, I sent these questions a few weeks back, but I think they got buried in the weekend emails, so I'm asking the same things again. Sorry for the spam. I'm using fieldtrip to do a MNE for EEG data with no subject MRIs and I have a few questions to which I can't get a straight answer from tutorials or from mailing list history. I guess this is sort of a sanity check. First, I'm wondering about the correct sourcemodel, as loading the standard_bem and setting the third mesh as the source points in ft_prepare_leadfield gives an error: Warning: dipole lies on boundary of volume model. Code: % Electrodes, vol, sourcemodel all set in same scale with ft_convert_units vol = load('standard_bem'); cfg = []; cfg.elec = elec_aligned; % electrodes aligned to skin surface cfg.grid.pos = vol.bnd(3).pnt; % source points cfg.grid.inside = 1:size(vol.bnd(3).pnt,1); cfg.vol = vol; cfg.reducerank = 3; leadfield = ft_prepare_leadfield(cfg); Using the code below works: vol = load('standard_bem'); sourcemodel = ft_read_headshape('cortex_8196.surf.gii'); cfg = []; cfg.elec = elec_aligned; % electrodes aligned to skin surface cfg.grid.pos = sourcemodel; % source points cfg.grid.inside = 1:size(sourcemodel,1); cfg.vol = vol; cfg.reducerank = 3; leadfield = ft_prepare_leadfield(cfg); But as the http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg seems to suggest the third mesh in vol should be the brain? Or is the third compartment there just for conduction calculations? As using the sourcemodel 'cortex_8196.surf.gii' at least gave an output I went forward with those for now, to see what other problems I'd encounter. Running the MNE: cfg = []; cfg.elec = elec_aligned; cfg.method = 'mne'; cfg.grid = leadfield; cfg.vol = vol; cfg.mne.prewhiten = 'yes'; cfg.mne.lambda = 60; %Hmmm? cfg.mne.scalesourcecov = 'yes'; cfg.mne.normalize = 'yes'; cfg.channel = 'all'; cond_12_source{subject_id} = ft_sourceanalysis(cfg,cond_12{subject_id}); So secondly, I'm concerned with the lambda value, as different tutorials give very different advice ranging from 3 to 1e8. Running the MNE with 3 seems to give very unstable results when comparing the results between subjects or conditions. The data is somewhat contaminated with leftover eye-movement artefacts (removed with ICA). And that 3 is from the tutorial where the data is from MEG. So a bigger lambda is in order, but how big? Or just let the minimumnormestimate.m calculate it from the data? I have to point out that the eye-movements are somewhat spread around the trial durations and not present in the calculation window of the .cov field from ft_timelockanalysis. Should I maybe calculate the .cov field from the whole trial? Third, there has been talk of MNE statistics in the mailing list, and it seems that the ft_timelockstatistics will do the job if a neighbours structure is provided. I build the neighbours structure from the sourcemodel mesh like this: sourcemodel = ft_read_headshape('cortex_8196.surf.gii'); nsources = length(sourcemodel.pnt); neighbours=struct; for i=1:nsources neighbours(i).label = num2str(i); neighb_nodes = sourcemodel.tri((sourcemodel.tri(:,1)==i | sourcemodel.tri(:,2)==i | sourcemodel.tri(:,3)==i),:); neighb_nodes = unique(neighb_nodes)'; idx = (neighb_nodes ~= i); neighb_nodes = neighb_nodes(idx); for k=1:length(neighb_nodes) neighbours(i).neighblabel{k} = num2str(neighb_nodes(k)); end end This seemed to give reasonable neighbours and just going by distance gave some sources that were on the other side of a gyrus. Although now with the above method the distances between the sources are not uniform. I also had to tweak the data structures a little bit, labels and such. Then I ran the tests with: cfg=[]; cfg.parameter = 'avg.pow'; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT'; cfg.parameter = 'avg'; cfg.correctm = 'cluster'; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.numrandomization = 1000; cfg.tail = 1; cfg.correcttail ='alpha'; cfg.alpha = 0.05; cfg.latency = [0.4 0.5]; cfg.avgovertime = 'yes'; cfg.neighbours = neighbours; cfg.design = [1:15 1:15;ones(1,15), ones(1,15)*2]; cfg.uvar = 1; cfg.ivar = 2; cond1_stat = ft_timelockstatistics(cfg, cond_11_source{:}, cond_12_source{:}); Looking at the resulting clusters from ft_timelockstatistics there were clusters that when plotted showed disconnected sources. For example, plotted like this for the first cluster: paint = ones(8196,3); indx = find(cond1_stat.posclusterslabelmat == 1); paint(indx,2) = 0; ft_plot_mesh(sourcemodel,'vertexcolor',paint); Gave the output in the attachment, in that case the third source is atleast close, but still not a neighbour to the two next to it. Is there maybe something I'm missing with using the ft_timelockstatistics like this? I hope someone can clarify some of these issues. Thank you already in advance! Tatu -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: disconnected_cluster.png Type: image/png Size: 83016 bytes Desc: not available URL: From noahertz6 at gmail.com Wed Apr 15 14:21:46 2015 From: noahertz6 at gmail.com (Noa Hertz) Date: Wed, 15 Apr 2015 15:21:46 +0300 Subject: [FieldTrip] Beamforming analysis in frequency band Message-ID: Hi all, I'm doing source analysis in the frequency domain of a resting-state data. when doing the source analysis, I want to use several frequency bands of interest, such as beta (13-30 Hz) and gamma (30-48 Hz). My problem is about the cfg.frequency parameter, which must be a scalar (whereas i'm interested in a frequency band). Arbitrarily choosing a frequency in the middle of the range doesn't seem right. What is the common practice when doing source analysis using this function? Does the cfg.tapsmofrq parameter is supposed to enable choosing frequency band instead of a single peak frequency? Any suggestions will be very much helpful! Thanks, Noa *This is the script I’m using: cfg = []; cfg.method ='mtmfft'; cfg.output ='fourier'; cfg.keeptapers = 'yes'; cfg.foilim = [30 48]; cfg.tapsmofrq = 2; freqClosed=ft_freqanalysis(cfg,eyesClosed); * cfg = []; cfg.method='pcc'; cfg.frequency = 39; % must be a scalar cfg.lambda = 0; cfg.vol = vol; cfg.grid = grid; cfg.feedback = 'textbar'; cfg.keepfilter='yes'; source1 = ft_sourceanalysis(cfg, freqClosed); -- My signature: http://www.documentarywire.com/earthlings/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Wed Apr 15 16:25:59 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 15 Apr 2015 16:25:59 +0200 Subject: [FieldTrip] next week: live broadcast of MEG/EEG toolkit lectures Message-ID: <827C8444-E803-4DA3-A475-78E0696A6C5C@donders.ru.nl> Dear FieldTrip users, Next Monday the 4-day MEG/EEG toolkit course will start at the Donders in Nijmegen. To maximize the impact of the course, we will be live broadcasting the lectures! The computer hands-on sessions are not suited for recording and live broadcasting, but following the corresponding lecture you might want to do some tutorials on your own. The program for the live broadcasts is (starting next Monday 20 April) Monday 09:45-10:45 Introduction to EEG/MEG and introduction to the FieldTrip toolbox Monday 15:15-16:30 Fundamentals of neuronal oscillations and synchrony Tuesday 11:00-12:15 Forward and inverse modeling Tuesday 13:00-14:00 Source reconstruction using beamformers Wednesday 09:00-10:00 Statistics using non-parametric randomization techniques Wednesday 13:00-14:00 Connectivity analysis in MEG and EEG data All indicated times are Central European Time (CET), i.e. the local time here in Nijmegen. You can watch the live lectures at our YouTube channel on https://www.youtube.com/user/FieldTripToolboxTV. If you go there now, you will already see that the live events have been scheduled. The full course program is on http://www.fieldtriptoolbox.org/workshop/toolkit2015, where it will be further updated during the next days. If at any moment in doubt during next week, please go to the toolkit2015 page to get the latest updates. I’ll also post the links to the youtube live streams there. best regards, Robert (on behalf of the FieldTrip team) PS this is the very first time for us to do a live broadcast. Of course we hope it will all work as planned, but we might run into some technical difficulties. As we cannot communicate all details to each of you individually, please keep an eye on http://www.fieldtriptoolbox.org/workshop/toolkit2015 for the latest news. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Wed Apr 15 16:41:41 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 15 Apr 2015 16:41:41 +0200 Subject: [FieldTrip] next week: live broadcast of MEG/EEG toolkit lectures Message-ID: <1299A68A-2F15-462A-9D13-6C4C5DE3AD1F@donders.ru.nl> Dear FieldTrip users, Next Monday the 4-day MEG/EEG toolkit course will start at the Donders in Nijmegen. To maximize the impact of the course, we will be live broadcasting the lectures! The computer hands-on sessions are not suited for recording and live broadcasting, but following the corresponding lecture you might want to do some tutorials on your own. The program for the live broadcasts is (starting next Monday 20 April) Monday 09:45-10:45 Introduction to EEG/MEG and introduction to the FieldTrip toolbox Monday 15:15-16:30 Fundamentals of neuronal oscillations and synchrony Tuesday 11:00-12:15 Forward and inverse modeling Tuesday 13:00-14:00 Source reconstruction using beamformers Wednesday 09:00-10:00 Statistics using non-parametric randomization techniques Wednesday 13:00-14:00 Connectivity analysis in MEG and EEG data All indicated times are Central European Time (CET), i.e. the local time here in Nijmegen. You can watch the live lectures at our YouTube channel on https://www.youtube.com/user/FieldTripToolboxTV. If you go there now, you will already see that the live events have been scheduled. The full course program is on http://www.fieldtriptoolbox.org/workshop/toolkit2015, where it will be further updated during the next days. If at any moment in doubt during next week, please go to the toolkit2015 page to get the latest updates. I’ll also post the links to the youtube live streams there. best regards, Robert (on behalf of the FieldTrip team) PS this is the very first time for us to do a live broadcast. Of course we hope it will all work as planned, but we might run into some technical difficulties. As we cannot communicate all details to each of you individually, please keep an eye on http://www.fieldtriptoolbox.org/workshop/toolkit2015 for the latest news. -------------- next part -------------- An HTML attachment was scrubbed... URL: From spa268 at nyu.edu Wed Apr 15 18:17:41 2015 From: spa268 at nyu.edu (Stephen Politzer-Ahles) Date: Wed, 15 Apr 2015 18:17:41 +0200 Subject: [FieldTrip] Why the general use of parametric test as observed test statistic for permutation cluster tests? Message-ID: Hi Peter, As far as I know this is just a default coded in fieldtrip, but can easily be replaced (by using your own statfun rather than e.g. depsamplesF, depsamplesT, etc.). According to Maris & Oostenveld (2007), the observed statistic used to calculate clusters can be anything, if I recall correctly. Best, Steve > Message: 2 > Date: Wed, 15 Apr 2015 00:06:33 +0000 > From: Peter Goodin > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] Why the general use of parametric test as > observed test statistic for permutation cluster tests? > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > Hi Fieldtrip list, > > I'm just wondering if someone can explain if there is a reasoning behind the > general use of a parametric test to calculate the initial step in the > permutation cluster test and not a non-parametric test (e.g t-test over Mann > Whitey U)? Is it just due to the assumption of a Gaussian distribution or is > there something deeper going on? > > Thanks, > > Peter > > _______________________ > Peter Goodin, > BSc (Hons), Ph.D Candidate (submitted). > > Brain and Psychological Sciences Research Centre (BPsych) > Swinburne University, > Hawthorn, Vic, 3122 > http://www.swinburne.edu.au/swinburneresearchers/index.php?fuseaction=profile&pid=4149 > > Monash Alfred Psychiatry Research Centre (MAPrc) > Level 4, 607 St Kilda Road, > Melbourne 3004 > Stephen Politzer-Ahles New York University, Abu Dhabi Neuroscience of Language Lab http://www.nyu.edu/projects/politzer-ahles/ From pgoodin at swin.edu.au Thu Apr 16 00:23:25 2015 From: pgoodin at swin.edu.au (Peter Goodin) Date: Wed, 15 Apr 2015 22:23:25 +0000 Subject: [FieldTrip] Why the general use of parametric test as observed test statistic for permutation cluster tests? In-Reply-To: References: Message-ID: Hi Steve, You recall correctly indeed! It was actually that statement that got me thinking about the default use of t-test rather than checking the initial distribution! Peter __________________________ Peter Goodin, BSc (Hons), Ph.D Candidate (submitted). Brain and Psychological Sciences Research Centre (BPsych) Swinburne University, Hawthorn, Vic, 3122 http://www.swinburne.edu.au/swinburneresearchers/index.php?fuseaction=profile&pid=4149 Monash Alfred Psychiatry Research Centre (MAPrc) Level 4, 607 St Kilda Road, Melbourne 3004 ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Stephen Politzer-Ahles [spa268 at nyu.edu] Sent: Thursday, 16 April 2015 2:17 AM To: fieldtrip at science.ru.nl Subject: Re: [FieldTrip] Why the general use of parametric test as observed test statistic for permutation cluster tests? Hi Peter, As far as I know this is just a default coded in fieldtrip, but can easily be replaced (by using your own statfun rather than e.g. depsamplesF, depsamplesT, etc.). According to Maris & Oostenveld (2007), the observed statistic used to calculate clusters can be anything, if I recall correctly. Best, Steve > Message: 2 > Date: Wed, 15 Apr 2015 00:06:33 +0000 > From: Peter Goodin > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] Why the general use of parametric test as > observed test statistic for permutation cluster tests? > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > Hi Fieldtrip list, > > I'm just wondering if someone can explain if there is a reasoning behind the > general use of a parametric test to calculate the initial step in the > permutation cluster test and not a non-parametric test (e.g t-test over Mann > Whitey U)? Is it just due to the assumption of a Gaussian distribution or is > there something deeper going on? > > Thanks, > > Peter > > _______________________ > Peter Goodin, > BSc (Hons), Ph.D Candidate (submitted). > > Brain and Psychological Sciences Research Centre (BPsych) > Swinburne University, > Hawthorn, Vic, 3122 > http://www.swinburne.edu.au/swinburneresearchers/index.php?fuseaction=profile&pid=4149 > > Monash Alfred Psychiatry Research Centre (MAPrc) > Level 4, 607 St Kilda Road, > Melbourne 3004 > Stephen Politzer-Ahles New York University, Abu Dhabi Neuroscience of Language Lab http://www.nyu.edu/projects/politzer-ahles/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From federica.ma at gmail.com Thu Apr 16 11:41:17 2015 From: federica.ma at gmail.com (Federica Mauro) Date: Thu, 16 Apr 2015 09:41:17 +0000 Subject: [FieldTrip] Problems with ft_freqanalysis Message-ID: <5cead4654ee14611ae745be82f0fcc49@EXPRD02.hosting.ru.nl> Hi everybody, I'm trying to compute coherence analyses following the coherence tutorial at http://www.fieldtriptoolbox.org/tutorial/coherence. Since a couple of days, I have this error message in computing ft_freqanalysis: Error using load Unable to read file precompute_dpss: No such file or directory. Error in dpss (line 9) load precompute_dpss Error in ft_specest_mtmfft>double_dpss (line 335) tap = dpss(double(a), double(b), varargin{:}); Error in ft_specest_mtmfft (line 151) tap = double_dpss(ndatsample,ndatsample*(tapsmofrq./fsample))'; Error in ft_freqanalysis (line 494) [spectrum,ntaper,foi] = ft_specest_mtmfft(dat, time, 'taper', cfg.taper, options{:}, 'feedback', fbopt); Is that a bug? Here is the code I'm using: cfg = []; cfg.output = 'powandcsd'; cfg.method = 'mtmfft'; cfg.foilim = [5 40]; cfg.tapsmofrq = 5; cfg.keeptrials = 'yes'; freq = ft_freqanalysis(cfg, eeg); Thank you in advance, Federica -------------- next part -------------- An HTML attachment was scrubbed... URL: From f.roux at bcbl.eu Thu Apr 16 11:50:06 2015 From: f.roux at bcbl.eu (=?utf-8?B?RnLDqWTDqXJpYw==?= Roux) Date: Thu, 16 Apr 2015 11:50:06 +0200 (CEST) Subject: [FieldTrip] [SPAM] Problems with ft_freqanalysis In-Reply-To: <5cead4654ee14611ae745be82f0fcc49@EXPRD02.hosting.ru.nl> Message-ID: <1216046341.56584.1429177806762.JavaMail.root@bcbl.eu> Hi Fredrica, this is most likely do to a path problem. Try adding this at the beginning of your script/function: restorde_defaultpath; addpath('/path2fieldtrip/fieldtrip-2015xxxx/'); ft_defaults; HTH -- Frédéric Roux Postdoctoral Scientist BCBL. Basque Center on Cognition, Brain % Language. f.roux at bcbl.eu Tel: +34 943 309 300 Ext 211 Fax: +34 943 309 052 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer --------------------------------------------------------------------------- ----- Original Message ----- From: "Federica Mauro" To: "donders fieldtrip" Sent: Thursday, April 16, 2015 11:41:17 AM Subject: [SPAM] [FieldTrip] Problems with ft_freqanalysis Hi everybody, I'm trying to compute coherence analyses following the coherence tutorial at http://www.fieldtriptoolbox.org/tutorial/coherence . Since a couple of days, I have this error message in computing ft_freqanalysis: Error using load Unable to read file precompute_dpss: No such file or directory. Error in dpss (line 9) load precompute_dpss Error in ft_specest_mtmfft>double_dpss (line 335) tap = dpss(double(a), double(b), varargin{:}); Error in ft_specest_mtmfft (line 151) tap = double_dpss(ndatsample,ndatsample*(tapsmofrq./fsample))'; Error in ft_freqanalysis (line 494) [spectrum,ntaper,foi] = ft_specest_mtmfft(dat, time, 'taper', cfg.taper, options{:}, 'feedback', fbopt); Is that a bug? Here is the code I'm using: cfg = []; cfg.output = 'powandcsd'; cfg.method = 'mtmfft'; cfg.foilim = [5 40]; cfg.tapsmofrq = 5; cfg.keeptrials = 'yes'; freq = ft_freqanalysis(cfg, eeg); Thank you in advance, Federica _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From r.oostenveld at donders.ru.nl Thu Apr 16 12:06:42 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 16 Apr 2015 12:06:42 +0200 Subject: [FieldTrip] Problems with ft_freqanalysis In-Reply-To: <5cead4654ee14611ae745be82f0fcc49@EXPRD02.hosting.ru.nl> References: <5cead4654ee14611ae745be82f0fcc49@EXPRD02.hosting.ru.nl> Message-ID: Hi Federica, The error message you run into relates to the presence (or absence) of the Mathworks signal processing toolbox. FieldTrip relies on a number of MATLAB toolboxes (see http://www.fieldtriptoolbox.org/faq/requirements). Where possible, we try to avoid extra commercial toolboxes. Therefore we have some drop-in replacement functions in fieldtrip/external/signal (which were obtained from the Octave project). For the DPSS function (used for multitapering) however we don’t have a fully satisfactory solution. The error message you get suggests that you are using the "fieldtrip/external/signal/dpss_hack” directory. That is one that should not be on your path, unless you explicitly add it. You should only add in case you don’t have the signal processing toolbox and know what you are doing (i.e. after having read the README in that directory). I suspect you have used add path(genpath(…)) or the GUI equivalent of it. Please see http://www.fieldtriptoolbox.org/faq/should_i_add_fieldtrip_with_all_subdirectories_to_my_matlab_path and remove the dpss_hack directory from your path. best Robert PS for the low frequency range you are interested in I suspect that multitapering won’t be the most optimal anyway. Better add cfg.taper=‘hanning’ to your analysis, and see Nietzsche explain it next Monday on https://www.youtube.com/watch?v=vwPpSglPJTE On 16 Apr 2015, at 11:41, Federica Mauro wrote: > Hi everybody, > > I'm trying to compute coherence analyses following the coherence tutorial at http://www.fieldtriptoolbox.org/tutorial/coherence. > Since a couple of days, I have this error message in computing ft_freqanalysis: > > Error using load > Unable to read file precompute_dpss: No such file or directory. > > Error in dpss (line 9) > load precompute_dpss > > Error in ft_specest_mtmfft>double_dpss (line 335) > tap = dpss(double(a), double(b), varargin{:}); > > Error in ft_specest_mtmfft (line 151) > tap = > double_dpss(ndatsample,ndatsample*(tapsmofrq./fsample))'; > > Error in ft_freqanalysis (line 494) > [spectrum,ntaper,foi] = ft_specest_mtmfft(dat, time, 'taper', > cfg.taper, options{:}, 'feedback', fbopt); > > Is that a bug? > > > Here is the code I'm using: > cfg = []; > cfg.output = 'powandcsd'; > cfg.method = 'mtmfft'; > cfg.foilim = [5 40]; > cfg.tapsmofrq = 5; > cfg.keeptrials = 'yes'; > > freq = ft_freqanalysis(cfg, eeg); > > > Thank you in advance, > Federica > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Thu Apr 16 13:53:41 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Thu, 16 Apr 2015 13:53:41 +0200 Subject: [FieldTrip] Beamforming analysis in frequency band In-Reply-To: References: Message-ID: <9BC70F24-9E97-4247-B0C0-365CCC154C70@uni-konstanz.de> Dear Noa, you should use frequency smoothening to achieve this. For example, a configuration of cfg.foilim = [20 20] ; and cfg.tapsmofrq = 10; will allow you to estimate sources in the 10 to 30 Hz band. > Hi all, > > I'm doing source analysis in the frequency domain of a resting-state data. > when doing the source analysis, I want to use several frequency bands of interest, such as beta (13-30 Hz) and gamma (30-48 Hz). > My problem is about the cfg.frequency parameter, which must be a scalar (whereas i'm interested in a frequency band). Arbitrarily choosing a frequency in the middle of the range doesn't seem right. > > What is the common practice when doing source analysis using this function? You could evaluate this tutorial: http://www.fieldtriptoolbox.org/tutorial/beamformer > Does the cfg.tapsmofrq parameter is supposed to enable choosing frequency band instead of a single peak frequency? and some detailed explanation in a pictorial form here: https://www.youtube.com/watch?v=7eS11DtbIPw best tzvetan > > Any suggestions will be very much helpful! > > Thanks, > Noa > > > This is the script I’m using: > > cfg = []; > cfg.method ='mtmfft'; > cfg.output ='fourier'; > cfg.keeptapers = 'yes'; > cfg.foilim = [30 48]; > cfg.tapsmofrq = 2; > freqClosed=ft_freqanalysis(cfg,eyesClosed); > > > > cfg = []; > cfg.method='pcc'; > cfg.frequency = 39; % must be a scalar > cfg.lambda = 0; > cfg.vol = vol; > cfg.grid = grid; > cfg.feedback = 'textbar'; > cfg.keepfilter='yes'; > source1 = ft_sourceanalysis(cfg, freqClosed); > > > -- > My signature: > > http://www.documentarywire.com/earthlings/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From federica.ma at gmail.com Thu Apr 16 16:44:18 2015 From: federica.ma at gmail.com (Federica Mauro) Date: Thu, 16 Apr 2015 16:44:18 +0200 Subject: [FieldTrip] [SPAM] Problems with ft_freqanalysis In-Reply-To: <1216046341.56584.1429177806762.JavaMail.root@bcbl.eu> References: <5cead4654ee14611ae745be82f0fcc49@EXPRD02.hosting.ru.nl> <1216046341.56584.1429177806762.JavaMail.root@bcbl.eu> Message-ID: Thanks, you've been really helpful. Thanks also for the tip on the taper cfg, Looking forward to the seminar! Federica 2015-04-16 11:50 GMT+02:00 Frédéric Roux : > Hi Fredrica, > > this is most likely do to a path problem. > > Try adding this at the beginning of your script/function: > > restorde_defaultpath; > addpath('/path2fieldtrip/fieldtrip-2015xxxx/'); > ft_defaults; > > HTH > > -- > Frédéric Roux > Postdoctoral Scientist > BCBL. Basque Center on Cognition, Brain % Language. > > f.roux at bcbl.eu > Tel: +34 943 309 300 Ext 211 > Fax: +34 943 309 052 > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > --------------------------------------------------------------------------- > > > ----- Original Message ----- > From: "Federica Mauro" > To: "donders fieldtrip" > Sent: Thursday, April 16, 2015 11:41:17 AM > Subject: [SPAM] [FieldTrip] Problems with ft_freqanalysis > > > > > > > > > > Hi everybody, > > I'm trying to compute coherence analyses following the coherence tutorial > at http://www.fieldtriptoolbox.org/tutorial/coherence . > Since a couple of days, I have this error message in computing > ft_freqanalysis: > > Error using load > Unable to read file precompute_dpss: No such file or directory. > > Error in dpss (line 9) > load precompute_dpss > > Error in ft_specest_mtmfft>double_dpss (line 335) > tap = dpss(double(a), double(b), varargin{:}); > > Error in ft_specest_mtmfft (line 151) > tap = > double_dpss(ndatsample,ndatsample*(tapsmofrq./fsample))'; > > Error in ft_freqanalysis (line 494) > [spectrum,ntaper,foi] = ft_specest_mtmfft(dat, time, 'taper', > cfg.taper, options{:}, 'feedback', fbopt); > > Is that a bug? > > > Here is the code I'm using: > cfg = []; > cfg.output = 'powandcsd'; > cfg.method = 'mtmfft'; > cfg.foilim = [5 40]; > cfg.tapsmofrq = 5; > cfg.keeptrials = 'yes'; > > freq = ft_freqanalysis(cfg, eeg); > > > Thank you in advance, > Federica > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From n.lam at donders.ru.nl Thu Apr 16 17:26:17 2015 From: n.lam at donders.ru.nl (Lam, N.H.L. (Nietzsche)) Date: Thu, 16 Apr 2015 15:26:17 +0000 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? Message-ID: Dear FieldTrip users, Next week we will provide a live broadcast of the lectures from the 4-day MEG/EEG toolkit course at the Donders in Nijmegen, on our YouTube channel https://www.youtube.com/user/FieldTripToolboxTV Please check whether the videos are available in your country (click on one of the scheduled live stream videos - you should see a clock that counts down to the lecture). If you get the message "Live streaming is not available in your country due to right issues" please reply to this email and state your country so that we can find a solution prior to the toolkit next week. We appreciate your help to make this a smooth broadcast. Best, Nietzsche (on behalf of the FieldTrip team) P.S. Full course program of the workshop http://www.fieldtriptoolbox.org/workshop/toolkit2015, Best, Nietzsche (on behalf of the FieldTrip team) -------------- next part -------------- An HTML attachment was scrubbed... URL: From tomh at kurage.nimh.nih.gov Thu Apr 16 17:39:50 2015 From: tomh at kurage.nimh.nih.gov (Tom Holroyd) Date: Thu, 16 Apr 2015 11:39:50 -0400 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: References: Message-ID: <20150416113950.253a352c@kurage.nimh.nih.gov> https://youtu.be/-RpQklxbCsg?list=PLbVcEw60xnKNuNKwBSWgzdZCXxNDMh3Gr I just watched that, no problems, and I get the countdowns for the newer links. Looking forward to it! I was almost surprised I didn't need to install a new Flash player or something. Thanks! On Thu, 16 Apr 2015 15:26:17 +0000 "Lam, N.H.L. (Nietzsche)" wrote: > Dear FieldTrip users, > > Next week we will provide a live broadcast of the lectures from the > 4-day MEG/EEG toolkit course at the Donders in Nijmegen, on our > YouTube channel https://www.youtube.com/user/FieldTripToolboxTV > > Please check whether the videos are available in your country (click > on one of the scheduled live stream videos - you should see a clock > that counts down to the lecture). If you get the message "Live > streaming is not available in your country due to right issues" > please reply to this email and state your country so that we can find > a solution prior to the toolkit next week. We appreciate your help > to make this a smooth broadcast. > > Best, > Nietzsche (on behalf of the FieldTrip team) > > P.S. Full course program of the workshop > http://www.fieldtriptoolbox.org/workshop/toolkit2015, > > > > > > > > > Best, > Nietzsche (on behalf of the FieldTrip team) -- Dr. Tom -- "There are not more than five musical notes, yet the combinations of these five give rise to more melodies than can ever be heard." -- Sun Tzu From Holger.Krause at med.uni-duesseldorf.de Thu Apr 16 17:45:03 2015 From: Holger.Krause at med.uni-duesseldorf.de (Holger Krause) Date: Thu, 16 Apr 2015 17:45:03 +0200 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: References: Message-ID: <201504161745.05273.Holger.Krause@med.uni-duesseldorf.de> Am Donnerstag, 16. April 2015 schrieb Lam, N.H.L. (Nietzsche): > Please check whether the videos are available in your country (click on one > of the scheduled live stream videos - you should see a clock that counts > down to the lecture). If you get the message "Live streaming is not > available in your country due to right issues" please reply to this email > and state your country so that we can find a solution prior to the toolkit > next week. We appreciate your help to make this a smooth broadcast. https://www.youtube.com/watch?v=ZBwh0Vm4fh4 Germany :-( "Live Streaming ist wegen Rechteproblemen in Deutschland leider nicht möglich." Best, Holger From kgm at tf.uni-kiel.de Thu Apr 16 17:52:39 2015 From: kgm at tf.uni-kiel.de (kgm) Date: Thu, 16 Apr 2015 17:52:39 +0200 Subject: [FieldTrip] =?utf-8?q?Can_you_view_the_Livestream_lectures_=28MEG?= =?utf-8?q?/EEG_toolkit=29=3F?= In-Reply-To: References: Message-ID: <8b25592765751ea3e1c8afa0e3936788@tf.uni-kiel.de> Dear all, I am a user from Germany and I get the message "Live streaming is not available in your country due to rights issues" when I click one of the scheduled videos. Looking forward for the solution. Thanks in advance! Best regards, Kidist G.Mideksa On 2015-04-16 17:26, Lam, N.H.L. (Nietzsche) wrote: > Dear FieldTrip users, > > Next week we will provide a live broadcast of the lectures from the > 4-day MEG/EEG toolkit course at the Donders in Nijmegen, on our > YouTube channel https://www.youtube.com/user/FieldTripToolboxTV > > Please CHECK WHETHER THE VIDEOS ARE AVAILABLE IN YOUR COUNTRY (click > on one of the scheduled live stream videos - you should see a clock > that counts down to the lecture). If you get the message "Live > streaming is not available in your country due to right issues" please > reply to this email and state your country so that we can find a > solution prior to the toolkit next week. We appreciate your help to > make this a smooth broadcast. > > Best, > Nietzsche (on behalf of the FieldTrip team) > > P.S. Full course program of the workshop > http://www.fieldtriptoolbox.org/workshop/toolkit2015 [1], > > Best, > Nietzsche (on behalf of the FieldTrip team) > > Links: > ------ > [1] http://www.fieldtriptoolbox.org/workshop/toolkit2015 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From david.schubring at uni-konstanz.de Thu Apr 16 18:07:43 2015 From: david.schubring at uni-konstanz.de (David Schubring) Date: Thu, 16 Apr 2015 18:07:43 +0200 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: <201504161745.05273.Holger.Krause@med.uni-duesseldorf.de> References: <201504161745.05273.Holger.Krause@med.uni-duesseldorf.de> Message-ID: <552FDE4F.3060501@uni-konstanz.de> Hello FieldTrip users, I don't know about the exact legal situation here, but since you probably won't stream copyrighted material a proxy plugin should be fine? At least it works for me (in germany) - which means, at the moment I can see the countdown. There is a ton of browser plugins for unblocking youtube, the one I use for Mozilla Firefox is called "ProxTube" (there should be one for Chrome as well): https://addons.mozilla.org/de/firefox/addon/proxtube/ Cheers, David Am 16.04.15 um 17:45 schrieb Holger Krause: > Am Donnerstag, 16. April 2015 schrieb Lam, N.H.L. (Nietzsche): >> Please check whether the videos are available in your country (click on one >> of the scheduled live stream videos - you should see a clock that counts >> down to the lecture). If you get the message "Live streaming is not >> available in your country due to right issues" please reply to this email >> and state your country so that we can find a solution prior to the toolkit >> next week. We appreciate your help to make this a smooth broadcast. > > https://www.youtube.com/watch?v=ZBwh0Vm4fh4 > > Germany :-( > > "Live Streaming ist wegen Rechteproblemen in Deutschland leider nicht > möglich." > > Best, > > Holger > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Dipl.-Psych. David Schubring Clinical Psychology University of Konstanz P.O. Box 905 78457 Konstanz Phone: +49-(0)7531-88-4889 From ingrid.sor at neuro.uu.se Fri Apr 17 09:43:44 2015 From: ingrid.sor at neuro.uu.se (=?windows-1252?Q?Ingrid_S=F6r?=) Date: Fri, 17 Apr 2015 09:43:44 +0200 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: References: Message-ID: <5530B9B0.9030104@neuro.uu.se> Hi, Works fine in Sweden! Looks like some interesting material. Best, Ingrid On 2015-04-16 17:26, Lam, N.H.L. (Nietzsche) wrote: > Dear FieldTrip users, > > Next week we will provide a live broadcast of the lectures from the > 4-day MEG/EEG toolkit course at the Donders in Nijmegen, on our > YouTube channel https://www.youtube.com/user/FieldTripToolboxTV > > Please*check whether the videos are available in your country* (click > on one of the scheduled live stream videos - you should see a clock > that counts down to the lecture). If you get the message "Live > streaming is not available in your country due to right issues" please > reply to this email and state your country so that we can find a > solution prior to the toolkit next week. We appreciate your help to > make this a smooth broadcast. > > Best, > Nietzsche (on behalf of the FieldTrip team) > > P.S. Full course program of the workshop > http://www.fieldtriptoolbox.org/workshop/toolkit2015, > > > > > > > > > Best, > Nietzsche (on behalf of the FieldTrip team) > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From mariya.kharaman at uni-konstanz.de Fri Apr 17 09:45:25 2015 From: mariya.kharaman at uni-konstanz.de (Mariya Kharaman) Date: Fri, 17 Apr 2015 09:45:25 +0200 Subject: [FieldTrip] =?utf-8?q?Can_you_view_the_Livestream_lectures_=28MEG?= =?utf-8?q?/EEG_toolkit=29=3F?= In-Reply-To: Message-ID: Dear all, I am in Germany and as it seems, I will not be able to watch the videos ("Live Streaming ist wegen Rechteproblemen in Deutschland leider nicht möglich." = "Live streaming is not available in your country due to right issues". I really hope the solution will be found! Thank you very much! Best wishes, Mariya Am Donnerstag, 16. April 2015 17:26 CEST, "Lam, N.H.L. (Nietzsche)" schrieb: > Dear FieldTrip users, > > Next week we will provide a live broadcast of the lectures from the 4-day MEG/EEG toolkit course at the Donders in Nijmegen, on our YouTube channel https://www.youtube.com/user/FieldTripToolboxTV > > Please check whether the videos are available in your country (click on one of the scheduled live stream videos - you should see a clock that counts down to the lecture). If you get the message "Live streaming is not available in your country due to right issues" please reply to this email and state your country so that we can find a solution prior to the toolkit next week. We appreciate your help to make this a smooth broadcast. > > Best, > Nietzsche (on behalf of the FieldTrip team) > > P.S. Full course program of the workshop http://www.fieldtriptoolbox.org/workshop/toolkit2015, > > > > > > > > > Best, > Nietzsche (on behalf of the FieldTrip team) From smoratti at psi.ucm.es Fri Apr 17 11:09:28 2015 From: smoratti at psi.ucm.es (smoratti at psi.ucm.es) Date: Fri, 17 Apr 2015 11:09:28 +0200 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: <201504161745.05273.Holger.Krause@med.uni-duesseldorf.de> References: <201504161745.05273.Holger.Krause@med.uni-duesseldorf.de> Message-ID: <04EC09B5-FE5B-491A-965A-5BACFC4C29EE@psi.ucm.es> in Spain it seems to work… best, Stephan ________________________________________________________ Stephan Moratti, PhD see: Stephan's research profile Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas Despacho (Office) 1326-0 28223 Pozuelo de Alarcón (Madrid) Spain and Center for Biomedical Technology Laboratory for Cognitive and Computational Neuroscience Parque Científico y Tecnológico de la Universidad Politecnica de Madrid Campus Montegancedo 28223 Pozuelo de Alarcón (Madrid) Spain email: smoratti at psi.ucm.es Tel.: +34 679219982 El 16/04/2015, a las 17:45, Holger Krause escribió: > Am Donnerstag, 16. April 2015 schrieb Lam, N.H.L. (Nietzsche): >> Please check whether the videos are available in your country (click on one >> of the scheduled live stream videos - you should see a clock that counts >> down to the lecture). If you get the message "Live streaming is not >> available in your country due to right issues" please reply to this email >> and state your country so that we can find a solution prior to the toolkit >> next week. We appreciate your help to make this a smooth broadcast. > > https://www.youtube.com/watch?v=ZBwh0Vm4fh4 > > Germany :-( > > "Live Streaming ist wegen Rechteproblemen in Deutschland leider nicht > möglich." > > Best, > > Holger > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From n.lam at donders.ru.nl Fri Apr 17 12:11:13 2015 From: n.lam at donders.ru.nl (Lam, N.H.L. (Nietzsche)) Date: Fri, 17 Apr 2015 10:11:13 +0000 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: <8b25592765751ea3e1c8afa0e3936788@tf.uni-kiel.de> References: , <8b25592765751ea3e1c8afa0e3936788@tf.uni-kiel.de> Message-ID: Dear FieldTrip Users, It seems that the viewing problem is only limited to Germany (we have checked in other countries as well). We suggest that you use a proxy plugin to circumvent the issue of not being able to view the video. A fellow FT user has suggested the following for Firefox https://addons.mozilla.org/de/firefox/addon/proxtube/ Similar proxy plugins exist for other web browsers (note that these were found on google, and have not be personally tested by the FieldTrip team): https://chrome.google.com/webstore/detail/proxxy/clkkaggocmafajhbcbknhcgnbmagjohi?hl=en http://www.chip.de/downloads/FoxyProxy-fuer-Chrome_53036930.html We suggest you determine a suitable proxy well in advance of the lecture(s), as it may be more than a 5 minute fix for some of you. Best, Nietzsche (on behalf of the FieldTrip team) ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of kgm [kgm at tf.uni-kiel.de] Sent: 16 April 2015 17:52 To: FieldTrip discussion list Subject: Re: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? Dear all, I am a user from Germany and I get the message "Live streaming is not available in your country due to rights issues" when I click one of the scheduled videos. Looking forward for the solution. Thanks in advance! Best regards, Kidist G.Mideksa On 2015-04-16 17:26, Lam, N.H.L. (Nietzsche) wrote: > Dear FieldTrip users, > > Next week we will provide a live broadcast of the lectures from the > 4-day MEG/EEG toolkit course at the Donders in Nijmegen, on our > YouTube channel https://www.youtube.com/user/FieldTripToolboxTV > > Please CHECK WHETHER THE VIDEOS ARE AVAILABLE IN YOUR COUNTRY (click > on one of the scheduled live stream videos - you should see a clock > that counts down to the lecture). If you get the message "Live > streaming is not available in your country due to right issues" please > reply to this email and state your country so that we can find a > solution prior to the toolkit next week. We appreciate your help to > make this a smooth broadcast. > > Best, > Nietzsche (on behalf of the FieldTrip team) > > P.S. Full course program of the workshop > http://www.fieldtriptoolbox.org/workshop/toolkit2015 [1], > > Best, > Nietzsche (on behalf of the FieldTrip team) > > Links: > ------ > [1] http://www.fieldtriptoolbox.org/workshop/toolkit2015 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From eva.patai at psych.ox.ac.uk Fri Apr 17 13:35:46 2015 From: eva.patai at psych.ox.ac.uk (Zita Eva Patai) Date: Fri, 17 Apr 2015 12:35:46 +0100 Subject: [FieldTrip] interpolation of bad channels matlab error Message-ID: Dear FTers I have been trying to fix some bad channels in my data through interpolation. It seems to not be working. My code is below. Please note my data object is converted from SPM (in case that matters). Thanks very much in advance, zita data = fsample: 250 label: {324x1 cell} trial: {1x505 cell} time: {1x505 cell} grad: [1x1 struct] triallist: {1x505 cell} >> cfg2 cfg2 = badchannel: {2x1 cell} method: 'nearest' neighbours: [1x306 struct] >> [interp]=ft_channelrepair(cfg2,data) the input is raw data with 324 channels and 505 trials using gradiometers specified in the data repairing channel MEG1132 using neighbour repairing channel MEG1421 using neighbour repairing bad channels for 505 trials .Error using * MTIMES is not supported for one sparse input and one single input. Error in ft_channelrepair (line 172) interp.trial{i} = repair * data.trial{i}; -- Eva Zita Patai, DPhil Postdoctoral Researcher Oxford Centre for Human Brain Activity University of Oxford -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri Apr 17 13:53:54 2015 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 17 Apr 2015 11:53:54 +0000 Subject: [FieldTrip] interpolation of bad channels matlab error In-Reply-To: References: Message-ID: <876E7EA3-688A-49EB-9B5A-2241570DD41D@fcdonders.ru.nl> Hi Eva, The MATLAB error suggests that your data is represented as single precision floating point numbers, and matrix multiplication is apparently not supported when you want to multiply with a sparse matrix. You could try and convert your data to double precision: data=ft_struct2double(data); and then call ft_channelrepair. Best, Jan-Mathijs On Apr 17, 2015, at 1:35 PM, Zita Eva Patai > wrote: Dear FTers I have been trying to fix some bad channels in my data through interpolation. It seems to not be working. My code is below. Please note my data object is converted from SPM (in case that matters). Thanks very much in advance, zita data = fsample: 250 label: {324x1 cell} trial: {1x505 cell} time: {1x505 cell} grad: [1x1 struct] triallist: {1x505 cell} >> cfg2 cfg2 = badchannel: {2x1 cell} method: 'nearest' neighbours: [1x306 struct] >> [interp]=ft_channelrepair(cfg2,data) the input is raw data with 324 channels and 505 trials using gradiometers specified in the data repairing channel MEG1132 using neighbour repairing channel MEG1421 using neighbour repairing bad channels for 505 trials .Error using * MTIMES is not supported for one sparse input and one single input. Error in ft_channelrepair (line 172) interp.trial{i} = repair * data.trial{i}; -- Eva Zita Patai, DPhil Postdoctoral Researcher Oxford Centre for Human Brain Activity University of Oxford _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jdien07 at mac.com Fri Apr 17 19:09:37 2015 From: jdien07 at mac.com (Joseph Dien) Date: Fri, 17 Apr 2015 13:09:37 -0400 Subject: [FieldTrip] Johns Hopkins Research Assistant Position Message-ID: General Description: Research of the Division is focused on improving aspects of cognition in humans, particularly those related to speech, communication, and cognitive control, in both normally developing individuals and in individuals with developmental and acquired disorders, such as autism, Lesch-Nyhan syndrome, and stroke. Studies use a mix of techniques from experimental psychology, transcranial Direct Current Stimulation (tDCS), structural imaging, fMRI, psychophysiological measures, and especially EEG. RA will be directly responsible for 1-2 projects themselves, and will assist with several other projects in the Division. Involvement will be in any and all aspects: library research; writing up research plans; subject recruitment; scheduling; testing (including psychological and experimental tasks); collecting data; cleaning data; maintaining files; initial analyses; draft and final write-ups. Interacts, as needed, with Institutional Review Board. Participates in regular laboratory research meetings. Maintains, monitors, and orders research supplies. Helps with statistical analyses, using software such as MATLAB, NetStation, SPM8, MRIcron, and SPSS. Reports directly to the Director of the Division, with delegated reporting to other faculty in the Division, faculty associated with the Division, and senior staff. Qualifications: Bachelor's degree in related discipline required. Some related experience required. Additional education may substitute for required experience and additional related experience may substitute for required education, to the extent permitted by the JHU equivalency formula. Must have ability to use a personal computer. Prefer experience with analytic tools, and with writing academic manuscripts and grants. Must be well-organized, efficient, accurate, responsible, and enthusiastic. Must be able to interact effectively with faculty, staff, and subjects. Experience administering and scoring cognitive and behavioral measures preferred. Experience with MS Word, Excel, SPSS, MATLAB, SPM8, and NetStation software preferred. Preferred Qualifications: Bachelor’s or Master’s Degree in Experimental Psychology, Cognitive Science, Neuroscience, or a related field preferred. Posting at: https://hrnt.jhu.edu/jhujobs/job_view.cfm?view_req_id=65838&view=sch Contact Joseph Dien (jdien1 at jhmi.edu ) for more information. Joe -------------------------------------------------------------------------------- Joseph Dien, PhD Research Associate Cognitive Neurology/Neuropsychology The Johns Hopkins University School of Medicine Lab E-mail: jdien1 at jhmi.edu Private E-mail: jdien07 at mac.com Office Phone: 410-614-3115 Cell Phone: 202-297-8117 Fax: 410-955-0188 http://joedien.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From vahidgerami.mse at gmail.com Sun Apr 19 08:28:14 2015 From: vahidgerami.mse at gmail.com (vahid gerami) Date: Sun, 19 Apr 2015 10:58:14 +0430 Subject: [FieldTrip] EEG from brain sensory motor area Message-ID: dear eeglab community i've recorded some eeg signals from sensory motor area. the signals are recorded while the right hand was moving regularly. now i want to detect the ERP changes on the signal caused by the hand movement. does any one have the same experience? how can i do the job? please help me about the procedure. regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From noahertz6 at gmail.com Sun Apr 19 12:57:46 2015 From: noahertz6 at gmail.com (Noa Hertz) Date: Sun, 19 Apr 2015 13:57:46 +0300 Subject: [FieldTrip] Beamforming analysis in frequency band In-Reply-To: <9BC70F24-9E97-4247-B0C0-365CCC154C70@uni-konstanz.de> References: <9BC70F24-9E97-4247-B0C0-365CCC154C70@uni-konstanz.de> Message-ID: Thank you Tzvetan! This raised two more question regarding the source analysis: 1. What is the difference between defining the frequency range under cfg.foi (such as cfg.foi=[30 48]) and defining if under the cfg.tapsmofrq (such as cfg.foi=[39 39] cfg.tapsmofrq=9)? 2. the cfg.tapsmofrq option only exist in the ft_freqanalysis function, and not in the ft_sourceanalysis function. in ft_sourceanalysis the only option is cfg.frequency which, as I mention, has to be a scalar. My question is whether defining the cfg.tapsmofrq in the ft_freqanalysis is also causing the source analysis to use the range of frequencies and not the single frequency. *Thanks a lot,* *Noa* 2015-04-16 14:53 GMT+03:00 Tzvetan Popov : > > Dear Noa, > > you should use frequency smoothening to achieve this. For example, a > configuration of cfg.foilim = [20 20] ; and cfg.tapsmofrq = 10; will allow > you to estimate sources in the 10 to 30 Hz band. > > Hi all, > > I'm doing source analysis in the frequency domain of a resting-state data. > when doing the source analysis, I want to use several frequency bands of > interest, such as beta (13-30 Hz) and gamma (30-48 Hz). > My problem is about the cfg.frequency parameter, which must be a scalar > (whereas i'm interested in a frequency band). Arbitrarily choosing a > frequency in the middle of the range doesn't seem right. > > What is the common practice when doing source analysis using this function? > > You could evaluate this tutorial: > http://www.fieldtriptoolbox.org/tutorial/beamformer > > Does the cfg.tapsmofrq parameter is supposed to enable choosing frequency > band instead of a single peak frequency? > > and some detailed explanation in a pictorial form here: > https://www.youtube.com/watch?v=7eS11DtbIPw > > best > tzvetan > > > Any suggestions will be very much helpful! > > Thanks, > Noa > > > > > > > > > > > > > > *This is the script I’m using: cfg = []; cfg.method ='mtmfft'; > cfg.output ='fourier'; cfg.keeptapers = 'yes'; cfg.foilim = [30 > 48]; cfg.tapsmofrq = 2; > freqClosed=ft_freqanalysis(cfg,eyesClosed); * > > cfg = []; > cfg.method='pcc'; > cfg.frequency = 39; % must be a scalar > cfg.lambda = 0; > cfg.vol = vol; > cfg.grid = grid; > cfg.feedback = 'textbar'; > cfg.keepfilter='yes'; > source1 = ft_sourceanalysis(cfg, freqClosed); > > > -- > My signature: > > http://www.documentarywire.com/earthlings/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- מעכשיו זאת החתימה שלי.. חובה לראות http://www.documentarywire.com/earthlings/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From stidimitriadis at gmail.com Sun Apr 19 19:03:09 2015 From: stidimitriadis at gmail.com (Stavros Dimitriadis) Date: Sun, 19 Apr 2015 10:03:09 -0700 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: <04EC09B5-FE5B-491A-965A-5BACFC4C29EE@psi.ucm.es> References: <201504161745.05273.Holger.Krause@med.uni-duesseldorf.de> <04EC09B5-FE5B-491A-965A-5BACFC4C29EE@psi.ucm.es> Message-ID: Dear All In Greece it works fine ! Best wishes Dimitriadis Stavros, PhD Research Fellow Aristotle University of Thessaloniki, Greece Department of Informatics http://users.auth.gr/~stdimitr/index.html 1)Artificial Intelligence Information Analysis lab Department of Informatics *Aristotle University of Thessaloniki * 2)NeuroInformatics.GRoup , AUTH, Greece 2015-04-17 2:09 GMT-07:00 smoratti at psi.ucm.es : > > in Spain it seems to work… > > best, > > Stephan > > ________________________________________________________ > Stephan Moratti, PhD > > see: Stephan's research profile > > > Universidad Complutense de Madrid > Facultad de Psicología > Departamento de Psicología Básica I > Campus de Somosaguas > Despacho (Office) 1326-0 > 28223 Pozuelo de Alarcón (Madrid) > Spain > > and > > Center for Biomedical Technology > Laboratory for Cognitive and Computational Neuroscience > Parque Científico y Tecnológico de la Universidad Politecnica de Madrid > Campus Montegancedo > 28223 Pozuelo de Alarcón (Madrid) > Spain > > > email: smoratti at psi.ucm.es > Tel.: +34 679219982 > > El 16/04/2015, a las 17:45, Holger Krause escribió: > > Am Donnerstag, 16. April 2015 schrieb Lam, N.H.L. (Nietzsche): > > Please check whether the videos are available in your country (click on one > > of the scheduled live stream videos - you should see a clock that counts > > down to the lecture). If you get the message "Live streaming is not > > available in your country due to right issues" please reply to this email > > and state your country so that we can find a solution prior to the toolkit > > next week. We appreciate your help to make this a smooth broadcast. > > > https://www.youtube.com/watch?v=ZBwh0Vm4fh4 > > Germany :-( > > "Live Streaming ist wegen Rechteproblemen in Deutschland leider nicht > möglich." > > Best, > > Holger > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From laura.marzetti at gmail.com Sun Apr 19 19:35:58 2015 From: laura.marzetti at gmail.com (Laura Marzetti) Date: Sun, 19 Apr 2015 19:35:58 +0200 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: References: <201504161745.05273.Holger.Krause@med.uni-duesseldorf.de> <04EC09B5-FE5B-491A-965A-5BACFC4C29EE@psi.ucm.es> Message-ID: In Italy as well :-) Best, Laura Inviato da iPhone > Il giorno 19/apr/2015, alle ore 07:03 PM, Stavros Dimitriadis ha scritto: > > Dear All > In Greece it works fine ! > > Best wishes > Dimitriadis Stavros, PhD > > Research Fellow > Aristotle University of Thessaloniki, Greece > Department of Informatics > http://users.auth.gr/~stdimitr/index.html > > 1)Artificial Intelligence Information Analysis lab Department of Informatics > Aristotle University of Thessaloniki > 2)NeuroInformatics.GRoup , AUTH, Greece > > > 2015-04-17 2:09 GMT-07:00 smoratti at psi.ucm.es : >> >> in Spain it seems to work… >> >> best, >> >> Stephan >> >> ________________________________________________________ >> Stephan Moratti, PhD >> >> see: Stephan's research profile >> >> Universidad Complutense de Madrid >> Facultad de Psicología >> Departamento de Psicología Básica I >> Campus de Somosaguas >> Despacho (Office) 1326-0 >> 28223 Pozuelo de Alarcón (Madrid) >> Spain >> >> and >> >> Center for Biomedical Technology >> Laboratory for Cognitive and Computational Neuroscience >> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid >> Campus Montegancedo >> 28223 Pozuelo de Alarcón (Madrid) >> Spain >> >> >> email: smoratti at psi.ucm.es >> Tel.: +34 679219982 >> >>> El 16/04/2015, a las 17:45, Holger Krause escribió: >>> >>> Am Donnerstag, 16. April 2015 schrieb Lam, N.H.L. (Nietzsche): >>>> Please check whether the videos are available in your country (click on one >>>> of the scheduled live stream videos - you should see a clock that counts >>>> down to the lecture). If you get the message "Live streaming is not >>>> available in your country due to right issues" please reply to this email >>>> and state your country so that we can find a solution prior to the toolkit >>>> next week. We appreciate your help to make this a smooth broadcast. >>> >>> https://www.youtube.com/watch?v=ZBwh0Vm4fh4 >>> >>> Germany :-( >>> >>> "Live Streaming ist wegen Rechteproblemen in Deutschland leider nicht >>> möglich." >>> >>> Best, >>> >>> Holger >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Sun Apr 19 19:49:20 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Sun, 19 Apr 2015 19:49:20 +0200 Subject: [FieldTrip] Beamforming analysis in frequency band In-Reply-To: References: <9BC70F24-9E97-4247-B0C0-365CCC154C70@uni-konstanz.de> Message-ID: <5F97C157-EB31-41B1-8F19-6DFB1D3E6E1C@uni-konstanz.de> Dear Noa, > Thank you Tzvetan! > > This raised two more question regarding the source analysis: > > 1. What is the difference between defining the frequency range under cfg.foi (such as cfg.foi=[30 48]) and defining if under the cfg.tapsmofrq (such as cfg.foi=[39 39] cfg.tapsmofrq=9)? The difference is that in the resulting output of ft_freqanalysis (lets name it freq) will contain a freq.freq field containing of 19 freq bins presuming frequency resolution of 1 Hz. Each of these is computed with smofrq of plus minus 9 Hz. In the second case freq.freq is one frequency bin namely 39 Hz. > 2. the cfg.tapsmofrq option only exist in the ft_freqanalysis function, and not in the ft_sourceanalysis function. in ft_sourceanalysis the only option is cfg.frequency which, as I mention, has to be a scalar. My question is whether defining the cfg.tapsmofrq in the ft_freqanalysis is also causing the source analysis to use the range of frequencies and not the single frequency. Yes. best tzvetan > > Thanks a lot, > Noa > > 2015-04-16 14:53 GMT+03:00 Tzvetan Popov : > > Dear Noa, > > you should use frequency smoothening to achieve this. For example, a configuration of cfg.foilim = [20 20] ; and cfg.tapsmofrq = 10; will allow you to estimate sources in the 10 to 30 Hz band. > >> Hi all, >> >> I'm doing source analysis in the frequency domain of a resting-state data. >> when doing the source analysis, I want to use several frequency bands of interest, such as beta (13-30 Hz) and gamma (30-48 Hz). >> My problem is about the cfg.frequency parameter, which must be a scalar (whereas i'm interested in a frequency band). Arbitrarily choosing a frequency in the middle of the range doesn't seem right. >> >> What is the common practice when doing source analysis using this function? > You could evaluate this tutorial: > http://www.fieldtriptoolbox.org/tutorial/beamformer > >> Does the cfg.tapsmofrq parameter is supposed to enable choosing frequency band instead of a single peak frequency? > and some detailed explanation in a pictorial form here: > https://www.youtube.com/watch?v=7eS11DtbIPw > > best > tzvetan > >> >> Any suggestions will be very much helpful! >> >> Thanks, >> Noa >> >> >> This is the script I’m using: >> >> cfg = []; >> cfg.method ='mtmfft'; >> cfg.output ='fourier'; >> cfg.keeptapers = 'yes'; >> cfg.foilim = [30 48]; >> cfg.tapsmofrq = 2; >> freqClosed=ft_freqanalysis(cfg,eyesClosed); >> >> >> >> cfg = []; >> cfg.method='pcc'; >> cfg.frequency = 39; % must be a scalar >> cfg.lambda = 0; >> cfg.vol = vol; >> cfg.grid = grid; >> cfg.feedback = 'textbar'; >> cfg.keepfilter='yes'; >> source1 = ft_sourceanalysis(cfg, freqClosed); >> >> >> -- >> My signature: >> >> http://www.documentarywire.com/earthlings/ >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > מעכשיו זאת החתימה שלי.. חובה לראות > > http://www.documentarywire.com/earthlings/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.maris at donders.ru.nl Tue Apr 21 07:38:52 2015 From: e.maris at donders.ru.nl (Maris, E.G.G. (Eric)) Date: Tue, 21 Apr 2015 05:38:52 +0000 Subject: [FieldTrip] coherence and group analyses In-Reply-To: References: Message-ID: <5B808383-6841-4F99-AEE9-73D64A807C47@donders.ru.nl> Dear Jean-Marc Lina, I’m sorry for this very late reply. Your post (which I requested) had slipped my attention. Involved in source analyses from MEG/EEG data, I am going through your papers related to statistical testing (Nonparametric stat testing of coherence differences, 2007 and stat testing in electrophys studies, 2012). Mostly concerned with coherence and coherency (either topography or tomography), I have some questions related to nonparametric statistical testing in the case where we have 2 groups (one group per condition, N subjects in each group) of individuals (n trials for each subjects). I will greatly appreciated some information that could help clarifying the followings: - how do we design the null distribution? permutations are among all subjects? How do we handle fixed/random effects? When you have multiple subjects, you should go for a random effects analysis. This implies that the ingredients for your statistical analysis are coherence values for every subject within every condition. What you do next depends on whether you have a within-groups or a between-groups design. In a within-groups design, every subject has participated in the multiple experimental conditions that you want to compare, and in a between-groups design, every subject has participated in only a single condition and you want to compare these conditions (e.g., patients versus controls, high-versus-low performers). In a within-groups design, the permutation distribution is obtained by randomly permuting the conditions within every subject. In a between-groups design, the permutation distribution is obtained by randomly permuting the subjects between the conditions. - Can we reproduce stricto sensu the Monte-Carlo approach described in the 2007 publication at the level of subjects (each subject being a UO) ? For an analysis that involves all subjects, the permutation distribution is obtained in a different way as described in the 2007 paper. In that paper, we had between-trials design, which is formally equivalent to a between-subjects designs (involving random permutations of trials between conditions). In a random effects analysis of the data of all subjects, one has to randomly permute the subject-level coherences between the conditions within every subject. - Can we use the stat defined as the difference of the imaginary part of the coherence ? (averaged over the subjects in a group?) Yes, you can use every statistic you expect to be sensitive for the phenomenon that you are investigating. Best, Eric With my anticipated thanks, Best JM Lina From: Robert Oostenveld > Cc: > To: FieldTrip discussion list > Date: 3 Mar 2015 21:54:55 CET Reply-To: FieldTrip discussion list > Subject: Re: [FieldTrip] Magnetic dipole fit vs Equiv. Current dipole fit Hi Jim You can do an inverse solution with any method (including dipole fitting) by specifying cfg.vol=[] in the corresponding high-level function (e.g. ft_prepare_leadfield, ft_dipolefitting or ft_sourceanalysis). This causes the forward model to be computed with a magnetic dipole. If you want to track this down to the lower lever code, have a look at these lines in the code “forward/ft_voltype.m" line 115 of 138 --83%-- col 11 “forward/ft_compute_leadfield.m" line 280 of 611 --45%-- col 12 My appologies for this not being documented better. I have been using this myself to check on the localization of the headcoils in the CTF “hz.ds” datasets, which worked fine. I hope you can get it to work for the Sandia Labs system. For the CTF system it is not needed to do these computations in MATLAB, since the CTF electronics does this in (alomst) real-time and the positions are streamed along with the MEG channel data. That makes this this http://fieldtrip.fcdonders.nl/getting_started/realtime_headlocalizer easy for the system we have in Nijmegen. Arjen and I have also been working on making it work for the Elekta system where the fitting has to be done in MATLAB, but have not been able sofar to get it to work robustly. You can find the experiences and (still open) report at http://bugzilla.fcdonders.nl/show_bug.cgi?id=1792. best regards Robert On 25 Feb 2015, at 22:40, Jim McKay > wrote: Hello Fieldtrippers, I am consulting with the Sandia Labs on development of an atomic magnetometer based MEG system prototype. One of the areas I am working on is head localization, so I was looking at the code for the realtime head localization in Fieldtrip. I was surprised to see that although the comments talk about using a magnetic dipole forward solution, it actually used the FT dipolefit code which is based on an equivalent current dipole, as far as I can tell. There should be a significant difference in the forward solutions between MD and ECD, so how does this work? Or am I just missing something? Cheers, Jim -- Jim McKay Candoo Systems Inc. - Magnetic field sensors, systems, and site surveys Tel. 778-840-0361 jim.mckay at candoosys.com www.candoosys.com _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From: Robert Oostenveld > To: FieldTrip discussion list > Date: 3 Mar 2015 22:14:42 CET Reply-To: FieldTrip discussion list > Subject: Re: [FieldTrip] inconsistent chanunit for Neuromag data Hi Steve The grad.chanunit pertains to the units that would be computed as the forward solution. The hdr.chanunit pertains to the units of the channel-level data. Using the ft_convert_units helper function you could convert the units of the gradiometer definition from cm to mm or m. This changes the baseline of the planar gradiometers with a factor of 10 or 100. However, the planar gradient chanel data is not updated simultaneously and remains in the same units (fieldstrength per distance). So it can happen that grad.chanunit and hdr.chanunit are inconsistent. The consequence (which many people on the list will have noticed, but might not have understood) is that the forward solution - and therefore the inverse solution - for the Elekta planar gradiometer channels can easily be incorrect: due to the data being in T/m and the forward solution in T/cm (or some other units, I don’t know the typical units from the top of my head). As long as you always use the same pipeline on hte planar gradiometers, you will most likely not notice since you will be interpreting the sourc estimates in “arbitrary units” anyway. But if you were to combine the planar channels with the magnetometers, the planar channels (fieldstrength per distance) would be affected differently than the manetometer channels (fieldstrength) by your choise of geometrical units. Using the ft_datatype_sens helper function you can ensure that the scaling of the grad structure (which affects the “coilpos" field but also the rows of the “tra" field that correspond to the planar channels) is consistent with your channel level data. If you specify all your data in SI units (T, m, V, etc.) the units of the forward computations will be correct and hence the units of the inverse estimates will also be consistent in SI units (e.g. dipole moment in A/m). The thing is that the different fieldtrip import functions (which come from various origins) return data in non-SI units more often than not :-( If you work with channel level data, SI units are often not nice. ERFs in Tesla are very small (10^-12). ERPs are usually expressed in uV. Also for anatomcial MRIs it is not convenient to express data in SI units (m) and mm is common. The CTF system by default expresses geometrical distance in cm. Etc… So all systems by themselves made their own “convenient” choices. But if all the data comes together with the physical model, it becomes a mess. The logical choice to solve the inconsistencies is to express it in SI units. I hope this helps in clarifying the situation. best regards, Robert PS if you search on bugzilla, you can see some (still open) bugs that pertain to this On 27 Feb 2015, at 03:53, Steve Patterson > wrote: Hello, I noticed that fieldtrip produces inconsistent channel units when I read in Neuromag (vectorview) data. For example: %%%%%%%%%%%%%%%%%%%%%%%% cfg = []; cfg.dataset = 'example.fif'; cfg.trialfun = 'ft_trialfun_general'; cfg.trialdef.eventtype = 'STI101'; cfg.trialdef.eventvalue = [17 18 20]; cfg.trialdef.prestim = 0.500; cfg.trialdef.poststim = 1.000; cfg = ft_definetrial(cfg); data = ft_preprocessing(cfg); disp(data.hdr.chanunit(1:6)); 'T/m' 'T/m' 'T' 'T/m' 'T/m' 'T' disp(data.grad.chanunit(1:6)); 'T' 'T' 'T' 'T' 'T' 'T' %%%%%%%%%%%%%%%%%%%%%%%% data.hdr.chanunit is correct and data.grad.chanunit is wrong. data.grad.chanunit must take precedence in further analysis, because I've noticed this causes problems downstream. For example, when using ft_dipolesimulation, the simulated data on the gradiometer channels is too small in amplitude by a factor of 1/(16.8E-3) (the distance between the gradiometer coil pair in meters). This is reflected in the grad.tra matrix, whose non-zero values are all 1's and -1's, whereas they should be 1's (magnetometers), and +/- 1/16.8E-3 (gradiometers). If you could fix this, it would be much appreciated! thanks, Steve _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From: Robert Oostenveld > To: FieldTrip discussion list > Date: 3 Mar 2015 22:18:34 CET Reply-To: FieldTrip discussion list > Subject: Re: [FieldTrip] eeglab2fieldtrip - Fieldtrip vs EEGLAB version Hi Omar, The eeglab2fieldtrip.m function lives on the boudary between the two projects. We (i.e. Arno and me) have decided to maintain it on the EEGLAB side and copy it to FieldTrip whenever needed. That is why it is in fieldtrip/external/eeglab. If you go to https://code.google.com/p/fieldtrip/source/list?path=/trunk/external/eeglab/eeglab2fieldtrip.m&start=10122 you can see the history. See also http://bugzilla.fcdonders.nl/show_bug.cgi?id=2770 In general for (almost) all code in fieldtrip/external it is being maintained externally, and often by people that are not directly related to the fieldtrip project. best Robert On 16 Feb 2015, at 16:38, Mian, Omar > wrote: Hello, There seem to be differences between the eeglab2fieldtrip.m when the Fieldtrip and EEGLAB versions are compared. Is this an oversight? Which one is “better” ? data.cfg.version.id contains a later date in the Fieldtrip version, but the file properties modified date is later in the EEGLAB version. The versions I am comparing are: \fieldtrip-20150109\external\eeglab\eeglab2fieldtrip.m \eeglab13_4_4b\plugins\dipfit2.3\eeglab2fieldtrip.m Thanks Omar --------------------------- Omar Mian, Phd Research Fellow School of Applied Sciences London South Bank University 103 Borough Road London SE1 0AA Copyright in this email and in any attachments belongs to London South Bank University. This email, and its attachments if any, may be confidential or legally privileged and is intended to be seen only by the person to whom it is addressed. If you are not the intended recipient, please note the following: (1) You should take immediate action to notify the sender and delete the original email and all copies from your computer systems; (2) You should not read copy or use the contents of the email nor disclose it or its existence to anyone else. The views expressed herein are those of the author(s) and should not be taken as those of London South Bank University, unless this is specifically stated. London South Bank University is a company limited by guarantee registered in England and Wales. The following details apply to London South Bank University: Company number - 00986761; Registered office and trading address - 103 Borough Road London SE1 0AA; VAT number - 778 1116 17 Email address - LSBUinfo at lsbu.ac.uk _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From: Tolga Ozkurt > To: > Date: 4 Mar 2015 09:54:53 CET Reply-To: FieldTrip discussion list > Subject: [FieldTrip] Visualization of Channels for Human Connectome Project MEG data Dear Fieldtrip list, I was seeing the MEG files uploaded by “Human Connectome Project”, which seem to be pre-processed by Fieldtrip. The resting data were collected in supine position with 4D Neuromag 248 channels. When I use the standard command for layout cfg.layout = '4D248.lay'; the channel locations do not seem to fit. (Please see the attached figure). I do not quite know the channel distribution of the system; but it seems some channels are out of the head. Could you give me an idea to project the channel layout properly? Thank you. Tolga -- Tolga Esat Özkurt, PhD Department of Health Informatics Middle East Technical University http://www.metu.edu.tr/~ozkurt/ From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Date: 4 Mar 2015 11:34:27 CET Reply-To: FieldTrip discussion list > Subject: Re: [FieldTrip] Visualization of Channels for Human Connectome Project MEG data Hi Tolga, There’s a layout that ‘better fits’ the projected channel locations, and which you can obtain from the megconnectome software that accompanies the HCP MEG data. The software can be obtained from here: humanconnectome.org/documentation/MEG1/meg-pipeline.html If you download one of the packages and unzip it, you’ll find a ‘template’ directory. Inside, there’s a 4D248.mat file (note that you need the ‘4D248.mat’ in cfg.layout in that case), which you can use as a layout for visualization. Best wishes, Jan-Mathijs On Mar 4, 2015, at 9:54 AM, Tolga Ozkurt > wrote: Dear Fieldtrip list, I was seeing the MEG files uploaded by “Human Connectome Project”, which seem to be pre-processed by Fieldtrip. The resting data were collected in supine position with 4D Neuromag 248 channels. When I use the standard command for layout cfg.layout = '4D248.lay'; the channel locations do not seem to fit. (Please see the attached figure). I do not quite know the channel distribution of the system; but it seems some channels are out of the head. Could you give me an idea to project the channel layout properly? Thank you. Tolga -- Tolga Esat Özkurt, PhD Department of Health Informatics Middle East Technical University http://www.metu.edu.tr/~ozkurt/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From joscha.schmiedt at esi-frankfurt.de Tue Apr 21 10:52:36 2015 From: joscha.schmiedt at esi-frankfurt.de (Schmiedt, Joscha) Date: Tue, 21 Apr 2015 08:52:36 +0000 Subject: [FieldTrip] A Fieldtrip data format? In-Reply-To: References: <5548CAB3-F9A2-4C6B-B958-3CF27CF2C27F@esi-frankfurt.de> , Message-ID: <17F994D43E9ADA418DE0040CC6F4A96B7FD2964A@UM-EXCDAG-A01.um.gwdg.de> Hey, For your information: there is a concerted effort by many big labs to create a standard data format for electrophysiology: https://crcns.org/NWB/Overview It will actually be based on HDF5. Joscha ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Schmiedt, Joscha [joscha.schmiedt at esi-frankfurt.de] Sent: Wednesday, April 01, 2015 2:03 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] A Fieldtrip data format? Hi Gio, Thanks for the info. The fcdc_matbin approach indeed would be suitable data for raw data. However, I’m looking for a fast solution for data that is already processed and cut into trials, in particular with varying trial length. Joscha > On Mar 31, 2015, at 22:39, Gio Piantoni wrote: > > Hi Joscha, > > FieldTrip already has its own simple uncompressed file format. > fcdc_matbin "It is not an official file format, but was invented here > at the FCDC. It consists of two files: a *.mat matlab file that > contains the header (and optionally the events) and a *.bin binary > file that contains the data." > http://www.fieldtriptoolbox.org/faq/reading_is_slow_can_i_write_my_raw_data_to_a_more_efficient_file_format > > If you want to look at the code: > https://github.com/fieldtrip/fieldtrip/blob/master/fileio/ft_write_data.m#L275 > > You should be able to read it as usual with ft_preprocessing. You can > convert your files to the fcdc_matbin using ft_preprocessing as well: > https://github.com/fieldtrip/fieldtrip/blob/master/ft_preprocessing.m#L581 > Be careful about not losing precision though. > > The only catch is that, as far as I know, you cannot export your > preprocessed data through ft_preprocessing at the moment, because > ft_write_data is now inside this if-part: > https://github.com/fieldtrip/fieldtrip/blob/master/ft_preprocessing.m#L252 > but it's only a matter of adapting that to your needs. > > Would this work for you? > > -g > > On Tue, Mar 31, 2015 at 9:09 AM, Schmiedt, Joscha > wrote: >> Hi, >> >> When working with Fieldtrip it is very convenient to store the data and >> analyses using MATLAB’s save and load functions. However, for large and/or >> complex data with many channels (>2GB) MATLAB enforces compression, which is >> pretty useless for electrophysiology data and slows down the load and save >> performance by a factor of up to 8 (see e.g. >> http://undocumentedmatlab.com/blog/improving-save-performance). The MATLAB >> file format is based on HDF5, which is generally an open and future-proof >> data format, but unfortunately MATLAB doesn’t allow you to disable the >> compression. >> >> An option to overcome this could be to develop a simple data format for >> Fieldtrip data that is also based on HDF5. Is or has there been any >> development going into that direction? Would there be any interest? Of >> course, creating yet another data format is almost never a good idea >> (https://xkcd.com/927/), but since HDF5 is well-documented and readable with >> almost any software, it might be worth thinking about it. >> >> I’d be happy to hear your thoughts. >> >> Joscha >> >> --------------------------------- >> Joscha Schmiedt >> PhD Student >> >> Ernst Strüngmann Institute (ESI) for Neuroscience >> in Cooperation with Max Planck Society >> Deutschordenstraße 46 >> 60528 Frankfurt am Main >> Germany >> >> Tel.: +49 (0)69 96769 241 >> >> Sitz der Gesellschaft: Frankfurt am Main >> Registergericht: Amtsgericht Frankfurt - HRB 84266 >> Geschäftsführer: Prof. Dr. Pascal Fries >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From anne.keller at sickkids.ca Tue Apr 21 18:59:07 2015 From: anne.keller at sickkids.ca (Anne Keller) Date: Tue, 21 Apr 2015 16:59:07 +0000 Subject: [FieldTrip] ICA before beamformer In-Reply-To: <69B46D4F7B3C33449A56153DF85867882EA7A0@SKMBXX02.sickkids.ca> References: <69B46D4F7B3C33449A56153DF85867882EA7A0@SKMBXX02.sickkids.ca> Message-ID: <69B46D4F7B3C33449A56153DF85867882EA7C8@SKMBXX02.sickkids.ca> Hi Fieldtrip-ers, I'm working with MEG data collected from children, and I am hoping to do source localization via beamformer. Our kids have lots of eye movement and blinks, so I was hoping to perform ICA prior to beamformer. How can I address the matrix regularization aspect after I remove components? Is there a fieldtrip function that corrects this? Due to lab requirements, I will be using SPM's beamformer (but Fieldtrip's ICA and reject components functions). Thanks so much in advance! Best, Anne ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. From drivolta81 at gmail.com Wed Apr 22 11:56:06 2015 From: drivolta81 at gmail.com (Davide Rivolta) Date: Wed, 22 Apr 2015 09:56:06 +0000 Subject: [FieldTrip] 20 PhD excellence scholarships at UEL Message-ID: Dear all, I just wish to let you know that 20 fully-funded UEL Excellence Studentships will be made available to PhD applicants, starting September 2015 (www.uel.ac.uk/studentships). For more information please do not hesitate to contact Ben Whitham in the Graduate School (B.Whitham at uel.ac.uk). Bests, Davide -- Davide Rivolta, PhD -------------- next part -------------- An HTML attachment was scrubbed... URL: From singhharsimrat at gmail.com Wed Apr 22 14:13:50 2015 From: singhharsimrat at gmail.com (Harsimrat Singh) Date: Wed, 22 Apr 2015 13:13:50 +0100 Subject: [FieldTrip] Compatibility of ft_layoutplot with MATLAB 2014b Message-ID: Hi Fieldtrippers I think I might have found a problem in ft_layoutplot compatibility with the newer versions of MATLAB. Now MATLAB doesn't let you add numeric values to an array of graphics objects - hence it throws an error Error using sprintf Function is not defined for 'matlab.ui.Figure' inputs. Best regards Harsimrat -------------------------------------------- *Dr Harsimrat Singh* *Department of Cancer and Surgery* *St. Marys Hospital Campus* *Imperial College London* *Praed Street, London W2 1NY* *harsimrat.singh at imperial.ac.uk * -------------- next part -------------- An HTML attachment was scrubbed... URL: From luke.bloy at gmail.com Wed Apr 22 22:55:14 2015 From: luke.bloy at gmail.com (Luke Bloy) Date: Wed, 22 Apr 2015 16:55:14 -0400 Subject: [FieldTrip] Source localizing resting state data Message-ID: Hi everyone, Following up on two recent email threads ( http://mailman.science.ru.nl/pipermail/fieldtrip/2015-April/009120.html and http://mailman.science.ru.nl/pipermail/fieldtrip/2015-January/008796.html) I'd like to ask the fieldtrip community what they feel is the best source localization methods for resting state data? Note that at this point i'm only thinking about simple things like localizing resting alpha and beta rhythms. -Thanks Luke -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Thu Apr 23 08:47:21 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Thu, 23 Apr 2015 08:47:21 +0200 Subject: [FieldTrip] Compatibility of ft_layoutplot with MATLAB 2014b In-Reply-To: References: Message-ID: <98A59F44-6729-41F0-AA81-D26E523B7584@uni-konstanz.de> Dear Harsimrat, Please update your FT version. This should solve the issue. Best Tzvetan > Am 22.04.2015 um 14:13 schrieb Harsimrat Singh : > > Hi Fieldtrippers > > I think I might have found a problem in ft_layoutplot compatibility with the newer versions of MATLAB. Now MATLAB doesn't let you add numeric values to an array of graphics objects - hence it throws an error > > Error using sprintf > Function is not defined for 'matlab.ui.Figure' inputs. > > Best regards > Harsimrat > > -------------------------------------------- > Dr Harsimrat Singh > Department of Cancer and Surgery > St. Marys Hospital Campus > Imperial College London > Praed Street, London W2 1NY > harsimrat.singh at imperial.ac.uk > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From ofcastaneda at outlook.com Thu Apr 23 15:58:27 2015 From: ofcastaneda at outlook.com (=?utf-8?B?T3NjYXIgRmVybmFuZG8gQ2FzdGHDsWVkYSBGZXJuw6FuZGV6?=) Date: Thu, 23 Apr 2015 13:58:27 +0000 Subject: [FieldTrip] =?utf-8?q?Using_Fieldtrip_with_BCI2000?= Message-ID: Dear community, My name is Oscar Castañeda and I’ve been using the Fieldtrip Buffer to extract samples from BCI2000; the samples were obtained using an Emotiv Headset. However, I have a problem with data adquisition: When I use the instruction ft_read_data(filename, ‘header’,hdr,‘begsample’,begsample,’endsample’,endsample,’chanindx’,chanindx) [where chanindx is a list going from number 1 to 14] and I compare the obtained data with the one stored in the corresponding BCI2000 .dat file, I find that the samples are equal for the first Emotiv cannel (AF3), just as we would expect. But for the rest of channels, the data returned by ft_read_data is not equal to the one from the .dat file, and varies in a non-constant proportion of 90% to 110% of the .dat sample. Why could this be happening? I would appreciate very much any kind of help. Thank you very much, Oscar -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.herring at donders.ru.nl Thu Apr 23 22:33:53 2015 From: j.herring at donders.ru.nl (Herring, J.D. (Jim)) Date: Thu, 23 Apr 2015 20:33:53 +0000 Subject: [FieldTrip] ICA before beamformer In-Reply-To: <69B46D4F7B3C33449A56153DF85867882EA7C8@SKMBXX02.sickkids.ca> References: <69B46D4F7B3C33449A56153DF85867882EA7A0@SKMBXX02.sickkids.ca> <69B46D4F7B3C33449A56153DF85867882EA7C8@SKMBXX02.sickkids.ca> Message-ID: <2E61E12F-DC21-4FB9-B91F-8FDD4843B311@donders.ru.nl> Dear Anne, If I am not mistaken SPM actually uses Fieldtrip’s DICS beamformer implementation. In any case, after doing ICA the grad field in your data structure should be corrected so you should be safe in using SPM's beamformer given that you use the grad contained in the data structure produced after cleaning with ICA in Fieldtrip. Best, Jim > On 21 Apr 2015, at 18:59, Anne Keller wrote: > > Hi Fieldtrip-ers, > > I'm working with MEG data collected from children, and I am hoping to do source localization via beamformer. Our kids have lots of eye movement and blinks, so I was hoping to perform ICA prior to beamformer. How can I address the matrix regularization aspect after I remove components? Is there a fieldtrip function that corrects this? Due to lab requirements, I will be using SPM's beamformer (but Fieldtrip's ICA and reject components functions). > > Thanks so much in advance! > > Best, > Anne > > ________________________________ > > This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From ronny.ibrahim at mq.edu.au Fri Apr 24 06:49:11 2015 From: ronny.ibrahim at mq.edu.au (Ronny Ibrahim) Date: Fri, 24 Apr 2015 14:49:11 +1000 Subject: [FieldTrip] MEG160 KIT layout file template Message-ID: Hi Community, I was wondering whether there is any fieldtrip '.lay' layout file for the MEG160 KIT system that I am currently using : This is a paper on the MEG system http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=783918 I have tried reading the coordinates using ft_read_header from the '*.con' file and trying to use this information to construct my own '.lay' file based on the Yokogawa's yokogawa440pg.lay planar gradiometer layout file ( while removing several sensors which weren't there in the MEG160 KIT system) but after plotting a few eye-blink responses, the topo_plot output does not seem to look right. Therefore, I would like to thank you for your kind help and inputs in resolving my simple issue here. Any help will be much appreciate it. Kind Regards, Ronny -------------- next part -------------- An HTML attachment was scrubbed... URL: From annika.notbohm at uni-oldenburg.de Fri Apr 24 11:51:37 2015 From: annika.notbohm at uni-oldenburg.de (Annika Notbohm) Date: Fri, 24 Apr 2015 11:51:37 +0200 Subject: [FieldTrip] PhD-Conference: Entrainment of Brain Oscillations (EBO) in Oldenburg, Germany Message-ID: <553A1229.3070500@uni-oldenburg.de> Dear (PhD-) students of brain oscillations and entrainment, we want to call your attention to our PhD conference: * **Entrainment of Brain Oscillations (EBO) * at 17th-18th September 2015 at the Hanse Wissenschaftskolleg (Delmenhorst, Germany). The conference is organized by four PhD students from the University of Oldenburg, together with Prof. Dr. Christoph Herrmann. Confirmed keynote speakers are /Prof. Dr. Ole Jensen (Donders Institute)/ and /Prof. Dr. Joachim Gross (University of Glasgow)/ who will also hold a one day workshop on "Analytical methods for studies of brain oscillations" as a pre-meeting to the conference. If you are interested in participating at our conference, please submit a poster abstract following the guidelines on our website (http://www.uni-oldenburg.de/ebo/abstract-submission). As we intend to realize a fair selection of poster abstracts, we kindly ask you to use the abstract template for blinded submission, as can be found on the link given above. POSTER DEADLINE: JUNE 20th 2015 Three symposia will be held during the conference which deal with entrainment of brain oscillations by using auditory, visual or electrical methods. The main focus in all three sessions will lie on basic research on the mechanism of entrainment as well as on causality of modified oscillations and behavior. We intend to create a platform that allows intensive exchange and potential collaborations between the participants. Therefore, the conference will be kept rather small (50 participants) and specific regarding the topic. More detailed information and a (preliminary) program can be found on the website www.uni-oldenburg.de/EBO. For further questions don't hesitate to contact us via EBO at uni-oldenburg.de. Please feel free to forward this e-mail to others who could be interested in our conference. Best regards, Alina Baltus, Anna-Katharina Bauer, Annika Notbohm and Johannes Vosskuhl -- Annika Notbohm, M.Sc. Experimental Psychology Lab Department of Psychology European Medical School Carl von Ossietzky Universität Ammerländer Heerstr. 114-118 26129 Oldenburg, Germany Tel: +49 441 798 2628 Mobile: +49 176 22716261 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mehmetakifozcoban at gmail.com Fri Apr 24 15:22:49 2015 From: mehmetakifozcoban at gmail.com (=?UTF-8?B?TWVobWV0IEFraWYgw5Z6w6dvYmFu?=) Date: Fri, 24 Apr 2015 16:22:49 +0300 Subject: [FieldTrip] =?utf-8?b?SMSx?= Message-ID: -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Fri Apr 24 17:02:49 2015 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Fri, 24 Apr 2015 17:02:49 +0200 Subject: [FieldTrip] =?utf-8?b?SMSx?= In-Reply-To: References: Message-ID: Hi! On 24 April 2015 at 15:22, Mehmet Akif Özçoban wrote: > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From haiteng.jiang at gmail.com Sun Apr 26 16:38:48 2015 From: haiteng.jiang at gmail.com (Haiteng Jiang) Date: Sun, 26 Apr 2015 16:38:48 +0200 Subject: [FieldTrip] Source localizing resting state data (Luke Bloy) Message-ID: Hi Luke, In my experience, the best way to deal with central bias issue is leadfield normalization on resting state . This is much more robust compared to neural activity index (NAI) across subjects. You can specify cfg.normalize = 'yes' when you compute leadfied using ft_prepare_leadfield function . This strategy gave me satisfactory results in the end. Hope this helps, Haiteng > > Message: 2 > Date: Wed, 22 Apr 2015 16:55:14 -0400 > From: Luke Bloy > To: FieldTrip list serve > Subject: [FieldTrip] Source localizing resting state data > Message-ID: > < > CAG5Ru-pJKH91o9EHD+kc53TQXc8F3X4Ogsa0UOC5wiJmLPvEvA at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi everyone, > > Following up on two recent email threads ( > http://mailman.science.ru.nl/pipermail/fieldtrip/2015-April/009120.html > and > http://mailman.science.ru.nl/pipermail/fieldtrip/2015-January/008796.html > ) > > I'd like to ask the fieldtrip community what they feel is the best source > localization methods for resting state data? Note that at this point i'm > only thinking about simple things like localizing resting alpha and beta > rhythms. > > -Thanks > Luke > > -- Haiteng Jiang PhD candidate Donders Institute for Brain, Cognition and Behaviour Neuronal Oscillations Group Computational Cognitive Neuroscience Lab https://sites.google.com/site/haitengjiang/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From Olaf.Hauk at mrc-cbu.cam.ac.uk Tue Apr 28 17:41:54 2015 From: Olaf.Hauk at mrc-cbu.cam.ac.uk (Olaf Hauk) Date: Tue, 28 Apr 2015 15:41:54 +0000 Subject: [FieldTrip] Methods Skills Survey Message-ID: Hello - I would be very grateful if you could participate in this methods skills survey, which will help the development of future methods training events. It is anonymous and should take about 10-15 minutes. Please participate only once. Please visit this link to go to the survey: https://www.surveymonkey.com/s/3JL2CZX Are you an undergraduate student, PhD student, or post-doc who is working or planning to work in the cognitive sciences? If so, then we would like to invite you to participate in an online survey that will help us develop more efficient methods training programmes for cognitive scientists and neuroscientists. Cognitive science and neuroscience are highly interdisciplinary, and it is important for us to know the skills of researchers who are moving into these fields. The survey should take you 10-15 minutes, and you will be asked some questions related to data analysis as well as about yourself (but you will remain anonymous). You will not receive any remuneration for your participation - but your information may benefit a large number of future students in the cognitive sciences. This is not an exam. Depending on your background, you may not be able to answer some or even many of these questions at all - but this information is also very useful to us. Please only participate in this survey once, and please do not consult the internet, books or friends to answer the questions. This survey is run by Dr. Olaf Hauk from the MRC Cognition and Brain Sciences Unit, Cambridge, UK. The data from this survey may be used in future presentations and publications. Olaf Hauk, PhD MRC Cognition and Brain Sciences Unit Phone: +44(0)1223 273702 Fax: +44(0)1223 359062 Web: http://www.mrc-cbu.cam.ac.uk/people/olaf.hauk/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From joseluisblues at gmail.com Wed Apr 29 09:35:47 2015 From: joseluisblues at gmail.com (Jose) Date: Wed, 29 Apr 2015 09:35:47 +0200 Subject: [FieldTrip] fast & coarse artifact rejection Message-ID: Dear fellows, My name is José Luis, I’m working with Micromed data in the Clinic Research Unit in Ville-Evrard in France. I succeed at importing and reading my data with Fieldtrip. I would like to do a superficial and fast ERP analysis (just for checking purposes), and I was wondering if there any way to tell Fieldtrip to remove trials that exceed a threshold (like -+80 uV). Meaning that I don’t want to go through ICA or any other method like this (for the moment). Is that possible?, Any hint would be appreciated. best, José Luis -- José Luis ULLOA FULGERI 33 (0)6.29.50.64.93 -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.herring at donders.ru.nl Wed Apr 29 09:54:49 2015 From: j.herring at donders.ru.nl (Herring, J.D. (Jim)) Date: Wed, 29 Apr 2015 07:54:49 +0000 Subject: [FieldTrip] fast & coarse artifact rejection In-Reply-To: References: Message-ID: <8D64FA7B-D59E-41F0-AC21-3A09289C4A84@donders.ru.nl> Hi Jose, Yes, using ft_artifact_zvalue you can z-transform your data and mark trials for rejection that exceed a certain threshold. Marked trials can be rejected with ft_rejectartifact. See http://www.fieldtriptoolbox.org/tutorial/automatic_artifact_rejection for a walkthrough and examples. Best, Jim On 29 Apr 2015, at 09:35, Jose > wrote: Dear fellows, My name is José Luis, I’m working with Micromed data in the Clinic Research Unit in Ville-Evrard in France. I succeed at importing and reading my data with Fieldtrip. I would like to do a superficial and fast ERP analysis (just for checking purposes), and I was wondering if there any way to tell Fieldtrip to remove trials that exceed a threshold (like -+80 uV). Meaning that I don’t want to go through ICA or any other method like this (for the moment). Is that possible?, Any hint would be appreciated. best, José Luis -- José Luis ULLOA FULGERI 33 (0)6.29.50.64.93 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From barbara.schorr at uni-ulm.de Wed Apr 29 11:01:30 2015 From: barbara.schorr at uni-ulm.de (Barbara Schorr) Date: Wed, 29 Apr 2015 11:01:30 +0200 Subject: [FieldTrip] Renormalized PDC In-Reply-To: References: Message-ID: <55409DEA.70404@uni-ulm.de> Dear Fieldtrippers, I am working on a connectivity analysis (partial directed coherence) in EEG data. I found this paper by Schelter, B.; Timmer, J.; Eichler, M. (2009). "Assesssing the strength of directed influences among neural signals using renormalized partial directed coherence"./J. Neurosci Methods/*179*(1): who suggest to rather use a renormalized PDC. Has anybody here used this before and could tell me how to calculate this rPDC in Fieldtrip? All the best, Barbara Am 27.04.2015 um 12:00 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 > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Re: Source localizing resting state data (Luke Bloy) > (Haiteng Jiang) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 26 Apr 2015 16:38:48 +0200 > From: Haiteng Jiang > To: fieldtrip at science.ru.nl > Subject: Re: [FieldTrip] Source localizing resting state data (Luke > Bloy) > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi Luke, > In my experience, the best way to deal with central bias issue is > leadfield normalization on resting state . This is much more robust > compared to neural activity index (NAI) across subjects. You can specify > cfg.normalize = 'yes' when you compute leadfied > using ft_prepare_leadfield function . This strategy gave me satisfactory > results in the end. > > Hope this helps, > Haiteng > > >> Message: 2 >> Date: Wed, 22 Apr 2015 16:55:14 -0400 >> From: Luke Bloy >> To: FieldTrip list serve >> Subject: [FieldTrip] Source localizing resting state data >> Message-ID: >> < >> CAG5Ru-pJKH91o9EHD+kc53TQXc8F3X4Ogsa0UOC5wiJmLPvEvA at mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi everyone, >> >> Following up on two recent email threads ( >> http://mailman.science.ru.nl/pipermail/fieldtrip/2015-April/009120.html >> and >> http://mailman.science.ru.nl/pipermail/fieldtrip/2015-January/008796.html >> ) >> >> I'd like to ask the fieldtrip community what they feel is the best source >> localization methods for resting state data? Note that at this point i'm >> only thinking about simple things like localizing resting alpha and beta >> rhythms. >> >> -Thanks >> Luke >> >> > -- Barbara Schorr, MSc Clinical and Biological Psychology University of Ulm Albert-Einstein-Allee 47 89069 Ulm Therapiezentrum Burgau Kapuzinerstraße 34 89331 Burgau -------------- next part -------------- An HTML attachment was scrubbed... URL: From guiraudh at gmail.com Wed Apr 29 14:45:56 2015 From: guiraudh at gmail.com (=?UTF-8?B?SMOpbMOobmUgR3VpcmF1ZA==?=) Date: Wed, 29 Apr 2015 14:45:56 +0200 Subject: [FieldTrip] Search for a template children. Message-ID: Dear community, My name is Hélène Guiraud and i'm working in DDL lab in Lyon (France) on speech perception in children using MEG. The children involved in the study don't pass MRI. We want to achieve source reconstruction from a template. However I can't find a template corresponding to the anatomy of a child (8-12 years). Can someone tell me if there are template children and where I can find them? Best, Hélène Guiraud -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.schneider at uke.uni-hamburg.de Wed Apr 29 15:53:13 2015 From: t.schneider at uke.uni-hamburg.de (Till Schneider) Date: Wed, 29 Apr 2015 15:53:13 +0200 Subject: [FieldTrip] Search for a template children. In-Reply-To: References: Message-ID: <5540E249.3000200@uke.uni-hamburg.de> Dear Helene, McGill University provides MNI brains for different age groups between 4.5y to 18y. http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1 You will probably find the template brain you are searching for in this database. Best regards, Till -- Till Schneider, PhD Cognitive and Clinical Neurophysiology Group Dept. of Neurophysiology and Pathophysiology University Medical Center Hamburg-Eppendorf Martinistr. 52 20246 Hamburg Germany phone +49-40-7410-53188 fax +49-40-7410-57126 www.uke.de/neurophysiologie Am 29.04.15 um 14:45 schrieb Hélène Guiraud: > Dear community, > > My name is Hélène Guiraud and i'm working in DDL lab in Lyon (France) > on speech perception in children using MEG. > The children involved in the study don't pass MRI. We want to achieve > source reconstruction from a template. However I can't find a template > corresponding to the anatomy of a child (8-12 years). > Can someone tell me if there are template children and where I can > find them? > > Best, > > Hélène Guiraud > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahjoory86 at gmail.com Wed Apr 29 16:25:35 2015 From: mahjoory86 at gmail.com (Keyvan Mahjoory) Date: Wed, 29 Apr 2015 16:25:35 +0200 Subject: [FieldTrip] ICBM 152 templates in FT Message-ID: Dear Fieldtrip Users, I perform source analysis in Fieldtrip with a template head model ( standard_bem ) and a template source model (cortex_5124.surf.gii ) to constarin estimated sources on cortex. These templates are based on Colin27, But I prefere to use the template ICBM152 instead. Does FT include ICBM template? I mean templates for both head model and cortical surfe. Many Thanks in advance, Keyvan -------------- next part -------------- An HTML attachment was scrubbed... URL: From RICHARDS at mailbox.sc.edu Thu Apr 30 14:12:22 2015 From: RICHARDS at mailbox.sc.edu (RICHARDS, JOHN) Date: Thu, 30 Apr 2015 12:12:22 +0000 Subject: [FieldTrip] re template for children Message-ID: We have a template for children‹actually have for infants from 2 weeks through adults at 89 years. We also have average electrode positions for EGI sensor nets (GSN128, HGSN128) and the 10-10 system; and segmented priors, stereotaxic atlases, and segmented heads (BEM, FEM). I also have been using this recently with FT for infants and child/adolescent/adult ages. WWW site: http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ Fro www site: This is a database of average MRIs and associated MRI volumes for developmental MRI work. It consists of average MRI templates, segmented partial volume estimate volumes for GM, WM, T2W-derived CSF (Description ). The database is separated into head-based and brain-based averages. The data are separated by ages in months, years, 6-month, or 5-year intervals (Ages and Templates ). The templates are grouped into first year (2 weeks through 12 months), early childhood (15 months through 4 years), childhood (4 years through 10 years), adolescence (10.5 years through 17.5 years) and adults (18 years through 89 years). Tools for cortical source analysis of EEG and ERP are provided. These tools are based on the average MRI templates, segmenting, and atlases. Also see my www site, jerlab.psych.sc.edu for publications describing this. We have a recent chapter that has a good description of the issues behind the database (with Wanze Xie). We have a paper accepted at Neuroimage for their upcoming ³Data Sharing² issue (with Carmen Sanchez, Michelle Phillips-Meek, and Wanze Xie). John *********************************************** John E. Richards Carolina Distinguished Professor Department of Psychology University of South Carolina Columbia, SC 29208 Dept Phone: 803 777 2079 Fax: 803 777 9558 Email: richards-john at sc.edu HTTP: jerlab.psych.sc.edu *********************************************** On 4/30/15, 6:00 AM, "fieldtrip-request at science.ru.nl" wrote: >Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > >To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > >You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of fieldtrip digest..." > > >Today's Topics: > > 1. Search for a template children. (H?l?ne Guiraud) > 2. Re: Search for a template children. (Till Schneider) > 3. ICBM 152 templates in FT (Keyvan Mahjoory) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Wed, 29 Apr 2015 14:45:56 +0200 >From: H?l?ne Guiraud >To: fieldtrip at science.ru.nl >Subject: [FieldTrip] Search for a template children. >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Dear community, > >My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) on >speech perception in children using MEG. >The children involved in the study don't pass MRI. We want to achieve >source reconstruction from a template. However I can't find a template >corresponding to the anatomy of a child (8-12 years). >Can someone tell me if there are template children and where I can find >them? > >Best, > >H?l?ne Guiraud >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >9b53e/attachment-0001.html> > >------------------------------ > >Message: 2 >Date: Wed, 29 Apr 2015 15:53:13 +0200 >From: Till Schneider >To: FieldTrip discussion list >Subject: Re: [FieldTrip] Search for a template children. >Message-ID: <5540E249.3000200 at uke.uni-hamburg.de> >Content-Type: text/plain; charset="windows-1252"; Format="flowed" > >Dear Helene, > >McGill University provides MNI brains for different age groups between >4.5y to 18y. >http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1 >You will probably find the template brain you are searching for in this >database. > >Best regards, >Till > >-- > >Till Schneider, PhD > >Cognitive and Clinical Neurophysiology Group >Dept. of Neurophysiology and Pathophysiology >University Medical Center Hamburg-Eppendorf >Martinistr. 52 >20246 Hamburg >Germany > >phone +49-40-7410-53188 >fax +49-40-7410-57126 >www.uke.de/neurophysiologie > > > >Am 29.04.15 um 14:45 schrieb H?l?ne Guiraud: >> Dear community, >> >> My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) >> on speech perception in children using MEG. >> The children involved in the study don't pass MRI. We want to achieve >> source reconstruction from a template. However I can't find a template >> corresponding to the anatomy of a child (8-12 years). >> Can someone tell me if there are template children and where I can >> find them? >> >> Best, >> >> H?l?ne Guiraud >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > >-- > >_____________________________________________________________________ > >Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen >Rechts; Gerichtsstand: Hamburg | www.uke.de >Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Prof. Dr. >Dr. Uwe Koch-Gromus, Joachim Pr?l?, Rainer Schoppik >_____________________________________________________________________ > >SAVE PAPER - THINK BEFORE PRINTING >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >44937/attachment-0001.html> > >------------------------------ > >Message: 3 >Date: Wed, 29 Apr 2015 16:25:35 +0200 >From: Keyvan Mahjoory >To: FieldTrip discussion list >Subject: [FieldTrip] ICBM 152 templates in FT >Message-ID: > >Content-Type: text/plain; charset="iso-8859-1" > >Dear Fieldtrip Users, > >I perform source analysis in Fieldtrip with a template head model ( >standard_bem ) and a >template source model (cortex_5124.surf.gii >) to constarin >estimated sources on cortex. These templates are based on Colin27, But I >prefere to use the template ICBM152 instead. >Does FT include ICBM template? I mean templates for both head model and >cortical surfe. > >Many Thanks in advance, >Keyvan >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >9daf3/attachment-0001.html> > >------------------------------ > >_______________________________________________ >fieldtrip mailing list >fieldtrip at donders.ru.nl >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >End of fieldtrip Digest, Vol 53, Issue 23 >***************************************** From frsantos at fpce.up.pt Thu Apr 30 17:34:23 2015 From: frsantos at fpce.up.pt (Fernando Ferreira-Santos) Date: Thu, 30 Apr 2015 15:34:23 +0000 Subject: [FieldTrip] Porto IV CAN: 4th Cognitive and Affective Neurophysiology Summer School Message-ID: <2BAB036A9BAEA44984A131DFCE4461080109B9E53D@SRVMBX02.fpceup.psi.up.pt> Dear colleagues, The Laboratory of Neuropsychopsysiology of the University of Porto (http://www.fpce.up.pt/labpsi/) is pleased to announce the 4th edition of the International Cognitive and Affective Neurophysiology Summer School: Acquisition, processing, and analysis of EEG signal. This summer school is focused on the application of Electroencephalography (EEG) and Event Related Potential (ERP) techniques to the study of cognitive and affective processes. The course will be fully taught in English and is aimed at an introductory level, so no previous experience with EEG or ERP is required. This event will take place from 7-12 of September 2015 in the lovely city of Porto. In last year’s edition the course was fully booked and, as such, we recommend early registration (course places are attributed by order of registration). For additional details and instructions on how to register, please consult our website (http://www.fpce.up.pt/labpsi/summerschool/). Please feel free to pass this information along to students or researchers that may be potentially interested. Thanks you and best wishes, -- Fernando Ferreira-Santos, PhD Lecturer Laboratory of Neuropsychophysiology Faculty of Psychology and Education Sciences University of Porto Rua Alfredo Allen, 4200-135 Porto (Portugal) Tel.: +351 226079700 (ext. 409) E-mail: frsantos at fpce.up.pt http://www.fpce.up.pt/labpsi/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From joscha.schmiedt at esi-frankfurt.de Wed Apr 1 14:03:27 2015 From: joscha.schmiedt at esi-frankfurt.de (Schmiedt, Joscha) Date: Wed, 1 Apr 2015 12:03:27 +0000 Subject: [FieldTrip] A Fieldtrip data format? In-Reply-To: References: <5548CAB3-F9A2-4C6B-B958-3CF27CF2C27F@esi-frankfurt.de> Message-ID: Hi Gio, Thanks for the info. The fcdc_matbin approach indeed would be suitable data for raw data. However, I’m looking for a fast solution for data that is already processed and cut into trials, in particular with varying trial length. Joscha > On Mar 31, 2015, at 22:39, Gio Piantoni wrote: > > Hi Joscha, > > FieldTrip already has its own simple uncompressed file format. > fcdc_matbin "It is not an official file format, but was invented here > at the FCDC. It consists of two files: a *.mat matlab file that > contains the header (and optionally the events) and a *.bin binary > file that contains the data." > http://www.fieldtriptoolbox.org/faq/reading_is_slow_can_i_write_my_raw_data_to_a_more_efficient_file_format > > If you want to look at the code: > https://github.com/fieldtrip/fieldtrip/blob/master/fileio/ft_write_data.m#L275 > > You should be able to read it as usual with ft_preprocessing. You can > convert your files to the fcdc_matbin using ft_preprocessing as well: > https://github.com/fieldtrip/fieldtrip/blob/master/ft_preprocessing.m#L581 > Be careful about not losing precision though. > > The only catch is that, as far as I know, you cannot export your > preprocessed data through ft_preprocessing at the moment, because > ft_write_data is now inside this if-part: > https://github.com/fieldtrip/fieldtrip/blob/master/ft_preprocessing.m#L252 > but it's only a matter of adapting that to your needs. > > Would this work for you? > > -g > > On Tue, Mar 31, 2015 at 9:09 AM, Schmiedt, Joscha > wrote: >> Hi, >> >> When working with Fieldtrip it is very convenient to store the data and >> analyses using MATLAB’s save and load functions. However, for large and/or >> complex data with many channels (>2GB) MATLAB enforces compression, which is >> pretty useless for electrophysiology data and slows down the load and save >> performance by a factor of up to 8 (see e.g. >> http://undocumentedmatlab.com/blog/improving-save-performance). The MATLAB >> file format is based on HDF5, which is generally an open and future-proof >> data format, but unfortunately MATLAB doesn’t allow you to disable the >> compression. >> >> An option to overcome this could be to develop a simple data format for >> Fieldtrip data that is also based on HDF5. Is or has there been any >> development going into that direction? Would there be any interest? Of >> course, creating yet another data format is almost never a good idea >> (https://xkcd.com/927/), but since HDF5 is well-documented and readable with >> almost any software, it might be worth thinking about it. >> >> I’d be happy to hear your thoughts. >> >> Joscha >> >> --------------------------------- >> Joscha Schmiedt >> PhD Student >> >> Ernst Strüngmann Institute (ESI) for Neuroscience >> in Cooperation with Max Planck Society >> Deutschordenstraße 46 >> 60528 Frankfurt am Main >> Germany >> >> Tel.: +49 (0)69 96769 241 >> >> Sitz der Gesellschaft: Frankfurt am Main >> Registergericht: Amtsgericht Frankfurt - HRB 84266 >> Geschäftsführer: Prof. Dr. Pascal Fries >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From orionblue8 at gmail.com Wed Apr 1 19:41:36 2015 From: orionblue8 at gmail.com (Orion) Date: Wed, 1 Apr 2015 12:41:36 -0500 Subject: [FieldTrip] how gamma power is calculated Message-ID: Does anyone in the Fieldtrip community calculate the "running gamma power"? This is what I call the parameter after doing a power analysis on each trial, and then to simplify the data by one dimension, averaging the bins within the 35-45 Hz or 30-94 Hz band. Coincidentally a plot of the running gamma power resembles a plot of the EEG first derivative (absolute value of). Can anyone explain why? Orion -------------- next part -------------- An HTML attachment was scrubbed... URL: From federica.ma at gmail.com Wed Apr 1 19:43:30 2015 From: federica.ma at gmail.com (Federica Mauro) Date: Wed, 1 Apr 2015 19:43:30 +0200 Subject: [FieldTrip] Spectral coherence Message-ID: Hi, I was starting to perform the tutorial on spectral coherence (the one is here: http://www.fieldtriptoolbox.org/tutorial/coherence?s[]=spectral&s[]=coherence), but, as I start with the first step I receive an error for the ft_freqanalysis function. The error is: freq = ft_freqanalysis(cfg, data); *??? Undefined function or variable 'abort'.* *Error in ==> ft_freqanalysis at 198* *if abort* what can I do? Thanks in advance! Federica -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.rotonda at gmail.com Thu Apr 2 02:33:52 2015 From: marco.rotonda at gmail.com (Marco Rotonda) Date: Thu, 2 Apr 2015 02:33:52 +0200 Subject: [FieldTrip] how gamma power is calculated In-Reply-To: References: Message-ID: Hi Orion, maybe you can have a look at: http://www.fieldtriptoolbox.org/example/ft_realtime_hilbert I did that code some years ago, so it's a bit outdated, but I think you can have an idea of what you're looking for. Marco On 1 April 2015 at 19:41, Orion wrote: > Does anyone in the Fieldtrip community calculate the "running gamma > power"? This is what I call the parameter after doing a power analysis on > each trial, and then to simplify the data by one dimension, averaging the > bins within the 35-45 Hz or 30-94 Hz band. > > Coincidentally a plot of the running gamma power resembles a plot of the > EEG first derivative (absolute value of). Can anyone explain why? > > Orion > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.sandeep29 at gmail.com Thu Apr 2 08:10:06 2015 From: b.sandeep29 at gmail.com (sandeep b) Date: Thu, 2 Apr 2015 11:40:06 +0530 Subject: [FieldTrip] Unable to download fieldtrip toolbox from the download link Message-ID: Dear Administrator, I am unable to download fieldtrip toolbox from the given link ( http://www.fieldtriptoolbox.org/download). Is there any other other way to get the toolbox. Kindly please suggest me to get the toolbox Thank you Sandeep -------------- next part -------------- An HTML attachment was scrubbed... URL: From dorothee-brigitte.hoppe at student.uni-tuebingen.de Thu Apr 2 15:44:05 2015 From: dorothee-brigitte.hoppe at student.uni-tuebingen.de (Dorothee Hoppe) Date: Thu, 02 Apr 2015 15:44:05 +0200 Subject: [FieldTrip] ICA on each trial or collapsing over all trials Message-ID: <20150402154405.14144i9yubvrxw2t@webmail.uni-tuebingen.de> Dear Discussion Group members, we want to use ICA for artifact correction, and now got stuck at the point of deciding whether to compute the ICs on the trial level or on the whole dataset for a subject. Using the whole dataset, the advantage is probably a higher power of the ICA because of the larger data input, so for example a blink component gets probably more distinctive. On the other hand, we observed, that artifacts that occur only in a small set of trials, like strong muscle artifacts cannot be detected that way, or even lead to a distortion of the components for that special trial. Would you recommend an ICA on each trial or collapsing over all trials (both options within each subject)? Are there other arguments to favor or reject these options? Best regards, Dorothée From mahjoory86 at gmail.com Thu Apr 2 15:51:23 2015 From: mahjoory86 at gmail.com (Keyvan Mahjoory) Date: Thu, 2 Apr 2015 15:51:23 +0200 Subject: [FieldTrip] Fwd: Power Maps on Surface In-Reply-To: References: Message-ID: Dear Fieldtrip Users, I used the surface file "cortex_5124.surf.gii" to restrict sources on cortex. I wonder how I can plot powermaps on surface? cfg.surffile=ft_read_headshape('cortex_5124.surf.gii'); even I save it's output in a new .mat file: "sourcemodel.mat" and tried cgf.surffile = 'sourcemodel.mat'; in either case the function "ft_sourceplot" gives error. cfg = []; cfg.method = 'surface'; cfg.funparameter = 'avg.pow'; cfg.funcolormap = 'jet'; cfg.surffile='sourcemodel.mat'; ft_sourceplot(cfg, src) In my code I have defined surface vertices and triangles, as well as power per vertex, I wonder What is wrong in my code? Many Thanks in advance, Best, Keyvan -------------- next part -------------- An HTML attachment was scrubbed... URL: From ayobimpe2004 at gmail.com Thu Apr 2 17:36:57 2015 From: ayobimpe2004 at gmail.com (Azeez Adebimpe) Date: Thu, 2 Apr 2015 17:36:57 +0200 Subject: [FieldTrip] Fwd: Power Maps on Surface In-Reply-To: References: Message-ID: Hello, Your code is right I also encouter the same problem but you can project on the surface with ft_plot_mesh ft_plot_mesh(bnd, 'vertexcolor', m); bnd is the your source modle and m is avg.pow value Azeez On Thu, Apr 2, 2015 at 3:51 PM, Keyvan Mahjoory wrote: > Dear Fieldtrip Users, > > > I used the surface file "cortex_5124.surf.gii" to restrict sources on > cortex. I wonder how I can plot powermaps on surface? > > cfg.surffile=ft_read_headshape('cortex_5124.surf.gii'); > > even I save it's output in a new .mat file: "sourcemodel.mat" and tried > cgf.surffile = 'sourcemodel.mat'; > > in either case the function "ft_sourceplot" gives error. > > cfg = []; > cfg.method = 'surface'; > cfg.funparameter = 'avg.pow'; > cfg.funcolormap = 'jet'; > cfg.surffile='sourcemodel.mat'; > ft_sourceplot(cfg, src) > > In my code I have defined surface vertices and triangles, as well as power > per vertex, I wonder What is wrong in my code? > > Many Thanks in advance, > Best, > Keyvan > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jorn at artinis.com Fri Apr 3 09:23:24 2015 From: jorn at artinis.com (=?utf-8?Q?J=C3=B6rn_M._Horschig?=) Date: Fri, 3 Apr 2015 09:23:24 +0200 Subject: [FieldTrip] Fwd: Power Maps on Surface In-Reply-To: References: Message-ID: <001b01d06ddf$12a60870$37f21950$@artinis.com> Hey. You should specify cfg.surffile really as the path to the file, and not read in the content apriori. This section here might help (the ‘exercise’ part of the tutorial lists a cfg-example for surface plotting). http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_sources_of_oscillatory_gamma-band_activity Best, Jörn -- Jörn M. Horschig, Software Engineer Artinis Medical Systems | +31 481 350 980 From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Azeez Adebimpe Sent: Thursday, April 2, 2015 5:37 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] Fwd: Power Maps on Surface Hello, Your code is right I also encouter the same problem but you can project on the surface with ft_plot_mesh ft_plot_mesh(bnd, 'vertexcolor', m); bnd is the your source modle and m is avg.pow value Azeez On Thu, Apr 2, 2015 at 3:51 PM, Keyvan Mahjoory > wrote: Dear Fieldtrip Users, I used the surface file "cortex_5124.surf.gii" to restrict sources on cortex. I wonder how I can plot powermaps on surface? cfg.surffile=ft_read_headshape('cortex_5124.surf.gii'); even I save it's output in a new .mat file: "sourcemodel.mat" and tried cgf.surffile = 'sourcemodel.mat'; in either case the function "ft_sourceplot" gives error. cfg = []; cfg.method = 'surface'; cfg.funparameter = 'avg.pow'; cfg.funcolormap = 'jet'; cfg.surffile='sourcemodel.mat'; ft_sourceplot(cfg, src) In my code I have defined surface vertices and triangles, as well as power per vertex, I wonder What is wrong in my code? Many Thanks in advance, Best, Keyvan _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From abarnyeu at hotmail.com Sun Apr 5 05:03:02 2015 From: abarnyeu at hotmail.com (Charles West) Date: Sat, 4 Apr 2015 20:03:02 -0700 Subject: [FieldTrip] cfg structure for plotting topographical maps Message-ID: Hi everyone, I am new to FieldTrip and am confused about the cfg structure that is required for running Field Trip functions. I would like to plot the topographical maps of a frequency range (e.g. 5 to 10 Hz) using Field Trip. I used the besa2fieldtrip function to create data. I receive the following error message when running ft_topoplotER. Please let me know why the following error appears. Many thanks! Charles West >>cfg.layout = 'layout.lay'; >>cfg.parameter = 'avg' >>ft_topoplotER(cfg, data); reading layout from file layout.lay the call to "ft_prepare_layout" took 0 seconds Attempt to reference field of non-structure array. Error in ft_datatype_sens (line 136) nchan = length(sens.label); Error in ft_datatype_timelock (line 99) timelock.elec = ft_datatype_sens(timelock.elec); Error in ft_checkdata (line 227) data = ft_datatype_timelock(data); Error in topoplot_common (line 74) data = ft_checkdata(data, 'datatype', {'comp', 'timelock', 'freq'}); Error in ft_topoplotER (line 192) cfg = topoplot_common(cfg, varargin{:}); -------------- next part -------------- An HTML attachment was scrubbed... URL: From rikkert.hindriks at upf.edu Wed Apr 8 09:32:37 2015 From: rikkert.hindriks at upf.edu (HINDRIKS, RIKKERT) Date: Wed, 8 Apr 2015 09:32:37 +0200 Subject: [FieldTrip] Unit of simulated EEG using openMEEG Message-ID: Dear all, Could anyone tell me what are the units of the entries in BEM leadfield matrices generated using openMEEG? For example, if I multiply the matrix with a vector of dipole moments in Am, do I get microVolts? (after taking the average reference) Thanks a lot, Rikkert -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at telecom-paristech.fr Wed Apr 8 10:08:02 2015 From: alexandre.gramfort at telecom-paristech.fr (Alexandre Gramfort) Date: Wed, 8 Apr 2015 10:08:02 +0200 Subject: [FieldTrip] Unit of simulated EEG using openMEEG In-Reply-To: References: Message-ID: hi, if your meshes are in meters then moments in Am produce volts. hope this helps Alex On Wed, Apr 8, 2015 at 9:32 AM, HINDRIKS, RIKKERT wrote: > > Dear all, > > Could anyone tell me what are the units of the entries in BEM leadfield > matrices generated using openMEEG? > > For example, if I multiply the matrix with a vector of dipole moments in Am, > do I get microVolts? (after taking the > average reference) > > Thanks a lot, > Rikkert > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From munsif.jatoi at gmail.com Wed Apr 8 10:08:28 2015 From: munsif.jatoi at gmail.com (Munsif Jatoi) Date: Wed, 8 Apr 2015 16:08:28 +0800 Subject: [FieldTrip] Unit of simulated EEG using openMEEG In-Reply-To: References: Message-ID: Dear Hindriks, The leadfield matrix has got orientation and moments of dipoles. When it is multiplied by dipole numbers say 1 or 2 at certain location, it will be generating the voltage matrix. Put it in a more simple way, V= KJ +e where, V= potential (volts), K= leadfield and J= current density (A/m2). So the generated data has units of microvolts or the units of voltage. I hope you got the point. Thanks, Munsif. On Wed, Apr 8, 2015 at 3:32 PM, HINDRIKS, RIKKERT wrote: > > Dear all, > > Could anyone tell me what are the units of the entries in BEM leadfield > matrices generated using openMEEG? > > For example, if I multiply the matrix with a vector of dipole moments in > Am, do I get microVolts? (after taking the > average reference) > > Thanks a lot, > Rikkert > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Munsif Ali H.Jatoi, Ph D Scholar, Centre for Intelligent Signals and Imaging Research, Universiti Teknologi PETRONAS, Malaysia. http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at telecom-paristech.fr Wed Apr 8 10:21:24 2015 From: alexandre.gramfort at telecom-paristech.fr (Alexandre Gramfort) Date: Wed, 8 Apr 2015 10:21:24 +0200 Subject: [FieldTrip] Unit of simulated EEG using openMEEG In-Reply-To: References: Message-ID: hi, OpenMEEG as used by default in Fieldtrip uses dipoles moments (not current density) so it's expressed in Am. Current density is also possible but not the default method exposed. Alex On Wed, Apr 8, 2015 at 10:08 AM, Munsif Jatoi wrote: > Dear Hindriks, > > The leadfield matrix has got orientation and moments of dipoles. When it is > multiplied by dipole numbers say 1 or 2 at certain location, it will be > generating the voltage matrix. Put it in a more simple way, V= KJ +e where, > V= potential (volts), K= leadfield and J= current density (A/m2). So the > generated data has units of microvolts or the units of voltage. I hope you > got the point. > > > Thanks, > > Munsif. > > > On Wed, Apr 8, 2015 at 3:32 PM, HINDRIKS, RIKKERT > wrote: >> >> >> Dear all, >> >> Could anyone tell me what are the units of the entries in BEM leadfield >> matrices generated using openMEEG? >> >> For example, if I multiply the matrix with a vector of dipole moments in >> Am, do I get microVolts? (after taking the >> average reference) >> >> Thanks a lot, >> Rikkert >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Munsif Ali H.Jatoi, > > Ph D Scholar, > Centre for Intelligent Signals and Imaging Research, > Universiti Teknologi PETRONAS, > Malaysia. > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > From rikkert.hindriks at upf.edu Wed Apr 8 11:20:46 2015 From: rikkert.hindriks at upf.edu (HINDRIKS, RIKKERT) Date: Wed, 8 Apr 2015 11:20:46 +0200 Subject: [FieldTrip] Unit of simulated EEG using openMEEG In-Reply-To: References: Message-ID: Hi Alex, I see, thanks. I have specified the meshes in mm's so a unit dipole moment is expressed in Amm right? Thus a homogeneous dipole field with moment x Amm leads to scalp potentials of 10^(-2)*L*x (where L is the computed leadfield matrix). The thing is that if I place a single dipole with moment Q = 10 nAm = 10^(-6) Amm (which is about the required value to pick up a measurable MEG signal), this gives scalp voltages LQ in the order of picoV (at most something of the order 10^(-11) for appropriately placed dipoles) while you would expect it to be in the order of microV no? Could it be that in the specification of the headmodel, I should use S/mm instead of S/m for the conductivities? (I use the "standard" values of 0.33 S/m , 0.0041 S/m, and 0.33 S/m for brain, skull, and scalp, resp.) Kind regards and thanks, Rikkert On Wed, Apr 8, 2015 at 10:08 AM, Alexandre Gramfort < alexandre.gramfort at telecom-paristech.fr> wrote: > hi, > > if your meshes are in meters then moments in Am produce volts. > > hope this helps > Alex > > On Wed, Apr 8, 2015 at 9:32 AM, HINDRIKS, RIKKERT > wrote: > > > > Dear all, > > > > Could anyone tell me what are the units of the entries in BEM leadfield > > matrices generated using openMEEG? > > > > For example, if I multiply the matrix with a vector of dipole moments in > Am, > > do I get microVolts? (after taking the > > average reference) > > > > Thanks a lot, > > Rikkert > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at telecom-paristech.fr Wed Apr 8 11:29:48 2015 From: alexandre.gramfort at telecom-paristech.fr (Alexandre Gramfort) Date: Wed, 8 Apr 2015 11:29:48 +0200 Subject: [FieldTrip] Unit of simulated EEG using openMEEG In-Reply-To: References: Message-ID: hi Rikkert, the unit of conductivities have no impact as it's only their ratio that is used in computation. For the rest run simple simulations to get more intuition. HTH Alex On Wed, Apr 8, 2015 at 11:20 AM, HINDRIKS, RIKKERT wrote: > Hi Alex, > > I see, thanks. I have specified the meshes in mm's so a unit dipole moment > is expressed in Amm right? > Thus a homogeneous dipole field with moment x Amm leads to scalp potentials > of 10^(-2)*L*x (where L > is the computed leadfield matrix). > > The thing is that if I place a single dipole with moment Q = 10 nAm = > 10^(-6) Amm (which is about the > required value to pick up a measurable MEG signal), this gives scalp > voltages LQ in the order of picoV > (at most something of the order 10^(-11) for appropriately placed dipoles) > while you would expect it to > be in the order of microV no? > > Could it be that in the specification of the headmodel, I should use S/mm > instead of S/m for the conductivities? > (I use the "standard" values of 0.33 S/m , 0.0041 S/m, and 0.33 S/m for > brain, skull, and scalp, resp.) > > > Kind regards and thanks, > Rikkert > > > On Wed, Apr 8, 2015 at 10:08 AM, Alexandre Gramfort > wrote: >> >> hi, >> >> if your meshes are in meters then moments in Am produce volts. >> >> hope this helps >> Alex >> >> On Wed, Apr 8, 2015 at 9:32 AM, HINDRIKS, RIKKERT >> wrote: >> > >> > Dear all, >> > >> > Could anyone tell me what are the units of the entries in BEM leadfield >> > matrices generated using openMEEG? >> > >> > For example, if I multiply the matrix with a vector of dipole moments in >> > Am, >> > do I get microVolts? (after taking the >> > average reference) >> > >> > Thanks a lot, >> > Rikkert >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From rikkert.hindriks at upf.edu Wed Apr 8 12:32:41 2015 From: rikkert.hindriks at upf.edu (HINDRIKS, RIKKERT) Date: Wed, 8 Apr 2015 12:32:41 +0200 Subject: [FieldTrip] Unit of simulated EEG using openMEEG In-Reply-To: References: Message-ID: Hi Alex, Ok, clear, thanks. But in any case, when using a typical dipole moment of 10 nAm, you would like to end up with voltages in the experimental range, that is, in the order of microVolts (after taking the average reference) I would appreciate it very much if someone could elucidate this for me. Kind regards, Rikkert On Wed, Apr 8, 2015 at 11:29 AM, Alexandre Gramfort < alexandre.gramfort at telecom-paristech.fr> wrote: > hi Rikkert, > > the unit of conductivities have no impact as it's only their ratio > that is used in computation. > > For the rest run simple simulations to get more intuition. > > HTH > Alex > > > On Wed, Apr 8, 2015 at 11:20 AM, HINDRIKS, RIKKERT > wrote: > > Hi Alex, > > > > I see, thanks. I have specified the meshes in mm's so a unit dipole > moment > > is expressed in Amm right? > > Thus a homogeneous dipole field with moment x Amm leads to scalp > potentials > > of 10^(-2)*L*x (where L > > is the computed leadfield matrix). > > > > The thing is that if I place a single dipole with moment Q = 10 nAm = > > 10^(-6) Amm (which is about the > > required value to pick up a measurable MEG signal), this gives scalp > > voltages LQ in the order of picoV > > (at most something of the order 10^(-11) for appropriately placed > dipoles) > > while you would expect it to > > be in the order of microV no? > > > > Could it be that in the specification of the headmodel, I should use S/mm > > instead of S/m for the conductivities? > > (I use the "standard" values of 0.33 S/m , 0.0041 S/m, and 0.33 S/m for > > brain, skull, and scalp, resp.) > > > > > > Kind regards and thanks, > > Rikkert > > > > > > On Wed, Apr 8, 2015 at 10:08 AM, Alexandre Gramfort > > wrote: > >> > >> hi, > >> > >> if your meshes are in meters then moments in Am produce volts. > >> > >> hope this helps > >> Alex > >> > >> On Wed, Apr 8, 2015 at 9:32 AM, HINDRIKS, RIKKERT > >> wrote: > >> > > >> > Dear all, > >> > > >> > Could anyone tell me what are the units of the entries in BEM > leadfield > >> > matrices generated using openMEEG? > >> > > >> > For example, if I multiply the matrix with a vector of dipole moments > in > >> > Am, > >> > do I get microVolts? (after taking the > >> > average reference) > >> > > >> > Thanks a lot, > >> > Rikkert > >> > > >> > _______________________________________________ > >> > fieldtrip mailing list > >> > fieldtrip at donders.ru.nl > >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at telecom-paristech.fr Wed Apr 8 16:32:57 2015 From: alexandre.gramfort at telecom-paristech.fr (Alexandre Gramfort) Date: Wed, 8 Apr 2015 16:32:57 +0200 Subject: [FieldTrip] Unit of simulated EEG using openMEEG In-Reply-To: References: Message-ID: hi, > But in any case, when using a typical dipole moment of 10 nAm, you would > like to end up with voltages in the experimental range, that is, in the > order > of microVolts (after taking the average reference) yes this should be the case if you use meshes in meters. A From Alexander.Hunold at tu-ilmenau.de Wed Apr 8 17:05:27 2015 From: Alexander.Hunold at tu-ilmenau.de (Hunold Alexander TU Ilmenau) Date: Wed, 8 Apr 2015 15:05:27 +0000 Subject: [FieldTrip] =?windows-1252?q?7th_International_Summer_School_in_B?= =?windows-1252?q?iomedical_Engineering_=84New_Instrumentation_for_brain_m?= =?windows-1252?q?easurements_and_stimulation=93=2C_17th_-_29th_August_201?= =?windows-1252?q?5_in_Lutherstadt_Wittenberg=2C_Germany?= Message-ID: <5B8562898ECA5A4594C9879007B90670395D7F5C@MB1.x.chg> Dear colleagues, we are pleased to announce the 7th International Summer School in Biomedical Engineering on "New Instrumentation for brain measurements and stimulation" August, 17-29, 2015 in Lutherstadt Wittenberg, Germany. This event stands in the tradition of a series of successful summer schools on hot themes in biomedical engineering, dedicated to intense learning in the fruitful atmosphere of tight interaction between students and world-leading specialists. This year’s summer school is devoted to new hardware technologies for measuring and stimulating the brain, such as dry electroencephalography (EEG) electrodes, optically pumped magnetic field sensors, neuronal current imaging based on low-field magnetic resonance and multichannel transcranial current stimulation. In particular, the 7th International Summer School on Biomedical Engineering will focus on ways how these new technical advances may help to overcome current limitations in human neurosciences and medicine. It will cover both theoretical foundations and practical applications. We aim at a thorough understanding of the underlying mechanisms. Thus, we will develop a critical view on current applications and possible future developments. The second important aim of the summer school consists in providing contact with both leading experts in the field and other students with similar interests, thereby facilitating the exchange of ideas on latest developments in the field. Target Group: - PhD students - Advanced Master students - Researchers entering the field of brain measurement and stimulation techniques Further Information about the 7th International Summer School in Biomedical Engineering: www.iss2015.org We would be happy to receive your application. Please pass this announcement to your colleagues who might be interested. Sincerely, Jens Haueisen and Thomas Knösche -------------- next part -------------- An HTML attachment was scrubbed... URL: From vanwijk.bernadette at gmail.com Wed Apr 8 17:07:42 2015 From: vanwijk.bernadette at gmail.com (Bernadette van Wijk) Date: Wed, 8 Apr 2015 16:07:42 +0100 Subject: [FieldTrip] SPM course for MEG/EEG in London: May 11-13 Message-ID: Dear all, We are pleased to announce that our annual *SPM course for MEG/EEG* will take place this year from *Monday May 11* to *Wednesday May 13 2015*. Hosted by University College London, the course will be held at Queen Square, a very central location in London (UK). The course will present instruction on the analysis of MEG and EEG data. The first two days will combine theoretical presentations with practical demonstrations of the different data analysis methods implemented in SPM. On the last day participants will have the opportunity to work on SPM tutorial data sets under the supervision of the course faculty. We also invite students to bring their own data for analysis. The course is suitable for both beginners and more advanced users. The topics that will be covered range from pre-processing and statistical analysis to source localization and dynamic causal modelling. The program is listed below. Registration is now open. We offer a reduced rate when attending both the MEG/EEG course and the fMRI course during the second half of the week. For full details of both courses see 'Statistical Parametric Mapping short courses' at http://www.ucl.ac.uk/ion/courses-viewer where you can also register. Available places are limited so please register as early as possible if you would like to attend! *Monday May 11th* 9.00 - 9.30 Registration 9.30 - 9.45 SPM introduction and resources *Guillaume Flandin* 9.45 - 10.30 What are we measuring with M/EEG? *Stefan Kiebel* 10.30 - 11.15 Data pre-processing *Holly Rossiter* *Coffee* 11.45 - 12.30 Data pre-processing - demo *Deborah Talmi, Megumi Fukuda* 12.30 - 13.15 General linear model and classical inference *Christophe Phillips* *Lunch* 14.15 - 15.00 Multiple comparisons problem and solutions *Gareth Barnes* 15.00 - 15.45 Bayesian inference *Chris Mathys* *Coffee* 16.15 - 18.00 Tutorial on group M/EEG dataset analysis *Vladimir Litvak, Jason Taylor* *Tuesday May 12th* 9.30 - 10.15 M/EEG source analysis *Saskia Helbling* 10.15 - 11.15 M/EEG source analysis - demo *Jose Lopez, Jason Taylor, Sofie Meyer* *Coffee* 11.45 - 12.30 The principles of DCM *Ryszard Auksztulewicz* 12.30 - 13.15 DCM for evoked responses *Harriet Brown* *Lunch* 14.15 - 15.00 DCM for steady state responses *Rosalyn Moran* 15.00 - 15.45 DCM for time-frequency responses *Bernadette van Wijk* 15.45 - 16.30 DCM - demo *Andre Marreiros, Martin Dietz * *Coffee* 17.00 - 17.45 Bayesian model selection and averaging *Will Penny* 17.45 - 18.45 Clinic - Questions & Answers session *Karl Friston* 19.00 onwards - Social Event *Wednesday May 13th* 9.30 – 17.00 Practical hands-on session in UCL computer class rooms. Participants can either work on SPM tutorial datasets or on their own data with the help of the faculty. There will also be an opportunity to ask questions in small tutorial groups for further discussions on the topics of the lectures. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Apr 9 09:04:11 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 9 Apr 2015 09:04:11 +0200 Subject: [FieldTrip] Call for applications for 15 early stage researchers Message-ID: Dear all Positions for 15 early stage researchers (doctoral students) are offered in a project aiming to develop and apply new brain research methods to study normal and atypical cognitive development of children. Applicants from all relevant academic disciplines are encouraged to apply, including cognitive neuroscience, computer science, educational sciences, engineering, medicine, mathematics, psychology, physics, statistics, and related disciplines. The selected doctoral students will enroll in the graduate school of the host institution and work towards their PhD. The multidisciplinary ChildBrain (Advancing brain research in children’s developmental neurocognitive disorders) project is funded by the Horizon 2020 Marie Skłodowska-Curie action of the European Union. It is part of the Innovative Training Network (ITN) actions. The positions are open at five top ranked academic institutions and three innovative companies in PhD projects under three broader themes of neurocognitive disorders, brain development and brain research methods (see project descriptions at www.childbrain.eu). The academic and private sector partners will offer the students project-specific research, scientific collaboration, secondments, workshops and courses on scientific and entrepreneurial skills, as well as excellent supervision. Salaries are competitive (please see details under specific ESR projects). Successful applicants should have a degree that allows a direct entry into doctoral studies and less than 4 years of experience in research; and not have lived more than 12 months during the last 3 years in the country where doctoral studies are started; this is due to emphasis on mobility in the ITN projects. Women and men from all countries are encouraged to apply. Please see details on the projects and how to apply at www.childbrain.eu. Deadline for the first round of applications is April 30th 2015 (June 30th 2015 for ESR projects 2, 5, 9 and 11). best regards, Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ChildBrain_call_for_applications.pdf Type: application/pdf Size: 204906 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Apr 9 13:50:31 2015 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 9 Apr 2015 13:50:31 +0200 Subject: [FieldTrip] Be careful with nonlinear warping of your individual grids to MNI Message-ID: Dear FieldTrip community, I have encountered a little problem inverse-MNI-warping the grids of my individual subjects for the purpose of averaging my beamformer results, in line with: http://www.fieldtriptoolbox.org/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space?s[]=grid When I visually checked the resultant individual grids, I found that 6 out of 25 subjects had severely distorted grids. See attached examples. A bit of distortion could be expected, but IMHO this is too much. It is the result of nonlinear warping (done in the example script mentioned above) and solved by using cfg.grid.nonlinear = 'no, in the following part of the script: cfg = []; cfg.grid.warpmni = 'yes'; cfg.grid.template = template_scm; cfg.grid.nonlinear = 'no'; cfg.mri = mri_segmented; grid = ft_prepare_sourcemodel(cfg); Ofcourse this is not a Fieldtrip bug in any way, but just something to be aware of, and a warning I wanted to share. And it really shows that it is important to check all of the warped individual grids! I will redo only these subjects with linear instead of nonlinear warping. That is, unless anyone has a better solution? All the best, Stephen Whitmarsh -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... 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Name: pp_20_headmodel_grid_a.png Type: image/png Size: 151143 bytes Desc: not available URL: From thismoment at 163.com Sun Apr 12 17:32:05 2015 From: thismoment at 163.com (thismoment) Date: Sun, 12 Apr 2015 23:32:05 +0800 Subject: [FieldTrip] error when I convert .mri data into mgz or other format Message-ID: <552A8FF2.2000705@163.com> Hi Experts, I got a set of MEG. The anatomical MRI was stored in .mri format (CTF device) and MEG was stored in a folder named by xxx.ds. I do not know how to do segmentation of .mri into scalp,skull and cortex. So I try to convert .mri into .mgz or other format so that it can be used in freesurfer for reconstruction. I used the following command. x=ft_read_mri('MEG619.mri','dataformat','ctf_mri4'); y=ft_write_mri('ddd',x,'dataformat','mgz', 'transform',x.transform) the error was >> y=ft_write_mri('ddd',x,'dataformat','mgz', 'transform',x.transform) Error using fwrite Cannot write value: unsupported class struct Error in save_mgh (line 107) fwrite(fid,vol,'float32'); Error in ft_write_mri (line 79) save_mgh(dat, filename, transform); I failed to do it. 1. Anyone know what happens ? 2. Freesurfer can use .mri directly to reconstruct ? 3. Are there other methods to convert .mri into .mgz or .dicom format? Best wishes, J. Zhang 2015-04-12 thismoment -------------- next part -------------- An HTML attachment was scrubbed... URL: From wanyu at gazzaleylab.ucsf.edu Tue Apr 14 00:48:45 2015 From: wanyu at gazzaleylab.ucsf.edu (WanYu Hsu) Date: Mon, 13 Apr 2015 15:48:45 -0700 Subject: [FieldTrip] questions about topoplot and notch filter Message-ID: Hi community, Recently I am analyzing EEG dataset with only 20 channels and I am focusing on coherence between frontal and posterior electrodes in frequency domain. I got two questions here: 1. I wanted to topoplot the coherence between each pair of electrodes that we're interested in, and I tried the following script: cfg = []; cfg.colorparam = 'plvspctrm'; cfg.layout = 'biosemi64.lay'; cfg.foi =[4]; ft_topoplotCC(cfg, plv_avg_stim); The electrode layout and coherence we wanted to see were in the plot, but the plot did not show coherence related to FP1, FP2, and FPz. Am I doing something wrong? 2. I would like to apply notch filter to remove 6 Hz and first I tried cfg.dftfilter ='yes'; cfg.dftfreq = [6] but the 6Hz signal was still there. Then I also tried cfg.bsfilter ='yes'; cfg.bsfreq =[5 7]; This worked well to remove 6Hz signal, but it also affected 5Hz and 7Hz. Is there any way to remove 6 Hz specificlly? Any help would be appreciated. Best, Wanyu Hsu -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue Apr 14 09:47:31 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 14 Apr 2015 09:47:31 +0200 Subject: [FieldTrip] error when I convert .mri data into mgz or other format In-Reply-To: <552A8FF2.2000705@163.com> References: <552A8FF2.2000705@163.com> Message-ID: <31465C27-5C1C-4076-929C-358CC7BD7AE6@donders.ru.nl> Hi Zhang, You should specify the anatomical data as a 3D array, not as a structure. So rather than ft_write_mri('ddd',x,'dataformat','mgz', 'transform',x.transform) you should do ft_write_mri('ddd’,x.anatomy,'dataformat','mgz', 'transform',x.transform) Note also that you should not expect an output from ft_write_mri. best regards, Robert On 12 Apr 2015, at 17:32, thismoment wrote: > Hi Experts, > > I got a set of MEG. The anatomical MRI was stored in .mri format (CTF device) and MEG was stored in a folder named by xxx.ds. > I do not know how to do segmentation of .mri into scalp,skull and cortex. So I try to convert .mri into .mgz or other format so > that it can be used in freesurfer for reconstruction. > I used the following command. > > x=ft_read_mri('MEG619.mri','dataformat','ctf_mri4'); > y=ft_write_mri('ddd',x,'dataformat','mgz', 'transform',x.transform) > > the error was > > >> y=ft_write_mri('ddd',x,'dataformat','mgz', 'transform',x.transform) > Error using fwrite > Cannot write value: unsupported class struct > > Error in save_mgh (line 107) > fwrite(fid,vol,'float32'); > > Error in ft_write_mri (line 79) > save_mgh(dat, filename, transform); > > I failed to do it. > 1. Anyone know what happens ? > 2. Freesurfer can use .mri directly to reconstruct ? > 3. Are there other methods to convert .mri into .mgz or .dicom format? > > Best wishes, > J. Zhang > > > 2015-04-12 > thismoment > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue Apr 14 09:52:31 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 14 Apr 2015 09:52:31 +0200 Subject: [FieldTrip] questions about topoplot and notch filter In-Reply-To: References: Message-ID: <62310C2D-1246-4BF3-83C7-AD2F23FDF98E@donders.ru.nl> Dear WanYu Regarding your first question: I am not sure what you expected to see in the figure, and what you actually did see. Perhaps you should be using ft_connectivityplot instead. Note that the high-level plotting functions (the ones that take a cfg as first input) are only there to help you to get started with the figures, you can always plot the actual data yourself using low-level matlab functions and using the helper functions in the fieldtrip/plotting directory. Regarding the second question, perhaps these address your question http://www.fieldtriptoolbox.org/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter http://www.fieldtriptoolbox.org/tag/filter?do=showtag&tag=filter best regards, Robert On 14 Apr 2015, at 00:48, WanYu Hsu wrote: > Hi community, > Recently I am analyzing EEG dataset with only 20 channels and I am focusing on coherence between frontal and posterior electrodes in frequency domain. > > I got two questions here: > > 1. I wanted to topoplot the coherence between each pair of electrodes that we're interested in, and I tried the following script: > > cfg = []; > cfg.colorparam = 'plvspctrm'; > cfg.layout = 'biosemi64.lay'; > cfg.foi =[4]; > ft_topoplotCC(cfg, plv_avg_stim); > > The electrode layout and coherence we wanted to see were in the plot, but the plot did not show coherence related to FP1, FP2, and FPz. Am I doing something wrong? > > > > 2. I would like to apply notch filter to remove 6 Hz and first I tried > > cfg.dftfilter ='yes'; > cfg.dftfreq = [6] > but the 6Hz signal was still there. > Then I also tried > > cfg.bsfilter ='yes'; > cfg.bsfreq =[5 7]; > > This worked well to remove 6Hz signal, but it also affected 5Hz and 7Hz. > > Is there any way to remove 6 Hz specificlly? > > Any help would be appreciated. > > > > Best, > > Wanyu Hsu > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue Apr 14 09:55:29 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 14 Apr 2015 09:55:29 +0200 Subject: [FieldTrip] MEG postdoctoral position at Karolinska Institutet Message-ID: <1348BCC9-DB8E-4DEF-8178-B2CB53476D8E@donders.ru.nl> Postdoctoral studies in Magnetoencephalography (scholarship) Karolinska Institutet, The Department of Neuroscience, Ehrsson Research groups at the Department of Neuroscience study different aspects of the function of the normal nervous system, as well as disturbances, injuries and diseases affecting the nervous system. Projects include a broad range of studies at the molecular and cellular levels, the network level and at the level of the overall organization of the nervous system. The department also conducts undergraduate education in neuroscience, anatomy and histology in a number of programs at Karolinska Institutet. To read more about our department, please visit our webpage; www.ki.se/en/neuro/startpage Duties We are seeking a highly talented and enthusiastic researcher with a PhD in neuroimaging awarded within the past three years to work on projects in which magnetoencephalography (MEG) is applied to the problem of how we come to experience limbs as part of our own body. The research will be conducted at the Brain, Body and Self Laboratory at the Department of Neuroscience (www.ehrssonlab.se). This center has widespread expertise in fMRI and human behavioural experiments. The MEG experiments will be conducted at the recently established the “National Facility Magnetoencephalography (www.natmeg.se) that is equipped with a state-of-the-art MEG system (Electa Neuromag TRIUX), complementary physiological recording devices (MEG compatible 128–channel EEG, plethysmography, EMG, ECG, eyetracking), and sophisticated stimulus delivery platforms (visual, auditory, olfactory, pain, somatosensory; including a robot system for tactile stimulation of the hands). The ideal candidate will have expertise in the acquisition and analysis of MEG data, (preferably on an Elekta Triux or Vectorview system), expertise in analysis of MEG data (preferably on FieldTrip and/or MNE), as well as excellent programming skills (preferably including MatLab and Neurobs Presentation). Expertise in analysis of EEG data would be an advantage. The candidate is expected to work on projects in which MEG methods are applied to questions relating to how multisensory signals from the body are integrated at the levels of cortical structures to give rise to dynamic changes in the feeling of ownership of limbs. Good social skills are important as the candidate is expected to actively collaborate with other members of the laboratory, in addition to running his or her own project. Applicants should be able to demonstrate a consistently good academic record, including publications in international journals. Entry requirements Scholarships to pursue postdoctoral studies may be awarded to individuals who come from other countries with the intention of remaining in Sweden only while obtaining all or part of their education. The head of the department determines whether their previous training and scholarly qualifications correspond to a Swedish PhD or higher. Having received a salary or other remuneration from Karolinska Institutet during the past two years may be disqualifying. One requirement for receiving a scholarship for postdoctoral studies is central registration as a postdoc. Type of scholarship Karolinska Institutet awards scholarships to pursue postdoctoral studies. This educational scholarship, which is paid for a maximum of two years within four years after the receipt of a PhD or the equivalent, is tax-exempt. The amount is set for twelve months at a time and is paid out on a monthly basis. In exceptional cases, shorter periods may be acceptable. Application process An application must contain the following documents in English: Curriculum vitae and qualifications, presented in accordance with Karolinska Institutet’s qualifications portfolio (http://ki.se/meritportfolj ) A complete list of publications A summary of current research (no more than one page) Verifications for crediting of illness, military service, work for labour unions or student organisations, parental leave or similar circumstances Verification from the thesis defence committee or the equivalent (only if the thesis defence is scheduled within three months after the application deadline) Contact details for two reference persons The application is to be submitted through the MyNetwork recruitment system. Karolinska Institutet is one of the world´s leading medical universities. Its mission is to contribute to the improvement of human health through research and education. 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Working hours: Full time First day of employment: As soon as possible Reference number: 2-1291/2015 Contact: Henrik Ehrsson, professor, henrik.ehrsson at ki.se Union representative: Peter Århem, SACO, 46-8 524 869 03 Anne Edgren, OFR, 08-616 16 29 Gunnar Stenberg, SEKO, 08-524 880 75 Published: 27.Mar.2015 Last application date: 07.May.2015 Contact Henrik Ehrsson, professor, henrik.ehrsson at ki.se Link to ad: http://ki.mynetworkglobal.com/what:job/jobID:61655/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: cid:134.gif Type: image/gif Size: 8101 bytes Desc: not available URL: From f.roux at bcbl.eu Tue Apr 14 18:12:26 2015 From: f.roux at bcbl.eu (=?utf-8?B?RnLDqWTDqXJpYw==?= Roux) Date: Tue, 14 Apr 2015 18:12:26 +0200 (CEST) Subject: [FieldTrip] missing samples after donwsampling In-Reply-To: <1130111699.32607.1429027894577.JavaMail.root@bcbl.eu> Message-ID: <1165544691.32620.1429027946414.JavaMail.root@bcbl.eu> Dear all, i've noticed that after invoking ft_resampledata not all trials have the same number of samples. For instance: cfg = []; cfg.resamplefs = 400; [meg_data] = ft_resamplefs(cfg,meg_data); will return length(meg_data.trial{1}) = 2601 whereas length(meg_data.trial{2}) = 2600 This is causing a conflict upstream in my analysis pipeline and I wanted to ask if there was a way to fix this? I am using fieldtrip-20150115. Any thoughts or help would be highly appreciated. Best, Fred -- Frédéric Roux Postdoctoral Scientist BCBL. Basque Center on Cognition, Brain % Language. f.roux at bcbl.eu Tel: +34 943 309 300 Ext 211 Fax: +34 943 309 052 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer --------------------------------------------------------------------------- From pgoodin at swin.edu.au Wed Apr 15 02:06:33 2015 From: pgoodin at swin.edu.au (Peter Goodin) Date: Wed, 15 Apr 2015 00:06:33 +0000 Subject: [FieldTrip] Why the general use of parametric test as observed test statistic for permutation cluster tests? Message-ID: Hi Fieldtrip list, I'm just wondering if someone can explain if there is a reasoning behind the general use of a parametric test to calculate the initial step in the permutation cluster test and not a non-parametric test (e.g t-test over Mann Whitey U)? Is it just due to the assumption of a Gaussian distribution or is there something deeper going on? Thanks, Peter _______________________ Peter Goodin, BSc (Hons), Ph.D Candidate (submitted). Brain and Psychological Sciences Research Centre (BPsych) Swinburne University, Hawthorn, Vic, 3122 http://www.swinburne.edu.au/swinburneresearchers/index.php?fuseaction=profile&pid=4149 Monash Alfred Psychiatry Research Centre (MAPrc) Level 4, 607 St Kilda Road, Melbourne 3004 From tamaonvaliaikainenmaili at gmail.com Wed Apr 15 10:32:32 2015 From: tamaonvaliaikainenmaili at gmail.com (hm ham) Date: Wed, 15 Apr 2015 11:32:32 +0300 Subject: [FieldTrip] EEG MNE with standard_bem and statistics sanity Message-ID: Hello fellow fieldtrippers, I sent these questions a few weeks back, but I think they got buried in the weekend emails, so I'm asking the same things again. Sorry for the spam. I'm using fieldtrip to do a MNE for EEG data with no subject MRIs and I have a few questions to which I can't get a straight answer from tutorials or from mailing list history. I guess this is sort of a sanity check. First, I'm wondering about the correct sourcemodel, as loading the standard_bem and setting the third mesh as the source points in ft_prepare_leadfield gives an error: Warning: dipole lies on boundary of volume model. Code: % Electrodes, vol, sourcemodel all set in same scale with ft_convert_units vol = load('standard_bem'); cfg = []; cfg.elec = elec_aligned; % electrodes aligned to skin surface cfg.grid.pos = vol.bnd(3).pnt; % source points cfg.grid.inside = 1:size(vol.bnd(3).pnt,1); cfg.vol = vol; cfg.reducerank = 3; leadfield = ft_prepare_leadfield(cfg); Using the code below works: vol = load('standard_bem'); sourcemodel = ft_read_headshape('cortex_8196.surf.gii'); cfg = []; cfg.elec = elec_aligned; % electrodes aligned to skin surface cfg.grid.pos = sourcemodel; % source points cfg.grid.inside = 1:size(sourcemodel,1); cfg.vol = vol; cfg.reducerank = 3; leadfield = ft_prepare_leadfield(cfg); But as the http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg seems to suggest the third mesh in vol should be the brain? Or is the third compartment there just for conduction calculations? As using the sourcemodel 'cortex_8196.surf.gii' at least gave an output I went forward with those for now, to see what other problems I'd encounter. Running the MNE: cfg = []; cfg.elec = elec_aligned; cfg.method = 'mne'; cfg.grid = leadfield; cfg.vol = vol; cfg.mne.prewhiten = 'yes'; cfg.mne.lambda = 60; %Hmmm? cfg.mne.scalesourcecov = 'yes'; cfg.mne.normalize = 'yes'; cfg.channel = 'all'; cond_12_source{subject_id} = ft_sourceanalysis(cfg,cond_12{subject_id}); So secondly, I'm concerned with the lambda value, as different tutorials give very different advice ranging from 3 to 1e8. Running the MNE with 3 seems to give very unstable results when comparing the results between subjects or conditions. The data is somewhat contaminated with leftover eye-movement artefacts (removed with ICA). And that 3 is from the tutorial where the data is from MEG. So a bigger lambda is in order, but how big? Or just let the minimumnormestimate.m calculate it from the data? I have to point out that the eye-movements are somewhat spread around the trial durations and not present in the calculation window of the .cov field from ft_timelockanalysis. Should I maybe calculate the .cov field from the whole trial? Third, there has been talk of MNE statistics in the mailing list, and it seems that the ft_timelockstatistics will do the job if a neighbours structure is provided. I build the neighbours structure from the sourcemodel mesh like this: sourcemodel = ft_read_headshape('cortex_8196.surf.gii'); nsources = length(sourcemodel.pnt); neighbours=struct; for i=1:nsources neighbours(i).label = num2str(i); neighb_nodes = sourcemodel.tri((sourcemodel.tri(:,1)==i | sourcemodel.tri(:,2)==i | sourcemodel.tri(:,3)==i),:); neighb_nodes = unique(neighb_nodes)'; idx = (neighb_nodes ~= i); neighb_nodes = neighb_nodes(idx); for k=1:length(neighb_nodes) neighbours(i).neighblabel{k} = num2str(neighb_nodes(k)); end end This seemed to give reasonable neighbours and just going by distance gave some sources that were on the other side of a gyrus. Although now with the above method the distances between the sources are not uniform. I also had to tweak the data structures a little bit, labels and such. Then I ran the tests with: cfg=[]; cfg.parameter = 'avg.pow'; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT'; cfg.parameter = 'avg'; cfg.correctm = 'cluster'; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.numrandomization = 1000; cfg.tail = 1; cfg.correcttail ='alpha'; cfg.alpha = 0.05; cfg.latency = [0.4 0.5]; cfg.avgovertime = 'yes'; cfg.neighbours = neighbours; cfg.design = [1:15 1:15;ones(1,15), ones(1,15)*2]; cfg.uvar = 1; cfg.ivar = 2; cond1_stat = ft_timelockstatistics(cfg, cond_11_source{:}, cond_12_source{:}); Looking at the resulting clusters from ft_timelockstatistics there were clusters that when plotted showed disconnected sources. For example, plotted like this for the first cluster: paint = ones(8196,3); indx = find(cond1_stat.posclusterslabelmat == 1); paint(indx,2) = 0; ft_plot_mesh(sourcemodel,'vertexcolor',paint); Gave the output in the attachment, in that case the third source is atleast close, but still not a neighbour to the two next to it. Is there maybe something I'm missing with using the ft_timelockstatistics like this? I hope someone can clarify some of these issues. Thank you already in advance! Tatu -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: disconnected_cluster.png Type: image/png Size: 83016 bytes Desc: not available URL: From noahertz6 at gmail.com Wed Apr 15 14:21:46 2015 From: noahertz6 at gmail.com (Noa Hertz) Date: Wed, 15 Apr 2015 15:21:46 +0300 Subject: [FieldTrip] Beamforming analysis in frequency band Message-ID: Hi all, I'm doing source analysis in the frequency domain of a resting-state data. when doing the source analysis, I want to use several frequency bands of interest, such as beta (13-30 Hz) and gamma (30-48 Hz). My problem is about the cfg.frequency parameter, which must be a scalar (whereas i'm interested in a frequency band). Arbitrarily choosing a frequency in the middle of the range doesn't seem right. What is the common practice when doing source analysis using this function? Does the cfg.tapsmofrq parameter is supposed to enable choosing frequency band instead of a single peak frequency? Any suggestions will be very much helpful! Thanks, Noa *This is the script I’m using: cfg = []; cfg.method ='mtmfft'; cfg.output ='fourier'; cfg.keeptapers = 'yes'; cfg.foilim = [30 48]; cfg.tapsmofrq = 2; freqClosed=ft_freqanalysis(cfg,eyesClosed); * cfg = []; cfg.method='pcc'; cfg.frequency = 39; % must be a scalar cfg.lambda = 0; cfg.vol = vol; cfg.grid = grid; cfg.feedback = 'textbar'; cfg.keepfilter='yes'; source1 = ft_sourceanalysis(cfg, freqClosed); -- My signature: http://www.documentarywire.com/earthlings/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Wed Apr 15 16:25:59 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 15 Apr 2015 16:25:59 +0200 Subject: [FieldTrip] next week: live broadcast of MEG/EEG toolkit lectures Message-ID: <827C8444-E803-4DA3-A475-78E0696A6C5C@donders.ru.nl> Dear FieldTrip users, Next Monday the 4-day MEG/EEG toolkit course will start at the Donders in Nijmegen. To maximize the impact of the course, we will be live broadcasting the lectures! The computer hands-on sessions are not suited for recording and live broadcasting, but following the corresponding lecture you might want to do some tutorials on your own. The program for the live broadcasts is (starting next Monday 20 April) Monday 09:45-10:45 Introduction to EEG/MEG and introduction to the FieldTrip toolbox Monday 15:15-16:30 Fundamentals of neuronal oscillations and synchrony Tuesday 11:00-12:15 Forward and inverse modeling Tuesday 13:00-14:00 Source reconstruction using beamformers Wednesday 09:00-10:00 Statistics using non-parametric randomization techniques Wednesday 13:00-14:00 Connectivity analysis in MEG and EEG data All indicated times are Central European Time (CET), i.e. the local time here in Nijmegen. You can watch the live lectures at our YouTube channel on https://www.youtube.com/user/FieldTripToolboxTV. If you go there now, you will already see that the live events have been scheduled. The full course program is on http://www.fieldtriptoolbox.org/workshop/toolkit2015, where it will be further updated during the next days. If at any moment in doubt during next week, please go to the toolkit2015 page to get the latest updates. I’ll also post the links to the youtube live streams there. best regards, Robert (on behalf of the FieldTrip team) PS this is the very first time for us to do a live broadcast. Of course we hope it will all work as planned, but we might run into some technical difficulties. As we cannot communicate all details to each of you individually, please keep an eye on http://www.fieldtriptoolbox.org/workshop/toolkit2015 for the latest news. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Wed Apr 15 16:41:41 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 15 Apr 2015 16:41:41 +0200 Subject: [FieldTrip] next week: live broadcast of MEG/EEG toolkit lectures Message-ID: <1299A68A-2F15-462A-9D13-6C4C5DE3AD1F@donders.ru.nl> Dear FieldTrip users, Next Monday the 4-day MEG/EEG toolkit course will start at the Donders in Nijmegen. To maximize the impact of the course, we will be live broadcasting the lectures! The computer hands-on sessions are not suited for recording and live broadcasting, but following the corresponding lecture you might want to do some tutorials on your own. The program for the live broadcasts is (starting next Monday 20 April) Monday 09:45-10:45 Introduction to EEG/MEG and introduction to the FieldTrip toolbox Monday 15:15-16:30 Fundamentals of neuronal oscillations and synchrony Tuesday 11:00-12:15 Forward and inverse modeling Tuesday 13:00-14:00 Source reconstruction using beamformers Wednesday 09:00-10:00 Statistics using non-parametric randomization techniques Wednesday 13:00-14:00 Connectivity analysis in MEG and EEG data All indicated times are Central European Time (CET), i.e. the local time here in Nijmegen. You can watch the live lectures at our YouTube channel on https://www.youtube.com/user/FieldTripToolboxTV. If you go there now, you will already see that the live events have been scheduled. The full course program is on http://www.fieldtriptoolbox.org/workshop/toolkit2015, where it will be further updated during the next days. If at any moment in doubt during next week, please go to the toolkit2015 page to get the latest updates. I’ll also post the links to the youtube live streams there. best regards, Robert (on behalf of the FieldTrip team) PS this is the very first time for us to do a live broadcast. Of course we hope it will all work as planned, but we might run into some technical difficulties. As we cannot communicate all details to each of you individually, please keep an eye on http://www.fieldtriptoolbox.org/workshop/toolkit2015 for the latest news. -------------- next part -------------- An HTML attachment was scrubbed... URL: From spa268 at nyu.edu Wed Apr 15 18:17:41 2015 From: spa268 at nyu.edu (Stephen Politzer-Ahles) Date: Wed, 15 Apr 2015 18:17:41 +0200 Subject: [FieldTrip] Why the general use of parametric test as observed test statistic for permutation cluster tests? Message-ID: Hi Peter, As far as I know this is just a default coded in fieldtrip, but can easily be replaced (by using your own statfun rather than e.g. depsamplesF, depsamplesT, etc.). According to Maris & Oostenveld (2007), the observed statistic used to calculate clusters can be anything, if I recall correctly. Best, Steve > Message: 2 > Date: Wed, 15 Apr 2015 00:06:33 +0000 > From: Peter Goodin > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] Why the general use of parametric test as > observed test statistic for permutation cluster tests? > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > Hi Fieldtrip list, > > I'm just wondering if someone can explain if there is a reasoning behind the > general use of a parametric test to calculate the initial step in the > permutation cluster test and not a non-parametric test (e.g t-test over Mann > Whitey U)? Is it just due to the assumption of a Gaussian distribution or is > there something deeper going on? > > Thanks, > > Peter > > _______________________ > Peter Goodin, > BSc (Hons), Ph.D Candidate (submitted). > > Brain and Psychological Sciences Research Centre (BPsych) > Swinburne University, > Hawthorn, Vic, 3122 > http://www.swinburne.edu.au/swinburneresearchers/index.php?fuseaction=profile&pid=4149 > > Monash Alfred Psychiatry Research Centre (MAPrc) > Level 4, 607 St Kilda Road, > Melbourne 3004 > Stephen Politzer-Ahles New York University, Abu Dhabi Neuroscience of Language Lab http://www.nyu.edu/projects/politzer-ahles/ From pgoodin at swin.edu.au Thu Apr 16 00:23:25 2015 From: pgoodin at swin.edu.au (Peter Goodin) Date: Wed, 15 Apr 2015 22:23:25 +0000 Subject: [FieldTrip] Why the general use of parametric test as observed test statistic for permutation cluster tests? In-Reply-To: References: Message-ID: Hi Steve, You recall correctly indeed! It was actually that statement that got me thinking about the default use of t-test rather than checking the initial distribution! Peter __________________________ Peter Goodin, BSc (Hons), Ph.D Candidate (submitted). Brain and Psychological Sciences Research Centre (BPsych) Swinburne University, Hawthorn, Vic, 3122 http://www.swinburne.edu.au/swinburneresearchers/index.php?fuseaction=profile&pid=4149 Monash Alfred Psychiatry Research Centre (MAPrc) Level 4, 607 St Kilda Road, Melbourne 3004 ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Stephen Politzer-Ahles [spa268 at nyu.edu] Sent: Thursday, 16 April 2015 2:17 AM To: fieldtrip at science.ru.nl Subject: Re: [FieldTrip] Why the general use of parametric test as observed test statistic for permutation cluster tests? Hi Peter, As far as I know this is just a default coded in fieldtrip, but can easily be replaced (by using your own statfun rather than e.g. depsamplesF, depsamplesT, etc.). According to Maris & Oostenveld (2007), the observed statistic used to calculate clusters can be anything, if I recall correctly. Best, Steve > Message: 2 > Date: Wed, 15 Apr 2015 00:06:33 +0000 > From: Peter Goodin > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] Why the general use of parametric test as > observed test statistic for permutation cluster tests? > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > Hi Fieldtrip list, > > I'm just wondering if someone can explain if there is a reasoning behind the > general use of a parametric test to calculate the initial step in the > permutation cluster test and not a non-parametric test (e.g t-test over Mann > Whitey U)? Is it just due to the assumption of a Gaussian distribution or is > there something deeper going on? > > Thanks, > > Peter > > _______________________ > Peter Goodin, > BSc (Hons), Ph.D Candidate (submitted). > > Brain and Psychological Sciences Research Centre (BPsych) > Swinburne University, > Hawthorn, Vic, 3122 > http://www.swinburne.edu.au/swinburneresearchers/index.php?fuseaction=profile&pid=4149 > > Monash Alfred Psychiatry Research Centre (MAPrc) > Level 4, 607 St Kilda Road, > Melbourne 3004 > Stephen Politzer-Ahles New York University, Abu Dhabi Neuroscience of Language Lab http://www.nyu.edu/projects/politzer-ahles/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From federica.ma at gmail.com Thu Apr 16 11:41:17 2015 From: federica.ma at gmail.com (Federica Mauro) Date: Thu, 16 Apr 2015 09:41:17 +0000 Subject: [FieldTrip] Problems with ft_freqanalysis Message-ID: <5cead4654ee14611ae745be82f0fcc49@EXPRD02.hosting.ru.nl> Hi everybody, I'm trying to compute coherence analyses following the coherence tutorial at http://www.fieldtriptoolbox.org/tutorial/coherence. Since a couple of days, I have this error message in computing ft_freqanalysis: Error using load Unable to read file precompute_dpss: No such file or directory. Error in dpss (line 9) load precompute_dpss Error in ft_specest_mtmfft>double_dpss (line 335) tap = dpss(double(a), double(b), varargin{:}); Error in ft_specest_mtmfft (line 151) tap = double_dpss(ndatsample,ndatsample*(tapsmofrq./fsample))'; Error in ft_freqanalysis (line 494) [spectrum,ntaper,foi] = ft_specest_mtmfft(dat, time, 'taper', cfg.taper, options{:}, 'feedback', fbopt); Is that a bug? Here is the code I'm using: cfg = []; cfg.output = 'powandcsd'; cfg.method = 'mtmfft'; cfg.foilim = [5 40]; cfg.tapsmofrq = 5; cfg.keeptrials = 'yes'; freq = ft_freqanalysis(cfg, eeg); Thank you in advance, Federica -------------- next part -------------- An HTML attachment was scrubbed... URL: From f.roux at bcbl.eu Thu Apr 16 11:50:06 2015 From: f.roux at bcbl.eu (=?utf-8?B?RnLDqWTDqXJpYw==?= Roux) Date: Thu, 16 Apr 2015 11:50:06 +0200 (CEST) Subject: [FieldTrip] [SPAM] Problems with ft_freqanalysis In-Reply-To: <5cead4654ee14611ae745be82f0fcc49@EXPRD02.hosting.ru.nl> Message-ID: <1216046341.56584.1429177806762.JavaMail.root@bcbl.eu> Hi Fredrica, this is most likely do to a path problem. Try adding this at the beginning of your script/function: restorde_defaultpath; addpath('/path2fieldtrip/fieldtrip-2015xxxx/'); ft_defaults; HTH -- Frédéric Roux Postdoctoral Scientist BCBL. Basque Center on Cognition, Brain % Language. f.roux at bcbl.eu Tel: +34 943 309 300 Ext 211 Fax: +34 943 309 052 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer --------------------------------------------------------------------------- ----- Original Message ----- From: "Federica Mauro" To: "donders fieldtrip" Sent: Thursday, April 16, 2015 11:41:17 AM Subject: [SPAM] [FieldTrip] Problems with ft_freqanalysis Hi everybody, I'm trying to compute coherence analyses following the coherence tutorial at http://www.fieldtriptoolbox.org/tutorial/coherence . Since a couple of days, I have this error message in computing ft_freqanalysis: Error using load Unable to read file precompute_dpss: No such file or directory. Error in dpss (line 9) load precompute_dpss Error in ft_specest_mtmfft>double_dpss (line 335) tap = dpss(double(a), double(b), varargin{:}); Error in ft_specest_mtmfft (line 151) tap = double_dpss(ndatsample,ndatsample*(tapsmofrq./fsample))'; Error in ft_freqanalysis (line 494) [spectrum,ntaper,foi] = ft_specest_mtmfft(dat, time, 'taper', cfg.taper, options{:}, 'feedback', fbopt); Is that a bug? Here is the code I'm using: cfg = []; cfg.output = 'powandcsd'; cfg.method = 'mtmfft'; cfg.foilim = [5 40]; cfg.tapsmofrq = 5; cfg.keeptrials = 'yes'; freq = ft_freqanalysis(cfg, eeg); Thank you in advance, Federica _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From r.oostenveld at donders.ru.nl Thu Apr 16 12:06:42 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 16 Apr 2015 12:06:42 +0200 Subject: [FieldTrip] Problems with ft_freqanalysis In-Reply-To: <5cead4654ee14611ae745be82f0fcc49@EXPRD02.hosting.ru.nl> References: <5cead4654ee14611ae745be82f0fcc49@EXPRD02.hosting.ru.nl> Message-ID: Hi Federica, The error message you run into relates to the presence (or absence) of the Mathworks signal processing toolbox. FieldTrip relies on a number of MATLAB toolboxes (see http://www.fieldtriptoolbox.org/faq/requirements). Where possible, we try to avoid extra commercial toolboxes. Therefore we have some drop-in replacement functions in fieldtrip/external/signal (which were obtained from the Octave project). For the DPSS function (used for multitapering) however we don’t have a fully satisfactory solution. The error message you get suggests that you are using the "fieldtrip/external/signal/dpss_hack” directory. That is one that should not be on your path, unless you explicitly add it. You should only add in case you don’t have the signal processing toolbox and know what you are doing (i.e. after having read the README in that directory). I suspect you have used add path(genpath(…)) or the GUI equivalent of it. Please see http://www.fieldtriptoolbox.org/faq/should_i_add_fieldtrip_with_all_subdirectories_to_my_matlab_path and remove the dpss_hack directory from your path. best Robert PS for the low frequency range you are interested in I suspect that multitapering won’t be the most optimal anyway. Better add cfg.taper=‘hanning’ to your analysis, and see Nietzsche explain it next Monday on https://www.youtube.com/watch?v=vwPpSglPJTE On 16 Apr 2015, at 11:41, Federica Mauro wrote: > Hi everybody, > > I'm trying to compute coherence analyses following the coherence tutorial at http://www.fieldtriptoolbox.org/tutorial/coherence. > Since a couple of days, I have this error message in computing ft_freqanalysis: > > Error using load > Unable to read file precompute_dpss: No such file or directory. > > Error in dpss (line 9) > load precompute_dpss > > Error in ft_specest_mtmfft>double_dpss (line 335) > tap = dpss(double(a), double(b), varargin{:}); > > Error in ft_specest_mtmfft (line 151) > tap = > double_dpss(ndatsample,ndatsample*(tapsmofrq./fsample))'; > > Error in ft_freqanalysis (line 494) > [spectrum,ntaper,foi] = ft_specest_mtmfft(dat, time, 'taper', > cfg.taper, options{:}, 'feedback', fbopt); > > Is that a bug? > > > Here is the code I'm using: > cfg = []; > cfg.output = 'powandcsd'; > cfg.method = 'mtmfft'; > cfg.foilim = [5 40]; > cfg.tapsmofrq = 5; > cfg.keeptrials = 'yes'; > > freq = ft_freqanalysis(cfg, eeg); > > > Thank you in advance, > Federica > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Thu Apr 16 13:53:41 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Thu, 16 Apr 2015 13:53:41 +0200 Subject: [FieldTrip] Beamforming analysis in frequency band In-Reply-To: References: Message-ID: <9BC70F24-9E97-4247-B0C0-365CCC154C70@uni-konstanz.de> Dear Noa, you should use frequency smoothening to achieve this. For example, a configuration of cfg.foilim = [20 20] ; and cfg.tapsmofrq = 10; will allow you to estimate sources in the 10 to 30 Hz band. > Hi all, > > I'm doing source analysis in the frequency domain of a resting-state data. > when doing the source analysis, I want to use several frequency bands of interest, such as beta (13-30 Hz) and gamma (30-48 Hz). > My problem is about the cfg.frequency parameter, which must be a scalar (whereas i'm interested in a frequency band). Arbitrarily choosing a frequency in the middle of the range doesn't seem right. > > What is the common practice when doing source analysis using this function? You could evaluate this tutorial: http://www.fieldtriptoolbox.org/tutorial/beamformer > Does the cfg.tapsmofrq parameter is supposed to enable choosing frequency band instead of a single peak frequency? and some detailed explanation in a pictorial form here: https://www.youtube.com/watch?v=7eS11DtbIPw best tzvetan > > Any suggestions will be very much helpful! > > Thanks, > Noa > > > This is the script I’m using: > > cfg = []; > cfg.method ='mtmfft'; > cfg.output ='fourier'; > cfg.keeptapers = 'yes'; > cfg.foilim = [30 48]; > cfg.tapsmofrq = 2; > freqClosed=ft_freqanalysis(cfg,eyesClosed); > > > > cfg = []; > cfg.method='pcc'; > cfg.frequency = 39; % must be a scalar > cfg.lambda = 0; > cfg.vol = vol; > cfg.grid = grid; > cfg.feedback = 'textbar'; > cfg.keepfilter='yes'; > source1 = ft_sourceanalysis(cfg, freqClosed); > > > -- > My signature: > > http://www.documentarywire.com/earthlings/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From federica.ma at gmail.com Thu Apr 16 16:44:18 2015 From: federica.ma at gmail.com (Federica Mauro) Date: Thu, 16 Apr 2015 16:44:18 +0200 Subject: [FieldTrip] [SPAM] Problems with ft_freqanalysis In-Reply-To: <1216046341.56584.1429177806762.JavaMail.root@bcbl.eu> References: <5cead4654ee14611ae745be82f0fcc49@EXPRD02.hosting.ru.nl> <1216046341.56584.1429177806762.JavaMail.root@bcbl.eu> Message-ID: Thanks, you've been really helpful. Thanks also for the tip on the taper cfg, Looking forward to the seminar! Federica 2015-04-16 11:50 GMT+02:00 Frédéric Roux : > Hi Fredrica, > > this is most likely do to a path problem. > > Try adding this at the beginning of your script/function: > > restorde_defaultpath; > addpath('/path2fieldtrip/fieldtrip-2015xxxx/'); > ft_defaults; > > HTH > > -- > Frédéric Roux > Postdoctoral Scientist > BCBL. Basque Center on Cognition, Brain % Language. > > f.roux at bcbl.eu > Tel: +34 943 309 300 Ext 211 > Fax: +34 943 309 052 > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > --------------------------------------------------------------------------- > > > ----- Original Message ----- > From: "Federica Mauro" > To: "donders fieldtrip" > Sent: Thursday, April 16, 2015 11:41:17 AM > Subject: [SPAM] [FieldTrip] Problems with ft_freqanalysis > > > > > > > > > > Hi everybody, > > I'm trying to compute coherence analyses following the coherence tutorial > at http://www.fieldtriptoolbox.org/tutorial/coherence . > Since a couple of days, I have this error message in computing > ft_freqanalysis: > > Error using load > Unable to read file precompute_dpss: No such file or directory. > > Error in dpss (line 9) > load precompute_dpss > > Error in ft_specest_mtmfft>double_dpss (line 335) > tap = dpss(double(a), double(b), varargin{:}); > > Error in ft_specest_mtmfft (line 151) > tap = > double_dpss(ndatsample,ndatsample*(tapsmofrq./fsample))'; > > Error in ft_freqanalysis (line 494) > [spectrum,ntaper,foi] = ft_specest_mtmfft(dat, time, 'taper', > cfg.taper, options{:}, 'feedback', fbopt); > > Is that a bug? > > > Here is the code I'm using: > cfg = []; > cfg.output = 'powandcsd'; > cfg.method = 'mtmfft'; > cfg.foilim = [5 40]; > cfg.tapsmofrq = 5; > cfg.keeptrials = 'yes'; > > freq = ft_freqanalysis(cfg, eeg); > > > Thank you in advance, > Federica > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From n.lam at donders.ru.nl Thu Apr 16 17:26:17 2015 From: n.lam at donders.ru.nl (Lam, N.H.L. (Nietzsche)) Date: Thu, 16 Apr 2015 15:26:17 +0000 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? Message-ID: Dear FieldTrip users, Next week we will provide a live broadcast of the lectures from the 4-day MEG/EEG toolkit course at the Donders in Nijmegen, on our YouTube channel https://www.youtube.com/user/FieldTripToolboxTV Please check whether the videos are available in your country (click on one of the scheduled live stream videos - you should see a clock that counts down to the lecture). If you get the message "Live streaming is not available in your country due to right issues" please reply to this email and state your country so that we can find a solution prior to the toolkit next week. We appreciate your help to make this a smooth broadcast. Best, Nietzsche (on behalf of the FieldTrip team) P.S. Full course program of the workshop http://www.fieldtriptoolbox.org/workshop/toolkit2015, Best, Nietzsche (on behalf of the FieldTrip team) -------------- next part -------------- An HTML attachment was scrubbed... URL: From tomh at kurage.nimh.nih.gov Thu Apr 16 17:39:50 2015 From: tomh at kurage.nimh.nih.gov (Tom Holroyd) Date: Thu, 16 Apr 2015 11:39:50 -0400 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: References: Message-ID: <20150416113950.253a352c@kurage.nimh.nih.gov> https://youtu.be/-RpQklxbCsg?list=PLbVcEw60xnKNuNKwBSWgzdZCXxNDMh3Gr I just watched that, no problems, and I get the countdowns for the newer links. Looking forward to it! I was almost surprised I didn't need to install a new Flash player or something. Thanks! On Thu, 16 Apr 2015 15:26:17 +0000 "Lam, N.H.L. (Nietzsche)" wrote: > Dear FieldTrip users, > > Next week we will provide a live broadcast of the lectures from the > 4-day MEG/EEG toolkit course at the Donders in Nijmegen, on our > YouTube channel https://www.youtube.com/user/FieldTripToolboxTV > > Please check whether the videos are available in your country (click > on one of the scheduled live stream videos - you should see a clock > that counts down to the lecture). If you get the message "Live > streaming is not available in your country due to right issues" > please reply to this email and state your country so that we can find > a solution prior to the toolkit next week. We appreciate your help > to make this a smooth broadcast. > > Best, > Nietzsche (on behalf of the FieldTrip team) > > P.S. Full course program of the workshop > http://www.fieldtriptoolbox.org/workshop/toolkit2015, > > > > > > > > > Best, > Nietzsche (on behalf of the FieldTrip team) -- Dr. Tom -- "There are not more than five musical notes, yet the combinations of these five give rise to more melodies than can ever be heard." -- Sun Tzu From Holger.Krause at med.uni-duesseldorf.de Thu Apr 16 17:45:03 2015 From: Holger.Krause at med.uni-duesseldorf.de (Holger Krause) Date: Thu, 16 Apr 2015 17:45:03 +0200 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: References: Message-ID: <201504161745.05273.Holger.Krause@med.uni-duesseldorf.de> Am Donnerstag, 16. April 2015 schrieb Lam, N.H.L. (Nietzsche): > Please check whether the videos are available in your country (click on one > of the scheduled live stream videos - you should see a clock that counts > down to the lecture). If you get the message "Live streaming is not > available in your country due to right issues" please reply to this email > and state your country so that we can find a solution prior to the toolkit > next week. We appreciate your help to make this a smooth broadcast. https://www.youtube.com/watch?v=ZBwh0Vm4fh4 Germany :-( "Live Streaming ist wegen Rechteproblemen in Deutschland leider nicht möglich." Best, Holger From kgm at tf.uni-kiel.de Thu Apr 16 17:52:39 2015 From: kgm at tf.uni-kiel.de (kgm) Date: Thu, 16 Apr 2015 17:52:39 +0200 Subject: [FieldTrip] =?utf-8?q?Can_you_view_the_Livestream_lectures_=28MEG?= =?utf-8?q?/EEG_toolkit=29=3F?= In-Reply-To: References: Message-ID: <8b25592765751ea3e1c8afa0e3936788@tf.uni-kiel.de> Dear all, I am a user from Germany and I get the message "Live streaming is not available in your country due to rights issues" when I click one of the scheduled videos. Looking forward for the solution. Thanks in advance! Best regards, Kidist G.Mideksa On 2015-04-16 17:26, Lam, N.H.L. (Nietzsche) wrote: > Dear FieldTrip users, > > Next week we will provide a live broadcast of the lectures from the > 4-day MEG/EEG toolkit course at the Donders in Nijmegen, on our > YouTube channel https://www.youtube.com/user/FieldTripToolboxTV > > Please CHECK WHETHER THE VIDEOS ARE AVAILABLE IN YOUR COUNTRY (click > on one of the scheduled live stream videos - you should see a clock > that counts down to the lecture). If you get the message "Live > streaming is not available in your country due to right issues" please > reply to this email and state your country so that we can find a > solution prior to the toolkit next week. We appreciate your help to > make this a smooth broadcast. > > Best, > Nietzsche (on behalf of the FieldTrip team) > > P.S. Full course program of the workshop > http://www.fieldtriptoolbox.org/workshop/toolkit2015 [1], > > Best, > Nietzsche (on behalf of the FieldTrip team) > > Links: > ------ > [1] http://www.fieldtriptoolbox.org/workshop/toolkit2015 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From david.schubring at uni-konstanz.de Thu Apr 16 18:07:43 2015 From: david.schubring at uni-konstanz.de (David Schubring) Date: Thu, 16 Apr 2015 18:07:43 +0200 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: <201504161745.05273.Holger.Krause@med.uni-duesseldorf.de> References: <201504161745.05273.Holger.Krause@med.uni-duesseldorf.de> Message-ID: <552FDE4F.3060501@uni-konstanz.de> Hello FieldTrip users, I don't know about the exact legal situation here, but since you probably won't stream copyrighted material a proxy plugin should be fine? At least it works for me (in germany) - which means, at the moment I can see the countdown. There is a ton of browser plugins for unblocking youtube, the one I use for Mozilla Firefox is called "ProxTube" (there should be one for Chrome as well): https://addons.mozilla.org/de/firefox/addon/proxtube/ Cheers, David Am 16.04.15 um 17:45 schrieb Holger Krause: > Am Donnerstag, 16. April 2015 schrieb Lam, N.H.L. (Nietzsche): >> Please check whether the videos are available in your country (click on one >> of the scheduled live stream videos - you should see a clock that counts >> down to the lecture). If you get the message "Live streaming is not >> available in your country due to right issues" please reply to this email >> and state your country so that we can find a solution prior to the toolkit >> next week. We appreciate your help to make this a smooth broadcast. > > https://www.youtube.com/watch?v=ZBwh0Vm4fh4 > > Germany :-( > > "Live Streaming ist wegen Rechteproblemen in Deutschland leider nicht > möglich." > > Best, > > Holger > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Dipl.-Psych. David Schubring Clinical Psychology University of Konstanz P.O. Box 905 78457 Konstanz Phone: +49-(0)7531-88-4889 From ingrid.sor at neuro.uu.se Fri Apr 17 09:43:44 2015 From: ingrid.sor at neuro.uu.se (=?windows-1252?Q?Ingrid_S=F6r?=) Date: Fri, 17 Apr 2015 09:43:44 +0200 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: References: Message-ID: <5530B9B0.9030104@neuro.uu.se> Hi, Works fine in Sweden! Looks like some interesting material. Best, Ingrid On 2015-04-16 17:26, Lam, N.H.L. (Nietzsche) wrote: > Dear FieldTrip users, > > Next week we will provide a live broadcast of the lectures from the > 4-day MEG/EEG toolkit course at the Donders in Nijmegen, on our > YouTube channel https://www.youtube.com/user/FieldTripToolboxTV > > Please*check whether the videos are available in your country* (click > on one of the scheduled live stream videos - you should see a clock > that counts down to the lecture). If you get the message "Live > streaming is not available in your country due to right issues" please > reply to this email and state your country so that we can find a > solution prior to the toolkit next week. We appreciate your help to > make this a smooth broadcast. > > Best, > Nietzsche (on behalf of the FieldTrip team) > > P.S. Full course program of the workshop > http://www.fieldtriptoolbox.org/workshop/toolkit2015, > > > > > > > > > Best, > Nietzsche (on behalf of the FieldTrip team) > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From mariya.kharaman at uni-konstanz.de Fri Apr 17 09:45:25 2015 From: mariya.kharaman at uni-konstanz.de (Mariya Kharaman) Date: Fri, 17 Apr 2015 09:45:25 +0200 Subject: [FieldTrip] =?utf-8?q?Can_you_view_the_Livestream_lectures_=28MEG?= =?utf-8?q?/EEG_toolkit=29=3F?= In-Reply-To: Message-ID: Dear all, I am in Germany and as it seems, I will not be able to watch the videos ("Live Streaming ist wegen Rechteproblemen in Deutschland leider nicht möglich." = "Live streaming is not available in your country due to right issues". I really hope the solution will be found! Thank you very much! Best wishes, Mariya Am Donnerstag, 16. April 2015 17:26 CEST, "Lam, N.H.L. (Nietzsche)" schrieb: > Dear FieldTrip users, > > Next week we will provide a live broadcast of the lectures from the 4-day MEG/EEG toolkit course at the Donders in Nijmegen, on our YouTube channel https://www.youtube.com/user/FieldTripToolboxTV > > Please check whether the videos are available in your country (click on one of the scheduled live stream videos - you should see a clock that counts down to the lecture). If you get the message "Live streaming is not available in your country due to right issues" please reply to this email and state your country so that we can find a solution prior to the toolkit next week. We appreciate your help to make this a smooth broadcast. > > Best, > Nietzsche (on behalf of the FieldTrip team) > > P.S. Full course program of the workshop http://www.fieldtriptoolbox.org/workshop/toolkit2015, > > > > > > > > > Best, > Nietzsche (on behalf of the FieldTrip team) From smoratti at psi.ucm.es Fri Apr 17 11:09:28 2015 From: smoratti at psi.ucm.es (smoratti at psi.ucm.es) Date: Fri, 17 Apr 2015 11:09:28 +0200 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: <201504161745.05273.Holger.Krause@med.uni-duesseldorf.de> References: <201504161745.05273.Holger.Krause@med.uni-duesseldorf.de> Message-ID: <04EC09B5-FE5B-491A-965A-5BACFC4C29EE@psi.ucm.es> in Spain it seems to work… best, Stephan ________________________________________________________ Stephan Moratti, PhD see: Stephan's research profile Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas Despacho (Office) 1326-0 28223 Pozuelo de Alarcón (Madrid) Spain and Center for Biomedical Technology Laboratory for Cognitive and Computational Neuroscience Parque Científico y Tecnológico de la Universidad Politecnica de Madrid Campus Montegancedo 28223 Pozuelo de Alarcón (Madrid) Spain email: smoratti at psi.ucm.es Tel.: +34 679219982 El 16/04/2015, a las 17:45, Holger Krause escribió: > Am Donnerstag, 16. April 2015 schrieb Lam, N.H.L. (Nietzsche): >> Please check whether the videos are available in your country (click on one >> of the scheduled live stream videos - you should see a clock that counts >> down to the lecture). If you get the message "Live streaming is not >> available in your country due to right issues" please reply to this email >> and state your country so that we can find a solution prior to the toolkit >> next week. We appreciate your help to make this a smooth broadcast. > > https://www.youtube.com/watch?v=ZBwh0Vm4fh4 > > Germany :-( > > "Live Streaming ist wegen Rechteproblemen in Deutschland leider nicht > möglich." > > Best, > > Holger > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From n.lam at donders.ru.nl Fri Apr 17 12:11:13 2015 From: n.lam at donders.ru.nl (Lam, N.H.L. (Nietzsche)) Date: Fri, 17 Apr 2015 10:11:13 +0000 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: <8b25592765751ea3e1c8afa0e3936788@tf.uni-kiel.de> References: , <8b25592765751ea3e1c8afa0e3936788@tf.uni-kiel.de> Message-ID: Dear FieldTrip Users, It seems that the viewing problem is only limited to Germany (we have checked in other countries as well). We suggest that you use a proxy plugin to circumvent the issue of not being able to view the video. A fellow FT user has suggested the following for Firefox https://addons.mozilla.org/de/firefox/addon/proxtube/ Similar proxy plugins exist for other web browsers (note that these were found on google, and have not be personally tested by the FieldTrip team): https://chrome.google.com/webstore/detail/proxxy/clkkaggocmafajhbcbknhcgnbmagjohi?hl=en http://www.chip.de/downloads/FoxyProxy-fuer-Chrome_53036930.html We suggest you determine a suitable proxy well in advance of the lecture(s), as it may be more than a 5 minute fix for some of you. Best, Nietzsche (on behalf of the FieldTrip team) ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of kgm [kgm at tf.uni-kiel.de] Sent: 16 April 2015 17:52 To: FieldTrip discussion list Subject: Re: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? Dear all, I am a user from Germany and I get the message "Live streaming is not available in your country due to rights issues" when I click one of the scheduled videos. Looking forward for the solution. Thanks in advance! Best regards, Kidist G.Mideksa On 2015-04-16 17:26, Lam, N.H.L. (Nietzsche) wrote: > Dear FieldTrip users, > > Next week we will provide a live broadcast of the lectures from the > 4-day MEG/EEG toolkit course at the Donders in Nijmegen, on our > YouTube channel https://www.youtube.com/user/FieldTripToolboxTV > > Please CHECK WHETHER THE VIDEOS ARE AVAILABLE IN YOUR COUNTRY (click > on one of the scheduled live stream videos - you should see a clock > that counts down to the lecture). If you get the message "Live > streaming is not available in your country due to right issues" please > reply to this email and state your country so that we can find a > solution prior to the toolkit next week. We appreciate your help to > make this a smooth broadcast. > > Best, > Nietzsche (on behalf of the FieldTrip team) > > P.S. Full course program of the workshop > http://www.fieldtriptoolbox.org/workshop/toolkit2015 [1], > > Best, > Nietzsche (on behalf of the FieldTrip team) > > Links: > ------ > [1] http://www.fieldtriptoolbox.org/workshop/toolkit2015 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From eva.patai at psych.ox.ac.uk Fri Apr 17 13:35:46 2015 From: eva.patai at psych.ox.ac.uk (Zita Eva Patai) Date: Fri, 17 Apr 2015 12:35:46 +0100 Subject: [FieldTrip] interpolation of bad channels matlab error Message-ID: Dear FTers I have been trying to fix some bad channels in my data through interpolation. It seems to not be working. My code is below. Please note my data object is converted from SPM (in case that matters). Thanks very much in advance, zita data = fsample: 250 label: {324x1 cell} trial: {1x505 cell} time: {1x505 cell} grad: [1x1 struct] triallist: {1x505 cell} >> cfg2 cfg2 = badchannel: {2x1 cell} method: 'nearest' neighbours: [1x306 struct] >> [interp]=ft_channelrepair(cfg2,data) the input is raw data with 324 channels and 505 trials using gradiometers specified in the data repairing channel MEG1132 using neighbour repairing channel MEG1421 using neighbour repairing bad channels for 505 trials .Error using * MTIMES is not supported for one sparse input and one single input. Error in ft_channelrepair (line 172) interp.trial{i} = repair * data.trial{i}; -- Eva Zita Patai, DPhil Postdoctoral Researcher Oxford Centre for Human Brain Activity University of Oxford -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri Apr 17 13:53:54 2015 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 17 Apr 2015 11:53:54 +0000 Subject: [FieldTrip] interpolation of bad channels matlab error In-Reply-To: References: Message-ID: <876E7EA3-688A-49EB-9B5A-2241570DD41D@fcdonders.ru.nl> Hi Eva, The MATLAB error suggests that your data is represented as single precision floating point numbers, and matrix multiplication is apparently not supported when you want to multiply with a sparse matrix. You could try and convert your data to double precision: data=ft_struct2double(data); and then call ft_channelrepair. Best, Jan-Mathijs On Apr 17, 2015, at 1:35 PM, Zita Eva Patai > wrote: Dear FTers I have been trying to fix some bad channels in my data through interpolation. It seems to not be working. My code is below. Please note my data object is converted from SPM (in case that matters). Thanks very much in advance, zita data = fsample: 250 label: {324x1 cell} trial: {1x505 cell} time: {1x505 cell} grad: [1x1 struct] triallist: {1x505 cell} >> cfg2 cfg2 = badchannel: {2x1 cell} method: 'nearest' neighbours: [1x306 struct] >> [interp]=ft_channelrepair(cfg2,data) the input is raw data with 324 channels and 505 trials using gradiometers specified in the data repairing channel MEG1132 using neighbour repairing channel MEG1421 using neighbour repairing bad channels for 505 trials .Error using * MTIMES is not supported for one sparse input and one single input. Error in ft_channelrepair (line 172) interp.trial{i} = repair * data.trial{i}; -- Eva Zita Patai, DPhil Postdoctoral Researcher Oxford Centre for Human Brain Activity University of Oxford _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jdien07 at mac.com Fri Apr 17 19:09:37 2015 From: jdien07 at mac.com (Joseph Dien) Date: Fri, 17 Apr 2015 13:09:37 -0400 Subject: [FieldTrip] Johns Hopkins Research Assistant Position Message-ID: General Description: Research of the Division is focused on improving aspects of cognition in humans, particularly those related to speech, communication, and cognitive control, in both normally developing individuals and in individuals with developmental and acquired disorders, such as autism, Lesch-Nyhan syndrome, and stroke. Studies use a mix of techniques from experimental psychology, transcranial Direct Current Stimulation (tDCS), structural imaging, fMRI, psychophysiological measures, and especially EEG. RA will be directly responsible for 1-2 projects themselves, and will assist with several other projects in the Division. Involvement will be in any and all aspects: library research; writing up research plans; subject recruitment; scheduling; testing (including psychological and experimental tasks); collecting data; cleaning data; maintaining files; initial analyses; draft and final write-ups. Interacts, as needed, with Institutional Review Board. Participates in regular laboratory research meetings. Maintains, monitors, and orders research supplies. Helps with statistical analyses, using software such as MATLAB, NetStation, SPM8, MRIcron, and SPSS. Reports directly to the Director of the Division, with delegated reporting to other faculty in the Division, faculty associated with the Division, and senior staff. Qualifications: Bachelor's degree in related discipline required. Some related experience required. Additional education may substitute for required experience and additional related experience may substitute for required education, to the extent permitted by the JHU equivalency formula. Must have ability to use a personal computer. Prefer experience with analytic tools, and with writing academic manuscripts and grants. Must be well-organized, efficient, accurate, responsible, and enthusiastic. Must be able to interact effectively with faculty, staff, and subjects. Experience administering and scoring cognitive and behavioral measures preferred. Experience with MS Word, Excel, SPSS, MATLAB, SPM8, and NetStation software preferred. Preferred Qualifications: Bachelor’s or Master’s Degree in Experimental Psychology, Cognitive Science, Neuroscience, or a related field preferred. Posting at: https://hrnt.jhu.edu/jhujobs/job_view.cfm?view_req_id=65838&view=sch Contact Joseph Dien (jdien1 at jhmi.edu ) for more information. Joe -------------------------------------------------------------------------------- Joseph Dien, PhD Research Associate Cognitive Neurology/Neuropsychology The Johns Hopkins University School of Medicine Lab E-mail: jdien1 at jhmi.edu Private E-mail: jdien07 at mac.com Office Phone: 410-614-3115 Cell Phone: 202-297-8117 Fax: 410-955-0188 http://joedien.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From vahidgerami.mse at gmail.com Sun Apr 19 08:28:14 2015 From: vahidgerami.mse at gmail.com (vahid gerami) Date: Sun, 19 Apr 2015 10:58:14 +0430 Subject: [FieldTrip] EEG from brain sensory motor area Message-ID: dear eeglab community i've recorded some eeg signals from sensory motor area. the signals are recorded while the right hand was moving regularly. now i want to detect the ERP changes on the signal caused by the hand movement. does any one have the same experience? how can i do the job? please help me about the procedure. regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From noahertz6 at gmail.com Sun Apr 19 12:57:46 2015 From: noahertz6 at gmail.com (Noa Hertz) Date: Sun, 19 Apr 2015 13:57:46 +0300 Subject: [FieldTrip] Beamforming analysis in frequency band In-Reply-To: <9BC70F24-9E97-4247-B0C0-365CCC154C70@uni-konstanz.de> References: <9BC70F24-9E97-4247-B0C0-365CCC154C70@uni-konstanz.de> Message-ID: Thank you Tzvetan! This raised two more question regarding the source analysis: 1. What is the difference between defining the frequency range under cfg.foi (such as cfg.foi=[30 48]) and defining if under the cfg.tapsmofrq (such as cfg.foi=[39 39] cfg.tapsmofrq=9)? 2. the cfg.tapsmofrq option only exist in the ft_freqanalysis function, and not in the ft_sourceanalysis function. in ft_sourceanalysis the only option is cfg.frequency which, as I mention, has to be a scalar. My question is whether defining the cfg.tapsmofrq in the ft_freqanalysis is also causing the source analysis to use the range of frequencies and not the single frequency. *Thanks a lot,* *Noa* 2015-04-16 14:53 GMT+03:00 Tzvetan Popov : > > Dear Noa, > > you should use frequency smoothening to achieve this. For example, a > configuration of cfg.foilim = [20 20] ; and cfg.tapsmofrq = 10; will allow > you to estimate sources in the 10 to 30 Hz band. > > Hi all, > > I'm doing source analysis in the frequency domain of a resting-state data. > when doing the source analysis, I want to use several frequency bands of > interest, such as beta (13-30 Hz) and gamma (30-48 Hz). > My problem is about the cfg.frequency parameter, which must be a scalar > (whereas i'm interested in a frequency band). Arbitrarily choosing a > frequency in the middle of the range doesn't seem right. > > What is the common practice when doing source analysis using this function? > > You could evaluate this tutorial: > http://www.fieldtriptoolbox.org/tutorial/beamformer > > Does the cfg.tapsmofrq parameter is supposed to enable choosing frequency > band instead of a single peak frequency? > > and some detailed explanation in a pictorial form here: > https://www.youtube.com/watch?v=7eS11DtbIPw > > best > tzvetan > > > Any suggestions will be very much helpful! > > Thanks, > Noa > > > > > > > > > > > > > > *This is the script I’m using: cfg = []; cfg.method ='mtmfft'; > cfg.output ='fourier'; cfg.keeptapers = 'yes'; cfg.foilim = [30 > 48]; cfg.tapsmofrq = 2; > freqClosed=ft_freqanalysis(cfg,eyesClosed); * > > cfg = []; > cfg.method='pcc'; > cfg.frequency = 39; % must be a scalar > cfg.lambda = 0; > cfg.vol = vol; > cfg.grid = grid; > cfg.feedback = 'textbar'; > cfg.keepfilter='yes'; > source1 = ft_sourceanalysis(cfg, freqClosed); > > > -- > My signature: > > http://www.documentarywire.com/earthlings/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- מעכשיו זאת החתימה שלי.. חובה לראות http://www.documentarywire.com/earthlings/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From stidimitriadis at gmail.com Sun Apr 19 19:03:09 2015 From: stidimitriadis at gmail.com (Stavros Dimitriadis) Date: Sun, 19 Apr 2015 10:03:09 -0700 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: <04EC09B5-FE5B-491A-965A-5BACFC4C29EE@psi.ucm.es> References: <201504161745.05273.Holger.Krause@med.uni-duesseldorf.de> <04EC09B5-FE5B-491A-965A-5BACFC4C29EE@psi.ucm.es> Message-ID: Dear All In Greece it works fine ! Best wishes Dimitriadis Stavros, PhD Research Fellow Aristotle University of Thessaloniki, Greece Department of Informatics http://users.auth.gr/~stdimitr/index.html 1)Artificial Intelligence Information Analysis lab Department of Informatics *Aristotle University of Thessaloniki * 2)NeuroInformatics.GRoup , AUTH, Greece 2015-04-17 2:09 GMT-07:00 smoratti at psi.ucm.es : > > in Spain it seems to work… > > best, > > Stephan > > ________________________________________________________ > Stephan Moratti, PhD > > see: Stephan's research profile > > > Universidad Complutense de Madrid > Facultad de Psicología > Departamento de Psicología Básica I > Campus de Somosaguas > Despacho (Office) 1326-0 > 28223 Pozuelo de Alarcón (Madrid) > Spain > > and > > Center for Biomedical Technology > Laboratory for Cognitive and Computational Neuroscience > Parque Científico y Tecnológico de la Universidad Politecnica de Madrid > Campus Montegancedo > 28223 Pozuelo de Alarcón (Madrid) > Spain > > > email: smoratti at psi.ucm.es > Tel.: +34 679219982 > > El 16/04/2015, a las 17:45, Holger Krause escribió: > > Am Donnerstag, 16. April 2015 schrieb Lam, N.H.L. (Nietzsche): > > Please check whether the videos are available in your country (click on one > > of the scheduled live stream videos - you should see a clock that counts > > down to the lecture). If you get the message "Live streaming is not > > available in your country due to right issues" please reply to this email > > and state your country so that we can find a solution prior to the toolkit > > next week. We appreciate your help to make this a smooth broadcast. > > > https://www.youtube.com/watch?v=ZBwh0Vm4fh4 > > Germany :-( > > "Live Streaming ist wegen Rechteproblemen in Deutschland leider nicht > möglich." > > Best, > > Holger > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From laura.marzetti at gmail.com Sun Apr 19 19:35:58 2015 From: laura.marzetti at gmail.com (Laura Marzetti) Date: Sun, 19 Apr 2015 19:35:58 +0200 Subject: [FieldTrip] Can you view the Livestream lectures (MEG/EEG toolkit)? In-Reply-To: References: <201504161745.05273.Holger.Krause@med.uni-duesseldorf.de> <04EC09B5-FE5B-491A-965A-5BACFC4C29EE@psi.ucm.es> Message-ID: In Italy as well :-) Best, Laura Inviato da iPhone > Il giorno 19/apr/2015, alle ore 07:03 PM, Stavros Dimitriadis ha scritto: > > Dear All > In Greece it works fine ! > > Best wishes > Dimitriadis Stavros, PhD > > Research Fellow > Aristotle University of Thessaloniki, Greece > Department of Informatics > http://users.auth.gr/~stdimitr/index.html > > 1)Artificial Intelligence Information Analysis lab Department of Informatics > Aristotle University of Thessaloniki > 2)NeuroInformatics.GRoup , AUTH, Greece > > > 2015-04-17 2:09 GMT-07:00 smoratti at psi.ucm.es : >> >> in Spain it seems to work… >> >> best, >> >> Stephan >> >> ________________________________________________________ >> Stephan Moratti, PhD >> >> see: Stephan's research profile >> >> Universidad Complutense de Madrid >> Facultad de Psicología >> Departamento de Psicología Básica I >> Campus de Somosaguas >> Despacho (Office) 1326-0 >> 28223 Pozuelo de Alarcón (Madrid) >> Spain >> >> and >> >> Center for Biomedical Technology >> Laboratory for Cognitive and Computational Neuroscience >> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid >> Campus Montegancedo >> 28223 Pozuelo de Alarcón (Madrid) >> Spain >> >> >> email: smoratti at psi.ucm.es >> Tel.: +34 679219982 >> >>> El 16/04/2015, a las 17:45, Holger Krause escribió: >>> >>> Am Donnerstag, 16. April 2015 schrieb Lam, N.H.L. (Nietzsche): >>>> Please check whether the videos are available in your country (click on one >>>> of the scheduled live stream videos - you should see a clock that counts >>>> down to the lecture). If you get the message "Live streaming is not >>>> available in your country due to right issues" please reply to this email >>>> and state your country so that we can find a solution prior to the toolkit >>>> next week. We appreciate your help to make this a smooth broadcast. >>> >>> https://www.youtube.com/watch?v=ZBwh0Vm4fh4 >>> >>> Germany :-( >>> >>> "Live Streaming ist wegen Rechteproblemen in Deutschland leider nicht >>> möglich." >>> >>> Best, >>> >>> Holger >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Sun Apr 19 19:49:20 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Sun, 19 Apr 2015 19:49:20 +0200 Subject: [FieldTrip] Beamforming analysis in frequency band In-Reply-To: References: <9BC70F24-9E97-4247-B0C0-365CCC154C70@uni-konstanz.de> Message-ID: <5F97C157-EB31-41B1-8F19-6DFB1D3E6E1C@uni-konstanz.de> Dear Noa, > Thank you Tzvetan! > > This raised two more question regarding the source analysis: > > 1. What is the difference between defining the frequency range under cfg.foi (such as cfg.foi=[30 48]) and defining if under the cfg.tapsmofrq (such as cfg.foi=[39 39] cfg.tapsmofrq=9)? The difference is that in the resulting output of ft_freqanalysis (lets name it freq) will contain a freq.freq field containing of 19 freq bins presuming frequency resolution of 1 Hz. Each of these is computed with smofrq of plus minus 9 Hz. In the second case freq.freq is one frequency bin namely 39 Hz. > 2. the cfg.tapsmofrq option only exist in the ft_freqanalysis function, and not in the ft_sourceanalysis function. in ft_sourceanalysis the only option is cfg.frequency which, as I mention, has to be a scalar. My question is whether defining the cfg.tapsmofrq in the ft_freqanalysis is also causing the source analysis to use the range of frequencies and not the single frequency. Yes. best tzvetan > > Thanks a lot, > Noa > > 2015-04-16 14:53 GMT+03:00 Tzvetan Popov : > > Dear Noa, > > you should use frequency smoothening to achieve this. For example, a configuration of cfg.foilim = [20 20] ; and cfg.tapsmofrq = 10; will allow you to estimate sources in the 10 to 30 Hz band. > >> Hi all, >> >> I'm doing source analysis in the frequency domain of a resting-state data. >> when doing the source analysis, I want to use several frequency bands of interest, such as beta (13-30 Hz) and gamma (30-48 Hz). >> My problem is about the cfg.frequency parameter, which must be a scalar (whereas i'm interested in a frequency band). Arbitrarily choosing a frequency in the middle of the range doesn't seem right. >> >> What is the common practice when doing source analysis using this function? > You could evaluate this tutorial: > http://www.fieldtriptoolbox.org/tutorial/beamformer > >> Does the cfg.tapsmofrq parameter is supposed to enable choosing frequency band instead of a single peak frequency? > and some detailed explanation in a pictorial form here: > https://www.youtube.com/watch?v=7eS11DtbIPw > > best > tzvetan > >> >> Any suggestions will be very much helpful! >> >> Thanks, >> Noa >> >> >> This is the script I’m using: >> >> cfg = []; >> cfg.method ='mtmfft'; >> cfg.output ='fourier'; >> cfg.keeptapers = 'yes'; >> cfg.foilim = [30 48]; >> cfg.tapsmofrq = 2; >> freqClosed=ft_freqanalysis(cfg,eyesClosed); >> >> >> >> cfg = []; >> cfg.method='pcc'; >> cfg.frequency = 39; % must be a scalar >> cfg.lambda = 0; >> cfg.vol = vol; >> cfg.grid = grid; >> cfg.feedback = 'textbar'; >> cfg.keepfilter='yes'; >> source1 = ft_sourceanalysis(cfg, freqClosed); >> >> >> -- >> My signature: >> >> http://www.documentarywire.com/earthlings/ >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > מעכשיו זאת החתימה שלי.. חובה לראות > > http://www.documentarywire.com/earthlings/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.maris at donders.ru.nl Tue Apr 21 07:38:52 2015 From: e.maris at donders.ru.nl (Maris, E.G.G. (Eric)) Date: Tue, 21 Apr 2015 05:38:52 +0000 Subject: [FieldTrip] coherence and group analyses In-Reply-To: References: Message-ID: <5B808383-6841-4F99-AEE9-73D64A807C47@donders.ru.nl> Dear Jean-Marc Lina, I’m sorry for this very late reply. Your post (which I requested) had slipped my attention. Involved in source analyses from MEG/EEG data, I am going through your papers related to statistical testing (Nonparametric stat testing of coherence differences, 2007 and stat testing in electrophys studies, 2012). Mostly concerned with coherence and coherency (either topography or tomography), I have some questions related to nonparametric statistical testing in the case where we have 2 groups (one group per condition, N subjects in each group) of individuals (n trials for each subjects). I will greatly appreciated some information that could help clarifying the followings: - how do we design the null distribution? permutations are among all subjects? How do we handle fixed/random effects? When you have multiple subjects, you should go for a random effects analysis. This implies that the ingredients for your statistical analysis are coherence values for every subject within every condition. What you do next depends on whether you have a within-groups or a between-groups design. In a within-groups design, every subject has participated in the multiple experimental conditions that you want to compare, and in a between-groups design, every subject has participated in only a single condition and you want to compare these conditions (e.g., patients versus controls, high-versus-low performers). In a within-groups design, the permutation distribution is obtained by randomly permuting the conditions within every subject. In a between-groups design, the permutation distribution is obtained by randomly permuting the subjects between the conditions. - Can we reproduce stricto sensu the Monte-Carlo approach described in the 2007 publication at the level of subjects (each subject being a UO) ? For an analysis that involves all subjects, the permutation distribution is obtained in a different way as described in the 2007 paper. In that paper, we had between-trials design, which is formally equivalent to a between-subjects designs (involving random permutations of trials between conditions). In a random effects analysis of the data of all subjects, one has to randomly permute the subject-level coherences between the conditions within every subject. - Can we use the stat defined as the difference of the imaginary part of the coherence ? (averaged over the subjects in a group?) Yes, you can use every statistic you expect to be sensitive for the phenomenon that you are investigating. Best, Eric With my anticipated thanks, Best JM Lina From: Robert Oostenveld > Cc: > To: FieldTrip discussion list > Date: 3 Mar 2015 21:54:55 CET Reply-To: FieldTrip discussion list > Subject: Re: [FieldTrip] Magnetic dipole fit vs Equiv. Current dipole fit Hi Jim You can do an inverse solution with any method (including dipole fitting) by specifying cfg.vol=[] in the corresponding high-level function (e.g. ft_prepare_leadfield, ft_dipolefitting or ft_sourceanalysis). This causes the forward model to be computed with a magnetic dipole. If you want to track this down to the lower lever code, have a look at these lines in the code “forward/ft_voltype.m" line 115 of 138 --83%-- col 11 “forward/ft_compute_leadfield.m" line 280 of 611 --45%-- col 12 My appologies for this not being documented better. I have been using this myself to check on the localization of the headcoils in the CTF “hz.ds” datasets, which worked fine. I hope you can get it to work for the Sandia Labs system. For the CTF system it is not needed to do these computations in MATLAB, since the CTF electronics does this in (alomst) real-time and the positions are streamed along with the MEG channel data. That makes this this http://fieldtrip.fcdonders.nl/getting_started/realtime_headlocalizer easy for the system we have in Nijmegen. Arjen and I have also been working on making it work for the Elekta system where the fitting has to be done in MATLAB, but have not been able sofar to get it to work robustly. You can find the experiences and (still open) report at http://bugzilla.fcdonders.nl/show_bug.cgi?id=1792. best regards Robert On 25 Feb 2015, at 22:40, Jim McKay > wrote: Hello Fieldtrippers, I am consulting with the Sandia Labs on development of an atomic magnetometer based MEG system prototype. One of the areas I am working on is head localization, so I was looking at the code for the realtime head localization in Fieldtrip. I was surprised to see that although the comments talk about using a magnetic dipole forward solution, it actually used the FT dipolefit code which is based on an equivalent current dipole, as far as I can tell. There should be a significant difference in the forward solutions between MD and ECD, so how does this work? Or am I just missing something? Cheers, Jim -- Jim McKay Candoo Systems Inc. - Magnetic field sensors, systems, and site surveys Tel. 778-840-0361 jim.mckay at candoosys.com www.candoosys.com _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From: Robert Oostenveld > To: FieldTrip discussion list > Date: 3 Mar 2015 22:14:42 CET Reply-To: FieldTrip discussion list > Subject: Re: [FieldTrip] inconsistent chanunit for Neuromag data Hi Steve The grad.chanunit pertains to the units that would be computed as the forward solution. The hdr.chanunit pertains to the units of the channel-level data. Using the ft_convert_units helper function you could convert the units of the gradiometer definition from cm to mm or m. This changes the baseline of the planar gradiometers with a factor of 10 or 100. However, the planar gradient chanel data is not updated simultaneously and remains in the same units (fieldstrength per distance). So it can happen that grad.chanunit and hdr.chanunit are inconsistent. The consequence (which many people on the list will have noticed, but might not have understood) is that the forward solution - and therefore the inverse solution - for the Elekta planar gradiometer channels can easily be incorrect: due to the data being in T/m and the forward solution in T/cm (or some other units, I don’t know the typical units from the top of my head). As long as you always use the same pipeline on hte planar gradiometers, you will most likely not notice since you will be interpreting the sourc estimates in “arbitrary units” anyway. But if you were to combine the planar channels with the magnetometers, the planar channels (fieldstrength per distance) would be affected differently than the manetometer channels (fieldstrength) by your choise of geometrical units. Using the ft_datatype_sens helper function you can ensure that the scaling of the grad structure (which affects the “coilpos" field but also the rows of the “tra" field that correspond to the planar channels) is consistent with your channel level data. If you specify all your data in SI units (T, m, V, etc.) the units of the forward computations will be correct and hence the units of the inverse estimates will also be consistent in SI units (e.g. dipole moment in A/m). The thing is that the different fieldtrip import functions (which come from various origins) return data in non-SI units more often than not :-( If you work with channel level data, SI units are often not nice. ERFs in Tesla are very small (10^-12). ERPs are usually expressed in uV. Also for anatomcial MRIs it is not convenient to express data in SI units (m) and mm is common. The CTF system by default expresses geometrical distance in cm. Etc… So all systems by themselves made their own “convenient” choices. But if all the data comes together with the physical model, it becomes a mess. The logical choice to solve the inconsistencies is to express it in SI units. I hope this helps in clarifying the situation. best regards, Robert PS if you search on bugzilla, you can see some (still open) bugs that pertain to this On 27 Feb 2015, at 03:53, Steve Patterson > wrote: Hello, I noticed that fieldtrip produces inconsistent channel units when I read in Neuromag (vectorview) data. For example: %%%%%%%%%%%%%%%%%%%%%%%% cfg = []; cfg.dataset = 'example.fif'; cfg.trialfun = 'ft_trialfun_general'; cfg.trialdef.eventtype = 'STI101'; cfg.trialdef.eventvalue = [17 18 20]; cfg.trialdef.prestim = 0.500; cfg.trialdef.poststim = 1.000; cfg = ft_definetrial(cfg); data = ft_preprocessing(cfg); disp(data.hdr.chanunit(1:6)); 'T/m' 'T/m' 'T' 'T/m' 'T/m' 'T' disp(data.grad.chanunit(1:6)); 'T' 'T' 'T' 'T' 'T' 'T' %%%%%%%%%%%%%%%%%%%%%%%% data.hdr.chanunit is correct and data.grad.chanunit is wrong. data.grad.chanunit must take precedence in further analysis, because I've noticed this causes problems downstream. For example, when using ft_dipolesimulation, the simulated data on the gradiometer channels is too small in amplitude by a factor of 1/(16.8E-3) (the distance between the gradiometer coil pair in meters). This is reflected in the grad.tra matrix, whose non-zero values are all 1's and -1's, whereas they should be 1's (magnetometers), and +/- 1/16.8E-3 (gradiometers). If you could fix this, it would be much appreciated! thanks, Steve _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From: Robert Oostenveld > To: FieldTrip discussion list > Date: 3 Mar 2015 22:18:34 CET Reply-To: FieldTrip discussion list > Subject: Re: [FieldTrip] eeglab2fieldtrip - Fieldtrip vs EEGLAB version Hi Omar, The eeglab2fieldtrip.m function lives on the boudary between the two projects. We (i.e. Arno and me) have decided to maintain it on the EEGLAB side and copy it to FieldTrip whenever needed. That is why it is in fieldtrip/external/eeglab. If you go to https://code.google.com/p/fieldtrip/source/list?path=/trunk/external/eeglab/eeglab2fieldtrip.m&start=10122 you can see the history. See also http://bugzilla.fcdonders.nl/show_bug.cgi?id=2770 In general for (almost) all code in fieldtrip/external it is being maintained externally, and often by people that are not directly related to the fieldtrip project. best Robert On 16 Feb 2015, at 16:38, Mian, Omar > wrote: Hello, There seem to be differences between the eeglab2fieldtrip.m when the Fieldtrip and EEGLAB versions are compared. Is this an oversight? Which one is “better” ? data.cfg.version.id contains a later date in the Fieldtrip version, but the file properties modified date is later in the EEGLAB version. The versions I am comparing are: \fieldtrip-20150109\external\eeglab\eeglab2fieldtrip.m \eeglab13_4_4b\plugins\dipfit2.3\eeglab2fieldtrip.m Thanks Omar --------------------------- Omar Mian, Phd Research Fellow School of Applied Sciences London South Bank University 103 Borough Road London SE1 0AA Copyright in this email and in any attachments belongs to London South Bank University. This email, and its attachments if any, may be confidential or legally privileged and is intended to be seen only by the person to whom it is addressed. If you are not the intended recipient, please note the following: (1) You should take immediate action to notify the sender and delete the original email and all copies from your computer systems; (2) You should not read copy or use the contents of the email nor disclose it or its existence to anyone else. The views expressed herein are those of the author(s) and should not be taken as those of London South Bank University, unless this is specifically stated. London South Bank University is a company limited by guarantee registered in England and Wales. The following details apply to London South Bank University: Company number - 00986761; Registered office and trading address - 103 Borough Road London SE1 0AA; VAT number - 778 1116 17 Email address - LSBUinfo at lsbu.ac.uk _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From: Tolga Ozkurt > To: > Date: 4 Mar 2015 09:54:53 CET Reply-To: FieldTrip discussion list > Subject: [FieldTrip] Visualization of Channels for Human Connectome Project MEG data Dear Fieldtrip list, I was seeing the MEG files uploaded by “Human Connectome Project”, which seem to be pre-processed by Fieldtrip. The resting data were collected in supine position with 4D Neuromag 248 channels. When I use the standard command for layout cfg.layout = '4D248.lay'; the channel locations do not seem to fit. (Please see the attached figure). I do not quite know the channel distribution of the system; but it seems some channels are out of the head. Could you give me an idea to project the channel layout properly? Thank you. Tolga -- Tolga Esat Özkurt, PhD Department of Health Informatics Middle East Technical University http://www.metu.edu.tr/~ozkurt/ From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Date: 4 Mar 2015 11:34:27 CET Reply-To: FieldTrip discussion list > Subject: Re: [FieldTrip] Visualization of Channels for Human Connectome Project MEG data Hi Tolga, There’s a layout that ‘better fits’ the projected channel locations, and which you can obtain from the megconnectome software that accompanies the HCP MEG data. The software can be obtained from here: humanconnectome.org/documentation/MEG1/meg-pipeline.html If you download one of the packages and unzip it, you’ll find a ‘template’ directory. Inside, there’s a 4D248.mat file (note that you need the ‘4D248.mat’ in cfg.layout in that case), which you can use as a layout for visualization. Best wishes, Jan-Mathijs On Mar 4, 2015, at 9:54 AM, Tolga Ozkurt > wrote: Dear Fieldtrip list, I was seeing the MEG files uploaded by “Human Connectome Project”, which seem to be pre-processed by Fieldtrip. The resting data were collected in supine position with 4D Neuromag 248 channels. When I use the standard command for layout cfg.layout = '4D248.lay'; the channel locations do not seem to fit. (Please see the attached figure). I do not quite know the channel distribution of the system; but it seems some channels are out of the head. Could you give me an idea to project the channel layout properly? Thank you. Tolga -- Tolga Esat Özkurt, PhD Department of Health Informatics Middle East Technical University http://www.metu.edu.tr/~ozkurt/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From joscha.schmiedt at esi-frankfurt.de Tue Apr 21 10:52:36 2015 From: joscha.schmiedt at esi-frankfurt.de (Schmiedt, Joscha) Date: Tue, 21 Apr 2015 08:52:36 +0000 Subject: [FieldTrip] A Fieldtrip data format? In-Reply-To: References: <5548CAB3-F9A2-4C6B-B958-3CF27CF2C27F@esi-frankfurt.de> , Message-ID: <17F994D43E9ADA418DE0040CC6F4A96B7FD2964A@UM-EXCDAG-A01.um.gwdg.de> Hey, For your information: there is a concerted effort by many big labs to create a standard data format for electrophysiology: https://crcns.org/NWB/Overview It will actually be based on HDF5. Joscha ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Schmiedt, Joscha [joscha.schmiedt at esi-frankfurt.de] Sent: Wednesday, April 01, 2015 2:03 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] A Fieldtrip data format? Hi Gio, Thanks for the info. The fcdc_matbin approach indeed would be suitable data for raw data. However, I’m looking for a fast solution for data that is already processed and cut into trials, in particular with varying trial length. Joscha > On Mar 31, 2015, at 22:39, Gio Piantoni wrote: > > Hi Joscha, > > FieldTrip already has its own simple uncompressed file format. > fcdc_matbin "It is not an official file format, but was invented here > at the FCDC. It consists of two files: a *.mat matlab file that > contains the header (and optionally the events) and a *.bin binary > file that contains the data." > http://www.fieldtriptoolbox.org/faq/reading_is_slow_can_i_write_my_raw_data_to_a_more_efficient_file_format > > If you want to look at the code: > https://github.com/fieldtrip/fieldtrip/blob/master/fileio/ft_write_data.m#L275 > > You should be able to read it as usual with ft_preprocessing. You can > convert your files to the fcdc_matbin using ft_preprocessing as well: > https://github.com/fieldtrip/fieldtrip/blob/master/ft_preprocessing.m#L581 > Be careful about not losing precision though. > > The only catch is that, as far as I know, you cannot export your > preprocessed data through ft_preprocessing at the moment, because > ft_write_data is now inside this if-part: > https://github.com/fieldtrip/fieldtrip/blob/master/ft_preprocessing.m#L252 > but it's only a matter of adapting that to your needs. > > Would this work for you? > > -g > > On Tue, Mar 31, 2015 at 9:09 AM, Schmiedt, Joscha > wrote: >> Hi, >> >> When working with Fieldtrip it is very convenient to store the data and >> analyses using MATLAB’s save and load functions. However, for large and/or >> complex data with many channels (>2GB) MATLAB enforces compression, which is >> pretty useless for electrophysiology data and slows down the load and save >> performance by a factor of up to 8 (see e.g. >> http://undocumentedmatlab.com/blog/improving-save-performance). The MATLAB >> file format is based on HDF5, which is generally an open and future-proof >> data format, but unfortunately MATLAB doesn’t allow you to disable the >> compression. >> >> An option to overcome this could be to develop a simple data format for >> Fieldtrip data that is also based on HDF5. Is or has there been any >> development going into that direction? Would there be any interest? Of >> course, creating yet another data format is almost never a good idea >> (https://xkcd.com/927/), but since HDF5 is well-documented and readable with >> almost any software, it might be worth thinking about it. >> >> I’d be happy to hear your thoughts. >> >> Joscha >> >> --------------------------------- >> Joscha Schmiedt >> PhD Student >> >> Ernst Strüngmann Institute (ESI) for Neuroscience >> in Cooperation with Max Planck Society >> Deutschordenstraße 46 >> 60528 Frankfurt am Main >> Germany >> >> Tel.: +49 (0)69 96769 241 >> >> Sitz der Gesellschaft: Frankfurt am Main >> Registergericht: Amtsgericht Frankfurt - HRB 84266 >> Geschäftsführer: Prof. Dr. Pascal Fries >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From anne.keller at sickkids.ca Tue Apr 21 18:59:07 2015 From: anne.keller at sickkids.ca (Anne Keller) Date: Tue, 21 Apr 2015 16:59:07 +0000 Subject: [FieldTrip] ICA before beamformer In-Reply-To: <69B46D4F7B3C33449A56153DF85867882EA7A0@SKMBXX02.sickkids.ca> References: <69B46D4F7B3C33449A56153DF85867882EA7A0@SKMBXX02.sickkids.ca> Message-ID: <69B46D4F7B3C33449A56153DF85867882EA7C8@SKMBXX02.sickkids.ca> Hi Fieldtrip-ers, I'm working with MEG data collected from children, and I am hoping to do source localization via beamformer. Our kids have lots of eye movement and blinks, so I was hoping to perform ICA prior to beamformer. How can I address the matrix regularization aspect after I remove components? Is there a fieldtrip function that corrects this? Due to lab requirements, I will be using SPM's beamformer (but Fieldtrip's ICA and reject components functions). Thanks so much in advance! Best, Anne ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. From drivolta81 at gmail.com Wed Apr 22 11:56:06 2015 From: drivolta81 at gmail.com (Davide Rivolta) Date: Wed, 22 Apr 2015 09:56:06 +0000 Subject: [FieldTrip] 20 PhD excellence scholarships at UEL Message-ID: Dear all, I just wish to let you know that 20 fully-funded UEL Excellence Studentships will be made available to PhD applicants, starting September 2015 (www.uel.ac.uk/studentships). For more information please do not hesitate to contact Ben Whitham in the Graduate School (B.Whitham at uel.ac.uk). Bests, Davide -- Davide Rivolta, PhD -------------- next part -------------- An HTML attachment was scrubbed... URL: From singhharsimrat at gmail.com Wed Apr 22 14:13:50 2015 From: singhharsimrat at gmail.com (Harsimrat Singh) Date: Wed, 22 Apr 2015 13:13:50 +0100 Subject: [FieldTrip] Compatibility of ft_layoutplot with MATLAB 2014b Message-ID: Hi Fieldtrippers I think I might have found a problem in ft_layoutplot compatibility with the newer versions of MATLAB. Now MATLAB doesn't let you add numeric values to an array of graphics objects - hence it throws an error Error using sprintf Function is not defined for 'matlab.ui.Figure' inputs. Best regards Harsimrat -------------------------------------------- *Dr Harsimrat Singh* *Department of Cancer and Surgery* *St. Marys Hospital Campus* *Imperial College London* *Praed Street, London W2 1NY* *harsimrat.singh at imperial.ac.uk * -------------- next part -------------- An HTML attachment was scrubbed... URL: From luke.bloy at gmail.com Wed Apr 22 22:55:14 2015 From: luke.bloy at gmail.com (Luke Bloy) Date: Wed, 22 Apr 2015 16:55:14 -0400 Subject: [FieldTrip] Source localizing resting state data Message-ID: Hi everyone, Following up on two recent email threads ( http://mailman.science.ru.nl/pipermail/fieldtrip/2015-April/009120.html and http://mailman.science.ru.nl/pipermail/fieldtrip/2015-January/008796.html) I'd like to ask the fieldtrip community what they feel is the best source localization methods for resting state data? Note that at this point i'm only thinking about simple things like localizing resting alpha and beta rhythms. -Thanks Luke -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Thu Apr 23 08:47:21 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Thu, 23 Apr 2015 08:47:21 +0200 Subject: [FieldTrip] Compatibility of ft_layoutplot with MATLAB 2014b In-Reply-To: References: Message-ID: <98A59F44-6729-41F0-AA81-D26E523B7584@uni-konstanz.de> Dear Harsimrat, Please update your FT version. This should solve the issue. Best Tzvetan > Am 22.04.2015 um 14:13 schrieb Harsimrat Singh : > > Hi Fieldtrippers > > I think I might have found a problem in ft_layoutplot compatibility with the newer versions of MATLAB. Now MATLAB doesn't let you add numeric values to an array of graphics objects - hence it throws an error > > Error using sprintf > Function is not defined for 'matlab.ui.Figure' inputs. > > Best regards > Harsimrat > > -------------------------------------------- > Dr Harsimrat Singh > Department of Cancer and Surgery > St. Marys Hospital Campus > Imperial College London > Praed Street, London W2 1NY > harsimrat.singh at imperial.ac.uk > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From ofcastaneda at outlook.com Thu Apr 23 15:58:27 2015 From: ofcastaneda at outlook.com (=?utf-8?B?T3NjYXIgRmVybmFuZG8gQ2FzdGHDsWVkYSBGZXJuw6FuZGV6?=) Date: Thu, 23 Apr 2015 13:58:27 +0000 Subject: [FieldTrip] =?utf-8?q?Using_Fieldtrip_with_BCI2000?= Message-ID: Dear community, My name is Oscar Castañeda and I’ve been using the Fieldtrip Buffer to extract samples from BCI2000; the samples were obtained using an Emotiv Headset. However, I have a problem with data adquisition: When I use the instruction ft_read_data(filename, ‘header’,hdr,‘begsample’,begsample,’endsample’,endsample,’chanindx’,chanindx) [where chanindx is a list going from number 1 to 14] and I compare the obtained data with the one stored in the corresponding BCI2000 .dat file, I find that the samples are equal for the first Emotiv cannel (AF3), just as we would expect. But for the rest of channels, the data returned by ft_read_data is not equal to the one from the .dat file, and varies in a non-constant proportion of 90% to 110% of the .dat sample. Why could this be happening? I would appreciate very much any kind of help. Thank you very much, Oscar -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.herring at donders.ru.nl Thu Apr 23 22:33:53 2015 From: j.herring at donders.ru.nl (Herring, J.D. (Jim)) Date: Thu, 23 Apr 2015 20:33:53 +0000 Subject: [FieldTrip] ICA before beamformer In-Reply-To: <69B46D4F7B3C33449A56153DF85867882EA7C8@SKMBXX02.sickkids.ca> References: <69B46D4F7B3C33449A56153DF85867882EA7A0@SKMBXX02.sickkids.ca> <69B46D4F7B3C33449A56153DF85867882EA7C8@SKMBXX02.sickkids.ca> Message-ID: <2E61E12F-DC21-4FB9-B91F-8FDD4843B311@donders.ru.nl> Dear Anne, If I am not mistaken SPM actually uses Fieldtrip’s DICS beamformer implementation. In any case, after doing ICA the grad field in your data structure should be corrected so you should be safe in using SPM's beamformer given that you use the grad contained in the data structure produced after cleaning with ICA in Fieldtrip. Best, Jim > On 21 Apr 2015, at 18:59, Anne Keller wrote: > > Hi Fieldtrip-ers, > > I'm working with MEG data collected from children, and I am hoping to do source localization via beamformer. Our kids have lots of eye movement and blinks, so I was hoping to perform ICA prior to beamformer. How can I address the matrix regularization aspect after I remove components? Is there a fieldtrip function that corrects this? Due to lab requirements, I will be using SPM's beamformer (but Fieldtrip's ICA and reject components functions). > > Thanks so much in advance! > > Best, > Anne > > ________________________________ > > This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From ronny.ibrahim at mq.edu.au Fri Apr 24 06:49:11 2015 From: ronny.ibrahim at mq.edu.au (Ronny Ibrahim) Date: Fri, 24 Apr 2015 14:49:11 +1000 Subject: [FieldTrip] MEG160 KIT layout file template Message-ID: Hi Community, I was wondering whether there is any fieldtrip '.lay' layout file for the MEG160 KIT system that I am currently using : This is a paper on the MEG system http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=783918 I have tried reading the coordinates using ft_read_header from the '*.con' file and trying to use this information to construct my own '.lay' file based on the Yokogawa's yokogawa440pg.lay planar gradiometer layout file ( while removing several sensors which weren't there in the MEG160 KIT system) but after plotting a few eye-blink responses, the topo_plot output does not seem to look right. Therefore, I would like to thank you for your kind help and inputs in resolving my simple issue here. Any help will be much appreciate it. Kind Regards, Ronny -------------- next part -------------- An HTML attachment was scrubbed... URL: From annika.notbohm at uni-oldenburg.de Fri Apr 24 11:51:37 2015 From: annika.notbohm at uni-oldenburg.de (Annika Notbohm) Date: Fri, 24 Apr 2015 11:51:37 +0200 Subject: [FieldTrip] PhD-Conference: Entrainment of Brain Oscillations (EBO) in Oldenburg, Germany Message-ID: <553A1229.3070500@uni-oldenburg.de> Dear (PhD-) students of brain oscillations and entrainment, we want to call your attention to our PhD conference: * **Entrainment of Brain Oscillations (EBO) * at 17th-18th September 2015 at the Hanse Wissenschaftskolleg (Delmenhorst, Germany). The conference is organized by four PhD students from the University of Oldenburg, together with Prof. Dr. Christoph Herrmann. Confirmed keynote speakers are /Prof. Dr. Ole Jensen (Donders Institute)/ and /Prof. Dr. Joachim Gross (University of Glasgow)/ who will also hold a one day workshop on "Analytical methods for studies of brain oscillations" as a pre-meeting to the conference. If you are interested in participating at our conference, please submit a poster abstract following the guidelines on our website (http://www.uni-oldenburg.de/ebo/abstract-submission). As we intend to realize a fair selection of poster abstracts, we kindly ask you to use the abstract template for blinded submission, as can be found on the link given above. POSTER DEADLINE: JUNE 20th 2015 Three symposia will be held during the conference which deal with entrainment of brain oscillations by using auditory, visual or electrical methods. The main focus in all three sessions will lie on basic research on the mechanism of entrainment as well as on causality of modified oscillations and behavior. We intend to create a platform that allows intensive exchange and potential collaborations between the participants. Therefore, the conference will be kept rather small (50 participants) and specific regarding the topic. More detailed information and a (preliminary) program can be found on the website www.uni-oldenburg.de/EBO. For further questions don't hesitate to contact us via EBO at uni-oldenburg.de. Please feel free to forward this e-mail to others who could be interested in our conference. Best regards, Alina Baltus, Anna-Katharina Bauer, Annika Notbohm and Johannes Vosskuhl -- Annika Notbohm, M.Sc. Experimental Psychology Lab Department of Psychology European Medical School Carl von Ossietzky Universität Ammerländer Heerstr. 114-118 26129 Oldenburg, Germany Tel: +49 441 798 2628 Mobile: +49 176 22716261 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mehmetakifozcoban at gmail.com Fri Apr 24 15:22:49 2015 From: mehmetakifozcoban at gmail.com (=?UTF-8?B?TWVobWV0IEFraWYgw5Z6w6dvYmFu?=) Date: Fri, 24 Apr 2015 16:22:49 +0300 Subject: [FieldTrip] =?utf-8?b?SMSx?= Message-ID: -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Fri Apr 24 17:02:49 2015 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Fri, 24 Apr 2015 17:02:49 +0200 Subject: [FieldTrip] =?utf-8?b?SMSx?= In-Reply-To: References: Message-ID: Hi! On 24 April 2015 at 15:22, Mehmet Akif Özçoban wrote: > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From haiteng.jiang at gmail.com Sun Apr 26 16:38:48 2015 From: haiteng.jiang at gmail.com (Haiteng Jiang) Date: Sun, 26 Apr 2015 16:38:48 +0200 Subject: [FieldTrip] Source localizing resting state data (Luke Bloy) Message-ID: Hi Luke, In my experience, the best way to deal with central bias issue is leadfield normalization on resting state . This is much more robust compared to neural activity index (NAI) across subjects. You can specify cfg.normalize = 'yes' when you compute leadfied using ft_prepare_leadfield function . This strategy gave me satisfactory results in the end. Hope this helps, Haiteng > > Message: 2 > Date: Wed, 22 Apr 2015 16:55:14 -0400 > From: Luke Bloy > To: FieldTrip list serve > Subject: [FieldTrip] Source localizing resting state data > Message-ID: > < > CAG5Ru-pJKH91o9EHD+kc53TQXc8F3X4Ogsa0UOC5wiJmLPvEvA at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi everyone, > > Following up on two recent email threads ( > http://mailman.science.ru.nl/pipermail/fieldtrip/2015-April/009120.html > and > http://mailman.science.ru.nl/pipermail/fieldtrip/2015-January/008796.html > ) > > I'd like to ask the fieldtrip community what they feel is the best source > localization methods for resting state data? Note that at this point i'm > only thinking about simple things like localizing resting alpha and beta > rhythms. > > -Thanks > Luke > > -- Haiteng Jiang PhD candidate Donders Institute for Brain, Cognition and Behaviour Neuronal Oscillations Group Computational Cognitive Neuroscience Lab https://sites.google.com/site/haitengjiang/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From Olaf.Hauk at mrc-cbu.cam.ac.uk Tue Apr 28 17:41:54 2015 From: Olaf.Hauk at mrc-cbu.cam.ac.uk (Olaf Hauk) Date: Tue, 28 Apr 2015 15:41:54 +0000 Subject: [FieldTrip] Methods Skills Survey Message-ID: Hello - I would be very grateful if you could participate in this methods skills survey, which will help the development of future methods training events. It is anonymous and should take about 10-15 minutes. Please participate only once. Please visit this link to go to the survey: https://www.surveymonkey.com/s/3JL2CZX Are you an undergraduate student, PhD student, or post-doc who is working or planning to work in the cognitive sciences? If so, then we would like to invite you to participate in an online survey that will help us develop more efficient methods training programmes for cognitive scientists and neuroscientists. Cognitive science and neuroscience are highly interdisciplinary, and it is important for us to know the skills of researchers who are moving into these fields. The survey should take you 10-15 minutes, and you will be asked some questions related to data analysis as well as about yourself (but you will remain anonymous). You will not receive any remuneration for your participation - but your information may benefit a large number of future students in the cognitive sciences. This is not an exam. Depending on your background, you may not be able to answer some or even many of these questions at all - but this information is also very useful to us. Please only participate in this survey once, and please do not consult the internet, books or friends to answer the questions. This survey is run by Dr. Olaf Hauk from the MRC Cognition and Brain Sciences Unit, Cambridge, UK. The data from this survey may be used in future presentations and publications. Olaf Hauk, PhD MRC Cognition and Brain Sciences Unit Phone: +44(0)1223 273702 Fax: +44(0)1223 359062 Web: http://www.mrc-cbu.cam.ac.uk/people/olaf.hauk/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From joseluisblues at gmail.com Wed Apr 29 09:35:47 2015 From: joseluisblues at gmail.com (Jose) Date: Wed, 29 Apr 2015 09:35:47 +0200 Subject: [FieldTrip] fast & coarse artifact rejection Message-ID: Dear fellows, My name is José Luis, I’m working with Micromed data in the Clinic Research Unit in Ville-Evrard in France. I succeed at importing and reading my data with Fieldtrip. I would like to do a superficial and fast ERP analysis (just for checking purposes), and I was wondering if there any way to tell Fieldtrip to remove trials that exceed a threshold (like -+80 uV). Meaning that I don’t want to go through ICA or any other method like this (for the moment). Is that possible?, Any hint would be appreciated. best, José Luis -- José Luis ULLOA FULGERI 33 (0)6.29.50.64.93 -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.herring at donders.ru.nl Wed Apr 29 09:54:49 2015 From: j.herring at donders.ru.nl (Herring, J.D. (Jim)) Date: Wed, 29 Apr 2015 07:54:49 +0000 Subject: [FieldTrip] fast & coarse artifact rejection In-Reply-To: References: Message-ID: <8D64FA7B-D59E-41F0-AC21-3A09289C4A84@donders.ru.nl> Hi Jose, Yes, using ft_artifact_zvalue you can z-transform your data and mark trials for rejection that exceed a certain threshold. Marked trials can be rejected with ft_rejectartifact. See http://www.fieldtriptoolbox.org/tutorial/automatic_artifact_rejection for a walkthrough and examples. Best, Jim On 29 Apr 2015, at 09:35, Jose > wrote: Dear fellows, My name is José Luis, I’m working with Micromed data in the Clinic Research Unit in Ville-Evrard in France. I succeed at importing and reading my data with Fieldtrip. I would like to do a superficial and fast ERP analysis (just for checking purposes), and I was wondering if there any way to tell Fieldtrip to remove trials that exceed a threshold (like -+80 uV). Meaning that I don’t want to go through ICA or any other method like this (for the moment). Is that possible?, Any hint would be appreciated. best, José Luis -- José Luis ULLOA FULGERI 33 (0)6.29.50.64.93 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From barbara.schorr at uni-ulm.de Wed Apr 29 11:01:30 2015 From: barbara.schorr at uni-ulm.de (Barbara Schorr) Date: Wed, 29 Apr 2015 11:01:30 +0200 Subject: [FieldTrip] Renormalized PDC In-Reply-To: References: Message-ID: <55409DEA.70404@uni-ulm.de> Dear Fieldtrippers, I am working on a connectivity analysis (partial directed coherence) in EEG data. I found this paper by Schelter, B.; Timmer, J.; Eichler, M. (2009). "Assesssing the strength of directed influences among neural signals using renormalized partial directed coherence"./J. Neurosci Methods/*179*(1): who suggest to rather use a renormalized PDC. Has anybody here used this before and could tell me how to calculate this rPDC in Fieldtrip? All the best, Barbara Am 27.04.2015 um 12:00 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 > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Re: Source localizing resting state data (Luke Bloy) > (Haiteng Jiang) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 26 Apr 2015 16:38:48 +0200 > From: Haiteng Jiang > To: fieldtrip at science.ru.nl > Subject: Re: [FieldTrip] Source localizing resting state data (Luke > Bloy) > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi Luke, > In my experience, the best way to deal with central bias issue is > leadfield normalization on resting state . This is much more robust > compared to neural activity index (NAI) across subjects. You can specify > cfg.normalize = 'yes' when you compute leadfied > using ft_prepare_leadfield function . This strategy gave me satisfactory > results in the end. > > Hope this helps, > Haiteng > > >> Message: 2 >> Date: Wed, 22 Apr 2015 16:55:14 -0400 >> From: Luke Bloy >> To: FieldTrip list serve >> Subject: [FieldTrip] Source localizing resting state data >> Message-ID: >> < >> CAG5Ru-pJKH91o9EHD+kc53TQXc8F3X4Ogsa0UOC5wiJmLPvEvA at mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi everyone, >> >> Following up on two recent email threads ( >> http://mailman.science.ru.nl/pipermail/fieldtrip/2015-April/009120.html >> and >> http://mailman.science.ru.nl/pipermail/fieldtrip/2015-January/008796.html >> ) >> >> I'd like to ask the fieldtrip community what they feel is the best source >> localization methods for resting state data? Note that at this point i'm >> only thinking about simple things like localizing resting alpha and beta >> rhythms. >> >> -Thanks >> Luke >> >> > -- Barbara Schorr, MSc Clinical and Biological Psychology University of Ulm Albert-Einstein-Allee 47 89069 Ulm Therapiezentrum Burgau Kapuzinerstraße 34 89331 Burgau -------------- next part -------------- An HTML attachment was scrubbed... URL: From guiraudh at gmail.com Wed Apr 29 14:45:56 2015 From: guiraudh at gmail.com (=?UTF-8?B?SMOpbMOobmUgR3VpcmF1ZA==?=) Date: Wed, 29 Apr 2015 14:45:56 +0200 Subject: [FieldTrip] Search for a template children. Message-ID: Dear community, My name is Hélène Guiraud and i'm working in DDL lab in Lyon (France) on speech perception in children using MEG. The children involved in the study don't pass MRI. We want to achieve source reconstruction from a template. However I can't find a template corresponding to the anatomy of a child (8-12 years). Can someone tell me if there are template children and where I can find them? Best, Hélène Guiraud -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.schneider at uke.uni-hamburg.de Wed Apr 29 15:53:13 2015 From: t.schneider at uke.uni-hamburg.de (Till Schneider) Date: Wed, 29 Apr 2015 15:53:13 +0200 Subject: [FieldTrip] Search for a template children. In-Reply-To: References: Message-ID: <5540E249.3000200@uke.uni-hamburg.de> Dear Helene, McGill University provides MNI brains for different age groups between 4.5y to 18y. http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1 You will probably find the template brain you are searching for in this database. Best regards, Till -- Till Schneider, PhD Cognitive and Clinical Neurophysiology Group Dept. of Neurophysiology and Pathophysiology University Medical Center Hamburg-Eppendorf Martinistr. 52 20246 Hamburg Germany phone +49-40-7410-53188 fax +49-40-7410-57126 www.uke.de/neurophysiologie Am 29.04.15 um 14:45 schrieb Hélène Guiraud: > Dear community, > > My name is Hélène Guiraud and i'm working in DDL lab in Lyon (France) > on speech perception in children using MEG. > The children involved in the study don't pass MRI. We want to achieve > source reconstruction from a template. However I can't find a template > corresponding to the anatomy of a child (8-12 years). > Can someone tell me if there are template children and where I can > find them? > > Best, > > Hélène Guiraud > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahjoory86 at gmail.com Wed Apr 29 16:25:35 2015 From: mahjoory86 at gmail.com (Keyvan Mahjoory) Date: Wed, 29 Apr 2015 16:25:35 +0200 Subject: [FieldTrip] ICBM 152 templates in FT Message-ID: Dear Fieldtrip Users, I perform source analysis in Fieldtrip with a template head model ( standard_bem ) and a template source model (cortex_5124.surf.gii ) to constarin estimated sources on cortex. These templates are based on Colin27, But I prefere to use the template ICBM152 instead. Does FT include ICBM template? I mean templates for both head model and cortical surfe. Many Thanks in advance, Keyvan -------------- next part -------------- An HTML attachment was scrubbed... URL: From RICHARDS at mailbox.sc.edu Thu Apr 30 14:12:22 2015 From: RICHARDS at mailbox.sc.edu (RICHARDS, JOHN) Date: Thu, 30 Apr 2015 12:12:22 +0000 Subject: [FieldTrip] re template for children Message-ID: We have a template for children‹actually have for infants from 2 weeks through adults at 89 years. We also have average electrode positions for EGI sensor nets (GSN128, HGSN128) and the 10-10 system; and segmented priors, stereotaxic atlases, and segmented heads (BEM, FEM). I also have been using this recently with FT for infants and child/adolescent/adult ages. WWW site: http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ Fro www site: This is a database of average MRIs and associated MRI volumes for developmental MRI work. It consists of average MRI templates, segmented partial volume estimate volumes for GM, WM, T2W-derived CSF (Description ). The database is separated into head-based and brain-based averages. The data are separated by ages in months, years, 6-month, or 5-year intervals (Ages and Templates ). The templates are grouped into first year (2 weeks through 12 months), early childhood (15 months through 4 years), childhood (4 years through 10 years), adolescence (10.5 years through 17.5 years) and adults (18 years through 89 years). Tools for cortical source analysis of EEG and ERP are provided. These tools are based on the average MRI templates, segmenting, and atlases. Also see my www site, jerlab.psych.sc.edu for publications describing this. We have a recent chapter that has a good description of the issues behind the database (with Wanze Xie). We have a paper accepted at Neuroimage for their upcoming ³Data Sharing² issue (with Carmen Sanchez, Michelle Phillips-Meek, and Wanze Xie). John *********************************************** John E. Richards Carolina Distinguished Professor Department of Psychology University of South Carolina Columbia, SC 29208 Dept Phone: 803 777 2079 Fax: 803 777 9558 Email: richards-john at sc.edu HTTP: jerlab.psych.sc.edu *********************************************** On 4/30/15, 6:00 AM, "fieldtrip-request at science.ru.nl" wrote: >Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > >To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > >You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of fieldtrip digest..." > > >Today's Topics: > > 1. Search for a template children. (H?l?ne Guiraud) > 2. Re: Search for a template children. (Till Schneider) > 3. ICBM 152 templates in FT (Keyvan Mahjoory) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Wed, 29 Apr 2015 14:45:56 +0200 >From: H?l?ne Guiraud >To: fieldtrip at science.ru.nl >Subject: [FieldTrip] Search for a template children. >Message-ID: > >Content-Type: text/plain; charset="utf-8" > >Dear community, > >My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) on >speech perception in children using MEG. >The children involved in the study don't pass MRI. We want to achieve >source reconstruction from a template. However I can't find a template >corresponding to the anatomy of a child (8-12 years). >Can someone tell me if there are template children and where I can find >them? > >Best, > >H?l?ne Guiraud >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >9b53e/attachment-0001.html> > >------------------------------ > >Message: 2 >Date: Wed, 29 Apr 2015 15:53:13 +0200 >From: Till Schneider >To: FieldTrip discussion list >Subject: Re: [FieldTrip] Search for a template children. >Message-ID: <5540E249.3000200 at uke.uni-hamburg.de> >Content-Type: text/plain; charset="windows-1252"; Format="flowed" > >Dear Helene, > >McGill University provides MNI brains for different age groups between >4.5y to 18y. >http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1 >You will probably find the template brain you are searching for in this >database. > >Best regards, >Till > >-- > >Till Schneider, PhD > >Cognitive and Clinical Neurophysiology Group >Dept. of Neurophysiology and Pathophysiology >University Medical Center Hamburg-Eppendorf >Martinistr. 52 >20246 Hamburg >Germany > >phone +49-40-7410-53188 >fax +49-40-7410-57126 >www.uke.de/neurophysiologie > > > >Am 29.04.15 um 14:45 schrieb H?l?ne Guiraud: >> Dear community, >> >> My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) >> on speech perception in children using MEG. >> The children involved in the study don't pass MRI. We want to achieve >> source reconstruction from a template. However I can't find a template >> corresponding to the anatomy of a child (8-12 years). >> Can someone tell me if there are template children and where I can >> find them? >> >> Best, >> >> H?l?ne Guiraud >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > >-- > >_____________________________________________________________________ > >Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen >Rechts; Gerichtsstand: Hamburg | www.uke.de >Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Prof. Dr. >Dr. Uwe Koch-Gromus, Joachim Pr?l?, Rainer Schoppik >_____________________________________________________________________ > >SAVE PAPER - THINK BEFORE PRINTING >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >44937/attachment-0001.html> > >------------------------------ > >Message: 3 >Date: Wed, 29 Apr 2015 16:25:35 +0200 >From: Keyvan Mahjoory >To: FieldTrip discussion list >Subject: [FieldTrip] ICBM 152 templates in FT >Message-ID: > >Content-Type: text/plain; charset="iso-8859-1" > >Dear Fieldtrip Users, > >I perform source analysis in Fieldtrip with a template head model ( >standard_bem ) and a >template source model (cortex_5124.surf.gii >) to constarin >estimated sources on cortex. These templates are based on Colin27, But I >prefere to use the template ICBM152 instead. >Does FT include ICBM template? I mean templates for both head model and >cortical surfe. > >Many Thanks in advance, >Keyvan >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >9daf3/attachment-0001.html> > >------------------------------ > >_______________________________________________ >fieldtrip mailing list >fieldtrip at donders.ru.nl >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >End of fieldtrip Digest, Vol 53, Issue 23 >***************************************** From frsantos at fpce.up.pt Thu Apr 30 17:34:23 2015 From: frsantos at fpce.up.pt (Fernando Ferreira-Santos) Date: Thu, 30 Apr 2015 15:34:23 +0000 Subject: [FieldTrip] Porto IV CAN: 4th Cognitive and Affective Neurophysiology Summer School Message-ID: <2BAB036A9BAEA44984A131DFCE4461080109B9E53D@SRVMBX02.fpceup.psi.up.pt> Dear colleagues, The Laboratory of Neuropsychopsysiology of the University of Porto (http://www.fpce.up.pt/labpsi/) is pleased to announce the 4th edition of the International Cognitive and Affective Neurophysiology Summer School: Acquisition, processing, and analysis of EEG signal. This summer school is focused on the application of Electroencephalography (EEG) and Event Related Potential (ERP) techniques to the study of cognitive and affective processes. The course will be fully taught in English and is aimed at an introductory level, so no previous experience with EEG or ERP is required. This event will take place from 7-12 of September 2015 in the lovely city of Porto. In last year’s edition the course was fully booked and, as such, we recommend early registration (course places are attributed by order of registration). For additional details and instructions on how to register, please consult our website (http://www.fpce.up.pt/labpsi/summerschool/). Please feel free to pass this information along to students or researchers that may be potentially interested. Thanks you and best wishes, -- Fernando Ferreira-Santos, PhD Lecturer Laboratory of Neuropsychophysiology Faculty of Psychology and Education Sciences University of Porto Rua Alfredo Allen, 4200-135 Porto (Portugal) Tel.: +351 226079700 (ext. 409) E-mail: frsantos at fpce.up.pt http://www.fpce.up.pt/labpsi/ -------------- next part -------------- An HTML attachment was scrubbed... URL: