From demiral.007 at gmail.com Sat Sep 1 16:29:35 2012 From: demiral.007 at gmail.com (Baris Demiral) Date: Sat, 1 Sep 2012 10:29:35 -0400 Subject: [FieldTrip] CTF data event/reading Message-ID: Hi Nedad, filedtrippers, I have continuous and epoched CTF data as well, and I want to import them into fieldtrip. The event types are previously edited in the early stages. When I looked at the event values with the ft_read_event(cfg.dataset) function, I see that some event values are empty '[ ]'. On the other hand, the initial triggers / event types have integer event values (type: 'front panel trigger', value: 222). Error is in " ft_preprocessing (line 511) ... tim = offset2time(offset, hdr.Fs, size(dat,2)); See below. Can you help me on that? What functions/lines of code shall I call? I followed the instructions on the web tutorials line by line, but nope. Sometimes it says " trialfun is not described." I also download fileio package. I am using the most recent version of FieldTrip. Do you think the event structure has anything to do with the errors, or I had to install some other package as well? Thanks Baris >> cfg.dataset = 'AFLLBCEAXXX_epoched.ds'; % name of CTF dataset data = ft_preprocessing(cfg) readCTFds: You are reading CTF data for use with a software-application tool that is not manufactured by VSM MedTech Ltd. and has not received marketing clearance for clinical applications. If CTF MEG data are processed by this tool, they should not be later employed for clinical and/or diagnostic purposes. undoing the G3BR balancing processing channel { 'UPPT001' 'SCLK01' 'BG1' 'BG2' 'BG3' 'BP1' 'BP2' 'BP3' 'BR1' 'BR2' 'BR3' 'G11' 'G12' 'G13' 'G22' 'G23' 'P11' 'P12' 'P22' 'P23' 'Q11' 'Q12' 'Q13' 'Q22' 'Q23' 'R11' 'R12' 'R13' 'R22' 'R23' 'MLC11' 'MLC12' 'MLC13' 'MLC14' 'MLC15' 'MLC16' 'MLC17' 'MLC21' 'MLC22' 'MLC23' 'MLC24' 'MLC25' 'MLC31' 'MLC32' 'MLC41' 'MLC42' 'MLC51' 'MLC52' 'MLC53' 'MLC54' 'MLC55' 'MLC61' 'MLC62' 'MLC63' 'MLF11' 'MLF12' 'MLF13' 'MLF14' 'MLF21' 'MLF22' 'MLF23' 'MLF24' 'MLF25' 'MLF31' 'MLF32' 'MLF33' 'MLF34' 'MLF35' 'MLF41' 'MLF42' 'MLF43' 'MLF44' 'MLF45' 'MLF46' 'MLF51' 'MLF52' 'MLF53' 'MLF54' 'MLF55' 'MLF56' 'MLF61' 'MLF62' 'MLF63' 'MLF64' 'MLF65' 'MLF66' 'MLF67' 'MLO11' 'MLO12' 'MLO13' 'MLO14' 'MLO21' 'MLO22' 'MLO23' 'MLO24' 'MLO31' 'MLO32' 'MLO33' 'MLO34' 'MLO41' 'MLO42' 'MLO43' 'MLO44' 'MLO51' 'MLO52' 'MLO53' 'MLP11' 'MLP12' 'MLP21' 'MLP22' 'MLP23' 'MLP31' 'MLP32' 'MLP33' 'MLP34' 'MLP35' 'MLP41' 'MLP42' 'MLP43' 'MLP44' 'MLP45' 'MLP51' 'MLP52' 'MLP53' 'MLP54' 'MLP55' 'MLP56' 'MLP57' 'MLT11' 'MLT12' 'MLT13' 'MLT14' 'MLT15' 'MLT16' 'MLT21' 'MLT22' 'MLT23' 'MLT24' 'MLT25' 'MLT26' 'MLT27' 'MLT31' 'MLT32' 'MLT33' 'MLT34' 'MLT35' 'MLT36' 'MLT37' 'MLT41' 'MLT42' 'MLT43' 'MLT44' 'MLT45' 'MLT46' 'MLT47' 'MLT51' 'MLT52' 'MLT53' 'MLT54' 'MLT55' 'MLT56' 'MLT57' 'MRC11' 'MRC12' 'MRC13' 'MRC14' 'MRC15' 'MRC16' 'MRC17' 'MRC21' 'MRC22' 'MRC23' 'MRC24' 'MRC25' 'MRC31' 'MRC32' 'MRC41' 'MRC42' 'MRC51' 'MRC52' 'MRC53' 'MRC54' 'MRC55' 'MRC61' 'MRC62' 'MRC63' 'MRF11' 'MRF12' 'MRF13' 'MRF14' 'MRF21' 'MRF22' 'MRF23' 'MRF24' 'MRF25' 'MRF31' 'MRF32' 'MRF33' 'MRF34' 'MRF35' 'MRF41' 'MRF42' 'MRF44' 'MRF45' 'MRF46' 'MRF51' 'MRF52' 'MRF53' 'MRF54' 'MRF55' 'MRF56' 'MRF61' 'MRF62' 'MRF63' 'MRF64' 'MRF65' 'MRF66' 'MRF67' 'MRO11' 'MRO12' 'MRO14' 'MRO21' 'MRO22' 'MRO23' 'MRO24' 'MRO31' 'MRO32' 'MRO33' 'MRO34' 'MRO41' 'MRO42' 'MRO43' 'MRO44' 'MRO51' 'MRO52' 'MRO53' 'MRP11' 'MRP12' 'MRP21' 'MRP22' 'MRP23' 'MRP31' 'MRP32' 'MRP33' 'MRP34' 'MRP35' 'MRP41' 'MRP42' 'MRP43' 'MRP44' 'MRP45' 'MRP51' 'MRP52' 'MRP53' 'MRP54' 'MRP55' 'MRP56' 'MRP57' 'MRT11' 'MRT12' 'MRT13' 'MRT14' 'MRT15' 'MRT16' 'MRT21' 'MRT22' 'MRT23' 'MRT24' 'MRT25' 'MRT26' 'MRT27' 'MRT31' 'MRT32' 'MRT33' 'MRT34' 'MRT35' 'MRT36' 'MRT37' 'MRT41' 'MRT42' 'MRT43' 'MRT44' 'MRT45' 'MRT46' 'MRT47' 'MRT51' 'MRT52' 'MRT53' 'MRT54' 'MRT55' 'MRT56' 'MRT57' 'MZC01' 'MZC02' 'MZC03' 'MZC04' 'MZF01' 'MZF02' 'MZF03' 'MZO01' 'MZO02' 'MZO03' 'MZP01' 'lip' 'HADC001' 'HADC002' 'HADC003' 'HDAC001' 'HDAC002' 'HDAC003' 'UADC003' 'UADC004' 'UADC016' 'HLC0011' 'HLC0012' 'HLC0013' 'HLC0021' 'HLC0022' 'HLC0023' 'HLC0031' 'HLC0032' 'HLC0033' 'HLC0018' 'HLC0028' 'HLC0038' 'HLC0014' 'HLC0015' 'HLC0016' 'HLC0017' 'HLC0024' 'HLC0025' 'HLC0026' 'HLC0027' 'HLC0034' 'HLC0035' 'HLC0036' 'HLC0037' } reading and preprocessing reading and preprocessing trial 1 from 72 Undefined function 'offset2time' for input arguments of type 'double'. Error in ft_preprocessing (line 511) tim = offset2time(offset, hdr.Fs, size(dat,2)); >> cfg.trialdef.eventtype = '?'; >> cfg = ft_definetrial(cfg); Warning: no trialfun was specified, using ft_trialfun_general > In ft_definetrial at 123 Undefined function 'ft_getuserfun' for input arguments of type 'char'. Error in ft_definetrial (line 140) cfg.trialfun = ft_getuserfun(cfg.trialfun, 'trialfun'); Thanks Baris On Thu, Aug 30, 2012 at 4:33 AM, Nenad Polomac wrote: > Hi, > > I am analyzing data obtained on CTF MEG 275 system. However, 4 sensors are > broken and data ended up with 271 sensor. So, my question is should I > interpolate the missing sensors with FT_CHANNELREPAIR? In the case I leave > data with 271 sensor, will those missing sensors influence neighbors > configuration in the statistic and the source localisation analysis? > > Thank you in advance! > > Kind regards! > > Nenad > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From r.oostenveld at donders.ru.nl Sun Sep 2 12:51:46 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Sun, 2 Sep 2012 12:51:46 +0200 Subject: [FieldTrip] neighbours In-Reply-To: References: Message-ID: <9BF899F9-DD29-482B-B964-CC07CEC56273@donders.ru.nl> Hi Nenad On 30 Aug 2012, at 10:33, Nenad Polomac wrote: > I am analyzing data obtained on CTF MEG 275 system. However, 4 sensors are broken and data ended up with 271 sensor. So, my question is should I interpolate the missing sensors with FT_CHANNELREPAIR? In the case I leave data with 271 sensor, will those missing sensors influence neighbors configuration in the statistic and the source localisation analysis? If the channels are consistently broken in all your subjects, you should better not interpolate them. If the channels are only missing in some, but not all subjects, interpolating will be of use for the channel-level statistics. For source reconstruction you should not interpolate the broken channels. Group statistics on source-level data is also not affected by having slight differences in the working channels over subjects. best regards Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Sun Sep 2 12:53:12 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Sun, 2 Sep 2012 12:53:12 +0200 Subject: [FieldTrip] neighbours In-Reply-To: <50406CB9.7090209@donders.ru.nl> References: <50406CB9.7090209@donders.ru.nl> Message-ID: whoops, I now see that Jorn has already provided a much better and elaborate answer. Better pay attention to what he writes and ignore my quick reply. Robert On 31 Aug 2012, at 9:50, Jörn M. Horschig wrote: > Hi Nenad, > > the question you are asking does not deserve a definite 'yes' or 'no'. In any case, note that when averaging over subjects, missing sensors for one subject will be removed for all other subjects as well. So, if you are talking about different missing sensors per subject, an interpolation will definitely be a wise thing to do. In case you choose for interpolating the missing channels, you can try to check out the new spherical spline interpolation method (see help ft_channelrepair) - theoretically that should result in a quite good reconstruction. But the (standard) nearest neighbour interpolation is fine as well. > > With respect to your second question: missing sensors will influence the neighbour configuration depending on the method you chose for neighbour selection. For the 'distance' and 'template' method, each neighbouring channel of the missing will have one sensor less (i.e. the missing one). The 'triangulation' method will create triangle neighbour no matter how many channels you have, so it will just ignore the whole in space. In any case, I'd propose that you check out how satisfied you personally are with the neighbours by calling ft_neighbourplot. Just last week, I added the new option that if you use cfg.enableedit='yes', you can interactively change the neighbourhood structure within the neighbourplot. If I were you, I would start from the template method. As an additional piece of information: I am currently working on improving the neighbour templates, and will upload them probably next week. > > All that advertised, let me also say that having 4 out of 275 sensors missing won't affect your statistics much. Here, it of course depends on your region if interest, research question etc. E.g. if you are interested in posterior alpha power, but miss four temporal channels, there is no reason to worry. So, without knowing what you are looking for and where the missing channels are, I cannot give you a general advise what to do. As a last remark, the sensitiviy of the statistics will of course be influenced by missing sensors, but I doubt that it will matter much. Btw, I am not quite sure how much the spherical spline interpolation will buy you here, you might give it a try. I bet that it will increase your sensitivity more than the nearest neighbour approach, although both might result in rather low increases. But this is just a general gut feeling rather than anything I empirically validated. > > Best, > Jörn > > On 8/30/2012 10:33 AM, Nenad Polomac wrote: >> Hi, >> >> I am analyzing data obtained on CTF MEG 275 system. However, 4 sensors are broken and data ended up with 271 sensor. So, my question is should I interpolate the missing sensors with FT_CHANNELREPAIR? In the case I leave data with 271 sensor, will those missing sensors influence neighbors configuration in the statistic and the source localisation analysis? >> >> Thank you in advance! >> >> Kind regards! >> >> Nenad >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Sun Sep 2 12:54:22 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Sun, 2 Sep 2012 12:54:22 +0200 Subject: [FieldTrip] CTF data event/reading In-Reply-To: References: Message-ID: Hi Baris, First something in general: This error > Undefined function 'offset2time' for input arguments > of type 'double'. > > Error in ft_preprocessing (line 511) > tim = offset2time(offset, hdr.Fs, size(dat,2)); should not happen with recent versions of FieldTrip (nor with older ones). The offset2time helper function is present in fieldtrip/private and can be found there by ft_preprocessing. Also the error > Undefined function 'ft_getuserfun' for input arguments > of type 'char'. > > Error in ft_definetrial (line 140) > cfg.trialfun = ft_getuserfun(cfg.trialfun, > 'trialfun'); suggests that your fieldtrip installation is broken. Please upgrade to the most recent version, that might resolve some (or all) of your problems. Don't move around the directories in the fieldtrip zip file, or rename them, otherwise ft_defaults is not able to set up the path correctly. See also http://fieldtrip.fcdonders.nl/faq/should_i_add_fieldtrip_with_all_subdirectories_to_my_matlab_path Then on to some other aspects of your question, which may be of interest to other CTF users as well. From the CTF channel naming scheme I can see that you have a CTF275 system. The 151 channel MEG system we started off with at the Donders in 2002 had an electronics rack which was placed such that there was a clear front and back side. Each side of the rack exposed 16 binary inputs (i.e. bits) for connecting external triggers. To the front we connected the button boxes, to the back we connected the stimulus presentation computer. The 16 bits from the front and from the back were combined in the 32 bit STIM channel. Given the connections of the button boxes and stimulus computers, in the analysis the 32 bit STIM channel did not match the users scripts with respect to button box and presentation trigger codes. Therefore the FieldTrip reading software was implemented to split the 32 bits into the 16 frontpanel and the 16 backpanel bits. This also shifts the bits to recover the trigger codes that were used in the presentation software by the users. This situation from early '2000 at the Donders in Nijmegen is still supported by FieldTrip. The “Subject01.ds” tutorial dataset is from that time, so that is why you see it in the tutorials. The front and back panel at other CTF sites with the old electronics rack may be (or have been) connected differently. Furthermore, the present CTF systems have more trigger input options and no front and back side any more, so better don't use those any more in your analyses. In many cases UPPT001 and similarly named channels are the interesting trigger channels. MEG data acquired with the older CTF systems uses the STIM channel. So please be aware that “frontpanel” and “backpanel” are Donders conventions that have ended up in FieldTrip, but may not be of any relevance to you. Another topic is that in Nijmegen (as many other CTF sites) we record the data continuously, and don't use the CTF software for epoching, classification of artifacts and trial marking. However FieldTrip does support the CTF ClassFile and Markerfile in FieldTrip. If you do ft_read_event('dataset.ds') you will see an event structure that combines all information. Some "events" are instantaneous, some "events" have a duration. This is explained in more detail at http://fieldtrip.fcdonders.nl/faq/what_is_the_relation_between_events_such_as_triggers_and_trials best regards, Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: From polomacnenad at gmail.com Sun Sep 2 16:51:31 2012 From: polomacnenad at gmail.com (Nenad Polomac) Date: Sun, 2 Sep 2012 16:51:31 +0200 Subject: [FieldTrip] neighbours Message-ID: Dear Jörn, Thank you very much for the thorough explanation! All the best! Nenad -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sun Sep 2 17:48:43 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sun, 2 Sep 2012 18:48:43 +0300 Subject: [FieldTrip] 'dml' variable Message-ID: Hello, I am trying to classify my data using ft_timelockstatistics function I am using the output of ft_timelockanalysis function and the following options: cfg.layout = 'CTF275.lay'; cfg.method = 'crossvalidate'; cfg.design = [ones(size(class1.trial,1),1); 2*ones(size(class2.trial,1),1)]'; But I got the following error: ??? Undefined variable "dml" or class "dml.standardizer". Error in ==> ft_statistics_crossvalidate at 44 cfg.mva = dml.analysis({ ... Error in ==> statistics_wrapper at 306 [stat] = statmethod(cfg, dat, design); Error in ==> ft_timelockstatistics at 110 [stat, cfg] = statistics_wrapper(cfg, varargin{:}); Did I forgot to add something?! Thanks -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghumana at upmc.edu Mon Sep 3 07:05:37 2012 From: ghumana at upmc.edu (Ghuman, Avniel) Date: Mon, 3 Sep 2012 05:05:37 +0000 Subject: [FieldTrip] A postdoc position in developing methods for MEG with atomic magnetometers In-Reply-To: <20385F716E75B746A7F52BBB3C46A1300226C790@MSXMBXNSPRD03.acct.upmchs.net> References: <20385F716E75B746A7F52BBB3C46A1300226C772@MSXMBXNSPRD03.acct.upmchs.net>, <20385F716E75B746A7F52BBB3C46A1300226C790@MSXMBXNSPRD03.acct.upmchs.net> Message-ID: <20385F716E75B746A7F52BBB3C46A1300226C809@MSXMBXNSPRD03.acct.upmchs.net> Post-doc in MEG with Atomic Magnetometers The Ghuman Lab at the University of Pittsburgh, in collaboration with the Romalis Group at Princeton University and Twinleaf LLC, is recruiting a Post doc to develop methods for atomic magnetometer based MEG and multimodal integration (simultaneous MEG-EEG and MEG-fNIRS). The position is available immediately. Responsibilities: • Develop novel solutions for MEG using atomic magnetometers concerning source localization, noise cancellation and head modeling • Acquire and analyze MEG, MEG-EEG, and MEG-fNIRS data • Develop novel methods for integrating multimodal data • Design and implement novel data analysis tools • Assist with preparation of progress reports • Prepare manuscripts and presentations • Work with Investigators to identify future problems and research opportunities Minimum Qualifications: • Ph.D. in Engineering, Physics, Neuroscience, Computer Science, Math, or related field. • Demonstrated expertise in solving MEG technological issues as shown through publication record, awards, successful patents and/or received applications. • Data analysis expertise includes independent components analysis, Bayesian algorithms, statistical parametric mapping, and MRI image processing. • Proficiency in creating software analysis tools and programs for investigators • MATLAB and Python programming knowledge preferred. Conditions of Employment: • Position available immediately • Salary: according to NIH postdoc salary scale • The University of Pittsburgh has excellent benefits, including health benefits and retirement plans with employer contributions. • The University of Pittsburgh values diversity and is committed to equal opportunity in employment. How to Apply: • E-mail Avniel Ghuman, Ph.D. (ghumana at upmc.edu) or Mike Romalis, Ph.D. (romalis at princeton.edu) From ghumana at upmc.edu Mon Sep 3 07:07:22 2012 From: ghumana at upmc.edu (Ghuman, Avniel) Date: Mon, 3 Sep 2012 05:07:22 +0000 Subject: [FieldTrip] A postdoc position in developing methods for MEG with atomic magnetometers In-Reply-To: <20385F716E75B746A7F52BBB3C46A1300226C790@MSXMBXNSPRD03.acct.upmchs.net> References: <20385F716E75B746A7F52BBB3C46A1300226C772@MSXMBXNSPRD03.acct.upmchs.net>, <20385F716E75B746A7F52BBB3C46A1300226C790@MSXMBXNSPRD03.acct.upmchs.net> Message-ID: <20385F716E75B746A7F52BBB3C46A1300226C827@MSXMBXNSPRD03.acct.upmchs.net> Post-doc in MEG with Atomic Magnetometers The Ghuman Lab at the University of Pittsburgh, in collaboration with the Romalis Group at Princeton University and Twinleaf LLC, is recruiting a Post doc to develop methods for atomic magnetometer based MEG and multimodal integration (simultaneous MEG-EEG and MEG-fNIRS). The position is available immediately. Responsibilities: • Develop novel solutions for MEG using atomic magnetometers concerning source localization, noise cancellation and head modeling • Acquire and analyze MEG, MEG-EEG, and MEG-fNIRS data • Develop novel methods for integrating multimodal data • Design and implement novel data analysis tools • Assist with preparation of progress reports • Prepare manuscripts and presentations • Work with Investigators to identify future problems and research opportunities Minimum Qualifications: • Ph.D. in Engineering, Physics, Neuroscience, Computer Science, Math, or related field. • Demonstrated expertise in solving MEG technological issues as shown through publication record, awards, successful patents and/or received applications. • Data analysis expertise includes independent components analysis, Bayesian algorithms, statistical parametric mapping, and MRI image processing. • Proficiency in creating software analysis tools and programs for investigators • MATLAB and Python programming knowledge preferred. Conditions of Employment: • Position available immediately • Salary: according to NIH postdoc salary scale • The University of Pittsburgh has excellent benefits, including health benefits and retirement plans with employer contributions. • The University of Pittsburgh values diversity and is committed to equal opportunity in employment. How to Apply: • E-mail Avniel Ghuman, Ph.D. (ghumana at upmc.edu) or Mike Romalis, Ph.D. (romalis at princeton.edu) From jm.horschig at donders.ru.nl Mon Sep 3 09:56:40 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 03 Sep 2012 09:56:40 +0200 Subject: [FieldTrip] 'dml' variable In-Reply-To: References: Message-ID: <504462B8.2060508@donders.ru.nl> Dear Hamza, 'crossvalidate' is part of the Donders Machine Learning Toolbox (DMLT). Formerly, it was known under a different name (afair MVA or multivariate toolbox) but recently it became an external toolbox and moved to the external/ folder. FieldTrip supports external toolboxes but takes no initiative in adding them automatically, so you need to it manually: addpath(genpath(fullfile('your_fieldtrip_folder', 'external', 'dmlt'))) See also here: http://fieldtrip.fcdonders.nl/tutorial/multivariateanalysis Since Marcel and others, who are developing this toolbox or have experience with using it, are on this mailinglist, feel free to post further questions concerning DMLT to this list anyhow. Best regards, Jörn On 9/2/2012 5:48 PM, Hamza Fawzi Altakroury (Student) wrote: > Hello, > > I am trying to classify my data using ft_timelockstatistics function > > I am using the output of ft_timelockanalysis function and the > following options: > > cfg.layout = 'CTF275.lay'; > cfg.method = 'crossvalidate'; > cfg.design = [ones(size(class1.trial,1),1); > 2*ones(size(class2.trial,1),1)]'; > > But I got the following error: > > ??? Undefined variable "dml" or class "dml.standardizer". > > Error in ==> ft_statistics_crossvalidate at 44 > cfg.mva = dml.analysis({ ... > > Error in ==> statistics_wrapper at 306 > [stat] = statmethod(cfg, dat, design); > > Error in ==> ft_timelockstatistics at 110 > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > Did I forgot to add something?! > > Thanks > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabanc? University > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From hubert.preissl at uni-tuebingen.de Mon Sep 3 14:08:21 2012 From: hubert.preissl at uni-tuebingen.de (Hubert Preissl) Date: Mon, 03 Sep 2012 14:08:21 +0200 Subject: [FieldTrip] 5th Autumn School Structure the Brain: 9th-11th October 2012, 2nd announcement In-Reply-To: References: Message-ID: <50449DB5.3000501@uni-tuebingen.de> Hello, we are pleased to announce the upcoming “5th Autumn School” in Tübingen organized by the MEG Center. For application and further information on the scientific program please visit our website: http://www.mp.uni-tuebingen.de/mp/index.php?id=400 Confirmed speakers: Christian Gaser, PhD, University of Jena, Germany Volkmar Glauche, MSc, University of Freiburg,Germany Matti Hämäläinen, PhD, Harvard Medical School, Boston, USA Risto Ilmoniemi, PhD, Aalto University, Aalto, Finland Svenja Knappe, PhD, National Institute of Standards and Technology, Boulder, USA Daniela Prayer, MD, University of Vienna, Austria Dana Small, PhD, The John B Pierce Laboratory and Yale University, USA Fabrice Wallois, PhD, University of Picardy,France We look forward meeting you in Tübingen! Best regards, Hubert Preissl -- Dr. Hubert Preissl MEG Center phone: ++49-(0)7071-2987704 Otfried Müller Str 47 fax: ++49-(0)7071-295706 72076 Tübingen, Germany email: hubert.preissl at uni-tuebingen.de From hamzaf at sabanciuniv.edu Mon Sep 3 17:22:02 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Mon, 3 Sep 2012 18:22:02 +0300 Subject: [FieldTrip] 'dml' variable In-Reply-To: <504462B8.2060508@donders.ru.nl> References: <504462B8.2060508@donders.ru.nl> Message-ID: Thank you Jörn, it works. Hamza On Mon, Sep 3, 2012 at 10:56 AM, "Jörn M. Horschig" < jm.horschig at donders.ru.nl> wrote: > Dear Hamza, > > 'crossvalidate' is part of the Donders Machine Learning Toolbox (DMLT). > Formerly, it was known under a different name (afair MVA or multivariate > toolbox) but recently it became an external toolbox and moved to the > external/ folder. FieldTrip supports external toolboxes but takes no > initiative in adding them automatically, so you need to it manually: > addpath(genpath(fullfile('your_fieldtrip_folder', 'external', 'dmlt'))) > > See also here: > http://fieldtrip.fcdonders.nl/tutorial/multivariateanalysis > > Since Marcel and others, who are developing this toolbox or have > experience with using it, are on this mailinglist, feel free to post > further questions concerning DMLT to this list anyhow. > > Best regards, > Jörn > > > On 9/2/2012 5:48 PM, Hamza Fawzi Altakroury (Student) wrote: > > Hello, > > I am trying to classify my data using ft_timelockstatistics function > > I am using the output of ft_timelockanalysis function and the following > options: > > cfg.layout = 'CTF275.lay'; > cfg.method = 'crossvalidate'; > cfg.design = [ones(size(class1.trial,1),1); > 2*ones(size(class2.trial,1),1)]'; > > But I got the following error: > > ??? Undefined variable "dml" or class "dml.standardizer". > > Error in ==> ft_statistics_crossvalidate at 44 > cfg.mva = dml.analysis({ ... > > Error in ==> statistics_wrapper at 306 > [stat] = statmethod(cfg, dat, design); > > Error in ==> ft_timelockstatistics at 110 > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > Did I forgot to add something?! > > Thanks > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From daria.laptinskaya at googlemail.com Mon Sep 3 17:22:58 2012 From: daria.laptinskaya at googlemail.com (Daria Laptinskaya) Date: Mon, 3 Sep 2012 17:22:58 +0200 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? Message-ID: Dear Fieldtrippers, I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip toolbox. The ERPs look perfect. The 'only' problem is, that my signals look to strong. It looks like if I get amplitutes (average) until 70 µV. I think it must be an intern amplifier for the signals. Does anyone know this problem with EGI-data? Or does anyone know, where I can see the amplifier? Greetings, Daria -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Mon Sep 3 19:04:47 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Mon, 3 Sep 2012 20:04:47 +0300 Subject: [FieldTrip] Changing the classifier Message-ID: Hello, I am dealing with ft_timelockstatistics function for classification, as I understand from the tutorail, the default classifier used is the SVM. I want to ask about the ability to change the classifier. Thanks for help. Best, -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Mon Sep 3 22:35:06 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 3 Sep 2012 22:35:06 +0200 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: References: Message-ID: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> Hi Daria, There might indeed be an incompatibility in the gain value applied to the data. If you are able to export the data using the EGI software in another format (e.g. EDF), you could read them both into FieldTrip and compare the timecourse aplitudes to check whether they are different. In case they are, I suggest to involve EGI support. They are aware of the FieldTrip reading functions and will know much more about the internals of their various file formats. best regards Robert On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: > Dear Fieldtrippers, > > I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip toolbox. > The ERPs look perfect. > The 'only' problem is, that my signals look to strong. > It looks like if I get amplitutes (average) until 70 µV. > I think it must be an intern amplifier for the signals. > Does anyone know this problem with EGI-data? > > Or does anyone know, where I can see the amplifier? > > > > > Greetings, > > Daria _______________________________________________ > 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 Mon Sep 3 23:02:21 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 3 Sep 2012 23:02:21 +0200 Subject: [FieldTrip] A postdoc position in developing methods for MEG with atomic magnetometers In-Reply-To: <20385F716E75B746A7F52BBB3C46A1300226C827@MSXMBXNSPRD03.acct.upmchs.net> References: <20385F716E75B746A7F52BBB3C46A1300226C772@MSXMBXNSPRD03.acct.upmchs.net>, <20385F716E75B746A7F52BBB3C46A1300226C790@MSXMBXNSPRD03.acct.upmchs.net> <20385F716E75B746A7F52BBB3C46A1300226C827@MSXMBXNSPRD03.acct.upmchs.net> Message-ID: <9D7A03F8-3318-498E-B2DD-BFE41B461548@donders.ru.nl> Dear Avniel (CC to the FieldTrip list) Thanks for announcing this interesting post doc position. Last week at the Biomag conference I attended the atomic/optical magnetic field sensor symposium and was very impressed with the progress that was presented. With respect to some of the tasks you outline (see below), I think that there is quite some overlap with the methods used in squid based MEG technology. E.g., the volume conduction modelling and forward solutions relate the equivalent current dipole strength in the model head to magnetic field strength outside the head. This is independent of the sensor technology, although the precise sensor geometry is of course different (as it also is between the various MEG systems). See for example http://fieldtrip.fcdonders.nl/faq/how_are_electrodes_magnetometers_or_gradiometers_described. The noise characteristics of the atomic magnetometers themselves will at the moment also be quite different for that of a squid-based system, but once the S/N gets good enough, a large fraction of the noise will be environmental and biological, again resulting in similar methods being applicable to deal with those parts of the noise (especially when compared to the magnetometer channels in some of the presently used MEG systems). I hope that it will be possible to develop methods for atomical magnetometer based MEG in close collaboration with the methods that are used and developed for conventional MEG. Actually it would be cool to implement support for the data formats that are being used by you and in Princeton in the FieldTrip toolbox. I believe that this would facilitate working together, not specifically with the Donders Institute in Nijmegen, but rather with the MEG field as a whole. It would also allow your data to be processed in the other large open source toolboxes (such as SPM and Nutmeg), as these all share the same data access functions and sensor representation. At the moment FieldTrip supports MEG data from about 15 different MEG systems (3x BTi, 2x Neuromag, 4x CTF, 4x Yokogawa, 2x ITAB, ranging from adult MEG to fetal MCG and even rodent MEG) and provides data processing and source reconstruction for all of them. Adding support for your data format and sensor arrangements is something that we could provide assistance with. I hope you will be able to attract a good candidate for the position and that the new atomic sensor technology will soon become available to the whole MEG community. best regards Robert ----------------------------------------------------------- Robert Oostenveld, PhD Senior Researcher & MEG Physicist Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen tel.: +31 (0)24 3619695 e-mail: r.oostenveld at donders.ru.nl web: http://www.ru.nl/neuroimaging skype: r.oostenveld ----------------------------------------------------------- On 3 Sep 2012, at 7:07, Ghuman, Avniel wrote: > Post-doc in MEG with Atomic Magnetometers > > The Ghuman Lab at the University of Pittsburgh, in collaboration with the Romalis Group at Princeton University and Twinleaf LLC, is recruiting a Post doc to develop methods for atomic magnetometer based MEG and multimodal integration (simultaneous MEG-EEG and MEG-fNIRS). The position is available immediately. > Responsibilities: > • Develop novel solutions for MEG using atomic magnetometers concerning source localization, noise cancellation and head modeling > • Acquire and analyze MEG, MEG-EEG, and MEG-fNIRS data > • Develop novel methods for integrating multimodal data > • Design and implement novel data analysis tools > • Assist with preparation of progress reports > • Prepare manuscripts and presentations > • Work with Investigators to identify future problems and research opportunities > > Minimum Qualifications: > • Ph.D. in Engineering, Physics, Neuroscience, Computer Science, Math, or related field. > • Demonstrated expertise in solving MEG technological issues as shown through publication record, awards, successful patents and/or received applications. > • Data analysis expertise includes independent components analysis, Bayesian algorithms, statistical parametric mapping, and MRI image processing. > • Proficiency in creating software analysis tools and programs for investigators > • MATLAB and Python programming knowledge preferred. > > Conditions of Employment: > • Position available immediately > • Salary: according to NIH postdoc salary scale > • The University of Pittsburgh has excellent benefits, including health benefits and retirement plans with employer contributions. > • The University of Pittsburgh values diversity and is committed to equal opportunity in employment. > > How to Apply: > • E-mail Avniel Ghuman, Ph.D. (ghumana at upmc.edu) or Mike Romalis, Ph.D. (romalis at princeton.edu) > > _______________________________________________ > 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 ayelet.landau at gmail.com Tue Sep 4 13:23:21 2012 From: ayelet.landau at gmail.com (Ayelet Landau) Date: Tue, 4 Sep 2012 13:23:21 +0200 Subject: [FieldTrip] problem with ft_rejectartifact Message-ID: Dear FieldTrip experts, I have encountered a strange behavior in ft_rejectartifact script. artifacts are defined in variables that contain two collumns and fed into this function as follows: cfg.artfctdef.eog.artifact =artifact_eog_all; other parameters I use are: cfg.trl=trl; cfg.artfctdef.reject = 'partial'; cfg.artfctdef.minaccepttim = .2; then I run ft_rejectartifact with this cfg (and many more categories of artifacts as exemplified above) and a structure containing my preprocessed data (with a the same trl I give in cfg.trl above). This is an example of what the data structure fed into ft_rejectartifact might looks like hdr: [1x1 struct] fsample: 1200 grad: [1x1 struct] sampleinfo: [50x2 double] trialinfo: [50x4 double] trial: {1x50 cell} time: {1x50 cell} label: {275x1 cell} cfg: [1x1 struct] and here is the error that I get: ??? Subscripted assignment dimension mismatch. Error in ==> ft_redefinetrial at 253 data.trialinfo(iTrl,:) = dataold.trialinfo(iTrlorig,:); Error in ==> ft_rejectartifact at 483 data = ft_redefinetrial(tmpcfg, data); When I run ft_rejectartifact with a cfg.data field calling my *.ds file, I get the following which I could probably use later as an adjusted trl for ft_preprocessing: datafile: 'XX_20120821_05.ds' trl: [79x7 double] artfctdef: [1x1 struct] trackconfig: 'off' checkconfig: 'loose' checksize: 100000 showcallinfo: 'yes' headerfile: 'XX_20120821_05.ds' trlold: [50x7 double] callinfo: [1x1 struct] version: [1x1 struct] Its a bit strange that my original approach stopped working. Any insights most welcome! -- Ayelet N. Landau Postdoctoral Scientist, Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society Deutschordenstr. 46, D-60528 Frankfurt Mobile: +49 (0)16 22733 110 Fax: +49 (0)69 96769 555 -------------- next part -------------- An HTML attachment was scrubbed... URL: From inieuwenhuis at berkeley.edu Tue Sep 4 22:00:03 2012 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Tue, 04 Sep 2012 13:00:03 -0700 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> Message-ID: <50465DC3.7080005@berkeley.edu> Hi Daria, Also, did you try looking at your raw data (so before the ERPs are made) in FieldTrip and in Net Station? So open your .raw data in NetStation. You can just look at a random participant's data, and check if the scale is the same. I'm pretty sure no amplification takes place when reading in the data into FieldTrip, this check can confirm that. Hope this helps, and let us know what you find. Cheers, Ingrid On 9/3/2012 1:35 PM, Robert Oostenveld wrote: > Hi Daria, > > There might indeed be an incompatibility in the gain value applied to > the data. > > If you are able to export the data using the EGI software in another > format (e.g. EDF), you could read them both into FieldTrip and compare > the timecourse aplitudes to check whether they are different. In case > they are, I suggest to involve EGI support. They are aware of the > FieldTrip reading functions and will know much more about the > internals of their various file formats. > > best regards > Robert > > > > > On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: > >> Dear Fieldtrippers, >> >> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip >> toolbox. >> The ERPs look perfect. >> The 'only' problem is, that my signals look to strong. >> It looks like if I get amplitutes (average) until 70 µV. >> I think it must be an intern amplifier for the signals. >> >> Does anyone know this problem with EGI-data? >> >> Or does anyone know, where I can see the amplifier? >> >> >> >> Greetings, >> >> Daria _______________________________________________ >> 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 -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jochem.rieger at uni-oldenburg.de Wed Sep 5 03:24:18 2012 From: jochem.rieger at uni-oldenburg.de (Jochem Rieger) Date: Wed, 05 Sep 2012 03:24:18 +0200 Subject: [FieldTrip] 1 post-doc and 1 PhD position in human auditory and motor neuroscience Message-ID: <5046A9C2.2020704@uni-oldenburg.de> The Department of Applied Neurocognitive Psychology at Oldenburg University, Germany, offers a *Post-doctoral position (E13/TVL, 3 years plus) * and a *PhD position (0.5*E13/TVL, initially 2 years)* The lab focuses on the fields of neural coding of complex movements and neural coding of speech in the human brain with the aim of developing brain-machine-interfaces. To extend our interdisciplinary team we seek for highly motivated candidates with strong quantitative and experimental skills. The post-doctoral position requires a PhD or comparable degree and the PhD position requires a masters or comparable degree. The post-doctoral position is initially limited to three years after with an option for an extension to obtain habilitation (post-doctoral degree, similar to a lecturer qualification). Successful candidates will perform cutting edge research in one of the lab's foci and should have a background in one or more of the following fields: non-invasive or invasive human neurophysiology of the motor or auditory system, statistical learning, brain-machine-interfacing. The positions offer an excellent interdisciplinary working environment with opportunities for international exchange. The lab is involved in the EU-project BRACOG (brain controlled grasping) and we have a close collaboration with UC Berkeley, USA. The University of Oldenburg was recently awarded a Cluster of Excellence in hearing research. The Dept. of Psychology will offer an attractive scientific environment with access to research dedicated state-of-the-art approaches to human neurophysiological techniques (fMRI, NIRS, EEG, ECoG, and MEG). Electronic applications are preferred and can be send to: Professor Dr. Jochem Rieger: Jochem.rieger at uni-oldenburg.de Please send paper applications until September 30^th 2012 to: Margrit Jung Dept. of Applied Neurocognitive Psychology Institute of Psychology Oldenburg University 26111 Oldenburg Germany Applications should include your CV and a list of most recent publications. Applications for the post-doctoral position should include a research statement (max. 3 pages). The University of Oldenburg aims to employ more women in this area and therefore particularly welcomes applications from women. We also welcome applications from disabled persons. -- Prof. Dr. rer. nat. Jochem Rieger Applied Neurocognitive Knight Lab Psychology Helen Wills Neuroscience Institute Faculty V University of California Carl-von-Ossietzky University 132 Barker Hall 26111 Oldenburg Berkeley, CA 94720-3192 Germany USA Phone: +49(0)4417984533 Fax: +49(0)4417983865 -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.piantoni at nin.knaw.nl Wed Sep 5 10:20:41 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Wed, 5 Sep 2012 10:20:41 +0200 Subject: [FieldTrip] freesurfer surfaces Message-ID: Dear Fieldtrip developers, I'd like to run source reconstruction on the cortical sheets obtained from Freesurfer and average them using the "sphere" approach of Freesurfer. I have these steps in mind: 1) create a 3-layer BEM ('outer_skin' 'inner_skull' 'brain' from the bem/watershed folder, which I think might be better than 'outer_skin' 'outer_skull' 'inner_skull' as in http://fieldtrip.fcdonders.nl/development/replicate_functionality_of_mne_software ) 2) create a forward model from a subset of points in "?h.smoothwm" (for computational purposes) 3) do source reconstruction on this subset of dipoles 4) source interpolate to the high resolution of ?h.smoothwm 5) project all the locations onto the ?h.sphere 6) interpolate to the points to the ?h.sphere of fsaverage 7) do 2-D statistics on the values of the ?h.sphere of fsaverage (and plot them using ?h.inflated of fsaverage) I was wondering if anybody has tried something similar and if there are steps I should be careful about. There was a discussion in January/February about doing statistics on cortical sheets: http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004749.html http://mailman.science.ru.nl/pipermail/fieldtrip/2012-February/004766.html Does anybody have suggestions about these steps? I promise I'll make a tutorial out of this, if it works out ;) A practical point I get stuck in is at steps 3) and 4). The interpolation from a subset of 2-D points to another subset of 2-D points gives a bit of nonsensical results. Code: %-get freesurfer surface bnd = ft_read_headshape('lh.smoothwm'); % get it from https://skydrive.live.com/redir?resid=6D9DCA0F726A645C!7000 % or any freesurfer surface you have %-downsample bnd_down = bnd; P.faces = bnd_down.tri; P.vertices = bnd_down.pnt; P = reducepatch(P, 0.05); bnd_down.tri = P.faces; bnd_down.pnt = P.vertices; %-create source source.pos = bnd_down.pnt; source.inside = true(size(source.pos,1),1); source.pow = bnd_down.pnt(:,3); % "fake" source reconstruction figure ft_plot_mesh(bnd_down, 'edgecolor', 'none', 'vertexcolor', source.pow) % the rainbow brain view(90, 0); camlight %-sourceinterpolate cfg = []; cfg.parameter = 'pow'; ana = []; ana.pnt = bnd_down.pnt; ana.orig = bnd; souinterp = ft_sourceinterpolate(cfg, source, ana); figure ft_plot_mesh(souinterp, 'edgecolor', 'none', 'vertexcolor', souinterp.pow) % the Arlecchino brain view(90, 0); camlight Should I file a bugzilla report for this? I haven't done it as I'm not even sure this is the correct input format. Thanks for any suggestion. Best wishes, Gio -- Giovanni Piantoni, MSc Dept. Sleep & Cognition Netherlands Institute for Neuroscience Meibergdreef 47 1105 BA Amsterdam (NL) www.gpiantoni.com From johanna.zumer at donders.ru.nl Wed Sep 5 12:41:38 2012 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Wed, 5 Sep 2012 12:41:38 +0200 Subject: [FieldTrip] FT_SCALPCURRENTDENSITY options and elec units In-Reply-To: References: Message-ID: Hi Akiko, Hopefully someone else can answer your main SCD question (although ft_scalpcurrentdensity provides the citations for the original papers on which these 2 methods are based). But for now, just a quick answer to your units question. The best way to convert the units of a FieldTrip data structure is with ft_convert_units, for example: elec_out = ft_convert_units(elec_in, 'm'). If elec.unit does not already exist in the structure, then either you can set it first if you know the units, or FT will do its best to assume which units the structure is in. Also note that the 'help' of ft_scalpcurrentdensity states that "the spatial distribution still will be correct" even if units do not match, which should explain why the topoplot shows the same results. Cheers, Johanna 2012/8/31 Akiko Ikkai > Hi, > > I'm trying to run plv analysis, first acquiring SCD of my data with > ft_scalcurrentdensity, and am confused about the difference between > cfg.method = 'finite' and 'spline.' Both gave similar results > short-range, but 'spline' gives higher plv at long range plv. I'd love it > if someone could explain or suggest reading on the difference between these > two methods (or is one method preferred over the other in some cases?). > > Also, I'm not sure whether or not I should convert my elec.pnt values, > since the code ft_scalcurrentdensity says that > "Note that the skin conductivity, electrode dimensions and the potential all > have to be expressed in the same SI units." My elec.pnt are in cm, and > I'm using the default conductivity (0.33 S/m). Do I need to do something > like elec.pnt = elec.pnt/100 to convert the unit from cm to m? With or > without conversion, I got the same results (viewed with ft_topoplotTFR), > and I'm a little confused... Thank you in advance for your time! Akiko > > -- > Akiko Ikkai, Ph.D. > Postdoctoral Fellow > Department of Psychological and Brain Sciences > Johns Hopkins University > Ames Hall, 3400 N. Charles St. > Baltimore, MD 21218 > > > > _______________________________________________ > 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 f.roux at bcbl.eu Wed Sep 5 14:47:29 2012 From: f.roux at bcbl.eu (Frederic Roux) Date: Wed, 05 Sep 2012 14:47:29 +0200 (CEST) Subject: [FieldTrip] left to right inversion after source interpolation In-Reply-To: Message-ID: <075a92dd-147e-45e9-a4d1-726999c597b1@thalamus_p> Dear fieldtrip users, I have noticed that after interpolating a dummy source volume with ft_sourceinterpolate, voxels that were located in the left side of the volume, apear to be located in the right side of the volume. The code that I use is as following: dummy is a dummy structure of an lcmv beamformer map with the fields dummy = dim : [15 18 17] time: [1x272662 double] pos: [4590x3 double] inside: [1x2144 double] outside: [1x2446 double] method: 'average' avg: [1x1 struct] voxpos = dummy.pos(dummy.inside,1);% get the coordinates of voxels inside the volume dummy.avg.pow(dummy.inside(sign(voxpos)==1)) = 0; % set activity in the left hemisphere to 0 dummy.avg.pow(dummy.inside(sign(voxpos)==-1)) = 1; % set activity in the left hemisphere to 1 cfg = []; cfg.parameters = 'all'; int_dummy = ft_sourceinterpolate(cfg,dummy,template_MNI_mri); cfg = []; cfg.funparameter = 'avg.pow'; cfg.method = 'ortho'; %plot the non-interpolated volume figure; ft_sourceplot(cfg,dummy); %plot the interpolated volume figure; ft_sourceplot(cfg,int_dummy); As you can see from the figure in the attachement, the voxels that corresponded to the left hemisphere prior to the interpolation, no appear to be located in the rigth hemisphere. This is also something that I have observed in real data. Does anybody have an explanation why this is happening? Am I doing something wrong? Best, Fred -------------- next part -------------- A non-text attachment was scrubbed... Name: non_interp_vs_interp.jpg Type: image/jpeg Size: 25092 bytes Desc: not available URL: From k.muesch at uke.uni-hamburg.de Wed Sep 5 16:30:49 2012 From: k.muesch at uke.uni-hamburg.de (=?iso-8859-1?Q?Kathrin_M=FCsch?=) Date: Wed, 5 Sep 2012 16:30:49 +0200 Subject: [FieldTrip] left to right inversion after source interpolation In-Reply-To: <075a92dd-147e-45e9-a4d1-726999c597b1@thalamus_p> References: <075a92dd-147e-45e9-a4d1-726999c597b1@thalamus_p> Message-ID: <44E1ACF5-2C6D-4BA2-8FA7-B0886FB8AF20@uke.uni-hamburg.de> Dear Fred, I encountered a similar thing a while ago and it was because spm8 seems to plot in radiological convention (i.e. left is plotted right and vice versa - http://mailman.science.ru.nl/pipermail/fieldtrip/2012-May/005229.html) so you're plots should actually be correct. If you use cfg.interactive = 'yes'; and click into the activated side of the brain, the first coordinate should be negative because you are in the left hemisphere. Hope that helps, Kathrin Am 05.09.2012 um 14:47 schrieb Frederic Roux: > Dear fieldtrip users, > > I have noticed that after interpolating a dummy source volume with ft_sourceinterpolate, > voxels that were located in the left side of the volume, apear to be located in the right > side of the volume. > > The code that I use is as following: > > dummy is a dummy structure of an lcmv beamformer map with the fields > > dummy = > dim : [15 18 17] > time: [1x272662 double] > pos: [4590x3 double] > inside: [1x2144 double] > outside: [1x2446 double] > method: 'average' > avg: [1x1 struct] > > voxpos = dummy.pos(dummy.inside,1);% get the coordinates of voxels inside the volume > dummy.avg.pow(dummy.inside(sign(voxpos)==1)) = 0; % set activity in the left hemisphere to 0 > dummy.avg.pow(dummy.inside(sign(voxpos)==-1)) = 1; % set activity in the left hemisphere to 1 > > cfg = []; > cfg.parameters = 'all'; > > int_dummy = ft_sourceinterpolate(cfg,dummy,template_MNI_mri); > > cfg = []; > cfg.funparameter = 'avg.pow'; > cfg.method = 'ortho'; > > %plot the non-interpolated volume > figure; > ft_sourceplot(cfg,dummy); > > %plot the interpolated volume > figure; > ft_sourceplot(cfg,int_dummy); > > As you can see from the figure in the attachement, the voxels that > corresponded to the left hemisphere prior to the interpolation, > no appear to be located in the rigth hemisphere. > > This is also something that I have observed in real data. > > Does anybody have an explanation why this is happening? > Am I doing something wrong? > > Best, > > Fred > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus From jdien07 at mac.com Thu Sep 6 03:17:03 2012 From: jdien07 at mac.com (Joseph Dien) Date: Wed, 05 Sep 2012 21:17:03 -0400 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: <50465DC3.7080005@berkeley.edu> References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> Message-ID: <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> The Simple Binary (.raw) files don't get corrected for gain when imported (I helped write them). I've experienced occasional unpredictable bugs with NetStation export routines where the files are generated with amplitudes many times too large, even with text format files. It's a bit disconcerting to say the least. I could take a look at your files if you'd like confirmation. Joe On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis wrote: > Hi Daria, > > Also, did you try looking at your raw data (so before the ERPs are made) in FieldTrip and in Net Station? So open your .raw data in NetStation. You can just look at a random participant's data, and check if the scale is the same. I'm pretty sure no amplification takes place when reading in the data into FieldTrip, this check can confirm that. Hope this helps, and let us know what you find. > > Cheers, > Ingrid > > > On 9/3/2012 1:35 PM, Robert Oostenveld wrote: >> Hi Daria, >> >> There might indeed be an incompatibility in the gain value applied to the data. >> >> If you are able to export the data using the EGI software in another format (e.g. EDF), you could read them both into FieldTrip and compare the timecourse aplitudes to check whether they are different. In case they are, I suggest to involve EGI support. They are aware of the FieldTrip reading functions and will know much more about the internals of their various file formats. >> >> best regards >> Robert >> >> >> >> >> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: >> >>> Dear Fieldtrippers, >>> >>> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip toolbox. >>> The ERPs look perfect. >>> The 'only' problem is, that my signals look to strong. >>> It looks like if I get amplitutes (average) until 70 µV. >>> I think it must be an intern amplifier for the signals. >>> Does anyone know this problem with EGI-data? >>> >>> Or does anyone know, where I can see the amplifier? >>> >>> >>> >>> >>> Greetings, >>> >>> Daria _______________________________________________ >>> 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 > > -- > Ingrid Nieuwenhuis PhD > Postdoctoral Fellow > Sleep and Neuroimaging Laboratory > Department of Psychology > University of California, Berkeley > California 94720-1650 > Tolman Hall, room 5305 > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07 at mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan.debener at uni-oldenburg.de Thu Sep 6 09:12:09 2012 From: stefan.debener at uni-oldenburg.de (Stefan Debener) Date: Thu, 06 Sep 2012 09:12:09 +0200 Subject: [FieldTrip] 1 post-doc and 1 PhD position in human auditory and motor neuroscience In-Reply-To: <5046A9C2.2020704@uni-oldenburg.de> References: <5046A9C2.2020704@uni-oldenburg.de> Message-ID: <50484CC9.2070601@uni-oldenburg.de> Lieber Jochem, ich habe vo ein paar Tagen Frau Straube gesprochen, die bei Prof. Kauss, Neurochirurgie Hannover, die Forschung leitet. Herr Krauss ist sehr kooperationsfreudig und es ist kein Problem an BG und Dystonie DBS Patienten zu kommen, das machen die wohl ziemlich häufig inzwischen (ca 1/Woche), und Ausleitung mehrere Tage danach ist auch kein Problem. Vielleicht solltest Du den Kontakt suchen, ist zwar nicht ecog, aber immerhin... lg, s Am 9/5/12 3:24 AM, schrieb Jochem Rieger: > The Department of Applied Neurocognitive Psychology at Oldenburg > University, Germany, offers a > > *Post-doctoral position (E13/TVL, 3 years plus) * > > and a > > *PhD position (0.5*E13/TVL, initially 2 years)* > > The lab focuses on the fields of neural coding of complex movements > and neural coding of speech in the human brain with the aim of > developing brain-machine-interfaces. > > To extend our interdisciplinary team we seek for highly motivated > candidates with strong quantitative and experimental skills. The > post-doctoral position requires a PhD or comparable degree and the PhD > position requires a masters or comparable degree. The post-doctoral > position is initially limited to three years after with an option for > an extension to obtain habilitation (post-doctoral degree, similar to > a lecturer qualification). Successful candidates will perform cutting > edge research in one of the lab's foci and should have a background in > one or more of the following fields: non-invasive or invasive human > neurophysiology of the motor or auditory system, statistical learning, > brain-machine-interfacing. The positions offer an excellent > interdisciplinary working environment with opportunities for > international exchange. The lab is involved in the EU-project BRACOG > (brain controlled grasping) and we have a close collaboration with UC > Berkeley, USA. The University of Oldenburg was recently awarded a > Cluster of Excellence in hearing research. The Dept. of Psychology > will offer an attractive scientific environment with access to > research dedicated state-of-the-art approaches to human > neurophysiological techniques (fMRI, NIRS, EEG, ECoG, and MEG). > > Electronic applications are preferred and can be send to: > Professor Dr. Jochem Rieger: Jochem.rieger at uni-oldenburg.de > > > Please send paper applications until September 30^th 2012 to: > > Margrit Jung > > Dept. of Applied Neurocognitive Psychology > > Institute of Psychology > > Oldenburg University > > 26111 Oldenburg > > Germany > > Applications should include your CV and a list of most recent > publications. Applications for the post-doctoral position should > include a research statement (max. 3 pages). The University of > Oldenburg aims to employ more women in this area and therefore > particularly welcomes applications from women. We also welcome > applications from disabled persons. > > > -- > Prof. Dr. rer. nat. Jochem Rieger > > Applied Neurocognitive Knight Lab > Psychology Helen Wills Neuroscience Institute > Faculty V University of California > Carl-von-Ossietzky University 132 Barker Hall > 26111 Oldenburg Berkeley, CA 94720-3192 > Germany USA > > Phone: +49(0)4417984533 > Fax: +49(0)4417983865 > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Prof. Dr. Stefan Debener Neuropsychology Lab Department of Psychology University of Oldenburg D-26111 Oldenburg Germany Office: A7 0-038 Phone: +49-441-798-4271 Fax: +49-441-798-5522 Email: stefan.debener at uni-oldenburg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.piantoni at nin.knaw.nl Thu Sep 6 10:21:58 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Thu, 6 Sep 2012 10:21:58 +0200 Subject: [FieldTrip] freesurfer surfaces In-Reply-To: References: Message-ID: I fixed the "Arlecchino brain" problem and committed the patch (r6433). I'd still appreciate if people had some suggestions about the analysis steps for the group-average. Best, Gio On Wed, Sep 5, 2012 at 10:20 AM, Gio Piantoni wrote: > Dear Fieldtrip developers, > > I'd like to run source reconstruction on the cortical sheets obtained > from Freesurfer and average them using the "sphere" approach of > Freesurfer. I have these steps in mind: > > 1) create a 3-layer BEM ('outer_skin' 'inner_skull' 'brain' from the > bem/watershed folder, which I think might be better than 'outer_skin' > 'outer_skull' 'inner_skull' as in > http://fieldtrip.fcdonders.nl/development/replicate_functionality_of_mne_software > ) > 2) create a forward model from a subset of points in "?h.smoothwm" > (for computational purposes) > 3) do source reconstruction on this subset of dipoles > 4) source interpolate to the high resolution of ?h.smoothwm > 5) project all the locations onto the ?h.sphere > 6) interpolate to the points to the ?h.sphere of fsaverage > 7) do 2-D statistics on the values of the ?h.sphere of fsaverage (and > plot them using ?h.inflated of fsaverage) > > I was wondering if anybody has tried something similar and if there > are steps I should be careful about. There was a discussion in > January/February about doing statistics on cortical sheets: > http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004749.html > http://mailman.science.ru.nl/pipermail/fieldtrip/2012-February/004766.html > > Does anybody have suggestions about these steps? I promise I'll make a > tutorial out of this, if it works out ;) > > A practical point I get stuck in is at steps 3) and 4). The > interpolation from a subset of 2-D points to another subset of 2-D > points gives a bit of nonsensical results. Code: > > %-get freesurfer surface > bnd = ft_read_headshape('lh.smoothwm'); > % get it from https://skydrive.live.com/redir?resid=6D9DCA0F726A645C!7000 > % or any freesurfer surface you have > > %-downsample > bnd_down = bnd; > P.faces = bnd_down.tri; > P.vertices = bnd_down.pnt; > P = reducepatch(P, 0.05); > bnd_down.tri = P.faces; > bnd_down.pnt = P.vertices; > > %-create source > source.pos = bnd_down.pnt; > source.inside = true(size(source.pos,1),1); > source.pow = bnd_down.pnt(:,3); % "fake" source reconstruction > > figure > ft_plot_mesh(bnd_down, 'edgecolor', 'none', 'vertexcolor', source.pow) > % the rainbow brain > view(90, 0); camlight > > %-sourceinterpolate > cfg = []; > cfg.parameter = 'pow'; > ana = []; > ana.pnt = bnd_down.pnt; > ana.orig = bnd; > souinterp = ft_sourceinterpolate(cfg, source, ana); > > figure > ft_plot_mesh(souinterp, 'edgecolor', 'none', 'vertexcolor', > souinterp.pow) % the Arlecchino brain > view(90, 0); camlight > > Should I file a bugzilla report for this? I haven't done it as I'm not > even sure this is the correct input format. > Thanks for any suggestion. > > Best wishes, > > Gio > > -- > Giovanni Piantoni, MSc > Dept. Sleep & Cognition > Netherlands Institute for Neuroscience > Meibergdreef 47 > 1105 BA Amsterdam (NL) > www.gpiantoni.com From stefan.debener at uni-oldenburg.de Thu Sep 6 12:22:46 2012 From: stefan.debener at uni-oldenburg.de (Stefan Debener) Date: Thu, 06 Sep 2012 12:22:46 +0200 Subject: [FieldTrip] 1 post-doc and 1 PhD position in human auditory and motor neuroscience In-Reply-To: <50484CC9.2070601@uni-oldenburg.de> References: <5046A9C2.2020704@uni-oldenburg.de> <50484CC9.2070601@uni-oldenburg.de> Message-ID: <50487976.7040900@uni-oldenburg.de> Apologies to all for spoiling this list with a personal mail, Stefan Am 9/5/12 3:24 AM, schrieb Jochem Rieger: >> The Department of Applied Neurocognitive Psychology at Oldenburg >> University, Germany, offers a >> >> *Post-doctoral position (E13/TVL, 3 years plus) * >> >> and a >> >> *PhD position (0.5*E13/TVL, initially 2 years)* >> >> The lab focuses on the fields of neural coding of complex movements >> and neural coding of speech in the human brain with the aim of >> developing brain-machine-interfaces. >> >> To extend our interdisciplinary team we seek for highly motivated >> candidates with strong quantitative and experimental skills. The >> post-doctoral position requires a PhD or comparable degree and the >> PhD position requires a masters or comparable degree. The >> post-doctoral position is initially limited to three years after with >> an option for an extension to obtain habilitation (post-doctoral >> degree, similar to a lecturer qualification). Successful candidates >> will perform cutting edge research in one of the lab's foci and >> should have a background in one or more of the following fields: >> non-invasive or invasive human neurophysiology of the motor or >> auditory system, statistical learning, brain-machine-interfacing. The >> positions offer an excellent interdisciplinary working environment >> with opportunities for international exchange. The lab is involved in >> the EU-project BRACOG (brain controlled grasping) and we have a close >> collaboration with UC Berkeley, USA. The University of Oldenburg was >> recently awarded a Cluster of Excellence in hearing research. The >> Dept. of Psychology will offer an attractive scientific environment >> with access to research dedicated state-of-the-art approaches to >> human neurophysiological techniques (fMRI, NIRS, EEG, ECoG, and MEG). >> >> Electronic applications are preferred and can be send to: >> Professor Dr. Jochem Rieger: Jochem.rieger at uni-oldenburg.de >> >> >> Please send paper applications until September 30^th 2012 to: >> >> Margrit Jung >> >> Dept. of Applied Neurocognitive Psychology >> >> Institute of Psychology >> >> Oldenburg University >> >> 26111 Oldenburg >> >> Germany >> >> Applications should include your CV and a list of most recent >> publications. Applications for the post-doctoral position should >> include a research statement (max. 3 pages). The University of >> Oldenburg aims to employ more women in this area and therefore >> particularly welcomes applications from women. We also welcome >> applications from disabled persons. >> >> >> -- >> Prof. Dr. rer. nat. Jochem Rieger >> >> Applied Neurocognitive Knight Lab >> Psychology Helen Wills Neuroscience Institute >> Faculty V University of California >> Carl-von-Ossietzky University 132 Barker Hall >> 26111 Oldenburg Berkeley, CA 94720-3192 >> Germany USA >> >> Phone: +49(0)4417984533 >> Fax: +49(0)4417983865 >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Prof. Dr. Stefan Debener > Neuropsychology Lab > Department of Psychology > University of Oldenburg > D-26111 Oldenburg > Germany > > Office: A7 0-038 > Phone: +49-441-798-4271 > Fax: +49-441-798-5522 > Email:stefan.debener at uni-oldenburg.de > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Prof. Dr. Stefan Debener Neuropsychology Lab Department of Psychology University of Oldenburg D-26111 Oldenburg Germany Office: A7 0-038 Phone: +49-441-798-4271 Fax: +49-441-798-5522 Email: stefan.debener at uni-oldenburg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From landpt at gmail.com Thu Sep 6 12:25:47 2012 From: landpt at gmail.com (Ricardo Jorge) Date: Thu, 6 Sep 2012 11:25:47 +0100 Subject: [FieldTrip] Having troubles with Emotiv + Fieldtrip + Matlab Message-ID: Hello there, I'm new to Fieldtrip: I've been assigned to work with signals acquired by Emotiv in Matlab environment, specially in real-time - or at least almost real-time - so I can work and study these signals with my own Matlab's functions. However, here's the bad thing: we did not expect it to be that complicated to extract signals directly to Matlab. While searching for any module, program, anything I could find, to help our problem, I found Fieldtrip. Correct me if I am wrong, but it seems that it is able to stream/buffer from emotiv's sdk to matlab. The problem is that we do not have that much experience with compiling C programs, hence I am having a really hard time to understand what do you mean with: "Compilation We provide a simple Makefile for the MinGW compiler, but you will need the Emotiv SDK. Please go to the realtime/datasource/emotiv directory and type make or mingw32-make. Note that you might need to compile the libbuffer library first." Here's what I did so far: 1. I have installed Matlab r2011b 64-bit and Emotiv SDK Research Edition; 2. I installed MinGW and set the path of the /bin in environmental variables; 3. I downloaded all these files from: http://code.google.com/p/fieldtrip/source/browse/trunk/realtime/datasource/emotiv/?r=1742 4. Then I went cmd and tried to do: mingw32-make -f makefile.gcc SHARED=1 UNICODE=1 BUILD=release which obviously failed: it said it was missing a file "Ftbuffer.h". I assumed it was the libbuffer library, however I can't seem to find it anywhere in the Internet (just some site that would ask me to install Makestuff application, which I did and was unsuccessful. I found a "buffer" folder in fieldtrip release but I dont think it's that. Hence I tried to download the Ftbuffer.h itself from internet and put it in the folder where emotiv2ft was. It worked, but then it started to ask others files.... and more.. and more.. So, obviously I'm stuck right here. Can you help me right here? What should I do? Have I done something wrong? I've read this discussion list and found one thread quite related to this - but his problem was not having research edition, which in fact, I do have it. I'm sorry bothering you with probably authentic beginner questions, but as I said, I only have high experience with Matlab. Best Regards, Ricardo From Lilla.Magyari at mpi.nl Thu Sep 6 14:45:55 2012 From: Lilla.Magyari at mpi.nl (Lilla.Magyari at mpi.nl) Date: Thu, 6 Sep 2012 14:45:55 +0200 (CEST) Subject: [FieldTrip] Having troubles with Emotiv + Fieldtrip + Matlab In-Reply-To: References: Message-ID: <49788.131.174.45.70.1346935555.squirrel@131.174.45.70> Hello Ricardo, I haven't tried to work with Emotiv, but I see an FtBuffer.h file in the latest version of FieldTrip in the realtime/src/buffer/cpp. I hope this helps. (It is also not clear for me if you downloaded only files related to emotive, or also the whole FieldTrip package (this latest is probably useful)). Best, Lilla > Hello there, > > I'm new to Fieldtrip: I've been assigned to work with signals acquired > by Emotiv in Matlab environment, specially in real-time - or at least > almost real-time - so I can work and study these signals with my own > Matlab's functions. However, here's the bad thing: we did not expect > it to be that complicated to extract signals directly to Matlab. > > While searching for any module, program, anything I could find, to > help our problem, I found Fieldtrip. Correct me if I am wrong, but it > seems that it is able to stream/buffer from emotiv's sdk to matlab. > > The problem is that we do not have that much experience with compiling > C programs, hence I am having a really hard time to understand what do > you mean with: > > "Compilation > We provide a simple Makefile for the MinGW compiler, but you will need > the Emotiv SDK. Please go to the realtime/datasource/emotiv directory > and type make or mingw32-make. Note that you might need to compile the > libbuffer library first." > > > Here's what I did so far: > > 1. I have installed Matlab r2011b 64-bit and Emotiv SDK Research Edition; > > 2. I installed MinGW and set the path of the /bin in environmental > variables; > > 3. I downloaded all these files from: > http://code.google.com/p/fieldtrip/source/browse/trunk/realtime/datasource/emotiv/?r=1742 > > 4. Then I went cmd and tried to do: mingw32-make -f makefile.gcc > SHARED=1 UNICODE=1 BUILD=release > which obviously failed: it said it was missing a file "Ftbuffer.h". I > assumed it was the libbuffer library, however I can't seem to find it > anywhere in the Internet (just some site that would ask me to install > Makestuff application, which I did and was unsuccessful. > I found a "buffer" folder in fieldtrip release but I dont think it's that. > Hence I tried to download the Ftbuffer.h itself from internet and put > it in the folder where emotiv2ft was. It worked, but then it started > to ask others files.... and more.. and more.. > > So, obviously I'm stuck right here. > Can you help me right here? What should I do? Have I done something wrong? > I've read this discussion list and found one thread quite related to > this - but his problem was not having research edition, which in fact, > I do have it. > > I'm sorry bothering you with probably authentic beginner questions, > but as I said, I only have high experience with Matlab. > > Best Regards, > Ricardo > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From r.oostenveld at donders.ru.nl Thu Sep 6 15:05:32 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 6 Sep 2012 15:05:32 +0200 Subject: [FieldTrip] Having troubles with Emotiv + Fieldtrip + Matlab In-Reply-To: References: Message-ID: <094D4EED-A39B-4788-BB7B-9C801AF65B78@donders.ru.nl> Dear Ricardo, We provide the full source code for you to investigate, modify and recompile, but we also provide pre-compiled binaries that you shoiuld be able to use to just get it to run. Rather than just grabbing a small section of the fieldtrip code, which you seem to have done, I suggest you get a complete fieldtrip version from http://fieldtrip.fcdonders.nl/download or through SVN (you want the complete trunk). In the fieldtrip/realtime/bin/win32 directory you will find the compiled emotiv2ft.exe program (it is present both in th ezip file from the ftp, as well as in the svn version). The emotiv2ft.exe application copies the data from the emotiv dll into the FT buffer, where you can access it from MATLAB using the methods described here http://fieldtrip.fcdonders.nl/getting_started/realtime for end-users and here http://fieldtrip.fcdonders.nl/development/realtime for developers. Hope this helps, Robert On 6 Sep 2012, at 12:25, Ricardo Jorge wrote: > Hello there, > > I'm new to Fieldtrip: I've been assigned to work with signals acquired > by Emotiv in Matlab environment, specially in real-time - or at least > almost real-time - so I can work and study these signals with my own > Matlab's functions. However, here's the bad thing: we did not expect > it to be that complicated to extract signals directly to Matlab. > > While searching for any module, program, anything I could find, to > help our problem, I found Fieldtrip. Correct me if I am wrong, but it > seems that it is able to stream/buffer from emotiv's sdk to matlab. > > The problem is that we do not have that much experience with compiling > C programs, hence I am having a really hard time to understand what do > you mean with: > > "Compilation > We provide a simple Makefile for the MinGW compiler, but you will need > the Emotiv SDK. Please go to the realtime/datasource/emotiv directory > and type make or mingw32-make. Note that you might need to compile the > libbuffer library first." > > > Here's what I did so far: > > 1. I have installed Matlab r2011b 64-bit and Emotiv SDK Research Edition; > > 2. I installed MinGW and set the path of the /bin in environmental variables; > > 3. I downloaded all these files from: > http://code.google.com/p/fieldtrip/source/browse/trunk/realtime/datasource/emotiv/?r=1742 > > 4. Then I went cmd and tried to do: mingw32-make -f makefile.gcc > SHARED=1 UNICODE=1 BUILD=release > which obviously failed: it said it was missing a file "Ftbuffer.h". I > assumed it was the libbuffer library, however I can't seem to find it > anywhere in the Internet (just some site that would ask me to install > Makestuff application, which I did and was unsuccessful. > I found a "buffer" folder in fieldtrip release but I dont think it's that. > Hence I tried to download the Ftbuffer.h itself from internet and put > it in the folder where emotiv2ft was. It worked, but then it started > to ask others files.... and more.. and more.. > > So, obviously I'm stuck right here. > Can you help me right here? What should I do? Have I done something wrong? > I've read this discussion list and found one thread quite related to > this - but his problem was not having research edition, which in fact, > I do have it. > > I'm sorry bothering you with probably authentic beginner questions, > but as I said, I only have high experience with Matlab. > > Best Regards, > Ricardo > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Jan.Hirschmann at med.uni-duesseldorf.de Thu Sep 6 15:06:02 2012 From: Jan.Hirschmann at med.uni-duesseldorf.de (Jan.Hirschmann at med.uni-duesseldorf.de) Date: Thu, 6 Sep 2012 15:06:02 +0200 Subject: [FieldTrip] phase difference between sources Message-ID: <72E993C35FB11743B79FF9286E5B6D8B04617307@Mail2-UKD.VMED.UKD> Dear fieldtrip experts, I was wondering how to get the mean phase difference between two sources A and B at a particular frequency f (mean across data segments). My idea was to use dics and to say cfg.refdip=A and cfg.keepcsd='yes'. Then I would get C, the cross spectral density between A and B, which is a 3x3 matrix with complex entries. Joachim Gross wrote that one could estimate csd in the dominant direction as the trace of C. So I guess I could get the phase difference by angle(trace(C)). Is this correct? If I wanted to use SVD to estimate the dominant direction instead of the trace, how would I get the phase difference then? And finally, if I wanted to have coherence not with the dipole orientation that maximizes power but with the orientation that maximizes phase difference, how would that work? Thanks for any remarks! Jan -- Jan Hirschmann MSc Neuroscience Institute of Clinical Neuroscience and Medical Psychology Heinrich Heine University Düsseldorf Universitätsstr. 1 40225 Düsseldorf Germany Tel: +49 (0)211 81 18415 Fax: +49 (0)211 81 19033 -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Sep 6 15:10:28 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 6 Sep 2012 15:10:28 +0200 Subject: [FieldTrip] left to right inversion after source interpolation In-Reply-To: <44E1ACF5-2C6D-4BA2-8FA7-B0886FB8AF20@uke.uni-hamburg.de> References: <075a92dd-147e-45e9-a4d1-726999c597b1@thalamus_p> <44E1ACF5-2C6D-4BA2-8FA7-B0886FB8AF20@uke.uni-hamburg.de> Message-ID: <7B18D5B7-9B69-4E09-AFD8-3B6D5B30D6A0@donders.ru.nl> Hi Fred, On http://fieldtrip.fcdonders.nl/faq/why_does_my_anatomical_mri_show_upside-down_when_plotting_it_with_ft_sourceplot there is an explanation to a related question. Also in your case FT_VOLUMERSLICE might be of use. See also http://fieldtrip.fcdonders.nl/faq/what_is_the_plotting_convention_for_anatomical_mris best Robert On 5 Sep 2012, at 16:30, Kathrin Müsch wrote: > Dear Fred, > > I encountered a similar thing a while ago and it was because spm8 seems to plot in radiological convention (i.e. left is plotted right and vice versa - http://mailman.science.ru.nl/pipermail/fieldtrip/2012-May/005229.html) so you're plots should actually be correct. > > If you use cfg.interactive = 'yes'; and click into the activated side of the brain, the first coordinate should be negative because you are in the left hemisphere. > > Hope that helps, > Kathrin > > > Am 05.09.2012 um 14:47 schrieb Frederic Roux: > >> Dear fieldtrip users, >> >> I have noticed that after interpolating a dummy source volume with ft_sourceinterpolate, >> voxels that were located in the left side of the volume, apear to be located in the right >> side of the volume. >> >> The code that I use is as following: >> >> dummy is a dummy structure of an lcmv beamformer map with the fields >> >> dummy = >> dim : [15 18 17] >> time: [1x272662 double] >> pos: [4590x3 double] >> inside: [1x2144 double] >> outside: [1x2446 double] >> method: 'average' >> avg: [1x1 struct] >> >> voxpos = dummy.pos(dummy.inside,1);% get the coordinates of voxels inside the volume >> dummy.avg.pow(dummy.inside(sign(voxpos)==1)) = 0; % set activity in the left hemisphere to 0 >> dummy.avg.pow(dummy.inside(sign(voxpos)==-1)) = 1; % set activity in the left hemisphere to 1 >> >> cfg = []; >> cfg.parameters = 'all'; >> >> int_dummy = ft_sourceinterpolate(cfg,dummy,template_MNI_mri); >> >> cfg = []; >> cfg.funparameter = 'avg.pow'; >> cfg.method = 'ortho'; >> >> %plot the non-interpolated volume >> figure; >> ft_sourceplot(cfg,dummy); >> >> %plot the interpolated volume >> figure; >> ft_sourceplot(cfg,int_dummy); >> >> As you can see from the figure in the attachement, the voxels that >> corresponded to the left hemisphere prior to the interpolation, >> no appear to be located in the rigth hemisphere. >> >> This is also something that I have observed in real data. >> >> Does anybody have an explanation why this is happening? >> Am I doing something wrong? >> >> Best, >> >> Fred >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): > > Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg > > Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From landpt at gmail.com Thu Sep 6 17:48:27 2012 From: landpt at gmail.com (Ricardo Jorge) Date: Thu, 6 Sep 2012 16:48:27 +0100 Subject: [FieldTrip] Having troubles with Emotiv + Fieldtrip + Matlab Message-ID: Hello there, Thanks! I'm a feeling a bit shamed because now they did seem like stupid questions but it really worked now - I had to read the walkthough to understand some definitions, and then I read your replies about the emotiv executable and really worked now! I was not understanding why I would need to compile again if there was an executable - I thought it was related to the fact that EPOC wouldn't allow the redistribution of their dlls or something like that, I don't know. Thanks again. Best, Ricardo Jorge From daria.laptinskaya at googlemail.com Thu Sep 6 18:52:44 2012 From: daria.laptinskaya at googlemail.com (Daria Laptinskaya) Date: Thu, 6 Sep 2012 18:52:44 +0200 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> Message-ID: Thanks you all for the answers! It seems to be a problem with reading the raw.-files. My collegue found a formula, maybe we can use it for microvolt-scaling. @Joe: It would be a great helf, if you could have a look at one of the files. Can I send you a dropbox-link? Best, Daria 2012/9/6 Joseph Dien > The Simple Binary (.raw) files don't get corrected for gain when imported > (I helped write them). I've experienced occasional unpredictable bugs with > NetStation export routines where the files are generated with amplitudes > many times too large, even with text format files. It's a bit > disconcerting to say the least. I could take a look at your files if you'd > like confirmation. > > Joe > > On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis > wrote: > > Hi Daria, > > Also, did you try looking at your raw data (so before the ERPs are made) > in FieldTrip and in Net Station? So open your .raw data in NetStation. You > can just look at a random participant's data, and check if the scale is the > same. I'm pretty sure no amplification takes place when reading in the data > into FieldTrip, this check can confirm that. Hope this helps, and let us > know what you find. > > Cheers, > Ingrid > > > On 9/3/2012 1:35 PM, Robert Oostenveld wrote: > > Hi Daria, > > There might indeed be an incompatibility in the gain value applied to > the data. > > If you are able to export the data using the EGI software in another > format (e.g. EDF), you could read them both into FieldTrip and compare the > timecourse aplitudes to check whether they are different. In case they are, > I suggest to involve EGI support. They are aware of the FieldTrip reading > functions and will know much more about the internals of their various file > formats. > > best regards > Robert > > > > > On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: > > Dear Fieldtrippers, > > I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip > toolbox. > The ERPs look perfect. > The 'only' problem is, that my signals look to strong. > It looks like if I get amplitutes (average) until 70 µV. > I think it must be an intern amplifier for the signals. > > Does anyone know this problem with EGI-data? > > Or does anyone know, where I can see the amplifier? > > > > Greetings, > Daria _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Ingrid Nieuwenhuis PhD > Postdoctoral Fellow > Sleep and Neuroimaging Laboratory > Department of Psychology > University of California, Berkeley > California 94720-1650 > Tolman Hall, room 5305 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mollison at gmail.com Thu Sep 6 19:01:42 2012 From: matt.mollison at gmail.com (Matt Mollison) Date: Thu, 6 Sep 2012 11:01:42 -0600 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> Message-ID: Joe, A few related questions: Does using the "calibrate data" option when exporting to raw (simple binary) correct for gain? Or is there a different solution/recommendation? Does exporting to MFF (Net Station 4.5.x only) or EGIS have this issue? I tend to use EGIS (faster to read than raw) and have no recollection of seeing unusually large voltages. Thanks, Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ On Wed, Sep 5, 2012 at 7:17 PM, Joseph Dien wrote: > The Simple Binary (.raw) files don't get corrected for gain when imported > (I helped write them). I've experienced occasional unpredictable bugs with > NetStation export routines where the files are generated with amplitudes > many times too large, even with text format files. It's a bit > disconcerting to say the least. I could take a look at your files if you'd > like confirmation. > > Joe > > On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis > wrote: > > Hi Daria, > > Also, did you try looking at your raw data (so before the ERPs are made) > in FieldTrip and in Net Station? So open your .raw data in NetStation. You > can just look at a random participant's data, and check if the scale is the > same. I'm pretty sure no amplification takes place when reading in the data > into FieldTrip, this check can confirm that. Hope this helps, and let us > know what you find. > > Cheers, > Ingrid > > > On 9/3/2012 1:35 PM, Robert Oostenveld wrote: > > Hi Daria, > > There might indeed be an incompatibility in the gain value applied to > the data. > > If you are able to export the data using the EGI software in another > format (e.g. EDF), you could read them both into FieldTrip and compare the > timecourse aplitudes to check whether they are different. In case they are, > I suggest to involve EGI support. They are aware of the FieldTrip reading > functions and will know much more about the internals of their various file > formats. > > best regards > Robert > > > > > On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: > > Dear Fieldtrippers, > > I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip > toolbox. > The ERPs look perfect. > The 'only' problem is, that my signals look to strong. > It looks like if I get amplitutes (average) until 70 µV. > I think it must be an intern amplifier for the signals. > > Does anyone know this problem with EGI-data? > > Or does anyone know, where I can see the amplifier? > > > > Greetings, > Daria _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Ingrid Nieuwenhuis PhD > Postdoctoral Fellow > Sleep and Neuroimaging Laboratory > Department of Psychology > University of California, Berkeley > California 94720-1650 > Tolman Hall, room 5305 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jdien07 at mac.com Fri Sep 7 02:58:43 2012 From: jdien07 at mac.com (Joseph Dien) Date: Thu, 06 Sep 2012 20:58:43 -0400 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> Message-ID: <293829E7-6D3C-4ED9-B592-5981F73098F8@mac.com> By all means! Joe On Sep 6, 2012, at 12:52 PM, Daria Laptinskaya wrote: > Thanks you all for the answers! > It seems to be a problem with reading the raw.-files. > My collegue found a formula, maybe we can use it for microvolt-scaling. > > @Joe: It would be a great helf, if you could have a look at one of the files. > Can I send you a dropbox-link? > > Best, > Daria > > > 2012/9/6 Joseph Dien > The Simple Binary (.raw) files don't get corrected for gain when imported (I helped write them). I've experienced occasional unpredictable bugs with NetStation export routines where the files are generated with amplitudes many times too large, even with text format files. It's a bit disconcerting to say the least. I could take a look at your files if you'd like confirmation. > > Joe > > On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis wrote: > >> Hi Daria, >> >> Also, did you try looking at your raw data (so before the ERPs are made) in FieldTrip and in Net Station? So open your .raw data in NetStation. You can just look at a random participant's data, and check if the scale is the same. I'm pretty sure no amplification takes place when reading in the data into FieldTrip, this check can confirm that. Hope this helps, and let us know what you find. >> >> Cheers, >> Ingrid >> >> >> On 9/3/2012 1:35 PM, Robert Oostenveld wrote: >>> Hi Daria, >>> >>> There might indeed be an incompatibility in the gain value applied to the data. >>> >>> If you are able to export the data using the EGI software in another format (e.g. EDF), you could read them both into FieldTrip and compare the timecourse aplitudes to check whether they are different. In case they are, I suggest to involve EGI support. They are aware of the FieldTrip reading functions and will know much more about the internals of their various file formats. >>> >>> best regards >>> Robert >>> >>> >>> >>> >>> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: >>> >>>> Dear Fieldtrippers, >>>> >>>> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip toolbox. >>>> The ERPs look perfect. >>>> The 'only' problem is, that my signals look to strong. >>>> It looks like if I get amplitutes (average) until 70 µV. >>>> I think it must be an intern amplifier for the signals. >>>> Does anyone know this problem with EGI-data? >>>> >>>> Or does anyone know, where I can see the amplifier? >>>> >>>> >>>> >>>> >>>> Greetings, >>>> >>>> Daria _______________________________________________ >>>> 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 >> >> -- >> Ingrid Nieuwenhuis PhD >> Postdoctoral Fellow >> Sleep and Neuroimaging Laboratory >> Department of Psychology >> University of California, Berkeley >> California 94720-1650 >> Tolman Hall, room 5305 >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07 at mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// -------------- next part -------------- An HTML attachment was scrubbed... URL: From jdien07 at mac.com Fri Sep 7 03:07:12 2012 From: jdien07 at mac.com (Joseph Dien) Date: Thu, 06 Sep 2012 21:07:12 -0400 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> Message-ID: <77D46473-6907-4AC1-96E1-F51756C119C0@mac.com> I don't recall ever seeing this problem with EGIS files, which is one of the reasons I prefer using this file format despite EGI's preference for newer Simple Binary format, but it's an unpredictable bug so I can't say it can't happen. I also can't say which versions of NetStation it happens with. It may have been fixed. I'm still trying to test out MFF so can't say anything about it. I had problems with the FieldTrip code for reading segmented MFF files (which is what I'm interested in). I also had trouble with writing them out from NetStation so I don't have a valid segmented test file and I'm still waiting for EGI to make one available so I can work them out. The simple binary file format (this is the original name for the EGI .raw file format and I prefer to use it over ".raw" as the BESA .raw file format is actually the .egis file format so it can get confusing) doesn't actually have separate calibration information for the channels (unlike EGIS), just one single gain value and no zeros values. So basically the simple binary format makes the assumption that calibration corrections have already been performed prior to generating the file. My understanding is that this is indeed what the "calibrate data" option is doing, but you'd have to confirm with EGI. Joe -------------------------------------------------------------------------------- On Sep 6, 2012, at 1:01 PM, Matt Mollison wrote: > Joe, > > A few related questions: > > Does using the "calibrate data" option when exporting to raw (simple binary) correct for gain? Or is there a different solution/recommendation? > Does exporting to MFF (Net Station 4.5.x only) or EGIS have this issue? I tend to use EGIS (faster to read than raw) and have no recollection of seeing unusually large voltages. > > Thanks, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > > On Wed, Sep 5, 2012 at 7:17 PM, Joseph Dien wrote: > The Simple Binary (.raw) files don't get corrected for gain when imported (I helped write them). I've experienced occasional unpredictable bugs with NetStation export routines where the files are generated with amplitudes many times too large, even with text format files. It's a bit disconcerting to say the least. I could take a look at your files if you'd like confirmation. > > Joe > > On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis wrote: > >> Hi Daria, >> >> Also, did you try looking at your raw data (so before the ERPs are made) in FieldTrip and in Net Station? So open your .raw data in NetStation. You can just look at a random participant's data, and check if the scale is the same. I'm pretty sure no amplification takes place when reading in the data into FieldTrip, this check can confirm that. Hope this helps, and let us know what you find. >> >> Cheers, >> Ingrid >> >> >> On 9/3/2012 1:35 PM, Robert Oostenveld wrote: >>> Hi Daria, >>> >>> There might indeed be an incompatibility in the gain value applied to the data. >>> >>> If you are able to export the data using the EGI software in another format (e.g. EDF), you could read them both into FieldTrip and compare the timecourse aplitudes to check whether they are different. In case they are, I suggest to involve EGI support. They are aware of the FieldTrip reading functions and will know much more about the internals of their various file formats. >>> >>> best regards >>> Robert >>> >>> >>> >>> >>> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: >>> >>>> Dear Fieldtrippers, >>>> >>>> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip toolbox. >>>> The ERPs look perfect. >>>> The 'only' problem is, that my signals look to strong. >>>> It looks like if I get amplitutes (average) until 70 µV. >>>> I think it must be an intern amplifier for the signals. >>>> Does anyone know this problem with EGI-data? >>>> >>>> Or does anyone know, where I can see the amplifier? >>>> >>>> >>>> >>>> >>>> Greetings, >>>> >>>> Daria _______________________________________________ >>>> 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 >> >> -- >> Ingrid Nieuwenhuis PhD >> Postdoctoral Fellow >> Sleep and Neuroimaging Laboratory >> Department of Psychology >> University of California, Berkeley >> California 94720-1650 >> Tolman Hall, room 5305 >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07 at mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// -------------- next part -------------- An HTML attachment was scrubbed... URL: From polomacnenad at gmail.com Fri Sep 7 12:36:05 2012 From: polomacnenad at gmail.com (Nenad Polomac) Date: Fri, 7 Sep 2012 12:36:05 +0200 Subject: [FieldTrip] problem with FT_MEGPLANAR Message-ID: Dear all, I would like to apply FT_MEGPLANAR on ERF data obtain from FT_TIMELOCKANALYSIS. According to tutorial that should be possible. This is the error I get: Error using ft_checkdata (line 376) This function requires ctf151, ctf275, bti148, bti248, itab153, yokogawa160 or yokogawa64 data as input, but you are giving ctf275 data. Error in ft_megplanar (line 109) data = ft_checkdata(data, 'datatype', {'raw' 'freq'}, 'feedback', 'yes', 'hassampleinfo', 'yes', 'ismeg', 'yes', 'senstype', {'ctf151', 'ctf275', 'bti148', 'bti248', 'itab153', 'yokogawa160', 'yokoga This is how looks like output form FT_TIMELOCKANALYSIS. On this data I would like to apply FT_MEGPLANAR. average32 = avg: [271x1440 double] var: [271x1440 double] time: [1x1440 double] dof: [271x1440 double] label: {271x1 cell} trial: [75x271x1440 double] dimord: 'rpt_chan_time' trialinfo: [75x1 double] cfg: [1x1 struct] My code: cfg = []; cfg.method = 'template'; cfg.template = 'CTF275_neighb.mat'; neighbours = ft_prepare_neighbours(cfg, grad); cfg=[]; cfg.neighbours=neighbours; cfg.planarmethod = 'orig'; cfg.trials = 'all'; planar32 = ft_megplanar(cfg, average32); *grad is structure obtained earlier with FT_PREPROCESSING Furthermore, I would also like to apply FT_MEGPLANAR on the other data obtained from ft_rejectcomponent (after ICA rejection) and this doesn't work as well. This error is the same as one I mentioned above. Thank you in advance! Nenad -------------- next part -------------- An HTML attachment was scrubbed... URL: From Markus.Butz at uni-duesseldorf.de Fri Sep 7 14:33:22 2012 From: Markus.Butz at uni-duesseldorf.de (Markus Butz) Date: Fri, 07 Sep 2012 13:33:22 +0100 Subject: [FieldTrip] Frontiers in Human Neuroscience - Research Topic: The Functional Role of Gamma Band Activity - Lessons from MEG Message-ID: <7620e04b44e3.5049f7a2@uni-duesseldorf.de> Dear FieldTrip list We are pleased to announce an upcoming Research Topic in Frontiers in Human Neuroscience on “The Functional Role of Gamma Band Activity – Lessons From MEG”. Further information can be found here: http://www.frontiersin.org/human_neuroscience/researchtopics/the_functional_role_of_gamma_b/962 Deadline for abstract submission: 01 Dec 2012 Deadline for full article submission: 01 Feb 2013 We are looking forward to your contributions! Please don’t hesitate to get in contact in case you have any further questions. Thank you very much for your consideration Krish & Markus -------------- next part -------------- An HTML attachment was scrubbed... URL: From tim.curran at Colorado.EDU Fri Sep 7 22:58:59 2012 From: tim.curran at Colorado.EDU (Tim Curran) Date: Fri, 7 Sep 2012 14:58:59 -0600 Subject: [FieldTrip] Colorado Computational Cognition Faculty Position In-Reply-To: References: Message-ID: <59F8E65D-69AE-4FCD-A985-1D0A28659020@colorado.edu> Computational Approaches to Cognition, Institute of Cognitive Science Tenure Track Position The Institute of Cognitive Science at the University of Colorado invites applications for a full-time tenure-track position in computational approaches to cognitive and/or affective processes at the assistant professor level with a starting date of Fall 2013. The Institute is a multidisciplinary unit with representation from the departments of Psychology & Neuroscience, Computer Science, Education, Philosophy, Linguistics, Architecture & Planning, and Speech, Language & Hearing Sciences. We seek applicants with a strong research program in theoretical and technical aspects of computational science. preferably with prior experience or interest in integrating cognitive science with state-of-the-art computational approaches. For example, individuals who utilize machine learning and statistical techniques to understand cognitive processes, such as language or learning, or to analyze high dimensional data from methods, such as functional magnetic resonance imaging, will be competitive for the position. Successful applicants could come from one of several fields, including cognitive science/cognitive neuroscience, computer science, statistics, biostatistics, physics, or other related disciplines. An ability for and commitment to interdisciplinary research is a priority, as is an approach that both exploits existing computational techniques to address questions relevant to cognitive science and advances machine-learning theory. Duties include research, research supervision, service, as well as graduate and undergraduate teaching. Applicants are directed to the CU online job application website: www.jobsatcu.com; Job Posting Number 818695. At this site you will be asked for a curriculum vitae, copies of representative publications, a teaching statement, a research summary, and letter from three referees. For fullest consideration, please apply by September 24th, 2012. Applications will continue to be accepted after this date until the position is filled. Email inquiries may be sent to Donna.Caccamise at colorado.edu. The University of Colorado is an Equal Opportunity Employer committed to building a diverse workforce. We encourage applications from women, racial and ethnic minorities, individuals with disabilities and veterans. Alternative formats of this ad can be provided upon request for individuals with disabilities by contacting the ADA Coordinator at hr-ada at colorado.edu. The University of Colorado Boulder conducts background checks on all final applicants being considered for employment. From jdien07 at mac.com Mon Sep 10 02:44:44 2012 From: jdien07 at mac.com (Joseph Dien) Date: Sun, 09 Sep 2012 20:44:44 -0400 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: <77D46473-6907-4AC1-96E1-F51756C119C0@mac.com> References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> <77D46473-6907-4AC1-96E1-F51756C119C0@mac.com> Message-ID: <3B494ED9-B6C3-46A3-840C-8EEEDAA85E5E@mac.com> Hey Daria, glad you were able to get it worked out! Thank Matt for his reminder (below) about the calibration option. Cheers! Joe > Hi Joe, > > > > I didn’t know that there is a function like this. > > The most of my colleagues use the RAW.-files they get from the file-exporter without problems. > > Not even NetStation-support could give me an answer. > > So I thought, it must be a problem between NetStation and fieldtrip. > > Because of your tip I opened an original datafile and tried to save a copy of the file. > > Doing so NetStation offers a possibility to ‘convert to microvolts’ and create a .ses –datafile. > > The .raw-files I get this way have microvolt as unit. > > I compared the signals I get this way with the signals I get by using the formula (5000 mircovolts / (2^16 bits) I send you. They are almost the same-that’s great!!! > > It seems to work now. > > Thank you very much!!! You were a great help!!! > > > Cheers, > > Daria > On Sep 6, 2012, at 9:07 PM, Joseph Dien wrote: > I don't recall ever seeing this problem with EGIS files, which is one of the reasons I prefer using this file format despite EGI's preference for newer Simple Binary format, but it's an unpredictable bug so I can't say it can't happen. I also can't say which versions of NetStation it happens with. It may have been fixed. I'm still trying to test out MFF so can't say anything about it. I had problems with the FieldTrip code for reading segmented MFF files (which is what I'm interested in). I also had trouble with writing them out from NetStation so I don't have a valid segmented test file and I'm still waiting for EGI to make one available so I can work them out. The simple binary file format (this is the original name for the EGI .raw file format and I prefer to use it over ".raw" as the BESA .raw file format is actually the .egis file format so it can get confusing) doesn't actually have separate calibration information for the channels (unlike EGIS), just one single gain value and no zeros values. So basically the simple binary format makes the assumption that calibration corrections have already been performed prior to generating the file. My understanding is that this is indeed what the "calibrate data" option is doing, but you'd have to confirm with EGI. > > Joe > > > -------------------------------------------------------------------------------- > > On Sep 6, 2012, at 1:01 PM, Matt Mollison wrote: > >> Joe, >> >> A few related questions: >> >> Does using the "calibrate data" option when exporting to raw (simple binary) correct for gain? Or is there a different solution/recommendation? >> Does exporting to MFF (Net Station 4.5.x only) or EGIS have this issue? I tend to use EGIS (faster to read than raw) and have no recollection of seeing unusually large voltages. >> >> Thanks, >> Matt >> >> -- >> Univ. of Colorado at Boulder >> Dept. of Psychology and Neuroscience >> matthew.mollison at colorado.edu >> http://psych.colorado.edu/~mollison/ >> >> On Wed, Sep 5, 2012 at 7:17 PM, Joseph Dien wrote: >> The Simple Binary (.raw) files don't get corrected for gain when imported (I helped write them). I've experienced occasional unpredictable bugs with NetStation export routines where the files are generated with amplitudes many times too large, even with text format files. It's a bit disconcerting to say the least. I could take a look at your files if you'd like confirmation. >> >> Joe >> >> On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis wrote: >> >>> Hi Daria, >>> >>> Also, did you try looking at your raw data (so before the ERPs are made) in FieldTrip and in Net Station? So open your .raw data in NetStation. You can just look at a random participant's data, and check if the scale is the same. I'm pretty sure no amplification takes place when reading in the data into FieldTrip, this check can confirm that. Hope this helps, and let us know what you find. >>> >>> Cheers, >>> Ingrid >>> >>> >>> On 9/3/2012 1:35 PM, Robert Oostenveld wrote: >>>> Hi Daria, >>>> >>>> There might indeed be an incompatibility in the gain value applied to the data. >>>> >>>> If you are able to export the data using the EGI software in another format (e.g. EDF), you could read them both into FieldTrip and compare the timecourse aplitudes to check whether they are different. In case they are, I suggest to involve EGI support. They are aware of the FieldTrip reading functions and will know much more about the internals of their various file formats. >>>> >>>> best regards >>>> Robert >>>> >>>> >>>> >>>> >>>> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: >>>> >>>>> Dear Fieldtrippers, >>>>> >>>>> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip toolbox. >>>>> The ERPs look perfect. >>>>> The 'only' problem is, that my signals look to strong. >>>>> It looks like if I get amplitutes (average) until 70 µV. >>>>> I think it must be an intern amplifier for the signals. >>>>> Does anyone know this problem with EGI-data? >>>>> >>>>> Or does anyone know, where I can see the amplifier? >>>>> >>>>> >>>>> >>>>> >>>>> Greetings, >>>>> >>>>> Daria _______________________________________________ >>>>> 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 >>> >>> -- >>> Ingrid Nieuwenhuis PhD >>> Postdoctoral Fellow >>> Sleep and Neuroimaging Laboratory >>> Department of Psychology >>> University of California, Berkeley >>> California 94720-1650 >>> Tolman Hall, room 5305 >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, >> Senior Research Scientist >> University of Maryland >> >> E-mail: jdien07 at mac.com >> Phone: 301-226-8848 >> Fax: 301-226-8811 >> http://joedien.com// >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07 at mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// -------------- next part -------------- An HTML attachment was scrubbed... URL: From sahand.babapoor at gmail.com Mon Sep 10 02:49:31 2012 From: sahand.babapoor at gmail.com (sahand babapoor) Date: Sun, 9 Sep 2012 20:49:31 -0400 Subject: [FieldTrip] Using WPLI od WPLI-debiased to do the coherence analysis Message-ID: Hi all, I am trying to do coherency analysis between ACC and FEF. I have tried both WPLI and WPLI-debiased methods to do the analysis. When I am using WPLI I find a very nice coherence pattern between ACC and FEF in the frequencies between ~11Hz to 20 Hz. However, when I am using WPLI-debiased method, the previous WPLI coherence pattern disappears and breaks into many sparse clusters across many time points and frequencies. Is there a way to know which method is the best for me. I should note that I am recording using tungsten microelectrodes advanced into the brain. I would appreciate if your help. Best, Sahand -------------- next part -------------- An HTML attachment was scrubbed... URL: From ivano_triggiani at yahoo.it Mon Sep 10 12:27:09 2012 From: ivano_triggiani at yahoo.it (Ivano Triggiani) Date: Mon, 10 Sep 2012 11:27:09 +0100 (BST) Subject: [FieldTrip] about overlap in PSD calculation In-Reply-To: References: Message-ID: <1347272829.31720.YahooMailNeo@web133103.mail.ir2.yahoo.com> Hi all. How can I obtain informations about the kind of overlapping performed by fiedltrip implemented method to obtain a Power Spectral Density ? I need to compare fieldtrip PSD with another spectral density, so I need to be sure of everything. I found docs about tapering, but I don't understand if using a kind of tapering the overlapping is given. Ivano   ------------------------------------------------------------------------ "No man can wear one face to himself and another to the multitude, without finally getting bewildered as to which one is true." Nathaniel Hawthorne ________________________________ Da: "fieldtrip-request at science.ru.nl" A: fieldtrip at science.ru.nl Inviato: Lunedì 10 Settembre 2012 12:00 Oggetto: fieldtrip Digest, Vol 22, Issue 17 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. Using WPLI od WPLI-debiased to do the coherence analysis       (sahand babapoor) ---------------------------------------------------------------------- Message: 1 Date: Sun, 9 Sep 2012 20:49:31 -0400 From: sahand babapoor To: fieldtrip at science.ru.nl Subject: [FieldTrip] Using WPLI od WPLI-debiased to do the coherence     analysis Message-ID:     Content-Type: text/plain; charset="iso-8859-1" Hi all, I am trying to do coherency analysis between ACC and FEF. I have tried both WPLI and WPLI-debiased methods to do the analysis. When I am using WPLI I find a very nice coherence pattern between ACC and FEF in the frequencies between ~11Hz to 20 Hz. However, when I am using WPLI-debiased method, the previous WPLI coherence pattern disappears and  breaks into many sparse clusters across many time points and frequencies. Is there a way to know which method is the best for me. I should note that I am recording using tungsten microelectrodes advanced into the brain. I would appreciate if your help. Best, Sahand -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip End of fieldtrip Digest, Vol 22, Issue 17 ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From bherrmann at cbs.mpg.de Mon Sep 10 13:16:09 2012 From: bherrmann at cbs.mpg.de (=?utf-8?Q?Bj=C3=B6rn_Herrmann?=) Date: Mon, 10 Sep 2012 13:16:09 +0200 (CEST) Subject: [FieldTrip] real-value spatial filter from FFT dipole localization? In-Reply-To: <380027886.2137.1347269068602.JavaMail.root@zimbra> Message-ID: <1396322041.3317.1347275769488.JavaMail.root@zimbra> Dear fieldtrip users, maybe someone can point me in the right direction. I try to obtain a spatial filter from localizing the sources of an auditory 3Hz peak in my FFT spectrum. I would like to apply the filter to my single trial real data, i.e. basically reducing my 204 gradiometer channels (neuromag system) to one or two channels in source space. I was using DICS beamformer and cfg.realfilter = 'yes' but the source localization results (NAI) looked not too well compared to the nice auditory gradiometer topographies. I then used ft_dipolefitting, however, I have trouble understanding the output. This is where I wondered whether someone could help me, in telling whether it is possible to obtain a real-value spatial filter from this: source = label: {204x1 cell} dip: [1x1 struct] Vdata: [204x408 double] Vmodel: [204x408 double] freq: 3 dimord: 'chan_freq' grad: [1x1 struct] cfg: [1x1 struct] source.dip = pos: [2x3 double] mom: [6x408 double] pot: [204x408 double] rv: [1x408 double] pow: 2.7948e+18 csd: [6x6 double] fourier: [6x204 double] I would appreciate helping comments, as I tested the different methods for some time now, but was unable to extract a reasonable real-value spatial filter for my auditory cortex activations. Best regards, Björn From wallisgj at gmail.com Mon Sep 10 14:22:20 2012 From: wallisgj at gmail.com (George Wallis) Date: Mon, 10 Sep 2012 13:22:20 +0100 Subject: [FieldTrip] Appending data.grad, after using D.ftraw(0) Message-ID: Dear fieldtrippers, if anyone can help me with this I'd be very grateful! I have a bunch of preprocessed and epoched data files in SPM format, and I'm converting them to fieldtrip format using the following: D = spm_eeg_load(fn); data = D.ftraw(0); ...which results in... data = fsample: 250 label: {350x1 cell} trial: {1x360 cell} time: {1x360 cell} Comparing this to data structures generated using fieldtrip alone, field like data.grad are missing. I can create something like a grad field by doing: D.sensors('MEG') ans = pnt: [510x3 double] ori: [510x3 double] tra: [306x510 double] unit: 'mm' label: {306x1 cell} If I then append this to the data: data.grad = D.sensors('MEG'); I get an error: --- Error using ft_chantype (line 56) the input that was provided to this function cannot be deciphered Error in ft_datatype_sens (line 128) sens.chantype = ft_chantype(sens); Error in ft_datatype_raw (line 99) data.grad = ft_datatype_sens(data.grad); Error in ft_checkdata (line 177) data = ft_datatype_raw(data, 'hassampleinfo', hassampleinfo); Error in ft_timelockanalysis (line 134) data = ft_checkdata(data, 'datatype', {'raw', 'comp'}, 'feedback', 'yes', 'hassampleinfo', 'yes'); Error in ft_SENS_ERF_grRep (line 82) avdat = ft_timelockanalysis(cfg,raw); --- ...when I try to do timelockanalysis on this data. If I leave the grad field off (i.e. not append it to the output of ftraw(0)) there's no problem, and the analysis runs fine. However, because I want to do spatial neighbour cluster analysis later, I think I need the .grad field, so I might as well get it incorporated at this stage. Going a bit further into the error messages above, the function ft_datatype_sens appears to convert the old format .ori, .pnt into the newer .coilori, .coilpos ... etc. But the next function in the chain, ft_chantype, looks for .pnt and .ori when doing: isgrad = isa(input, 'struct') && isfield(input, 'pnt') && isfield(input, 'ori'); I'm wondering if this could be the problem? Sorry for the long message! I'd be very grateful if anyone can help out. Best wishes, George -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Mon Sep 10 15:55:26 2012 From: smoratti at psi.ucm.es (smoratti at psi.ucm.es) Date: Mon, 10 Sep 2012 15:55:26 +0200 Subject: [FieldTrip] Appending data.grad, after using D.ftraw(0) In-Reply-To: References: Message-ID: <44D6E4E8-E44D-4D08-B012-C3B506F6E935@psi.ucm.es> Dear George, Your approach was right, and it would have worked with older versions of field trip. Now in field trip the grad field contents have changed a little bit. Now it contains balance: [1x1 struct] chanori: [306x3 double] chanpos: [306x3 double] chantype: {306x1 cell} chanunit: {306x1 cell} coilori: [510x3 double] coilpos: [510x3 double] label: {306x1 cell} tra: [306x510 double] unit: 'cm' so the field put would be chanpos, ori would be chanori (or coilpos/ coilori depending on your MEG system). So check this out and you can easily adapt the structure. I think SPM does not go with the últimate field trip version. I hope this helps, best, Stephan ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 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 10/09/2012, a las 14:22, George Wallis escribió: > Dear fieldtrippers, > > if anyone can help me with this I'd be very grateful! > > I have a bunch of preprocessed and epoched data files in SPM format, and I'm converting them to fieldtrip format using the following: > > D = spm_eeg_load(fn); > data = D.ftraw(0); > > ...which results in... > > data = > > fsample: 250 > label: {350x1 cell} > trial: {1x360 cell} > time: {1x360 cell} > > Comparing this to data structures generated using fieldtrip alone, field like data.grad are missing. > > I can create something like a grad field by doing: > > D.sensors('MEG') > > ans = > > pnt: [510x3 double] > ori: [510x3 double] > tra: [306x510 double] > unit: 'mm' > label: {306x1 cell} > > If I then append this to the data: > > data.grad = D.sensors('MEG'); > > I get an error: > > --- > > Error using ft_chantype (line 56) > the input that was provided to this function cannot be deciphered > > Error in ft_datatype_sens (line 128) > sens.chantype = ft_chantype(sens); > > Error in ft_datatype_raw (line 99) > data.grad = ft_datatype_sens(data.grad); > > Error in ft_checkdata (line 177) > data = ft_datatype_raw(data, 'hassampleinfo', hassampleinfo); > > Error in ft_timelockanalysis (line 134) > data = ft_checkdata(data, 'datatype', {'raw', 'comp'}, 'feedback', 'yes', 'hassampleinfo', > 'yes'); > > Error in ft_SENS_ERF_grRep (line 82) > avdat = ft_timelockanalysis(cfg,raw); > > --- > > ...when I try to do timelockanalysis on this data. If I leave the grad field off (i.e. not append it to the output of ftraw(0)) there's no problem, and the analysis runs fine. However, because I want to do spatial neighbour cluster analysis later, I think I need the .grad field, so I might as well get it incorporated at this stage. > > Going a bit further into the error messages above, the function ft_datatype_sens appears to convert the old format .ori, .pnt into the newer .coilori, .coilpos ... etc. But the next function in the chain, ft_chantype, looks for .pnt and .ori when doing: > > isgrad = isa(input, 'struct') && isfield(input, 'pnt') && isfield(input, 'ori'); > > I'm wondering if this could be the problem? > > Sorry for the long message! I'd be very grateful if anyone can help out. > > Best wishes, > George > _______________________________________________ > 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 wallisgj at gmail.com Mon Sep 10 18:21:36 2012 From: wallisgj at gmail.com (George Wallis) Date: Mon, 10 Sep 2012 17:21:36 +0100 Subject: [FieldTrip] Appending data.grad, after using D.ftraw(0) Message-ID: Hi Stephan, Thanks very much for your reply (and sorry for not replying to the thread; I get a digest, and couldn't figure out how to reply to an individual message). So, SPM will produce an outdated .grad format, which can be corrected. There is one thing I don't get, which is why ft_chantype looks for the older fields, viz: *isgrad = isa(input, 'struct') && isfield(input, 'pnt') && isfield(input, 'ori');* It seems like the function ft_chantype is called from, ft_datatype_sens, automatically corrects the old grad format before passing the structure (now called 'sens') to ft_chantype: % sensor description is a MEG sensor-array, containing oriented coils [chanpos, chanori, chanlab] = channelposition(sens, 'channel', 'all'); sens.coilori = sens.ori; sens = rmfield(sens, 'ori'); sens.coilpos = sens.pnt; sens = rmfield(sens, 'pnt'); sens.chanpos = chanpos; sens.chanori = chanori; Did the new format not propagate through? best wishes, George On Mon, Sep 10, 2012 at 2:55 PM, 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. about overlap in PSD calculation (Ivano Triggiani) > 2. real-value spatial filter from FFT dipole localization? > (Bj?rn Herrmann) > 3. Appending data.grad, after using D.ftraw(0) (George Wallis) > 4. Re: Appending data.grad, after using D.ftraw(0) > (smoratti at psi.ucm.es) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 10 Sep 2012 11:27:09 +0100 (BST) > From: Ivano Triggiani > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] about overlap in PSD calculation > Message-ID: > <1347272829.31720.YahooMailNeo at web133103.mail.ir2.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all. > > How can I obtain informations about the kind of overlapping performed by > fiedltrip implemented method to obtain a Power Spectral Density ? > > I need to compare fieldtrip PSD with another spectral density, so I need > to be sure of everything. I found docs about tapering, but I don't > understand if using a kind of tapering the overlapping is given. > Ivano > > ? > ------------------------------------------------------------------------ > > > > > "No man can wear one face to himself > and another to the multitude, > without finally getting bewildered > as to which one is true." > > > Nathaniel Hawthorne > > > ________________________________ > Da: "fieldtrip-request at science.ru.nl" > A: fieldtrip at science.ru.nl > Inviato: Luned? 10 Settembre 2012 12:00 > Oggetto: fieldtrip Digest, Vol 22, Issue 17 > > 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. Using WPLI od WPLI-debiased to do the coherence analysis > ? ? ? (sahand babapoor) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 9 Sep 2012 20:49:31 -0400 > From: sahand babapoor > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Using WPLI od WPLI-debiased to do the coherence > ??? analysis > Message-ID: > ??? > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > > I am trying to do coherency analysis between ACC and FEF. I have tried both > WPLI and WPLI-debiased methods to do the analysis. When I am using WPLI I > find a very nice coherence pattern between ACC and FEF in the frequencies > between ~11Hz to 20 Hz. However, when I am using WPLI-debiased method, the > previous WPLI coherence pattern disappears and? breaks into many sparse > clusters across many time points and frequencies. Is there a way to know > which method is the best for me. I should note that I am recording using > tungsten microelectrodes advanced into the brain. I would appreciate if > your help. > > Best, > Sahand > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120909/2a47bbc7/attachment-0001.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 22, Issue 17 > ***************************************** > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120910/448a5494/attachment-0001.html > > > > ------------------------------ > > Message: 2 > Date: Mon, 10 Sep 2012 13:16:09 +0200 (CEST) > From: Bj?rn Herrmann > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] real-value spatial filter from FFT dipole > localization? > Message-ID: <1396322041.3317.1347275769488.JavaMail.root at zimbra> > Content-Type: text/plain; charset=utf-8 > > Dear fieldtrip users, > > maybe someone can point me in the right direction. I try to obtain a > spatial filter from localizing the sources of an auditory 3Hz peak in my > FFT spectrum. I would like to apply the filter to my single trial real > data, i.e. basically reducing my 204 gradiometer channels (neuromag system) > to one or two channels in source space. > I was using DICS beamformer and cfg.realfilter = 'yes' but the source > localization results (NAI) looked not too well compared to the nice > auditory gradiometer topographies. > I then used ft_dipolefitting, however, I have trouble understanding the > output. This is where I wondered whether someone could help me, in telling > whether it is possible to obtain a real-value spatial filter from this: > > source = > label: {204x1 cell} > dip: [1x1 struct] > Vdata: [204x408 double] > Vmodel: [204x408 double] > freq: 3 > dimord: 'chan_freq' > grad: [1x1 struct] > cfg: [1x1 struct] > > source.dip = > pos: [2x3 double] > mom: [6x408 double] > pot: [204x408 double] > rv: [1x408 double] > pow: 2.7948e+18 > csd: [6x6 double] > fourier: [6x204 double] > > I would appreciate helping comments, as I tested the different methods for > some time now, but was unable to extract a reasonable real-value spatial > filter for my auditory cortex activations. > > Best regards, > > Bj?rn > > > > > > ------------------------------ > > Message: 3 > Date: Mon, 10 Sep 2012 13:22:20 +0100 > From: George Wallis > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Appending data.grad, after using D.ftraw(0) > Message-ID: > < > CADqk8UgZ-wUf-FAjLL9K0hScW6ZTWrOVJKaR0S+PVhvuKx31-w at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear fieldtrippers, > > if anyone can help me with this I'd be very grateful! > > I have a bunch of preprocessed and epoched data files in SPM format, and > I'm converting them to fieldtrip format using the following: > > D = spm_eeg_load(fn); > data = D.ftraw(0); > > ...which results in... > > data = > > fsample: 250 > label: {350x1 cell} > trial: {1x360 cell} > time: {1x360 cell} > > Comparing this to data structures generated using fieldtrip alone, field > like data.grad are missing. > > I can create something like a grad field by doing: > > D.sensors('MEG') > > ans = > > pnt: [510x3 double] > ori: [510x3 double] > tra: [306x510 double] > unit: 'mm' > label: {306x1 cell} > > If I then append this to the data: > > data.grad = D.sensors('MEG'); > > I get an error: > > --- > > Error using ft_chantype (line 56) > the input that was provided to this function cannot be deciphered > > Error in ft_datatype_sens (line 128) > sens.chantype = ft_chantype(sens); > > Error in ft_datatype_raw (line 99) > data.grad = ft_datatype_sens(data.grad); > > Error in ft_checkdata (line 177) > data = ft_datatype_raw(data, 'hassampleinfo', hassampleinfo); > > Error in ft_timelockanalysis (line 134) > data = ft_checkdata(data, 'datatype', {'raw', 'comp'}, 'feedback', 'yes', > 'hassampleinfo', > 'yes'); > > Error in ft_SENS_ERF_grRep (line 82) > avdat = ft_timelockanalysis(cfg,raw); > > --- > > ...when I try to do timelockanalysis on this data. If I leave the grad > field off (i.e. not append it to the output of ftraw(0)) there's no > problem, and the analysis runs fine. However, because I want to do spatial > neighbour cluster analysis later, I think I need the .grad field, so I > might as well get it incorporated at this stage. > > Going a bit further into the error messages above, the function > ft_datatype_sens appears to convert the old format .ori, .pnt into the > newer .coilori, .coilpos ... etc. But the next function in the chain, > ft_chantype, looks for .pnt and .ori when doing: > > isgrad = isa(input, 'struct') && isfield(input, 'pnt') && isfield(input, > 'ori'); > > I'm wondering if this could be the problem? > > Sorry for the long message! I'd be very grateful if anyone can help out. > > Best wishes, > George > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120910/8418e2de/attachment-0001.html > > > > ------------------------------ > > Message: 4 > Date: Mon, 10 Sep 2012 15:55:26 +0200 > From: "smoratti at psi.ucm.es" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Appending data.grad, after using D.ftraw(0) > Message-ID: <44D6E4E8-E44D-4D08-B012-C3B506F6E935 at psi.ucm.es> > Content-Type: text/plain; charset="iso-8859-1" > > Dear George, > > Your approach was right, and it would have worked with older versions of > field trip. Now in field trip the grad field contents have changed a little > bit. > > Now it contains > > balance: [1x1 struct] > chanori: [306x3 double] > chanpos: [306x3 double] > chantype: {306x1 cell} > chanunit: {306x1 cell} > coilori: [510x3 double] > coilpos: [510x3 double] > label: {306x1 cell} > tra: [306x510 double] > unit: 'cm' > > so the field put would be chanpos, ori would be chanori (or coilpos/ > coilori depending on your MEG system). > > So check this out and you can easily adapt the structure. I think SPM does > not go with the ?ltimate field trip version. > > I hope this helps, > > best, > > Stephan > > ________________________________________________________ > Stephan Moratti, PhD > > see also: http://web.me.com/smoratti/ > > Universidad Complutense de Madrid > Facultad de Psicolog?a > Departamento de Psicolog?a B?sica I > Campus de Somosaguas > 28223 Pozuelo de Alarc?n (Madrid) > Spain > > and > > Center for Biomedical Technology > Laboratory for Cognitive and Computational Neuroscience > Parque Cient?fico y Tecnol?gico de la Universidad Politecnica de Madrid > Campus Montegancedo > 28223 Pozuelo de Alarc?n (Madrid) > Spain > > > email: smoratti at psi.ucm.es > Tel.: +34 679219982 > > El 10/09/2012, a las 14:22, George Wallis escribi?: > > > Dear fieldtrippers, > > > > if anyone can help me with this I'd be very grateful! > > > > I have a bunch of preprocessed and epoched data files in SPM format, and > I'm converting them to fieldtrip format using the following: > > > > D = spm_eeg_load(fn); > > data = D.ftraw(0); > > > > ...which results in... > > > > data = > > > > fsample: 250 > > label: {350x1 cell} > > trial: {1x360 cell} > > time: {1x360 cell} > > > > Comparing this to data structures generated using fieldtrip alone, field > like data.grad are missing. > > > > I can create something like a grad field by doing: > > > > D.sensors('MEG') > > > > ans = > > > > pnt: [510x3 double] > > ori: [510x3 double] > > tra: [306x510 double] > > unit: 'mm' > > label: {306x1 cell} > > > > If I then append this to the data: > > > > data.grad = D.sensors('MEG'); > > > > I get an error: > > > > --- > > > > Error using ft_chantype (line 56) > > the input that was provided to this function cannot be deciphered > > > > Error in ft_datatype_sens (line 128) > > sens.chantype = ft_chantype(sens); > > > > Error in ft_datatype_raw (line 99) > > data.grad = ft_datatype_sens(data.grad); > > > > Error in ft_checkdata (line 177) > > data = ft_datatype_raw(data, 'hassampleinfo', hassampleinfo); > > > > Error in ft_timelockanalysis (line 134) > > data = ft_checkdata(data, 'datatype', {'raw', 'comp'}, 'feedback', > 'yes', 'hassampleinfo', > > 'yes'); > > > > Error in ft_SENS_ERF_grRep (line 82) > > avdat = ft_timelockanalysis(cfg,raw); > > > > --- > > > > ...when I try to do timelockanalysis on this data. If I leave the grad > field off (i.e. not append it to the output of ftraw(0)) there's no > problem, and the analysis runs fine. However, because I want to do spatial > neighbour cluster analysis later, I think I need the .grad field, so I > might as well get it incorporated at this stage. > > > > Going a bit further into the error messages above, the function > ft_datatype_sens appears to convert the old format .ori, .pnt into the > newer .coilori, .coilpos ... etc. But the next function in the chain, > ft_chantype, looks for .pnt and .ori when doing: > > > > isgrad = isa(input, 'struct') && isfield(input, 'pnt') && > isfield(input, 'ori'); > > > > I'm wondering if this could be the problem? > > > > Sorry for the long message! I'd be very grateful if anyone can help out. > > > > Best wishes, > > George > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120910/444962f9/attachment.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 22, Issue 18 > ***************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Mon Sep 10 18:36:02 2012 From: litvak.vladimir at gmail.com (litvak.vladimir at gmail.com) Date: Mon, 10 Sep 2012 16:36:02 +0000 Subject: [FieldTrip] Appending data.grad, after using D.ftraw(0) In-Reply-To: References: Message-ID: <1665240477-1347294953-cardhu_decombobulator_blackberry.rim.net-1232560809-@b18.c20.bise7.blackberry> Dear George, Yes, what you describe is still a bug in Fieldtrip because the conversion from the old to new grad format should be automatic. This might be related to a similar bug I reported on Bugzilla last Friday. The problem was specific to Neuromag data. The next SPM8 update will include an updated Fieldtrip version and will work with the new sensor formats. I hope the FT team will look at this soon. Vladimir Sent using BlackBerry® from Orange -----Original Message----- From: George Wallis Sender: fieldtrip-bounces at science.ru.nl Date: Mon, 10 Sep 2012 17:21:36 To: Reply-To: FieldTrip discussion list Subject: [FieldTrip] Appending data.grad, after using D.ftraw(0) _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From martin.maier at student.hu-berlin.de Tue Sep 11 14:06:38 2012 From: martin.maier at student.hu-berlin.de (Martin Maier) Date: Tue, 11 Sep 2012 14:06:38 +0200 Subject: [FieldTrip] example cross-frequency analysis In-Reply-To: References: Message-ID: Hi there, I'm trying to analyse my data for phase-amplitude cross-frequency coupling.The example script (http://fieldtrip.fcdonders.nl/example/crossfreq/phalow_amphigh) still uses ft_freqdescriptives to get the coherence-spectrum, but this has since been implemented in ft_connectivityanalysis. My question concerns the channelcombination when using ft_connectivityanalysis. When calculating the coherence between power and raw, I get the following error message: "??? Error using ==> univariate2bivariate at 25 no channel combinations are specified" I did specify channel combinations, but somehow ft_connectivityanalysis doesn't get them. Does the function need a different format when setting the channels to be combined? Or should I use a different function to calculate the coherence spectra (instead of ft_connectivityanalysis)? Thanks, Martin From member at linkedin.com Wed Sep 12 01:26:18 2012 From: member at linkedin.com (=?UTF-8?Q?Alicia_Gonz=C3=A1lez_Moreno_via_LinkedIn?=) Date: Tue, 11 Sep 2012 23:26:18 +0000 (UTC) Subject: [FieldTrip] Join my network on LinkedIn Message-ID: <1377830396.2855738.1347405978358.JavaMail.app@ela4-app2314.prod> LinkedIn ------------ Alicia González Moreno requested to add you as a connection on LinkedIn: ------------------------------------------ I'd like to add you to my professional network on LinkedIn. Accept invitation from Alicia González Moreno http://www.linkedin.com/e/-deyl8h-h6zmqar3-2j/2ql61bZWrtgNAx4NauUqWbaswiGNhc8KtyoV/blk/I214712724_50/0UcDpKqiRzolZKqiRybmRSrCBvrmRLoORIrmkZt5YCpnlOt3RApnhMpmdzgmhxrSNBszYMdlYQczsOcjsQcj99bTtdszl6sCl4bPsRc3oNcjsMdzwLrCBxbOYWrSlI/eml-comm_invm-b-in_ac-inv28/?hs=false&tok=2DIcL0uIu-Glo1 View profile of Alicia González Moreno http://www.linkedin.com/e/-deyl8h-h6zmqar3-2j/rso/203786050/UX0W/name/51465358_I214712724_50/?hs=false&tok=1RKIB_Kum-Glo1 ------------------------------------------ You are receiving Invitation emails. This email was intended for lin wang. Learn why this is included: http://www.linkedin.com/e/-deyl8h-h6zmqar3-2j/plh/http%3A%2F%2Fhelp%2Elinkedin%2Ecom%2Fapp%2Fanswers%2Fdetail%2Fa_id%2F4788/-GXI/?hs=false&tok=2C0EwII2W-Glo1 (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA. -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.hartmann at th-ht.de Wed Sep 12 14:57:37 2012 From: thomas.hartmann at th-ht.de (Thomas Hartmann) Date: Wed, 12 Sep 2012 14:57:37 +0200 Subject: [FieldTrip] units after beamforming Message-ID: <505086C1.9010004@th-ht.de> hi all, i do lcmv beamforming on meg data and use cfg.method='localspheres' and cfg.singlesphere='yes' as options to call ft_prepare_localspheres. i was wondering about the units of the resulting spatial filter. does anyone know, what those might be? thanks a lot! best, thomas -- Dr. Thomas Hartmann CIMeC - Center for Mind/Brain Sciences Università degli Studi di Trento via delle Regole, 101 38060 Mattarello (TN) ITALY Tel: +39 0461 28 2779 Fax: +39 0461 28 3066 Email: thomas.hartmann at th-ht.de Homepage: http://sites.google.com/site/obobcimec/ "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle) From elizabeth.bock at mcgill.ca Wed Sep 12 20:32:39 2012 From: elizabeth.bock at mcgill.ca (Elizabeth Anne Bock, Ms) Date: Wed, 12 Sep 2012 18:32:39 +0000 Subject: [FieldTrip] realtime buffer does not exit Message-ID: <86D86365C4E767468A79EB52DFBFB46F0510F73C@exmbx2010-8.campus.MCGILL.CA> I am using the realtime buffer and I have found I cannot exit the buffer within the Matlab command window. I am forced to exit Matlab or, more often, must kill the process manually from the windows task manager. I am using Windows XP to host the buffer and Linux to run acqftx. Here is what I am seeing: >> buffer('tcpserver', 'exit', ft_host, ft_port) In main: requesting cancelation of tcpserver thread >> buffer('tcpserver', 'init', ft_host, ft_port) ??? Error using ==> buffer thread is already running Any suggestions? Thanks, Elizabeth ------------------------------------------------------------------------------------------ Elizabeth Bock / MEG System Engineer McConnell Brain Imaging Centre / Montreal Neurological Institute McGill University / 3801 University St. / Montreal, QC H3A 2B4 MEG Lab: 514.398.6056 Mobile: 514.718.6342 From daria.laptinskaya at googlemail.com Thu Sep 13 09:21:00 2012 From: daria.laptinskaya at googlemail.com (Daria Laptinskaya) Date: Thu, 13 Sep 2012 09:21:00 +0200 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: <3B494ED9-B6C3-46A3-840C-8EEEDAA85E5E@mac.com> References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> <77D46473-6907-4AC1-96E1-F51756C119C0@mac.com> <3B494ED9-B6C3-46A3-840C-8EEEDAA85E5E@mac.com> Message-ID: Yes, it works fine now-thank you!!! @Matt: Do you know a calibration-function for existing raw-files? Best, Daria 2012/9/10 Joseph Dien > Hey Daria, > glad you were able to get it worked out! Thank Matt for his reminder > (below) about the calibration option. > > Cheers! > > Joe > > > Hi Joe, > > > I didn’t know that there is a function like this. > > The most of my colleagues use the RAW.-files they get from the > file-exporter without problems. > > Not even NetStation-support could give me an answer. > > So I thought, it must be a problem between NetStation and fieldtrip. > > Because of your tip I opened an original datafile and tried to save a copy > of the file. > > Doing so NetStation offers a possibility to ‘convert to microvolts’ and > create a .ses –datafile. > > The .raw-files I get this way have microvolt as unit. > > I compared the signals I get this way with the signals I get by using the > formula (5000 mircovolts / (2^16 bits) I send you. They are almost the > same-that’s great!!! > > It seems to work now. > > Thank you very much!!! You were a great help!!! > > > Cheers, > > Daria > > On Sep 6, 2012, at 9:07 PM, Joseph Dien wrote: > > I don't recall ever seeing this problem with EGIS files, which is one of > the reasons I prefer using this file format despite EGI's preference for > newer Simple Binary format, but it's an unpredictable bug so I can't say it > can't happen. I also can't say which versions of NetStation it happens > with. It may have been fixed. I'm still trying to test out MFF so can't > say anything about it. I had problems with the FieldTrip code for reading > segmented MFF files (which is what I'm interested in). I also had trouble > with writing them out from NetStation so I don't have a valid segmented > test file and I'm still waiting for EGI to make one available so I can work > them out. The simple binary file format (this is the original name for the > EGI .raw file format and I prefer to use it over ".raw" as the BESA .raw > file format is actually the .egis file format so it can get confusing) > doesn't actually have separate calibration information for the channels > (unlike EGIS), just one single gain value and no zeros values. So > basically the simple binary format makes the assumption that calibration > corrections have already been performed prior to generating the file. My > understanding is that this is indeed what the "calibrate data" option is > doing, but you'd have to confirm with EGI. > > Joe > > > > -------------------------------------------------------------------------------- > > On Sep 6, 2012, at 1:01 PM, Matt Mollison wrote: > > Joe, > > A few related questions: > > Does using the "calibrate data" option when exporting to raw (simple > binary) correct for gain? Or is there a different solution/recommendation? > Does exporting to MFF (Net Station 4.5.x only) or EGIS have this issue? I > tend to use EGIS (faster to read than raw) and have no recollection of > seeing unusually large voltages. > > Thanks, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > > On Wed, Sep 5, 2012 at 7:17 PM, Joseph Dien wrote: > >> The Simple Binary (.raw) files don't get corrected for gain when imported >> (I helped write them). I've experienced occasional unpredictable bugs with >> NetStation export routines where the files are generated with amplitudes >> many times too large, even with text format files. It's a bit >> disconcerting to say the least. I could take a look at your files if you'd >> like confirmation. >> >> Joe >> >> On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis >> wrote: >> >> Hi Daria, >> >> Also, did you try looking at your raw data (so before the ERPs are made) >> in FieldTrip and in Net Station? So open your .raw data in NetStation. You >> can just look at a random participant's data, and check if the scale is the >> same. I'm pretty sure no amplification takes place when reading in the data >> into FieldTrip, this check can confirm that. Hope this helps, and let us >> know what you find. >> >> Cheers, >> Ingrid >> >> >> On 9/3/2012 1:35 PM, Robert Oostenveld wrote: >> >> Hi Daria, >> >> There might indeed be an incompatibility in the gain value applied to >> the data. >> >> If you are able to export the data using the EGI software in another >> format (e.g. EDF), you could read them both into FieldTrip and compare the >> timecourse aplitudes to check whether they are different. In case they are, >> I suggest to involve EGI support. They are aware of the FieldTrip reading >> functions and will know much more about the internals of their various file >> formats. >> >> best regards >> Robert >> >> >> >> >> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: >> >> Dear Fieldtrippers, >> >> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip >> toolbox. >> The ERPs look perfect. >> The 'only' problem is, that my signals look to strong. >> It looks like if I get amplitutes (average) until 70 µV. >> I think it must be an intern amplifier for the signals. >> >> Does anyone know this problem with EGI-data? >> >> Or does anyone know, where I can see the amplifier? >> >> >> >> Greetings, >> Daria _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> _______________________________________________ >> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -- >> Ingrid Nieuwenhuis PhD >> Postdoctoral Fellow >> Sleep and Neuroimaging Laboratory >> Department of Psychology >> University of California, Berkeley >> California 94720-1650 >> Tolman Hall, room 5305 >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, >> Senior Research Scientist >> University of Maryland >> >> E-mail: jdien07 at mac.com >> Phone: 301-226-8848 >> Fax: 301-226-8811 >> http://joedien.com// >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > > > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joscha.schmiedt at esi-frankfurt.de Thu Sep 13 09:46:19 2012 From: joscha.schmiedt at esi-frankfurt.de (Schmiedt, Joscha) Date: Thu, 13 Sep 2012 07:46:19 +0000 Subject: [FieldTrip] Verbosity of fieldtrip functions Message-ID: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> Hi, I was wondering whether there is any option to suppress the printed output of a fieldtrip function or whether there are any plans for implementing a cfg.verbose option. Whenever I'm running some kind of loop I'd be glad to be able to use my own progress feedback without interruption from all the involved functions. Best, Joscha --------------------------- Joscha Schmiedt, MS 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 411 -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu Sep 13 10:03:19 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 13 Sep 2012 10:03:19 +0200 Subject: [FieldTrip] Verbosity of fieldtrip functions In-Reply-To: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> References: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> Message-ID: Hi Joscha, At the moment, we are thinking about implementing a generic logging mechanism in FieldTrip. Such a mechanism would allow you to specify the level of feedback you desire on the console, and also allow people to conveniently store log files for e.g. posting on this list for debugging. But given that (1) our thinking about this is still in its early stages, and (2) it requires a replace of all fprintf() statements in the entire codebase, it could be a while before this is fully implemented. But, to repeat, this is something we plan to do in the (near) future. Best, Eelke On 13 September 2012 09:46, Schmiedt, Joscha wrote: > Hi, > > I was wondering whether there is any option to suppress the printed output > of a fieldtrip function or whether there are any plans for implementing a > cfg.verbose option. Whenever I'm running some kind of loop I'd be glad to be > able to use my own progress feedback without interruption from all the > involved functions. > > Best, > Joscha > > > --------------------------- > Joscha Schmiedt, MS > 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 411 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From eelke.spaak at donders.ru.nl Thu Sep 13 10:03:19 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 13 Sep 2012 10:03:19 +0200 Subject: [FieldTrip] Verbosity of fieldtrip functions In-Reply-To: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> References: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> Message-ID: Hi Joscha, At the moment, we are thinking about implementing a generic logging mechanism in FieldTrip. Such a mechanism would allow you to specify the level of feedback you desire on the console, and also allow people to conveniently store log files for e.g. posting on this list for debugging. But given that (1) our thinking about this is still in its early stages, and (2) it requires a replace of all fprintf() statements in the entire codebase, it could be a while before this is fully implemented. But, to repeat, this is something we plan to do in the (near) future. Best, Eelke On 13 September 2012 09:46, Schmiedt, Joscha wrote: > Hi, > > I was wondering whether there is any option to suppress the printed output > of a fieldtrip function or whether there are any plans for implementing a > cfg.verbose option. Whenever I'm running some kind of loop I'd be glad to be > able to use my own progress feedback without interruption from all the > involved functions. > > Best, > Joscha > > > --------------------------- > Joscha Schmiedt, MS > 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 411 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From g.piantoni at nin.knaw.nl Thu Sep 13 10:28:31 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Thu, 13 Sep 2012 10:28:31 +0200 Subject: [FieldTrip] Verbosity of fieldtrip functions In-Reply-To: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> References: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> Message-ID: Hi Joscha, A quick and dirty solution is evalc: [~, data] = evalc('yourfunction(cfg)'); Cheers, Gio On Thu, Sep 13, 2012 at 9:46 AM, Schmiedt, Joscha wrote: > Hi, > > I was wondering whether there is any option to suppress the printed output > of a fieldtrip function or whether there are any plans for implementing a > cfg.verbose option. Whenever I'm running some kind of loop I'd be glad to be > able to use my own progress feedback without interruption from all the > involved functions. > > Best, > Joscha > > > --------------------------- > Joscha Schmiedt, MS > 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 411 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From smoratti at psi.ucm.es Thu Sep 13 10:36:05 2012 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Thu, 13 Sep 2012 10:36:05 +0200 Subject: [FieldTrip] Verbosity of fieldtrip functions In-Reply-To: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> References: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> Message-ID: <2EF4BF72-E8CE-4134-9DEB-7657B034C167@psi.ucm.es> Hi Joscha, Sometimes you can suppress some outputs with cfg.feedback = 'no'; Best, Stephan El 13/09/2012, a las 09:46, Schmiedt, Joscha escribió: > Hi, > > I was wondering whether there is any option to suppress the printed output of a fieldtrip function or whether there are any plans for implementing a cfg.verbose option. Whenever I'm running some kind of loop I'd be glad to be able to use my own progress feedback without interruption from all the involved functions. > > Best, > Joscha > > > --------------------------- > Joscha Schmiedt, MS > 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 411 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Thu Sep 13 10:36:05 2012 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Thu, 13 Sep 2012 10:36:05 +0200 Subject: [FieldTrip] Verbosity of fieldtrip functions In-Reply-To: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> References: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> Message-ID: <2EF4BF72-E8CE-4134-9DEB-7657B034C167@psi.ucm.es> Hi Joscha, Sometimes you can suppress some outputs with cfg.feedback = 'no'; Best, Stephan El 13/09/2012, a las 09:46, Schmiedt, Joscha escribió: > Hi, > > I was wondering whether there is any option to suppress the printed output of a fieldtrip function or whether there are any plans for implementing a cfg.verbose option. Whenever I'm running some kind of loop I'd be glad to be able to use my own progress feedback without interruption from all the involved functions. > > Best, > Joscha > > > --------------------------- > Joscha Schmiedt, MS > 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 411 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Thu Sep 13 10:55:55 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Thu, 13 Sep 2012 11:55:55 +0300 Subject: [FieldTrip] Making your own trialfun Message-ID: Hello, I tried to run the example in the following page: http://fieldtrip.fcdonders.nl/example/making_your_own_trialfun_for_conditional_trial_definition I did the required modifications so it can be run using biosemi system. But I don't know what to put instead of the variable "trigger" in the following statement: for j = 1:(length(trigger)-1) Could you help me Best, -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu Sep 13 11:02:32 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 13 Sep 2012 11:02:32 +0200 Subject: [FieldTrip] Making your own trialfun In-Reply-To: References: Message-ID: Hi Hamza, This is a bug in the example code; apologies. The "trigger" variable here actually refers to "value", so the vector of trigger values, assigned a few lines earlier. I will update the wiki. Best, Eelke On 13 September 2012 10:55, Hamza Fawzi Altakroury (Student) wrote: > Hello, > > I tried to run the example in the following page: > http://fieldtrip.fcdonders.nl/example/making_your_own_trialfun_for_conditional_trial_definition > > I did the required modifications so it can be run using biosemi system. > > But I don't know what to put instead of the variable "trigger" in the > following statement: > > for j = 1:(length(trigger)-1) > > > Could you help me > > Best, > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From eelke.spaak at donders.ru.nl Thu Sep 13 11:02:32 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 13 Sep 2012 11:02:32 +0200 Subject: [FieldTrip] Making your own trialfun In-Reply-To: References: Message-ID: Hi Hamza, This is a bug in the example code; apologies. The "trigger" variable here actually refers to "value", so the vector of trigger values, assigned a few lines earlier. I will update the wiki. Best, Eelke On 13 September 2012 10:55, Hamza Fawzi Altakroury (Student) wrote: > Hello, > > I tried to run the example in the following page: > http://fieldtrip.fcdonders.nl/example/making_your_own_trialfun_for_conditional_trial_definition > > I did the required modifications so it can be run using biosemi system. > > But I don't know what to put instead of the variable "trigger" in the > following statement: > > for j = 1:(length(trigger)-1) > > > Could you help me > > Best, > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From a.stolk at fcdonders.ru.nl Thu Sep 13 11:05:20 2012 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Thu, 13 Sep 2012 11:05:20 +0200 (CEST) Subject: [FieldTrip] realtime buffer does not exit In-Reply-To: <86D86365C4E767468A79EB52DFBFB46F0510F73C@exmbx2010-8.campus.MCGILL.CA> Message-ID: <3342976.328678.1347527120171.JavaMail.root@sculptor.zimbra.ru.nl> Hi Elizabeth, Could you try and start the buffer from outside matlab using 'demo_buffer.exe' (to be found in the 'realtime/bin/win32' directory)? This application may operate smoother than when starting the buffer from a single matlab thread. Best, Arjen ----- Oorspronkelijk bericht ----- > Van: "Elizabeth Anne Bock, Ms" > Aan: fieldtrip at science.ru.nl > Verzonden: Woensdag 12 september 2012 20:32:39 > Onderwerp: [FieldTrip] realtime buffer does not exit > I am using the realtime buffer and I have found I cannot exit the > buffer within the Matlab command window. I am forced to exit Matlab > or, more often, must kill the process manually from the windows task > manager. I am using Windows XP to host the buffer and Linux to run > acqftx. Here is what I am seeing: > > >> buffer('tcpserver', 'exit', ft_host, ft_port) > In main: requesting cancelation of tcpserver thread > > >> buffer('tcpserver', 'init', ft_host, ft_port) > ??? Error using ==> buffer > thread is already running > > Any suggestions? > Thanks, > Elizabeth > > > ------------------------------------------------------------------------------------------ > > Elizabeth Bock / MEG System Engineer > > McConnell Brain Imaging Centre / Montreal Neurological Institute > > McGill University / 3801 University St. / Montreal, QC H3A 2B4 > > > > MEG Lab: 514.398.6056 > > Mobile: 514.718.6342 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From hamzaf at sabanciuniv.edu Thu Sep 13 11:13:20 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Thu, 13 Sep 2012 12:13:20 +0300 Subject: [FieldTrip] Making your own trialfun In-Reply-To: References: Message-ID: Thank you Eelke, it works now. Best, Hamza On Thu, Sep 13, 2012 at 12:02 PM, Eelke Spaak wrote: > Hi Hamza, > > This is a bug in the example code; apologies. The "trigger" variable > here actually refers to "value", so the vector of trigger values, > assigned a few lines earlier. > > I will update the wiki. > > Best, > Eelke > > On 13 September 2012 10:55, Hamza Fawzi Altakroury (Student) > wrote: > > Hello, > > > > I tried to run the example in the following page: > > > http://fieldtrip.fcdonders.nl/example/making_your_own_trialfun_for_conditional_trial_definition > > > > I did the required modifications so it can be run using biosemi system. > > > > But I don't know what to put instead of the variable "trigger" in the > > following statement: > > > > for j = 1:(length(trigger)-1) > > > > > > Could you help me > > > > Best, > > > > -- > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabancı University > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Thu Sep 13 11:19:37 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Thu, 13 Sep 2012 12:19:37 +0300 Subject: [FieldTrip] ft_realtime_selectiveaverage Message-ID: Hello, I am tried to run the ft_realtime_selectiveaverage function but I got the following error: (note: the error appears after showing a plot with title: condition 255, ntrials = 1.) Could you tell me what is the problem. (exactly what does "connet read data before the begin of the file"). Best, ??? Error using ==> ft_read_data at 243 cannot read data before the begin of the file Error in ==> ft_realtime_selectiveaverage at 94 dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', chanindx, 'checkboundary', false); Error in ==> online1 at 48 ft_realtime_selectiveaverage(cfg) Statements: cfg = []; cfg.channel = {'A1'}; cfg.dataset = 'buffer://localhost:1972'; %cfg.trialfun = 'myfun'; cfg.trialdef.eventtype = 'stimulus'; % By placing '?' we can see the eventtype that we have. cfg.trialdef.eventvalue = 255; cfg.trialdef.pre = 0; cfg.trialdef.post = 1.0; cfg = ft_definetrial(cfg); ft_realtime_selectiveaverage(cfg) -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Sep 13 12:19:26 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 13 Sep 2012 05:19:26 -0500 Subject: [FieldTrip] Verbosity of fieldtrip functions In-Reply-To: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> References: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> Message-ID: <7638A242-2EF9-46AF-AB27-9448413A153E@donders.ru.nl> Hi Joscha There is indeed such a plan, see http://bugzilla.fcdonders.nl/show_bug.cgi?id=1686. If you want, you can provide your comments or ideas there. best Robert On 13 Sep 2012, at 2:46, Schmiedt, Joscha wrote: > Hi, > > I was wondering whether there is any option to suppress the printed output of a fieldtrip function or whether there are any plans for implementing a cfg.verbose option. Whenever I'm running some kind of loop I'd be glad to be able to use my own progress feedback without interruption from all the involved functions. > > Best, > Joscha > > > --------------------------- > Joscha Schmiedt, MS > 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 411 > > _______________________________________________ > 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 Duncan.Astle at mrc-cbu.cam.ac.uk Thu Sep 13 12:46:49 2012 From: Duncan.Astle at mrc-cbu.cam.ac.uk (Duncan Astle) Date: Thu, 13 Sep 2012 10:46:49 +0000 Subject: [FieldTrip] Problem with clustering across electrode neighbours Message-ID: Dear Fieldtrippers, I am rather new to this, but am attempting to do some cluster stats on my ERP sensor level data. It is working well, and I can cluster across time, but I can't get it to cluster across electrode locations. I think it is because of a mistake that I am making in my 'neighbours' file, although it looks fine when I inspect it. This is the error message that I get: ??? Cell contents reference from a non-cell array object. Error in ==> clusterstat>makechanneighbstructmat at 520 [seld] = match_str(cfg.channel, cfg.neighbours{chan}.label); Error in ==> clusterstat at 60 channeighbstructmat = makechanneighbstructmat(cfg); Error in ==> statistics_montecarlo at 322 [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); Error in ==> statistics_wrapper at 285 [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); Error in ==> ft_timelockstatistics at 119 [stat, cfg] = statistics_wrapper(cfg, varargin{:}); Can anyone spot what I am doing wrong? This is how I make my neighbour file: cfg = []; cfg.layout = 'EEG1010.lay'; % try 'distance' as well cfg.feedback = 'yes'; % show a neighbour plot cfg.method = 'template'; cfg.neighbourdist = 'number'; cfg.template = 'EEG1010_neighb.mat' cfg.channel = 'all' cfg.feedback = 'yes'; neighbours = ft_prepare_neighbours(cfg, Load5Hard); % define neighbouring channels This is how I then try the stats: cfg = []; cfg.channel = 'all'; cfg.latency = [0.1 1.3]; cfg.avgovertime = 'no'; cfg.avgoverchannel = 'no'; cfg.parameter = 'individual'; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT' cfg.alpha = 0.05; cfg.correctm = 'cluster'; cfg.correcttail = 'prob'; cfg.numrandomization = 1000; cfg.feedback = 'yes'; % show a neighbour plot cfg.neighbours = neighbours; %cfg.minnbchan = 2; cfg.clusterstatistic = 'maxsum'; cfg.clusterthreshold = 'nonparametric'; cfg.clusteralpha = 0.01; cfg.clustercritval = 0.06; % cfg.clustertail = 0; cfg.tail = 0; Nsub = 19; cfg.design(1,1:2*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub)]; cfg.design(2,1:2*Nsub) = [1:Nsub 1:Nsub]; cfg.ivar = 1; % the 1st row in cfg.design contains the independent variable cfg.uvar = 2; % the 2nd row in cfg.design contains the subject number [stat] = ft_timelockstatistics(cfg, Load3Hard, Load3Easy) Any suggestions very gratefully received. Thanks, Duncan ________________________________________________ Dr. Duncan Astle, Programme Leader Track, British Academy Research Fellow, MRC Cognition and Brain Sciences Unit, Chaucer Road, Cambridge. Duncan.Astle at mrc-cbu.cam.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu Sep 13 12:55:34 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 13 Sep 2012 12:55:34 +0200 Subject: [FieldTrip] Problem with clustering across electrode neighbours In-Reply-To: References: Message-ID: Dear Duncan, Jörn can correct me if I'm wrong, but I think it is sufficient to write cfg = []; cfg.method = 'template'; cfg.template = 'EEG1010_neighb.mat'; neighbours = ft_prepare_neighbours(cfg); if you want to use the neighbourhood structure template. So, specifying all those other options might have confused ft_prepare_neighbours. Best, Eelke On 13 September 2012 12:46, Duncan Astle wrote: > Dear Fieldtrippers, > > > > I am rather new to this, but am attempting to do some cluster stats on my > ERP sensor level data. It is working well, and I can cluster across time, > but I can’t get it to cluster across electrode locations. I think it is > because of a mistake that I am making in my ‘neighbours’ file, although it > looks fine when I inspect it. This is the error message that I get: > > > > ??? Cell contents reference from a non-cell array object. > > > > Error in ==> clusterstat>makechanneighbstructmat at 520 > > [seld] = match_str(cfg.channel, cfg.neighbours{chan}.label); > > > > Error in ==> clusterstat at 60 > > channeighbstructmat = makechanneighbstructmat(cfg); > > > > Error in ==> statistics_montecarlo at 322 > > [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); > > > > Error in ==> statistics_wrapper at 285 > > [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); > > > > Error in ==> ft_timelockstatistics at 119 > > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > > > Can anyone spot what I am doing wrong? > > > > This is how I make my neighbour file: > > > > cfg = []; > > cfg.layout = 'EEG1010.lay'; % try 'distance' as well > > cfg.feedback = 'yes'; % show a neighbour plot > > cfg.method = 'template'; > > cfg.neighbourdist = 'number'; > > cfg.template = 'EEG1010_neighb.mat' > > cfg.channel = 'all' > > cfg.feedback = 'yes'; > > neighbours = ft_prepare_neighbours(cfg, Load5Hard); % define > neighbouring channels > > > > This is how I then try the stats: > > > > cfg = []; > > cfg.channel = 'all'; > > cfg.latency = [0.1 1.3]; > > cfg.avgovertime = 'no'; > > cfg.avgoverchannel = 'no'; > > cfg.parameter = 'individual'; > > cfg.method = 'montecarlo'; > > cfg.statistic = 'depsamplesT' > > cfg.alpha = 0.05; > > cfg.correctm = 'cluster'; > > cfg.correcttail = 'prob'; > > cfg.numrandomization = 1000; > > cfg.feedback = 'yes'; % show a neighbour plot > > cfg.neighbours = neighbours; > > %cfg.minnbchan = 2; > > cfg.clusterstatistic = 'maxsum'; > > cfg.clusterthreshold = 'nonparametric'; > > cfg.clusteralpha = 0.01; > > cfg.clustercritval = 0.06; > > % cfg.clustertail = 0; > > cfg.tail = 0; > > Nsub = 19; > > cfg.design(1,1:2*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub)]; > > cfg.design(2,1:2*Nsub) = [1:Nsub 1:Nsub]; > > cfg.ivar = 1; % the 1st row in cfg.design contains the > independent variable > > cfg.uvar = 2; % the 2nd row in cfg.design contains the > subject number > > > > > > [stat] = ft_timelockstatistics(cfg, Load3Hard, Load3Easy) > > > > Any suggestions very gratefully received. > > > > Thanks, > > Duncan > > ________________________________________________ > > Dr. Duncan Astle, > > Programme Leader Track, > > British Academy Research Fellow, > > MRC Cognition and Brain Sciences Unit, > > Chaucer Road, > > Cambridge. > > Duncan.Astle at mrc-cbu.cam.ac.uk > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Thu Sep 13 13:11:15 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 13 Sep 2012 13:11:15 +0200 Subject: [FieldTrip] Problem with clustering across electrode neighbours In-Reply-To: References: Message-ID: <5051BF53.5030606@donders.ru.nl> Hey Duncan, it looks pretty much like you are using an old FieldTrip version with a new neighbourhood-structure. Could you check the with the most recent version again? Some months (about a year?) ago we changed the neighbour definition from cell arrays to structure arrays, so any attempt to access cfg.neighbours{i} will fail, cause it has to be cfg.neighbours(i) instead. But as I already said, this has been changed quite some time back in the past :) Essentially, your code is fine, but some note that cfg.neighbourdist should be a scalar, not the string 'number', but only if cfg.method='distance'. If you choose cfg.method = 'template' then cfg.neighbourdist is not used, cause a template is loaded. Best, Jörn On 9/13/2012 12:46 PM, Duncan Astle wrote: > > Dear Fieldtrippers, > > I am rather new to this, but am attempting to do some cluster stats on > my ERP sensor level data. It is working well, and I can cluster across > time, but I can't get it to cluster across electrode locations. I > think it is because of a mistake that I am making in my 'neighbours' > file, although it looks fine when I inspect it. This is the error > message that I get: > > ??? Cell contents reference from a non-cell array object. > > Error in ==> clusterstat>makechanneighbstructmat at 520 > > [seld] = match_str(cfg.channel, cfg.neighbours{chan}.label); > > Error in ==> clusterstat at 60 > > channeighbstructmat = makechanneighbstructmat(cfg); > > Error in ==> statistics_montecarlo at 322 > > [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); > > Error in ==> statistics_wrapper at 285 > > [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); > > Error in ==> ft_timelockstatistics at 119 > > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > Can anyone spot what I am doing wrong? > > This is how I make my neighbour file: > > cfg = []; > > cfg.layout = 'EEG1010.lay'; % try 'distance' as well > > cfg.feedback = 'yes'; % show a neighbour plot > > cfg.method = 'template'; > > cfg.neighbourdist = 'number'; > > cfg.template = 'EEG1010_neighb.mat' > > cfg.channel = 'all' > > cfg.feedback = 'yes'; > > neighbours = ft_prepare_neighbours(cfg, Load5Hard); % define > neighbouring channels > > This is how I then try the stats: > > cfg = []; > > cfg.channel = 'all'; > > cfg.latency = [0.1 1.3]; > > cfg.avgovertime = 'no'; > > cfg.avgoverchannel = 'no'; > > cfg.parameter = 'individual'; > > cfg.method = 'montecarlo'; > > cfg.statistic = 'depsamplesT' > > cfg.alpha = 0.05; > > cfg.correctm = 'cluster'; > > cfg.correcttail = 'prob'; > > cfg.numrandomization = 1000; > > cfg.feedback = 'yes'; % show a neighbour plot > > cfg.neighbours = neighbours; > > %cfg.minnbchan = 2; > > cfg.clusterstatistic = 'maxsum'; > > cfg.clusterthreshold = 'nonparametric'; > > cfg.clusteralpha = 0.01; > > cfg.clustercritval = 0.06; > > % cfg.clustertail = 0; > > cfg.tail = 0; > > Nsub = 19; > > cfg.design(1,1:2*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub)]; > > cfg.design(2,1:2*Nsub) = [1:Nsub 1:Nsub]; > > cfg.ivar = 1; % the 1st row in cfg.design contains > the independent variable > > cfg.uvar = 2; % the 2nd row in cfg.design contains > the subject number > > [stat] = ft_timelockstatistics(cfg, Load3Hard, Load3Easy) > > Any suggestions very gratefully received. > > Thanks, > > Duncan > > ________________________________________________ > > Dr. Duncan Astle, > > Programme Leader Track, > > British Academy Research Fellow, > > MRC Cognition and Brain Sciences Unit, > > Chaucer Road, > > Cambridge. > > Duncan.Astle at mrc-cbu.cam.ac.uk > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From elizabeth.bock at mcgill.ca Thu Sep 13 14:51:42 2012 From: elizabeth.bock at mcgill.ca (Elizabeth Anne Bock, Ms) Date: Thu, 13 Sep 2012 12:51:42 +0000 Subject: [FieldTrip] realtime buffer does not exit In-Reply-To: <3342976.328678.1347527120171.JavaMail.root@sculptor.zimbra.ru.nl> References: <86D86365C4E767468A79EB52DFBFB46F0510F73C@exmbx2010-8.campus.MCGILL.CA>, <3342976.328678.1347527120171.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <86D86365C4E767468A79EB52DFBFB46F05110836@exmbx2010-8.campus.MCGILL.CA> Thanks for the feedback. However, I would like to read the header and the data from the buffer into Matlab (I am doing realtime processing of the data). Is this possible to run the buffer in the windows environment and then read from it in Matlab? hdr = buffer('get_hdr', [], ft_host, ft_port) ??? Error using ==> buffer ERROR: failed to create socket (1) Thanks, Beth ------------------------------------------------------------------------------------------ Elizabeth Bock / MEG System Engineer McConnell Brain Imaging Centre / Montreal Neurological Institute McGill University / 3801 University St. / Montreal, QC H3A 2B4 MEG Lab: 514.398.6056 Mobile: 514.718.6342 ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Stolk, A. [a.stolk at fcdonders.ru.nl] Sent: Thursday, September 13, 2012 5:05 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] realtime buffer does not exit Hi Elizabeth, Could you try and start the buffer from outside matlab using 'demo_buffer.exe' (to be found in the 'realtime/bin/win32' directory)? This application may operate smoother than when starting the buffer from a single matlab thread. Best, Arjen ----- Oorspronkelijk bericht ----- > Van: "Elizabeth Anne Bock, Ms" > Aan: fieldtrip at science.ru.nl > Verzonden: Woensdag 12 september 2012 20:32:39 > Onderwerp: [FieldTrip] realtime buffer does not exit > I am using the realtime buffer and I have found I cannot exit the > buffer within the Matlab command window. I am forced to exit Matlab > or, more often, must kill the process manually from the windows task > manager. I am using Windows XP to host the buffer and Linux to run > acqftx. Here is what I am seeing: > > >> buffer('tcpserver', 'exit', ft_host, ft_port) > In main: requesting cancelation of tcpserver thread > > >> buffer('tcpserver', 'init', ft_host, ft_port) > ??? Error using ==> buffer > thread is already running > > Any suggestions? > Thanks, > Elizabeth > > > ------------------------------------------------------------------------------------------ > > Elizabeth Bock / MEG System Engineer > > McConnell Brain Imaging Centre / Montreal Neurological Institute > > McGill University / 3801 University St. / Montreal, QC H3A 2B4 > > > > MEG Lab: 514.398.6056 > > Mobile: 514.718.6342 > > _______________________________________________ > 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 wallisgj at gmail.com Thu Sep 13 15:26:55 2012 From: wallisgj at gmail.com (George Wallis) Date: Thu, 13 Sep 2012 14:26:55 +0100 Subject: [FieldTrip] Dimension mismatch in .grad struct for neuromag data Message-ID: Dear fieldtrippers, With neuromag306 data, after the old style of .grad gets converted to the new style, the field have dimensions as follows: data.grad: ans = unit: 'mm' label: {306x1 cell} coilori: [510x3 double] coilpos: [510x3 double] lab: {102x3 cell} chanpos: [102x3 double] chanori: [102x3 double] balance: [1x1 struct] Because there are three sensors in each location, there are 1/3 as many elements in chanpos as in coilpos. However, in ft_combineplanar, where the function remakes the .grad field to match the new list of channels (where the gradiometers have been combined), is uses a list of channel indices 'sel' which is concatenated vertically: sel = [sel_comb(:);sel_other(:)]; ...and indexes into newgrad.chanpos. As above, newgrad.chanpos is 102x3, but sel is 204x1: 102 combined gradiometers ('sel_comb') plus 102 magnetometers ('sel_other'). There is therefore a dimension mismatch, because the different channel types are 'overlaid' in 'chanpos' but not in 'sel'. Have I set up my .chanpos, .chanori incorrectly? Thanks for any tips, George -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mollison at gmail.com Thu Sep 13 16:50:58 2012 From: matt.mollison at gmail.com (Matt Mollison) Date: Thu, 13 Sep 2012 08:50:58 -0600 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> <77D46473-6907-4AC1-96E1-F51756C119C0@mac.com> <3B494ED9-B6C3-46A3-840C-8EEEDAA85E5E@mac.com> Message-ID: Daria, I do not know any calibration function for raw files that were exported without calibration, but maybe it is a simple formula? You might want to contact EGI. Let us know if you find anything out. Best, Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ On Thu, Sep 13, 2012 at 1:21 AM, Daria Laptinskaya < daria.laptinskaya at googlemail.com> wrote: > Yes, it works fine now-thank you!!! > > @Matt: Do you know a calibration-function for existing raw-files? > > > > Best, > > Daria > > > 2012/9/10 Joseph Dien > >> Hey Daria, >> glad you were able to get it worked out! Thank Matt for his reminder >> (below) about the calibration option. >> >> Cheers! >> >> Joe >> >> >> Hi Joe, >> >> >> I didn’t know that there is a function like this. >> >> The most of my colleagues use the RAW.-files they get from the >> file-exporter without problems. >> >> Not even NetStation-support could give me an answer. >> >> So I thought, it must be a problem between NetStation and fieldtrip. >> >> Because of your tip I opened an original datafile and tried to save a >> copy of the file. >> >> Doing so NetStation offers a possibility to ‘convert to microvolts’ and >> create a .ses –datafile. >> >> The .raw-files I get this way have microvolt as unit. >> >> I compared the signals I get this way with the signals I get by using the >> formula (5000 mircovolts / (2^16 bits) I send you. They are almost the >> same-that’s great!!! >> >> It seems to work now. >> >> Thank you very much!!! You were a great help!!! >> >> >> Cheers, >> >> Daria >> >> On Sep 6, 2012, at 9:07 PM, Joseph Dien wrote: >> >> I don't recall ever seeing this problem with EGIS files, which is one of >> the reasons I prefer using this file format despite EGI's preference for >> newer Simple Binary format, but it's an unpredictable bug so I can't say it >> can't happen. I also can't say which versions of NetStation it happens >> with. It may have been fixed. I'm still trying to test out MFF so can't >> say anything about it. I had problems with the FieldTrip code for reading >> segmented MFF files (which is what I'm interested in). I also had trouble >> with writing them out from NetStation so I don't have a valid segmented >> test file and I'm still waiting for EGI to make one available so I can work >> them out. The simple binary file format (this is the original name for the >> EGI .raw file format and I prefer to use it over ".raw" as the BESA .raw >> file format is actually the .egis file format so it can get confusing) >> doesn't actually have separate calibration information for the channels >> (unlike EGIS), just one single gain value and no zeros values. So >> basically the simple binary format makes the assumption that calibration >> corrections have already been performed prior to generating the file. My >> understanding is that this is indeed what the "calibrate data" option is >> doing, but you'd have to confirm with EGI. >> >> Joe >> >> >> >> -------------------------------------------------------------------------------- >> >> On Sep 6, 2012, at 1:01 PM, Matt Mollison >> wrote: >> >> Joe, >> >> A few related questions: >> >> Does using the "calibrate data" option when exporting to raw (simple >> binary) correct for gain? Or is there a different solution/recommendation? >> Does exporting to MFF (Net Station 4.5.x only) or EGIS have this issue? I >> tend to use EGIS (faster to read than raw) and have no recollection of >> seeing unusually large voltages. >> >> Thanks, >> Matt >> >> On Wed, Sep 5, 2012 at 7:17 PM, Joseph Dien wrote: >> >>> The Simple Binary (.raw) files don't get corrected for gain when >>> imported (I helped write them). I've experienced occasional unpredictable >>> bugs with NetStation export routines where the files are generated with >>> amplitudes many times too large, even with text format files. It's a bit >>> disconcerting to say the least. I could take a look at your files if you'd >>> like confirmation. >>> >>> Joe >>> >>> On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis < >>> inieuwenhuis at BERKELEY.EDU> wrote: >>> >>> Hi Daria, >>> >>> Also, did you try looking at your raw data (so before the ERPs are made) >>> in FieldTrip and in Net Station? So open your .raw data in NetStation. You >>> can just look at a random participant's data, and check if the scale is the >>> same. I'm pretty sure no amplification takes place when reading in the data >>> into FieldTrip, this check can confirm that. Hope this helps, and let us >>> know what you find. >>> >>> Cheers, >>> Ingrid >>> >>> >>> On 9/3/2012 1:35 PM, Robert Oostenveld wrote: >>> >>> Hi Daria, >>> >>> There might indeed be an incompatibility in the gain value applied to >>> the data. >>> >>> If you are able to export the data using the EGI software in another >>> format (e.g. EDF), you could read them both into FieldTrip and compare the >>> timecourse aplitudes to check whether they are different. In case they are, >>> I suggest to involve EGI support. They are aware of the FieldTrip reading >>> functions and will know much more about the internals of their various file >>> formats. >>> >>> best regards >>> Robert >>> >>> >>> >>> >>> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: >>> >>> Dear Fieldtrippers, >>> >>> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip >>> toolbox. >>> The ERPs look perfect. >>> The 'only' problem is, that my signals look to strong. >>> It looks like if I get amplitutes (average) until 70 µV. >>> I think it must be an intern amplifier for the signals. >>> >>> Does anyone know this problem with EGI-data? >>> >>> Or does anyone know, where I can see the amplifier? >>> >>> >>> >>> Greetings, >>> Daria _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> -- >>> Ingrid Nieuwenhuis PhD >>> Postdoctoral Fellow >>> Sleep and Neuroimaging Laboratory >>> Department of Psychology >>> University of California, Berkeley >>> California 94720-1650 >>> Tolman Hall, room 5305 >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> Joseph Dien, >>> Senior Research Scientist >>> University of Maryland >>> >>> E-mail: jdien07 at mac.com >>> Phone: 301-226-8848 >>> Fax: 301-226-8811 >>> http://joedien.com// >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, >> Senior Research Scientist >> University of Maryland >> >> E-mail: jdien07 at mac.com >> Phone: 301-226-8848 >> Fax: 301-226-8811 >> http://joedien.com// >> >> >> >> >> >> >> >> >> >> >> >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, >> Senior Research Scientist >> University of Maryland >> >> E-mail: jdien07 at mac.com >> Phone: 301-226-8848 >> Fax: 301-226-8811 >> http://joedien.com// >> >> >> >> >> >> >> >> >> >> >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From daria.laptinskaya at googlemail.com Thu Sep 13 17:14:37 2012 From: daria.laptinskaya at googlemail.com (Daria Laptinskaya) Date: Thu, 13 Sep 2012 17:14:37 +0200 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> <77D46473-6907-4AC1-96E1-F51756C119C0@mac.com> <3B494ED9-B6C3-46A3-840C-8EEEDAA85E5E@mac.com> Message-ID: There is a formula in the NetStation-manual: (5000 mircovolts / (2^16 bits). You can convert bits to microvolts by multiplicating all signals with the factor 0,076293945 in fieldtrip. This solution isn't perfect, because it doesn't consider gains. We asked EGI for an other formula, but didn't yet get an answer. I compare the two methods and for little N the gains don't make a great difference. Best, Daria 2012/9/13 Matt Mollison > Daria, > > I do not know any calibration function for raw files that were exported > without calibration, but maybe it is a simple formula? You might want to > contact EGI. Let us know if you find anything out. > > Best, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > > On Thu, Sep 13, 2012 at 1:21 AM, Daria Laptinskaya < > daria.laptinskaya at googlemail.com> wrote: > >> Yes, it works fine now-thank you!!! >> >> @Matt: Do you know a calibration-function for existing raw-files? >> >> >> >> Best, >> >> Daria >> >> >> 2012/9/10 Joseph Dien >> >>> Hey Daria, >>> glad you were able to get it worked out! Thank Matt for his reminder >>> (below) about the calibration option. >>> >>> Cheers! >>> >>> Joe >>> >>> >>> Hi Joe, >>> >>> >>> I didn’t know that there is a function like this. >>> >>> The most of my colleagues use the RAW.-files they get from the >>> file-exporter without problems. >>> >>> Not even NetStation-support could give me an answer. >>> >>> So I thought, it must be a problem between NetStation and fieldtrip. >>> >>> Because of your tip I opened an original datafile and tried to save a >>> copy of the file. >>> >>> Doing so NetStation offers a possibility to ‘convert to microvolts’ and >>> create a .ses –datafile. >>> >>> The .raw-files I get this way have microvolt as unit. >>> >>> I compared the signals I get this way with the signals I get by using >>> the formula (5000 mircovolts / (2^16 bits) I send you. They are almost the >>> same-that’s great!!! >>> >>> It seems to work now. >>> >>> Thank you very much!!! You were a great help!!! >>> >>> >>> Cheers, >>> >>> Daria >>> >>> On Sep 6, 2012, at 9:07 PM, Joseph Dien wrote: >>> >>> I don't recall ever seeing this problem with EGIS files, which is one of >>> the reasons I prefer using this file format despite EGI's preference for >>> newer Simple Binary format, but it's an unpredictable bug so I can't say it >>> can't happen. I also can't say which versions of NetStation it happens >>> with. It may have been fixed. I'm still trying to test out MFF so can't >>> say anything about it. I had problems with the FieldTrip code for reading >>> segmented MFF files (which is what I'm interested in). I also had trouble >>> with writing them out from NetStation so I don't have a valid segmented >>> test file and I'm still waiting for EGI to make one available so I can work >>> them out. The simple binary file format (this is the original name for the >>> EGI .raw file format and I prefer to use it over ".raw" as the BESA .raw >>> file format is actually the .egis file format so it can get confusing) >>> doesn't actually have separate calibration information for the channels >>> (unlike EGIS), just one single gain value and no zeros values. So >>> basically the simple binary format makes the assumption that calibration >>> corrections have already been performed prior to generating the file. My >>> understanding is that this is indeed what the "calibrate data" option is >>> doing, but you'd have to confirm with EGI. >>> >>> Joe >>> >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> On Sep 6, 2012, at 1:01 PM, Matt Mollison >>> wrote: >>> >>> Joe, >>> >>> A few related questions: >>> >>> Does using the "calibrate data" option when exporting to raw (simple >>> binary) correct for gain? Or is there a different solution/recommendation? >>> Does exporting to MFF (Net Station 4.5.x only) or EGIS have this issue? >>> I tend to use EGIS (faster to read than raw) and have no recollection of >>> seeing unusually large voltages. >>> >>> Thanks, >>> Matt >>> >>> On Wed, Sep 5, 2012 at 7:17 PM, Joseph Dien wrote: >>> >>>> The Simple Binary (.raw) files don't get corrected for gain when >>>> imported (I helped write them). I've experienced occasional unpredictable >>>> bugs with NetStation export routines where the files are generated with >>>> amplitudes many times too large, even with text format files. It's a bit >>>> disconcerting to say the least. I could take a look at your files if you'd >>>> like confirmation. >>>> >>>> Joe >>>> >>>> On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis < >>>> inieuwenhuis at BERKELEY.EDU> wrote: >>>> >>>> Hi Daria, >>>> >>>> Also, did you try looking at your raw data (so before the ERPs are >>>> made) in FieldTrip and in Net Station? So open your .raw data in >>>> NetStation. You can just look at a random participant's data, and check if >>>> the scale is the same. I'm pretty sure no amplification takes place when >>>> reading in the data into FieldTrip, this check can confirm that. Hope this >>>> helps, and let us know what you find. >>>> >>>> Cheers, >>>> Ingrid >>>> >>>> >>>> On 9/3/2012 1:35 PM, Robert Oostenveld wrote: >>>> >>>> Hi Daria, >>>> >>>> There might indeed be an incompatibility in the gain value applied >>>> to the data. >>>> >>>> If you are able to export the data using the EGI software in another >>>> format (e.g. EDF), you could read them both into FieldTrip and compare the >>>> timecourse aplitudes to check whether they are different. In case they are, >>>> I suggest to involve EGI support. They are aware of the FieldTrip reading >>>> functions and will know much more about the internals of their various file >>>> formats. >>>> >>>> best regards >>>> Robert >>>> >>>> >>>> >>>> >>>> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: >>>> >>>> Dear Fieldtrippers, >>>> >>>> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip >>>> toolbox. >>>> The ERPs look perfect. >>>> The 'only' problem is, that my signals look to strong. >>>> It looks like if I get amplitutes (average) until 70 µV. >>>> I think it must be an intern amplifier for the signals. >>>> >>>> Does anyone know this problem with EGI-data? >>>> >>>> Or does anyone know, where I can see the amplifier? >>>> >>>> >>>> >>>> Greetings, >>>> Daria _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> >>>> -- >>>> Ingrid Nieuwenhuis PhD >>>> Postdoctoral Fellow >>>> Sleep and Neuroimaging Laboratory >>>> Department of Psychology >>>> University of California, Berkeley >>>> California 94720-1650 >>>> Tolman Hall, room 5305 >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> >>>> >>>> >>>> -------------------------------------------------------------------------------- >>>> >>>> Joseph Dien, >>>> Senior Research Scientist >>>> University of Maryland >>>> >>>> E-mail: jdien07 at mac.com >>>> Phone: 301-226-8848 >>>> Fax: 301-226-8811 >>>> http://joedien.com// >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> Joseph Dien, >>> Senior Research Scientist >>> University of Maryland >>> >>> E-mail: jdien07 at mac.com >>> Phone: 301-226-8848 >>> Fax: 301-226-8811 >>> http://joedien.com// >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> Joseph Dien, >>> Senior Research Scientist >>> University of Maryland >>> >>> E-mail: jdien07 at mac.com >>> Phone: 301-226-8848 >>> Fax: 301-226-8811 >>> http://joedien.com// >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bherrmann at cbs.mpg.de Fri Sep 14 10:23:14 2012 From: bherrmann at cbs.mpg.de (=?utf-8?Q?Bj=C3=B6rn_Herrmann?=) Date: Fri, 14 Sep 2012 10:23:14 +0200 (CEST) Subject: [FieldTrip] How to impove dics realfilter solution In-Reply-To: <612757646.1088.1347610775726.JavaMail.root@zimbra> Message-ID: <736231433.1128.1347610993969.JavaMail.root@zimbra> Dear fieldtrip user, I am using the DICS beamformer to localize a 3Hz FFT power topographical distribution (using a neuromag system). The topographies are very clear auditory in single subjects, thus it shouldn't be a problem finding the "right" solution. When I use the beamformer to obtain complex-value spatial filters, the solution looks very good (using NAI). No problem here. However, using cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real values, the localization completely breaks down, sometimes even finding a strong peak in the opposite hemisphere than visible in the sensor topography (the head is centered in the sensor array). Does someone have a suggestion how to improve the solution using realfilter = 'yes'. I use the following settings. They are rather standard I guess. cfg = []; cfg.method = 'dics'; cfg.frequency = 3; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.keepfilter = 'yes'; cfg.dics.realfilter = 'yes'; cfg.dics.fixedori = 'no'; If someone has a suggestion, I would appreciate it. Thanks in advance, best, Björn From r.oostenveld at donders.ru.nl Fri Sep 14 11:25:54 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 14 Sep 2012 04:25:54 -0500 Subject: [FieldTrip] fieldtrip wiki website unstable In-Reply-To: References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> <77D46473-6907-4AC1-96E1-F51756C119C0@mac.com> <3B494ED9-B6C3-46A3-840C-8EEEDAA85E5E@mac.com> Message-ID: <8FD34ABA-CEDF-4E8C-B024-9F175E1CD573@donders.ru.nl> Dear FieldTrip users, As you may have noticed, we have some issues with the FieldTrip wiki. The underlying cause is that the file server hosting the webserver, bugzilla, svn and the ftp server is acting weird, causing temporary failures of the online services. Our ICT group is working on it. So if you notice that either the FieldTrip wiki or one of the related servers is not doing what you expect, please try again later. best regards Robert From b.reuderink at donders.ru.nl Fri Sep 14 12:21:52 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Fri, 14 Sep 2012 12:21:52 +0200 Subject: [FieldTrip] realtime buffer does not exit In-Reply-To: <86D86365C4E767468A79EB52DFBFB46F05110836@exmbx2010-8.campus.MCGILL.CA> References: <86D86365C4E767468A79EB52DFBFB46F0510F73C@exmbx2010-8.campus.MCGILL.CA>, <3342976.328678.1347527120171.JavaMail.root@sculptor.zimbra.ru.nl> <86D86365C4E767468A79EB52DFBFB46F05110836@exmbx2010-8.campus.MCGILL.CA> Message-ID: <81D26A77-1088-4A8A-89FF-AA9B199F0320@donders.ru.nl> Dear Elizabeth, It is indeed possible (perhaps preferable) to run the FieldTrip buffer outside of the MATLAB environment. Basically, the 'demo_buffer.exe' functions as a stand-alone server that holds the neuro data. Then, you would need a client, that reads from your acquisition hardware and writes new samples and events to the server. FieldTrip has programs for many different acquisition systems, see [1]. Your MATLAB program can then act as another client and read form the buffer. The advantage of this setup is that you can restart your MATLAB session without disrupting the FieldTrip real-time buffer. You can even run the serving buffer and your MATLAB code on different computers in you lab. Without additional details I can only guess why you got the error message you described. Perhaps the ft_host and ft_port are not set correctly? For ft_host you could try 'localhost' or '127.0.0.1', and for ft_port the default is 1972. These settings tell FieldTrip to connect to a buffer (=server) on the same computer. If you can't get it to work, please don't hesitate to ask. BTW, some background information on real-time signal processing with FieldTrip can be found on [2] — perhaps that is useful. Best regards, Boris Reuderink [1] http://fieldtrip.fcdonders.nl/development/realtime/implementation [2] http://fieldtrip.fcdonders.nl/development/realtime/buffer_overview -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl On 13 sep. 2012, at 14:51, "Elizabeth Anne Bock, Ms" wrote: > Thanks for the feedback. However, I would like to read the header and the data from the buffer into Matlab (I am doing realtime processing of the data). Is this possible to run the buffer in the windows environment and then read from it in Matlab? > > hdr = buffer('get_hdr', [], ft_host, ft_port) > ??? Error using ==> buffer > ERROR: failed to create socket (1) > > Thanks, > Beth > > ------------------------------------------------------------------------------------------ > > Elizabeth Bock / MEG System Engineer > > McConnell Brain Imaging Centre / Montreal Neurological Institute > > McGill University / 3801 University St. / Montreal, QC H3A 2B4 > > > > MEG Lab: 514.398.6056 > > Mobile: 514.718.6342 > > ________________________________________ > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Stolk, A. [a.stolk at fcdonders.ru.nl] > Sent: Thursday, September 13, 2012 5:05 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] realtime buffer does not exit > > Hi Elizabeth, > > Could you try and start the buffer from outside matlab using 'demo_buffer.exe' (to be found in the 'realtime/bin/win32' directory)? This application may operate smoother than when starting the buffer from a single matlab thread. > > Best, > Arjen > > ----- Oorspronkelijk bericht ----- >> Van: "Elizabeth Anne Bock, Ms" >> Aan: fieldtrip at science.ru.nl >> Verzonden: Woensdag 12 september 2012 20:32:39 >> Onderwerp: [FieldTrip] realtime buffer does not exit >> I am using the realtime buffer and I have found I cannot exit the >> buffer within the Matlab command window. I am forced to exit Matlab >> or, more often, must kill the process manually from the windows task >> manager. I am using Windows XP to host the buffer and Linux to run >> acqftx. Here is what I am seeing: >> >>>> buffer('tcpserver', 'exit', ft_host, ft_port) >> In main: requesting cancelation of tcpserver thread >> >>>> buffer('tcpserver', 'init', ft_host, ft_port) >> ??? Error using ==> buffer >> thread is already running >> >> Any suggestions? >> Thanks, >> Elizabeth >> >> >> ------------------------------------------------------------------------------------------ >> >> Elizabeth Bock / MEG System Engineer >> >> McConnell Brain Imaging Centre / Montreal Neurological Institute >> >> McGill University / 3801 University St. / Montreal, QC H3A 2B4 >> >> >> >> MEG Lab: 514.398.6056 >> >> Mobile: 514.718.6342 >> >> _______________________________________________ >> 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 andrea.brovelli at univ-amu.fr Fri Sep 14 12:27:59 2012 From: andrea.brovelli at univ-amu.fr (andrea brovelli) Date: Fri, 14 Sep 2012 12:27:59 +0200 Subject: [FieldTrip] Data prewhitening Message-ID: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> Dear all, I was wondering whether we can whiten the data using the cfg options in the ft_preprocessing function. Does anyone know ? Or does anyone have some code for prewhitening raw data ? Thanks a lot Andrea From jan.schoffelen at donders.ru.nl Fri Sep 14 12:41:41 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 14 Sep 2012 12:41:41 +0200 Subject: [FieldTrip] Data prewhitening In-Reply-To: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> References: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> Message-ID: Caro Andrea, I think you could achieve this with ft_componentanalysis (but have never tried it myself): try: cfg = []; cfg.method = 'fastica'; cfg.fastica.only = 'white'; data2 = ft_componentanalysis(cfg, data); the fastica toolbox is in fieldtrip/external/ Check out the documentation in fastica.m Ciao, JM On Sep 14, 2012, at 12:27 PM, andrea brovelli wrote: > Dear all, > > I was wondering whether we can whiten the data using the cfg options in the ft_preprocessing function. Does anyone know ? > > Or does anyone have some code for prewhitening raw data ? > > Thanks a lot > > Andrea > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.vandermeij at donders.ru.nl Fri Sep 14 13:03:32 2012 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Fri, 14 Sep 2012 13:03:32 +0200 Subject: [FieldTrip] Data prewhitening In-Reply-To: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> References: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> Message-ID: Hi Andrea, Are you referring to pre-whitening by removing the first parameter of an auto-regressive model, thereby removing most (if not all) of the 1/f shape in the spectrum? If so, this can be done by taking the first temporal derivative of the raw-data, effectively setting the first AR parameter to 0. This is implemented by setting cfg.derivative = 'yes' in preprocessing. I don't know of any good references for this trick though, so if anybody else can help out, that'd be great. Best, Roemer On Fri, Sep 14, 2012 at 12:27 PM, andrea brovelli < andrea.brovelli at univ-amu.fr> wrote: > Dear all, > > I was wondering whether we can whiten the data using the cfg options in > the ft_preprocessing function. Does anyone know ? > > Or does anyone have some code for prewhitening raw data ? > > Thanks a lot > > Andrea > > > ______________________________**_________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip > -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri Sep 14 13:52:43 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 14 Sep 2012 13:52:43 +0200 Subject: [FieldTrip] Data prewhitening In-Reply-To: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> References: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> Message-ID: <55DE5D38-8A8E-4452-AE65-1326CE686A97@donders.ru.nl> Hi Andrea, As a follow up to my previous mail. There even seems to be a cfg.method = 'white' in ft_componentanalysis. As an addition to Roemers suggestion: if you want to spectrally whiten your data, his approach can be used. I interpreted your question as that you want to achieve spatial whitening. Best, JM On Sep 14, 2012, at 12:27 PM, andrea brovelli wrote: > Dear all, > > I was wondering whether we can whiten the data using the cfg options in the ft_preprocessing function. Does anyone know ? > > Or does anyone have some code for prewhitening raw data ? > > Thanks a lot > > Andrea > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrea.brovelli at univ-amu.fr Fri Sep 14 14:09:43 2012 From: andrea.brovelli at univ-amu.fr (andrea brovelli) Date: Fri, 14 Sep 2012 14:09:43 +0200 Subject: [FieldTrip] Data prewhitening In-Reply-To: References: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> Message-ID: <20120914140943.11107al822gjc39c@wmelperso1.univmed.fr> Thank you all for these suggestions, I'll try them out. bye Andrea ----- Message de r.vandermeij at donders.ru.nl --------- Date : Fri, 14 Sep 2012 13:03:32 +0200 De : Roemer van der Meij Répondre à : FieldTrip discussion list Objet : Re: [FieldTrip] Data prewhitening À : FieldTrip discussion list > Hi Andrea, > > Are you referring to pre-whitening by removing the first parameter of > an auto-regressive model, thereby removing most (if not all) of the 1/f > shape in the spectrum? If so, this can be done by taking the first > temporal derivative of the raw-data, effectively setting the first AR > parameter to 0. This is implemented by setting cfg.derivative = 'yes' in > preprocessing. > I don't know of any good references for this trick though, so if anybody > else can help out, that'd be great. > > Best, > Roemer > > > On Fri, Sep 14, 2012 at 12:27 PM, andrea brovelli < > andrea.brovelli at univ-amu.fr> wrote: > >> Dear all, >> >> I was wondering whether we can whiten the data using the cfg options in >> the ft_preprocessing function. Does anyone know ? >> >> Or does anyone have some code for prewhitening raw data ? >> >> Thanks a lot >> >> Andrea >> >> >> ______________________________**_________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip >> > > > > -- > Roemer van der Meij M.Sc. > PhD student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > Tel: +31(0)24 3655932 > E-mail: r.vandermeij at donders.ru.nl > ----- Fin du message de r.vandermeij at donders.ru.nl ----- -- NEW EMAIL: andrea.brovelli at univ-amu.fr From eelke.spaak at donders.ru.nl Fri Sep 14 14:27:54 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Fri, 14 Sep 2012 14:27:54 +0200 Subject: [FieldTrip] Data prewhitening In-Reply-To: <20120914140943.11107al822gjc39c@wmelperso1.univmed.fr> References: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> <20120914140943.11107al822gjc39c@wmelperso1.univmed.fr> Message-ID: Hi Andrea, To add to Roemer's suggestion: it's not exactly a reference perhaps, but Robert posted on the list a while ago some explanation behind using the temporal derivative to remove 1/f power (=whitening). See http://mailman.science.ru.nl/pipermail/fieldtrip/2011-October/004390.html Best, Eelke On 14 September 2012 14:09, andrea brovelli wrote: > Thank you all for these suggestions, I'll try them out. > > bye > > Andrea > > > ----- Message de r.vandermeij at donders.ru.nl --------- > Date : Fri, 14 Sep 2012 13:03:32 +0200 > De : Roemer van der Meij > Répondre à : FieldTrip discussion list > Objet : Re: [FieldTrip] Data prewhitening > À : FieldTrip discussion list > > >> Hi Andrea, >> >> Are you referring to pre-whitening by removing the first parameter of >> an auto-regressive model, thereby removing most (if not all) of the 1/f >> shape in the spectrum? If so, this can be done by taking the first >> temporal derivative of the raw-data, effectively setting the first AR >> parameter to 0. This is implemented by setting cfg.derivative = 'yes' in >> preprocessing. >> I don't know of any good references for this trick though, so if anybody >> else can help out, that'd be great. >> >> Best, >> Roemer >> >> >> On Fri, Sep 14, 2012 at 12:27 PM, andrea brovelli < >> andrea.brovelli at univ-amu.fr> wrote: >> >>> Dear all, >>> >>> I was wondering whether we can whiten the data using the cfg options in >>> the ft_preprocessing function. Does anyone know ? >>> >>> Or does anyone have some code for prewhitening raw data ? >>> >>> Thanks a lot >>> >>> Andrea >>> >>> >>> ______________________________**_________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> >>> http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> Roemer van der Meij M.Sc. >> PhD student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognition >> P.O. Box 9104 >> 6500 HE Nijmegen >> The Netherlands >> Tel: +31(0)24 3655932 >> E-mail: r.vandermeij at donders.ru.nl >> > > > ----- Fin du message de r.vandermeij at donders.ru.nl ----- > > > > -- > > NEW EMAIL: andrea.brovelli at univ-amu.fr > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Fri Sep 14 14:42:10 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 14 Sep 2012 14:42:10 +0200 Subject: [FieldTrip] improved edge behavior for cfg.boxcar in ft_preprocessing Message-ID: Dear all, I just pushed an improved version of boxcar smoothing to the svn-repository (will be available for download as of tonight). I just want to mention it, because it behaves slightly different from what you are used to (provided you actually ever use the option cfg.boxcar in ft_preprocessing). In a nutshell, the old implementation did an implicit zero-padding when performing the boxcar convolution. This could sometimes lead to ugly edges, if the local mean of the data (close to the edge) significantly deviated from 0. Therefore I implemented an explicit padding with the local mean value. You can read the code in ft_preproc_smooth. Since I think this change entails a significant improvement, and the old implementation was far from ideal, I decided to not support backward compatibility in this case. This means that you will not be able to reproduce the bad edge behavior of FT's boxcar functionality on your data anymore. Too bad. Happy computing and with best wishes, Jan-Mathijs Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.m.groppe at gmail.com Fri Sep 14 14:54:23 2012 From: david.m.groppe at gmail.com (David Groppe) Date: Fri, 14 Sep 2012 08:54:23 -0400 Subject: [FieldTrip] Data prewhitening In-Reply-To: References: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> <20120914140943.11107al822gjc39c@wmelperso1.univmed.fr> Message-ID: Here's a reference for whitening: Applications of spectral methods in functional brain imaging. D. Kleinfeld and P. P. Mitra. In Imaging: A Laboratory Manual (Book 1) R. Yuste, editor and series editor, 2011, Cold Spring Harbor Laboratory Press, NY, Chapter 12, 143-158. http://physics.ucsd.edu/neurophysics/publications/12_08_IMG.pdf And thanks to Robert Oostenveld for that original email response to my question about removing 1/f power trends. -David On Fri, Sep 14, 2012 at 8:27 AM, Eelke Spaak wrote: > Hi Andrea, > > To add to Roemer's suggestion: it's not exactly a reference perhaps, > but Robert posted on the list a while ago some explanation behind > using the temporal derivative to remove 1/f power (=whitening). See > http://mailman.science.ru.nl/pipermail/fieldtrip/2011-October/004390.html > > Best, > Eelke > > On 14 September 2012 14:09, andrea brovelli wrote: >> Thank you all for these suggestions, I'll try them out. >> >> bye >> >> Andrea >> >> >> ----- Message de r.vandermeij at donders.ru.nl --------- >> Date : Fri, 14 Sep 2012 13:03:32 +0200 >> De : Roemer van der Meij >> Répondre à : FieldTrip discussion list >> Objet : Re: [FieldTrip] Data prewhitening >> À : FieldTrip discussion list >> >> >>> Hi Andrea, >>> >>> Are you referring to pre-whitening by removing the first parameter of >>> an auto-regressive model, thereby removing most (if not all) of the 1/f >>> shape in the spectrum? If so, this can be done by taking the first >>> temporal derivative of the raw-data, effectively setting the first AR >>> parameter to 0. This is implemented by setting cfg.derivative = 'yes' in >>> preprocessing. >>> I don't know of any good references for this trick though, so if anybody >>> else can help out, that'd be great. >>> >>> Best, >>> Roemer >>> >>> >>> On Fri, Sep 14, 2012 at 12:27 PM, andrea brovelli < >>> andrea.brovelli at univ-amu.fr> wrote: >>> >>>> Dear all, >>>> >>>> I was wondering whether we can whiten the data using the cfg options in >>>> the ft_preprocessing function. Does anyone know ? >>>> >>>> Or does anyone have some code for prewhitening raw data ? >>>> >>>> Thanks a lot >>>> >>>> Andrea >>>> >>>> >>>> ______________________________**_________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> >>>> http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip >>>> >>> >>> >>> >>> -- >>> Roemer van der Meij M.Sc. >>> PhD student >>> Donders Institute for Brain, Cognition and Behaviour >>> Centre for Cognition >>> P.O. Box 9104 >>> 6500 HE Nijmegen >>> The Netherlands >>> Tel: +31(0)24 3655932 >>> E-mail: r.vandermeij at donders.ru.nl >>> >> >> >> ----- Fin du message de r.vandermeij at donders.ru.nl ----- >> >> >> >> -- >> >> NEW EMAIL: andrea.brovelli at univ-amu.fr >> >> >> _______________________________________________ >> 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 -- David Groppe, Ph.D. Postdoctoral Researcher North Shore LIJ Health System New Hyde Park, New York http://www.cogsci.ucsd.edu/~dgroppe/ From elizabeth.bock at mcgill.ca Fri Sep 14 16:23:51 2012 From: elizabeth.bock at mcgill.ca (Elizabeth Anne Bock, Ms) Date: Fri, 14 Sep 2012 14:23:51 +0000 Subject: [FieldTrip] realtime buffer does not exit In-Reply-To: <81D26A77-1088-4A8A-89FF-AA9B199F0320@donders.ru.nl> References: <86D86365C4E767468A79EB52DFBFB46F0510F73C@exmbx2010-8.campus.MCGILL.CA>, <3342976.328678.1347527120171.JavaMail.root@sculptor.zimbra.ru.nl> <86D86365C4E767468A79EB52DFBFB46F05110836@exmbx2010-8.campus.MCGILL.CA>, <81D26A77-1088-4A8A-89FF-AA9B199F0320@donders.ru.nl> Message-ID: <86D86365C4E767468A79EB52DFBFB46F05110DDE@exmbx2010-8.campus.MCGILL.CA> Thanks! This works great. Elizabeth ------------------------------------------------------------------------------------------ Elizabeth Bock / MEG System Engineer McConnell Brain Imaging Centre / Montreal Neurological Institute McGill University / 3801 University St. / Montreal, QC H3A 2B4 MEG Lab: 514.398.6056 Mobile: 514.718.6342 ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Boris Reuderink [b.reuderink at donders.ru.nl] Sent: Friday, September 14, 2012 6:21 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] realtime buffer does not exit Dear Elizabeth, It is indeed possible (perhaps preferable) to run the FieldTrip buffer outside of the MATLAB environment. Basically, the 'demo_buffer.exe' functions as a stand-alone server that holds the neuro data. Then, you would need a client, that reads from your acquisition hardware and writes new samples and events to the server. FieldTrip has programs for many different acquisition systems, see [1]. Your MATLAB program can then act as another client and read form the buffer. The advantage of this setup is that you can restart your MATLAB session without disrupting the FieldTrip real-time buffer. You can even run the serving buffer and your MATLAB code on different computers in you lab. Without additional details I can only guess why you got the error message you described. Perhaps the ft_host and ft_port are not set correctly? For ft_host you could try 'localhost' or '127.0.0.1', and for ft_port the default is 1972. These settings tell FieldTrip to connect to a buffer (=server) on the same computer. If you can't get it to work, please don't hesitate to ask. BTW, some background information on real-time signal processing with FieldTrip can be found on [2] — perhaps that is useful. Best regards, Boris Reuderink [1] http://fieldtrip.fcdonders.nl/development/realtime/implementation [2] http://fieldtrip.fcdonders.nl/development/realtime/buffer_overview -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl On 13 sep. 2012, at 14:51, "Elizabeth Anne Bock, Ms" wrote: > Thanks for the feedback. However, I would like to read the header and the data from the buffer into Matlab (I am doing realtime processing of the data). Is this possible to run the buffer in the windows environment and then read from it in Matlab? > > hdr = buffer('get_hdr', [], ft_host, ft_port) > ??? Error using ==> buffer > ERROR: failed to create socket (1) > > Thanks, > Beth > > ------------------------------------------------------------------------------------------ > > Elizabeth Bock / MEG System Engineer > > McConnell Brain Imaging Centre / Montreal Neurological Institute > > McGill University / 3801 University St. / Montreal, QC H3A 2B4 > > > > MEG Lab: 514.398.6056 > > Mobile: 514.718.6342 > > ________________________________________ > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Stolk, A. [a.stolk at fcdonders.ru.nl] > Sent: Thursday, September 13, 2012 5:05 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] realtime buffer does not exit > > Hi Elizabeth, > > Could you try and start the buffer from outside matlab using 'demo_buffer.exe' (to be found in the 'realtime/bin/win32' directory)? This application may operate smoother than when starting the buffer from a single matlab thread. > > Best, > Arjen > > ----- Oorspronkelijk bericht ----- >> Van: "Elizabeth Anne Bock, Ms" >> Aan: fieldtrip at science.ru.nl >> Verzonden: Woensdag 12 september 2012 20:32:39 >> Onderwerp: [FieldTrip] realtime buffer does not exit >> I am using the realtime buffer and I have found I cannot exit the >> buffer within the Matlab command window. I am forced to exit Matlab >> or, more often, must kill the process manually from the windows task >> manager. I am using Windows XP to host the buffer and Linux to run >> acqftx. Here is what I am seeing: >> >>>> buffer('tcpserver', 'exit', ft_host, ft_port) >> In main: requesting cancelation of tcpserver thread >> >>>> buffer('tcpserver', 'init', ft_host, ft_port) >> ??? Error using ==> buffer >> thread is already running >> >> Any suggestions? >> Thanks, >> Elizabeth >> >> >> ------------------------------------------------------------------------------------------ >> >> Elizabeth Bock / MEG System Engineer >> >> McConnell Brain Imaging Centre / Montreal Neurological Institute >> >> McGill University / 3801 University St. / Montreal, QC H3A 2B4 >> >> >> >> MEG Lab: 514.398.6056 >> >> Mobile: 514.718.6342 >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Duncan.Astle at mrc-cbu.cam.ac.uk Fri Sep 14 16:58:26 2012 From: Duncan.Astle at mrc-cbu.cam.ac.uk (Duncan Astle) Date: Fri, 14 Sep 2012 14:58:26 +0000 Subject: [FieldTrip] Problem with clustering across electrode neighbours In-Reply-To: <5051BF53.5030606@donders.ru.nl> References: <5051BF53.5030606@donders.ru.nl> Message-ID: Thanks for your help. You were spot on; now the version is updated it runs perfectly. Thanks, Duncan ________________________________________________ Dr. Duncan Astle, Programme Leader Track, British Academy Research Fellow, MRC Cognition and Brain Sciences Unit, Chaucer Road, Cambridge. Duncan.Astle at mrc-cbu.cam.ac.uk From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig" Sent: 13 September 2012 12:11 To: FieldTrip discussion list Subject: Re: [FieldTrip] Problem with clustering across electrode neighbours Hey Duncan, it looks pretty much like you are using an old FieldTrip version with a new neighbourhood-structure. Could you check the with the most recent version again? Some months (about a year?) ago we changed the neighbour definition from cell arrays to structure arrays, so any attempt to access cfg.neighbours{i} will fail, cause it has to be cfg.neighbours(i) instead. But as I already said, this has been changed quite some time back in the past :) Essentially, your code is fine, but some note that cfg.neighbourdist should be a scalar, not the string 'number', but only if cfg.method='distance'. If you choose cfg.method = 'template' then cfg.neighbourdist is not used, cause a template is loaded. Best, Jörn On 9/13/2012 12:46 PM, Duncan Astle wrote: Dear Fieldtrippers, I am rather new to this, but am attempting to do some cluster stats on my ERP sensor level data. It is working well, and I can cluster across time, but I can't get it to cluster across electrode locations. I think it is because of a mistake that I am making in my 'neighbours' file, although it looks fine when I inspect it. This is the error message that I get: ??? Cell contents reference from a non-cell array object. Error in ==> clusterstat>makechanneighbstructmat at 520 [seld] = match_str(cfg.channel, cfg.neighbours{chan}.label); Error in ==> clusterstat at 60 channeighbstructmat = makechanneighbstructmat(cfg); Error in ==> statistics_montecarlo at 322 [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); Error in ==> statistics_wrapper at 285 [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); Error in ==> ft_timelockstatistics at 119 [stat, cfg] = statistics_wrapper(cfg, varargin{:}); Can anyone spot what I am doing wrong? This is how I make my neighbour file: cfg = []; cfg.layout = 'EEG1010.lay'; % try 'distance' as well cfg.feedback = 'yes'; % show a neighbour plot cfg.method = 'template'; cfg.neighbourdist = 'number'; cfg.template = 'EEG1010_neighb.mat' cfg.channel = 'all' cfg.feedback = 'yes'; neighbours = ft_prepare_neighbours(cfg, Load5Hard); % define neighbouring channels This is how I then try the stats: cfg = []; cfg.channel = 'all'; cfg.latency = [0.1 1.3]; cfg.avgovertime = 'no'; cfg.avgoverchannel = 'no'; cfg.parameter = 'individual'; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT' cfg.alpha = 0.05; cfg.correctm = 'cluster'; cfg.correcttail = 'prob'; cfg.numrandomization = 1000; cfg.feedback = 'yes'; % show a neighbour plot cfg.neighbours = neighbours; %cfg.minnbchan = 2; cfg.clusterstatistic = 'maxsum'; cfg.clusterthreshold = 'nonparametric'; cfg.clusteralpha = 0.01; cfg.clustercritval = 0.06; % cfg.clustertail = 0; cfg.tail = 0; Nsub = 19; cfg.design(1,1:2*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub)]; cfg.design(2,1:2*Nsub) = [1:Nsub 1:Nsub]; cfg.ivar = 1; % the 1st row in cfg.design contains the independent variable cfg.uvar = 2; % the 2nd row in cfg.design contains the subject number [stat] = ft_timelockstatistics(cfg, Load3Hard, Load3Easy) Any suggestions very gratefully received. Thanks, Duncan ________________________________________________ Dr. Duncan Astle, Programme Leader Track, British Academy Research Fellow, MRC Cognition and Brain Sciences Unit, Chaucer Road, Cambridge. Duncan.Astle at mrc-cbu.cam.ac.uk _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sat Sep 15 07:49:07 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sat, 15 Sep 2012 08:49:07 +0300 Subject: [FieldTrip] example: ft_realtime_selectiveaverage Message-ID: Hello, Did any of you dealt before with ft_realtime_selectiveaverage function. If so, could I have a simple code so I can see how it is run? Best, -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From dmitri89 at ut.ee Tue Sep 18 10:00:35 2012 From: dmitri89 at ut.ee (Dmitri Filimonov) Date: Tue, 18 Sep 2012 11:00:35 +0300 Subject: [FieldTrip] channel repair script Message-ID: <259e43dd8af0ecf135e3965765705a76.squirrel@mailhost.ut.ee> Dear Sir/Madam, My name is Dmitri Filimonov, I am a master student in University of Tartu (Estonia), using fieldtrip for EEG data analysis. I would like to ask some assistance with fieldtrip script. The task is to repair some EEG channels, so need to use ft_channelrepair. And I tried to do that after artifact rejection, so I could first see, which channels are noisy or disabled. I tried multiple combinations, yet there are still problems with the script. It looks like: >> channels_to_repair={'Fp1', 'Fp2'}; layout_file=('C:\ fieldtrip-20120703\template\layout\EEG1010.lay'); cfg=[]; cfg.layout = 'EEG1010.lay'; data.elec = ft_prepare_layout(cfg); neighbours = ft_prepare_neighbours(cfg, good_data) cfg = ft_checkconfig(cfg, 'required', {'method'}); cfg.method = 'distance'; (or ‘nearest’) cfg.badchannel=channels_to_repair; cfg.neighbours = ft_prepare_neighbours (cfg, good_data); G_data = ft_channelrepair(cfg, dood_data); (Good_data –is a processed and filtered data, yet containing channels, which have to be repaired.) After processing the program gives me several errors: reading layout from file EEG1010.lay the call to "ft_prepare_layout" took 0 seconds and an estimated NaN MB ??? Error using ==> ft_checkconfig at 151 The field cfg.method is required Error in ==> ft_prepare_neighbours at 77 cfg = ft_checkconfig(cfg, 'required', {'method'}); Other combinations emerge similar errors, or Error in ==> ft_neighbourselection at 30 neighbours = ft_prepare_neighbours(varargin{:}); Can you give me some help, what kind of ‘method’ exactly program wants me to mention (type)? Yours sincerely, Dmitri From Joachim.Gross at glasgow.ac.uk Tue Sep 18 11:00:34 2012 From: Joachim.Gross at glasgow.ac.uk (Joachim Gross) Date: Tue, 18 Sep 2012 10:00:34 +0100 Subject: [FieldTrip] Five PostDoc Positions in Glasgow Message-ID: Research Associate (5 posts available) University of Glasgow - Institute of Neuroscience and Psychology You will contribute to Wellcome Trust funded research entitled "Natural and modulated neural communication: State-dependent decoding and driving of human Brain Oscillations" (Joint Investigators: Gregor Thut, Joachim Gross). This is one of 5 simultaneously filled 5-year Research Associate positions covering different aspects of the above project. The job requires working in an interdisciplinary team of researchers on longstanding questions of how brain oscillations orchestrate brain functions, or relate to brain dysfunction. Depending on the position within the team, this will involve the development and/or application of new analysis methods to eavesdrop on brain communication and decode some of the information coded in brain oscillations (MEG/EEG), or using this knowledge for controlled intervention into brain oscillations by transcranial stimulation to modulate brain function (combined TMS/tACS-EEG). For more information on the position and environment please write to Joachim.Gross at glasgow.ac.uk, or Gregor.Thut at glasgow.ac.uk This post has funding available until 31 December 2017 Ref: 002653 Please apply here: http://www.gla.ac.uk/about/jobs/ Salary: Grade 7, £31,948 - £35,938 per annum Closing date: 15 October 2012 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Tue Sep 18 12:34:01 2012 From: jm.horschig at donders.ru.nl (=?UTF-8?B?IkrDtnJuIE0uIEhvcnNjaGlnIg==?=) Date: Tue, 18 Sep 2012 12:34:01 +0200 Subject: [FieldTrip] channel repair script In-Reply-To: <259e43dd8af0ecf135e3965765705a76.squirrel@mailhost.ut.ee> References: <259e43dd8af0ecf135e3965765705a76.squirrel@mailhost.ut.ee> Message-ID: <50584E19.3090300@donders.ru.nl> Dear Dmitri, I think you are confusing things here. Note that you are calling two FieldTrip functions subsequently. The error message you are receiving results from ft_prepare_neighbours. ft_prepare_neighbours needs a different cfg than ft_channelrepair. The call you are making, does however not make much sense, because you already called that function a few lines before. So just drop that cfg.neighbours = ft_prepare_neighbours(...) line and replace it by cfg.neighbours = neighbours. Thereby, you are removing the function call that results in an error (and you already did that call), and I guess everything will work fine. Best, Jörn On 9/18/2012 10:00 AM, Dmitri Filimonov wrote: > Dear Sir/Madam, > > My name is Dmitri Filimonov, I am a master student in University of Tartu > (Estonia), using fieldtrip for EEG data analysis. I would like to ask some > assistance with fieldtrip script. > The task is to repair some EEG channels, so need to use ft_channelrepair. > And I tried to do that after artifact rejection, so I could first see, > which channels are noisy or disabled. I tried multiple combinations, yet > there are still problems with the script. > It looks like: > >>> channels_to_repair={'Fp1', 'Fp2'}; > layout_file=('C:\ fieldtrip-20120703\template\layout\EEG1010.lay'); > > cfg=[]; > cfg.layout = 'EEG1010.lay'; > data.elec = ft_prepare_layout(cfg); > neighbours = ft_prepare_neighbours(cfg, good_data) > cfg = ft_checkconfig(cfg, 'required', {'method'}); > cfg.method = 'distance'; (or ‘nearest’) > cfg.badchannel=channels_to_repair; > cfg.neighbours = ft_prepare_neighbours (cfg, good_data); > G_data = ft_channelrepair(cfg, dood_data); > (Good_data –is a processed and filtered data, yet containing channels, > which have to be repaired.) > After processing the program gives me several errors: > > reading layout from file EEG1010.lay > the call to "ft_prepare_layout" took 0 seconds and an estimated NaN MB > ??? Error using ==> ft_checkconfig at 151 > The field cfg.method is required > Error in ==> ft_prepare_neighbours at 77 > cfg = ft_checkconfig(cfg, 'required', {'method'}); > > Other combinations emerge similar errors, or > > Error in ==> ft_neighbourselection at 30 > neighbours = ft_prepare_neighbours(varargin{:}); > > Can you give me some help, what kind of ‘method’ exactly program wants me > to mention (type)? > > Yours sincerely, > Dmitri > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From r.vandermeij at donders.ru.nl Wed Sep 19 11:20:12 2012 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Wed, 19 Sep 2012 11:20:12 +0200 Subject: [FieldTrip] Question of implementing Fieldtrip In-Reply-To: <201209190328.q8J3SNa4008385@melipona.ucdavis.edu> References: <201209190328.q8J3SNa4008385@melipona.ucdavis.edu> Message-ID: Hi Jinghao, I forwarded your question to the Fieldtrip mailing list. I don't entirely understand what you mean only saving clusters with psychological meaning. Given the parameters that you chose, you get a certain number of clusters, all of which are significant as a whole. In analogy, this means that the whole 'mountain range' is significant or not, not the 'individual peaks'. You could of course focus on a few of those clusters in your report, as long as you mention the other clusters. You could also try to set your parameters a little more stringent (i.e. a lower cfg.clusteralpha), this would 'reduce the number of peaks in your mountain range', as some peaks would then fall below the threshold. Hopefully, your clusters with 'psychological meaning' would still show up, albeit a little smaller/shorter. Hope this helps, Roemer > Well in fact I'm doing an intracranial EEG project currently where the data > should be analyzed statistically. The permutation analysis seems a good > choice and first I ran it with sample-specific independent t-test to get a > rough idea of the data in different conditions. > > I'm wondering how to apply cluster-based permutation in single sensor > analysis where I would like to save only the time clusters with > psychological meaning. I could not find the guidance of how to do this in > Fieldtrip. Could you please share with me the approach? That'll be really > helpful. > > Best Regards, > Jinghao Lu > > > Dept. of Physics > Zhejiang University > 866 Yuhangtang Road > Hangzhou > 310058 ZHEJIANG > CHINA > > Temporary Affiliate > Dynamic Memory Lab > UC Davis > > > Jinghao Lu > > > Dept. of Physics > Zhejiang University > 866 Yuhangtang Road > Hangzhou > 310058 ZHEJIANG > CHINA > > Temporary Affiliate > Dynamic Memory Lab > UC Davis > -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From politzerahless at gmail.com Wed Sep 19 13:46:19 2012 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Wed, 19 Sep 2012 06:46:19 -0500 Subject: [FieldTrip] Question of implementing Fieldtrip Message-ID: Hi Jinghao, You can use cfg.latency to limit the time period in which the test will look for clusters (for example, if you expect a difference to show up in a particular small time window and you are only interested in that difference, and don't want to test earlier or later differences); the tutorial has some more information. The choice of time window should be made based on predictions you had before the experiment, not based on inspection of the data. But like Roemer points out, it's not possible to save "only clusters with psychological meaning", as the statistical test doesn't know whether or not clusters have psychological meaning. Best, Steve > Message: 2 > Date: Wed, 19 Sep 2012 11:20:12 +0200 > From: Roemer van der Meij > To: Email discussion list for the FieldTrip project > > Cc: Jinghao Lu > Subject: Re: [FieldTrip] Question of implementing Fieldtrip > Message-ID: > < > CA+WpQ37dfrEoQV4gLuVTHWbMrBKexo8HFRprSJ9d5t8w45ZvYg at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Jinghao, > > I forwarded your question to the Fieldtrip mailing list. I don't entirely > understand what you mean only saving clusters with psychological meaning. > Given the parameters that you chose, you get a certain number of clusters, > all of which are significant as a whole. In analogy, this means that the > whole 'mountain range' is significant or not, not the 'individual peaks'. > You could of course focus on a few of those clusters in your report, as > long as you mention the other clusters. You could also try to set your > parameters a little more stringent (i.e. a lower cfg.clusteralpha), this > would 'reduce the number of peaks in your mountain range', as some peaks > would then fall below the threshold. Hopefully, your clusters with > 'psychological meaning' would still show up, albeit a little > smaller/shorter. > > Hope this helps, > Roemer > > > > > > Well in fact I'm doing an intracranial EEG project currently where the > data > > should be analyzed statistically. The permutation analysis seems a good > > choice and first I ran it with sample-specific independent t-test to get > a > > rough idea of the data in different conditions. > > > > I'm wondering how to apply cluster-based permutation in single sensor > > analysis where I would like to save only the time clusters with > > psychological meaning. I could not find the guidance of how to do this in > > Fieldtrip. Could you please share with me the approach? That'll be really > > helpful. > > > > Best Regards, > > Jinghao Lu > > > > > > Dept. of Physics > > Zhejiang University > > 866 Yuhangtang Road > > Hangzhou > > 310058 ZHEJIANG > > CHINA > > > > Temporary Affiliate > > Dynamic Memory Lab > > UC Davis > > > > > > Jinghao Lu > > > > > > Dept. of Physics > > Zhejiang University > > 866 Yuhangtang Road > > Hangzhou > > 310058 ZHEJIANG > > CHINA > > > > Temporary Affiliate > > Dynamic Memory Lab > > UC Davis > > > > > > -- > Roemer van der Meij M.Sc. > PhD student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > Tel: +31(0)24 3655932 > E-mail: r.vandermeij at donders.ru.nl > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120919/bc3080b9/attachment-0001.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 22, Issue 35 > ***************************************** > -- Stephen Politzer-Ahles University of Kansas Linguistics Department http://www.linguistics.ku.edu/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From haiteng.jiang at gmail.com Wed Sep 19 15:39:15 2012 From: haiteng.jiang at gmail.com (Haiteng Jiang) Date: Wed, 19 Sep 2012 15:39:15 +0200 Subject: [FieldTrip] Problems plotting TFR with different frequency sacle Message-ID: Dear Fieldtripers , I try to plot the TFR with Fieldtrip , but I find the frequency shift in the plotting when I use different frequency scale. Please see the attached two examples (4-30Hz versus 4-100Hz). The TFR within 4-30Hz is centered in alpha band while it is switched to beta band with the 4-100Hz. scale . Regarding to the TFR, I calculate it by using an adaptive sliding time window of four cycles length (Δt = 4/f) and a Hanning taper for lower frequencies (4–30 Hz), and a sliding time window of fixed length (200ms) and three orthogonal Slepian tapers resulting in ±10 Hz smoothing (29) for higher frequencies (30–100 Hz). Any suggestion ? All the best, Haiteng -- Haiteng Jiang PhD candidate Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Visiting address Room 2.32 Donders Centre for Cognitive Neuroimaging Kapittelweg 29 6525 EN Nijmegen the Netherlands Tel.: +31 (0)243668291 Web: https://sites.google.com/site/haitengjiang/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TFR_4-30.jpg Type: image/jpeg Size: 84855 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TFR_4-100.jpg Type: image/jpeg Size: 76534 bytes Desc: not available URL: From r.vandermeij at donders.ru.nl Wed Sep 19 16:04:19 2012 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Wed, 19 Sep 2012 16:04:19 +0200 Subject: [FieldTrip] Question of implementing Fieldtrip In-Reply-To: <201209191150.q8JBoQsp022660@phaenicia.ucdavis.edu> References: <201209191150.q8JBoQsp022660@phaenicia.ucdavis.edu> Message-ID: Hi Jinghao, If you are talking about only looking at a single channel and using those for analyses, you can use cfg.channel for this purpose. It might be a good idea as well to run through the respective tutorial, which can be found at: http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock. My previous suggestion will also aid in reducing small clusters popping up. Best, Roemer On Wed, Sep 19, 2012 at 1:50 PM, Jinghao Lu wrote: > > > As for my question, what I mean is that I want to apply the cluster-based > permutation on the data from a single intracranial electrode just like what > Maris did in his paper 'Nonparametric statistical testing of EEG- and MEG- > data'. In this way, the scattered clusters will reduce to only several. > Some discrete sample with significant difference may disappear as well. > > In Fieldtrip, if I choose cfg.correctm = 'cluster', then a neighborhood is > required. However, I only have one electrode and want to apply it on > time(or further frequency). How can I set cfg? > > -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Wed Sep 19 16:07:09 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 19 Sep 2012 16:07:09 +0200 Subject: [FieldTrip] Problems plotting TFR with different frequency sacle In-Reply-To: References: Message-ID: <5059D18D.4070705@donders.ru.nl> Hi Haiteng, I'm gonna drop by since you are in the office next door ;) Best, Jörn On 9/19/2012 3:39 PM, Haiteng Jiang wrote: > Dear Fieldtripers , > I try to plot the TFR with Fieldtrip , but I find the frequency > shift in the plotting when I use different frequency scale. Please > see the attached two examples (4-30Hz versus 4-100Hz). The TFR within > 4-30Hz is centered in alpha band while it is switched to beta band > with the 4-100Hz. scale . Regarding to the TFR, I calculate it by > using an adaptive sliding time window of four cycles length (?t = 4/f) > and a Hanning taper for lower frequencies (4--30 Hz), and a sliding > time window of fixed length (200ms) and three orthogonal Slepian > tapers resulting in ±10 Hz smoothing (29) for higher frequencies > (30--100 Hz). > Any suggestion ? > All the best, > Haiteng > -- > Haiteng Jiang > PhD candidate > Neuronal Oscillations Group > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > > Visiting address > Room 2.32 > Donders Centre for Cognitive Neuroimaging > Kapittelweg 29 > 6525 EN Nijmegen > the Netherlands > > Tel.: +31 (0)243668291 > Web: https://sites.google.com/site/haitengjiang/ > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From Markus.Butz at uni-duesseldorf.de Wed Sep 19 16:25:33 2012 From: Markus.Butz at uni-duesseldorf.de (Markus Butz) Date: Wed, 19 Sep 2012 15:25:33 +0100 Subject: [FieldTrip] ft_checkcoordsys outdated? Message-ID: <7630d250a5f1.5059e3ed@uni-duesseldorf.de> Dear list the headmodel tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the function ft_checkcoordsys. This function is also explained here http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. However, as far as I can see it is not existent in the fieldtrip version I am using right now, ie 20111101. How come? Is it outdated or do I miss something here? Best wishes Markus -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at donders.ru.nl Wed Sep 19 18:17:43 2012 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Wed, 19 Sep 2012 18:17:43 +0200 Subject: [FieldTrip] ft_checkcoordsys outdated? In-Reply-To: <7630d250a5f1.5059e3ed@uni-duesseldorf.de> References: <7630d250a5f1.5059e3ed@uni-duesseldorf.de> Message-ID: Hi Markus, Indeed it is outdated. It has been renamed to ft_determine_coordsys and moved to utilities: http://code.google.com/p/fieldtrip/source/detail?spec=svn3219&r=3219 Thanks for spotting that on the tutorial, as it should be updated. Cheers, Johanna 2012/9/19 Markus Butz > Dear list > > the headmodel tutorial ( > http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the > function ft_checkcoordsys. > This function is also explained here > http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. > However, as far as I can see it is not existent in the fieldtrip version I > am using right now, ie 20111101. > How come? Is it outdated or do I miss something here? > > Best wishes > Markus > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Sep 19 19:06:12 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 19 Sep 2012 19:06:12 +0200 Subject: [FieldTrip] ft_checkcoordsys outdated? In-Reply-To: References: <7630d250a5f1.5059e3ed@uni-duesseldorf.de> Message-ID: ...and the good thing about a wiki is: anybody can update it! ;-) Best, Jan-Mathijs On Sep 19, 2012, at 6:17 PM, Johanna Zumer wrote: > Hi Markus, > > Indeed it is outdated. It has been renamed to ft_determine_coordsys and moved to utilities: http://code.google.com/p/fieldtrip/source/detail?spec=svn3219&r=3219 > Thanks for spotting that on the tutorial, as it should be updated. > > Cheers, > Johanna > > 2012/9/19 Markus Butz > Dear list > > the headmodel tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the function ft_checkcoordsys. > This function is also explained here http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. > However, as far as I can see it is not existent in the fieldtrip version I am using right now, ie 20111101. > How come? Is it outdated or do I miss something here? > > Best wishes > Markus > > > > > > _______________________________________________ > 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 Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jhlu at ucdavis.edu Thu Sep 20 00:29:25 2012 From: jhlu at ucdavis.edu (Jinghao Lu) Date: Wed, 19 Sep 2012 15:29:25 -0700 (PDT) Subject: [FieldTrip] problem of implementing fieldtrip Message-ID: <201209192229.q8JMTPtA023532@syrphus.ucdavis.edu> Hi Roemer, the more exact problem may be like this: 1. I used eeglab to do all the erps and time-frequency and then used 'eeglab2fieldtrip(preprocessing, which seems the only way)' 2. then ran ft_timelockanalysis to generate erps, with cfg.channel = {'naLeft1'}(only one channel) 3. ran permutation with cfg.correctm = 'cluster' and subsequent cfg settings. However, an error message came out saying: "Error using ==> statistics_wrapper at 249 You need to specify a neighbourstructure" Which part did I set wrong? Best, Jinghao > 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: Question of implementing Fieldtrip (Roemer van der Meij) > 2. Re: Problems plotting TFR with different frequency sacle > (J?rn M. Horschig) > 3. ft_checkcoordsys outdated? (Markus Butz) > 4. Re: ft_checkcoordsys outdated? (Johanna Zumer) > 5. Re: ft_checkcoordsys outdated? (jan-mathijs schoffelen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 19 Sep 2012 16:04:19 +0200 > From: Roemer van der Meij > To: Email discussion list for the FieldTrip project > > Subject: Re: [FieldTrip] Question of implementing Fieldtrip > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Jinghao, > > If you are talking about only looking at a single channel and using those > for analyses, you can use cfg.channel for this purpose. It might be a > good > idea as well to run through the respective tutorial, which can be found > at: http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock. > My previous suggestion will also aid in reducing small clusters popping > up. > > Best, > Roemer > > > > On Wed, Sep 19, 2012 at 1:50 PM, Jinghao Lu wrote: > > > > > > > As for my question, what I mean is that I want to apply the > cluster-based > > permutation on the data from a single intracranial electrode just like > what > > Maris did in his paper 'Nonparametric statistical testing of EEG- and > MEG- > > data'. In this way, the scattered clusters will reduce to only several. > > Some discrete sample with significant difference may disappear as well. > > > > In Fieldtrip, if I choose cfg.correctm = 'cluster', then a neighborhood > is > > required. However, I only have one electrode and want to apply it on > > time(or further frequency). How can I set cfg? > > > > > -- > Roemer van der Meij M.Sc. > PhD student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > Tel: +31(0)24 3655932 > E-mail: r.vandermeij at donders.ru.nl > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Message: 2 > Date: Wed, 19 Sep 2012 16:07:09 +0200 > From: "J?rn M. Horschig" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Problems plotting TFR with different > frequency sacle > Message-ID: <5059D18D.4070705 at donders.ru.nl> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hi Haiteng, > > I'm gonna drop by since you are in the office next door ;) > > Best, > J?rn > > On 9/19/2012 3:39 PM, Haiteng Jiang wrote: > > Dear Fieldtripers , > > I try to plot the TFR with Fieldtrip , but I find the frequency > > shift in the plotting when I use different frequency scale. Please > > see the attached two examples (4-30Hz versus 4-100Hz). The TFR within > > 4-30Hz is centered in alpha band while it is switched to beta band > > with the 4-100Hz. scale . Regarding to the TFR, I calculate it by > > using an adaptive sliding time window of four cycles length (?t = 4/f) > > and a Hanning taper for lower frequencies (4--30 Hz), and a sliding > > time window of fixed length (200ms) and three orthogonal Slepian > > tapers resulting in ?10 Hz smoothing (29) for higher frequencies > > (30--100 Hz). > > Any suggestion ? > > All the best, > > Haiteng > > -- > > Haiteng Jiang > > PhD candidate > > Neuronal Oscillations Group > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > > > Visiting address > > Room 2.32 > > Donders Centre for Cognitive Neuroimaging > > Kapittelweg 29 > > 6525 EN Nijmegen > > the Netherlands > > > > Tel.: +31 (0)243668291 > > Web: https://sites.google.com/site/haitengjiang/ > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > J?rn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Message: 3 > Date: Wed, 19 Sep 2012 15:25:33 +0100 > From: Markus Butz > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] ft_checkcoordsys outdated? > Message-ID: <7630d250a5f1.5059e3ed at uni-duesseldorf.de> > Content-Type: text/plain; charset="us-ascii" > > Dear list > > the headmodel tutorial > (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the > function ft_checkcoordsys. > This function is also explained here > http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. > However, as far as I can see it is not existent in the fieldtrip version I > am using right now, ie 20111101. > How come? Is it outdated or do I miss something here? > > Best wishes > Markus > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Message: 4 > Date: Wed, 19 Sep 2012 18:17:43 +0200 > From: Johanna Zumer > To: Markus.Butz at uni-duesseldorf.de, FieldTrip discussion list > > Subject: Re: [FieldTrip] ft_checkcoordsys outdated? > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Markus, > > Indeed it is outdated. It has been renamed to ft_determine_coordsys and > moved to utilities: > http://code.google.com/p/fieldtrip/source/detail?spec=svn3219&r=3219 > Thanks for spotting that on the tutorial, as it should be updated. > > Cheers, > Johanna > > 2012/9/19 Markus Butz > > > Dear list > > > > the headmodel tutorial ( > > http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the > > function ft_checkcoordsys. > > This function is also explained here > > http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. > > However, as far as I can see it is not existent in the fieldtrip version > I > > am using right now, ie 20111101. > > How come? Is it outdated or do I miss something here? > > > > Best wishes > > Markus > > > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Message: 5 > Date: Wed, 19 Sep 2012 19:06:12 +0200 > From: jan-mathijs schoffelen > To: FieldTrip discussion list > Subject: Re: [FieldTrip] ft_checkcoordsys outdated? > Message-ID: > Content-Type: text/plain; charset="us-ascii" > > ...and the good thing about a wiki is: anybody can update it! ;-) > > Best, > Jan-Mathijs > > > On Sep 19, 2012, at 6:17 PM, Johanna Zumer wrote: > > > Hi Markus, > > > > Indeed it is outdated. It has been renamed to ft_determine_coordsys and > moved to utilities: > http://code.google.com/p/fieldtrip/source/detail?spec=svn3219&r=3219 > > Thanks for spotting that on the tutorial, as it should be updated. > > > > Cheers, > > Johanna > > > > 2012/9/19 Markus Butz > > Dear list > > > > the headmodel tutorial > (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the > function ft_checkcoordsys. > > This function is also explained here > http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. > > However, as far as I can see it is not existent in the fieldtrip version > I am using right now, ie 20111101. > > How come? Is it outdated or do I miss something here? > > > > Best wishes > > Markus > > > > > > > > > > > > _______________________________________________ > > 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 > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 22, Issue 37 > ***************************************** > Jinghao Lu Dept. of Physics Zhejiang University 866 Yuhangtang Road Hangzhou 310058 ZHEJIANG CHINA Temporary Affiliate Dynamic Memory Lab UC Davis From dmitri89 at ut.ee Thu Sep 20 09:54:59 2012 From: dmitri89 at ut.ee (Dmitri Filimonov) Date: Thu, 20 Sep 2012 10:54:59 +0300 Subject: [FieldTrip] channel repair script In-Reply-To: <50584E19.3090300@donders.ru.nl> References: <259e43dd8af0ecf135e3965765705a76.squirrel@mailhost.ut.ee> <50584E19.3090300@donders.ru.nl> Message-ID: Dear Jörn, Thank you for answering, but unfortunately it doesn't work anyway. I tried that also. It always gives "The field cfg.method is required" I've put several possible cfg.methods = *(like cfg.method = 'mtmfft' (in case if program wants me to set spectra calculating parameters); or 'nearest' (in case of neighbour selection method). Non of this works, yet I am trying to deal with it now. Best wishes, Dmitri > Dear Dmitri, > > I think you are confusing things here. > Note that you are calling two FieldTrip functions subsequently. The > error message you are receiving results from ft_prepare_neighbours. > ft_prepare_neighbours needs a different cfg than ft_channelrepair. The > call you are making, does however not make much sense, because you > already called that function a few lines before. So just drop that > cfg.neighbours = ft_prepare_neighbours(...) line and replace it by > cfg.neighbours = neighbours. Thereby, you are removing the function call > that results in an error (and you already did that call), and I guess > everything will work fine. > > Best, > Jörn > > On 9/18/2012 10:00 AM, Dmitri Filimonov wrote: >> Dear Sir/Madam, >> >> My name is Dmitri Filimonov, I am a master student in University of >> Tartu >> (Estonia), using fieldtrip for EEG data analysis. I would like to ask >> some >> assistance with fieldtrip script. >> The task is to repair some EEG channels, so need to use >> ft_channelrepair. >> And I tried to do that after artifact rejection, so I could first see, >> which channels are noisy or disabled. I tried multiple combinations, yet >> there are still problems with the script. >> It looks like: >> >>>> channels_to_repair={'Fp1', 'Fp2'}; >> layout_file=('C:\ fieldtrip-20120703\template\layout\EEG1010.lay'); >> >> cfg=[]; >> cfg.layout = 'EEG1010.lay'; >> data.elec = ft_prepare_layout(cfg); >> neighbours = ft_prepare_neighbours(cfg, good_data) >> cfg = ft_checkconfig(cfg, 'required', {'method'}); >> cfg.method = 'distance'; (or ‘nearest’) >> cfg.badchannel=channels_to_repair; >> cfg.neighbours = ft_prepare_neighbours (cfg, good_data); >> G_data = ft_channelrepair(cfg, dood_data); >> (Good_data –is a processed and filtered data, yet containing channels, >> which have to be repaired.) >> After processing the program gives me several errors: >> >> reading layout from file EEG1010.lay >> the call to "ft_prepare_layout" took 0 seconds and an estimated NaN MB >> ??? Error using ==> ft_checkconfig at 151 >> The field cfg.method is required >> Error in ==> ft_prepare_neighbours at 77 >> cfg = ft_checkconfig(cfg, 'required', {'method'}); >> >> Other combinations emerge similar errors, or >> >> Error in ==> ft_neighbourselection at 30 >> neighbours = ft_prepare_neighbours(varargin{:}); >> >> Can you give me some help, what kind of ‘method’ exactly program wants >> me >> to mention (type)? >> >> Yours sincerely, >> Dmitri >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Thu Sep 20 09:59:27 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 20 Sep 2012 09:59:27 +0200 Subject: [FieldTrip] problem of implementing fieldtrip In-Reply-To: <201209192229.q8JMTPtA023532@syrphus.ucdavis.edu> References: <201209192229.q8JMTPtA023532@syrphus.ucdavis.edu> Message-ID: <505ACCDF.6020100@donders.ru.nl> Dear Jinghao, you need to specify cfg.avgoverchan='yes' prior to calling ft_timelockstatistics to tell fieldtrip that no clustering in space is needed. It should work fine then. Best, Jörn On 9/20/2012 12:29 AM, Jinghao Lu wrote: > Hi Roemer, > > the more exact problem may be like this: > > 1. I used eeglab to do all the erps and time-frequency and then used > 'eeglab2fieldtrip(preprocessing, which seems the only way)' > > 2. then ran ft_timelockanalysis to generate erps, with cfg.channel = > {'naLeft1'}(only one channel) > > 3. ran permutation with cfg.correctm = 'cluster' and subsequent cfg > settings. However, an error message came out saying: > > > "Error using ==> statistics_wrapper at 249 > You need to specify a neighbourstructure" > > Which part did I set wrong? > > Best, > Jinghao > > > > > >> 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: Question of implementing Fieldtrip (Roemer van der Meij) >> 2. Re: Problems plotting TFR with different frequency sacle >> (J?rn M. Horschig) >> 3. ft_checkcoordsys outdated? (Markus Butz) >> 4. Re: ft_checkcoordsys outdated? (Johanna Zumer) >> 5. Re: ft_checkcoordsys outdated? (jan-mathijs schoffelen) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Wed, 19 Sep 2012 16:04:19 +0200 >> From: Roemer van der Meij >> To: Email discussion list for the FieldTrip project >> >> Subject: Re: [FieldTrip] Question of implementing Fieldtrip >> Message-ID: >> XXYb5Wb0vcyG_j=8g at mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi Jinghao, >> >> If you are talking about only looking at a single channel and using those >> for analyses, you can use cfg.channel for this purpose. It might be a >> good >> idea as well to run through the respective tutorial, which can be found >> at: http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock. >> My previous suggestion will also aid in reducing small clusters popping >> up. >> >> Best, >> Roemer >> >> >> >> On Wed, Sep 19, 2012 at 1:50 PM, Jinghao Lu wrote: >> >>> >>> As for my question, what I mean is that I want to apply the >> cluster-based >>> permutation on the data from a single intracranial electrode just like >> what >>> Maris did in his paper 'Nonparametric statistical testing of EEG- and >> MEG- >>> data'. In this way, the scattered clusters will reduce to only several. >>> Some discrete sample with significant difference may disappear as well. >>> >>> In Fieldtrip, if I choose cfg.correctm = 'cluster', then a neighborhood >> is >>> required. However, I only have one electrode and want to apply it on >>> time(or further frequency). How can I set cfg? >>> >>> >> -- >> Roemer van der Meij M.Sc. >> PhD student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognition >> P.O. Box 9104 >> 6500 HE Nijmegen >> The Netherlands >> Tel: +31(0)24 3655932 >> E-mail: r.vandermeij at donders.ru.nl >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> > 56cf/attachment-0001.html> >> ------------------------------ >> >> Message: 2 >> Date: Wed, 19 Sep 2012 16:07:09 +0200 >> From: "J?rn M. Horschig" >> To: FieldTrip discussion list >> Subject: Re: [FieldTrip] Problems plotting TFR with different >> frequency sacle >> Message-ID: <5059D18D.4070705 at donders.ru.nl> >> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" >> >> Hi Haiteng, >> >> I'm gonna drop by since you are in the office next door ;) >> >> Best, >> J?rn >> >> On 9/19/2012 3:39 PM, Haiteng Jiang wrote: >>> Dear Fieldtripers , >>> I try to plot the TFR with Fieldtrip , but I find the frequency >>> shift in the plotting when I use different frequency scale. Please >>> see the attached two examples (4-30Hz versus 4-100Hz). The TFR within >>> 4-30Hz is centered in alpha band while it is switched to beta band >>> with the 4-100Hz. scale . Regarding to the TFR, I calculate it by >>> using an adaptive sliding time window of four cycles length (?t = 4/f) >>> and a Hanning taper for lower frequencies (4--30 Hz), and a sliding >>> time window of fixed length (200ms) and three orthogonal Slepian >>> tapers resulting in ?10 Hz smoothing (29) for higher frequencies >>> (30--100 Hz). >>> Any suggestion ? >>> All the best, >>> Haiteng >>> -- >>> Haiteng Jiang >>> PhD candidate >>> Neuronal Oscillations Group >>> Donders Institute for Brain, Cognition and Behaviour >>> Centre for Cognitive Neuroimaging >>> Radboud University Nijmegen >>> >>> Visiting address >>> Room 2.32 >>> Donders Centre for Cognitive Neuroimaging >>> Kapittelweg 29 >>> 6525 EN Nijmegen >>> the Netherlands >>> >>> Tel.: +31 (0)243668291 >>> Web: https://sites.google.com/site/haitengjiang/ >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> -- >> J?rn M. Horschig >> PhD Student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> Neuronal Oscillations Group >> FieldTrip Development Team >> >> P.O. Box 9101 >> NL-6500 HB Nijmegen >> The Netherlands >> >> Contact: >> E-Mail: jm.horschig at donders.ru.nl >> Tel: +31-(0)24-36-68493 >> Web: http://www.ru.nl/donders >> >> Visiting address: >> Trigon, room 2.30 >> Kapittelweg 29 >> NL-6525 EN Nijmegen >> The Netherlands >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> > dfd7/attachment-0001.html> >> ------------------------------ >> >> Message: 3 >> Date: Wed, 19 Sep 2012 15:25:33 +0100 >> From: Markus Butz >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] ft_checkcoordsys outdated? >> Message-ID: <7630d250a5f1.5059e3ed at uni-duesseldorf.de> >> Content-Type: text/plain; charset="us-ascii" >> >> Dear list >> >> the headmodel tutorial >> (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the >> function ft_checkcoordsys. >> This function is also explained here >> http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. >> However, as far as I can see it is not existent in the fieldtrip version > I >> am using right now, ie 20111101. >> How come? Is it outdated or do I miss something here? >> >> Best wishes >> Markus >> >> >> >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> > 9565/attachment-0001.html> >> ------------------------------ >> >> Message: 4 >> Date: Wed, 19 Sep 2012 18:17:43 +0200 >> From: Johanna Zumer >> To: Markus.Butz at uni-duesseldorf.de, FieldTrip discussion list >> >> Subject: Re: [FieldTrip] ft_checkcoordsys outdated? >> Message-ID: >> 8FHxUvcAhG0Or35B=Ow at mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi Markus, >> >> Indeed it is outdated. It has been renamed to ft_determine_coordsys and >> moved to utilities: >> http://code.google.com/p/fieldtrip/source/detail?spec=svn3219&r=3219 >> Thanks for spotting that on the tutorial, as it should be updated. >> >> Cheers, >> Johanna >> >> 2012/9/19 Markus Butz >> >>> Dear list >>> >>> the headmodel tutorial ( >>> http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the >>> function ft_checkcoordsys. >>> This function is also explained here >>> http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. >>> However, as far as I can see it is not existent in the fieldtrip > version >> I >>> am using right now, ie 20111101. >>> How come? Is it outdated or do I miss something here? >>> >>> Best wishes >>> Markus >>> >>> >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> > 1c05/attachment-0001.html> >> ------------------------------ >> >> Message: 5 >> Date: Wed, 19 Sep 2012 19:06:12 +0200 >> From: jan-mathijs schoffelen >> To: FieldTrip discussion list >> Subject: Re: [FieldTrip] ft_checkcoordsys outdated? >> Message-ID: >> Content-Type: text/plain; charset="us-ascii" >> >> ...and the good thing about a wiki is: anybody can update it! ;-) >> >> Best, >> Jan-Mathijs >> >> >> On Sep 19, 2012, at 6:17 PM, Johanna Zumer wrote: >> >>> Hi Markus, >>> >>> Indeed it is outdated. It has been renamed to ft_determine_coordsys > and >> moved to utilities: >> http://code.google.com/p/fieldtrip/source/detail?spec=svn3219&r=3219 >>> Thanks for spotting that on the tutorial, as it should be updated. >>> >>> Cheers, >>> Johanna >>> >>> 2012/9/19 Markus Butz >>> Dear list >>> >>> the headmodel tutorial >> (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the >> function ft_checkcoordsys. >>> This function is also explained here >> http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. >>> However, as far as I can see it is not existent in the fieldtrip > version >> I am using right now, ie 20111101. >>> How come? Is it outdated or do I miss something here? >>> >>> Best wishes >>> Markus >>> >>> >>> >>> >>> >>> _______________________________________________ >>> 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 >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> > 674f/attachment.html> >> ------------------------------ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> End of fieldtrip Digest, Vol 22, Issue 37 >> ***************************************** >> > Jinghao Lu > > > Dept. of Physics > Zhejiang University > 866 Yuhangtang Road > Hangzhou > 310058 ZHEJIANG > CHINA > > Temporary Affiliate > Dynamic Memory Lab > UC Davis > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From jm.horschig at donders.ru.nl Thu Sep 20 10:09:53 2012 From: jm.horschig at donders.ru.nl (=?UTF-8?B?IkrDtnJuIE0uIEhvcnNjaGlnIg==?=) Date: Thu, 20 Sep 2012 10:09:53 +0200 Subject: [FieldTrip] channel repair script In-Reply-To: References: <259e43dd8af0ecf135e3965765705a76.squirrel@mailhost.ut.ee> <50584E19.3090300@donders.ru.nl> Message-ID: <505ACF51.4040706@donders.ru.nl> Hi Dmitri, looking at your script it seems that the error occurs even right at the start. You said you are doing this (the very first lines that you pasted) cfg=[]; cfg.layout = 'EEG1010.lay'; data.elec = ft_prepare_layout(cfg); neighbours = ft_prepare_neighbours(cfg, good_data) which means that you call ft_prepare_neighbours with a configuration structure which only has cfg.layout and nothing else. However, you did not specify a method how neighbours should be defined. If you look up the help from ft_prepare_neighbours, you will see what methods are available. Note that these are distinct from cfg.method for other functions. Every function has it's own cfg-settings, which are mostly independent from those of other functions. For example 'nearest' is not an method for ft_prepare_neighbours but for ft_channelrepair. Likewise, 'mtmfft' is a method for ft_freqanalysis, but not for any other method. I would strongly advise you to start with FieldTrip by going through our tutorials: http://fieldtrip.fcdonders.nl/tutorial This is the easiest way to get acquainted and used to the way FieldTrip works with cfg-and data-structures. And then check our frequently asked questions: http://fieldtrip.fcdonders.nl/faq In your case, especially http://fieldtrip.fcdonders.nl/faq/how_can_i_define_neighbouring_sensors http://fieldtrip.fcdonders.nl/faq/how_does_ft_prepare_neighbours_work Should you need any more assistance, feel free to ask. Best, Jörn On 9/20/2012 9:54 AM, Dmitri Filimonov wrote: > Dear Jörn, > > Thank you for answering, but unfortunately it doesn't work anyway. I tried > that also. It always gives > > "The field cfg.method is required" > > I've put several possible cfg.methods = *(like cfg.method = 'mtmfft' (in > case if program wants me to set spectra calculating parameters); or > 'nearest' (in case of neighbour selection method). Non of this works, yet > I am trying to deal with it now. > > Best wishes, > Dmitri > > > > >> Dear Dmitri, >> >> I think you are confusing things here. >> Note that you are calling two FieldTrip functions subsequently. The >> error message you are receiving results from ft_prepare_neighbours. >> ft_prepare_neighbours needs a different cfg than ft_channelrepair. The >> call you are making, does however not make much sense, because you >> already called that function a few lines before. So just drop that >> cfg.neighbours = ft_prepare_neighbours(...) line and replace it by >> cfg.neighbours = neighbours. Thereby, you are removing the function call >> that results in an error (and you already did that call), and I guess >> everything will work fine. >> >> Best, >> Jörn >> >> On 9/18/2012 10:00 AM, Dmitri Filimonov wrote: >>> Dear Sir/Madam, >>> >>> My name is Dmitri Filimonov, I am a master student in University of >>> Tartu >>> (Estonia), using fieldtrip for EEG data analysis. I would like to ask >>> some >>> assistance with fieldtrip script. >>> The task is to repair some EEG channels, so need to use >>> ft_channelrepair. >>> And I tried to do that after artifact rejection, so I could first see, >>> which channels are noisy or disabled. I tried multiple combinations, yet >>> there are still problems with the script. >>> It looks like: >>> >>>>> channels_to_repair={'Fp1', 'Fp2'}; >>> layout_file=('C:\ fieldtrip-20120703\template\layout\EEG1010.lay'); >>> >>> cfg=[]; >>> cfg.layout = 'EEG1010.lay'; >>> data.elec = ft_prepare_layout(cfg); >>> neighbours = ft_prepare_neighbours(cfg, good_data) >>> cfg = ft_checkconfig(cfg, 'required', {'method'}); >>> cfg.method = 'distance'; (or ‘nearest’) >>> cfg.badchannel=channels_to_repair; >>> cfg.neighbours = ft_prepare_neighbours (cfg, good_data); >>> G_data = ft_channelrepair(cfg, dood_data); >>> (Good_data –is a processed and filtered data, yet containing channels, >>> which have to be repaired.) >>> After processing the program gives me several errors: >>> >>> reading layout from file EEG1010.lay >>> the call to "ft_prepare_layout" took 0 seconds and an estimated NaN MB >>> ??? Error using ==> ft_checkconfig at 151 >>> The field cfg.method is required >>> Error in ==> ft_prepare_neighbours at 77 >>> cfg = ft_checkconfig(cfg, 'required', {'method'}); >>> >>> Other combinations emerge similar errors, or >>> >>> Error in ==> ft_neighbourselection at 30 >>> neighbours = ft_prepare_neighbours(varargin{:}); >>> >>> Can you give me some help, what kind of ‘method’ exactly program wants >>> me >>> to mention (type)? >>> >>> Yours sincerely, >>> Dmitri >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> -- >> Jörn M. Horschig >> PhD Student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> Neuronal Oscillations Group >> FieldTrip Development Team >> >> P.O. Box 9101 >> NL-6500 HB Nijmegen >> The Netherlands >> >> Contact: >> E-Mail: jm.horschig at donders.ru.nl >> Tel: +31-(0)24-36-68493 >> Web: http://www.ru.nl/donders >> >> Visiting address: >> Trigon, room 2.30 >> Kapittelweg 29 >> NL-6525 EN Nijmegen >> The Netherlands >> >> _______________________________________________ >> 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 -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From b.reuderink at donders.ru.nl Thu Sep 20 11:16:27 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Thu, 20 Sep 2012 11:16:27 +0200 Subject: [FieldTrip] ft_realtime_selectiveaverage In-Reply-To: References: Message-ID: Dear Hamza, I guess that the function is trying to samples form the FieldTrip buffer form the period before it was started, i.e. samples with negative indices. This might be related to the triggers you have and your trial fun. Your best bet is to start the MATLAB debugger, and just step through the code until the error occurs. Inspection of variables might give a clue on what is happening. In the mean-time, I'll try to update the examples with some extra information on how to call these functions. Best regards, Boris -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl On 13 sep. 2012, at 11:19, Hamza Fawzi Altakroury (Student) wrote: > Hello, > > I am tried to run the ft_realtime_selectiveaverage function but I got the following error: > (note: the error appears after showing a plot with title: condition 255, ntrials = 1.) > > Could you tell me what is the problem. (exactly what does "connet read data before the begin of the file"). > > Best, > > ??? Error using ==> ft_read_data at 243 > cannot read data before the begin of the file > > Error in ==> ft_realtime_selectiveaverage at 94 > dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', chanindx, 'checkboundary', false); > > Error in ==> online1 at 48 > ft_realtime_selectiveaverage(cfg) > > Statements: > > cfg = []; > cfg.channel = {'A1'}; > cfg.dataset = 'buffer://localhost:1972'; > %cfg.trialfun = 'myfun'; > cfg.trialdef.eventtype = 'stimulus'; % By placing '?' we can see the eventtype that we have. > cfg.trialdef.eventvalue = 255; > cfg.trialdef.pre = 0; > cfg.trialdef.post = 1.0; > cfg = ft_definetrial(cfg); > ft_realtime_selectiveaverage(cfg) > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From hamzaf at sabanciuniv.edu Thu Sep 20 11:29:48 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Thu, 20 Sep 2012 12:29:48 +0300 Subject: [FieldTrip] ft_realtime_selectiveaverage In-Reply-To: References: Message-ID: Thank you Boris Best, Hamza On Thu, Sep 20, 2012 at 12:16 PM, Boris Reuderink wrote: > Dear Hamza, > > I guess that the function is trying to samples form the FieldTrip buffer > form the period before it was started, i.e. samples with negative indices. > This might be related to the triggers you have and your trial fun. > > Your best bet is to start the MATLAB debugger, and just step through the > code until the error occurs. Inspection of variables might give a clue on > what is happening. > > In the mean-time, I'll try to update the examples with some extra > information on how to call these functions. > > Best regards, > > Boris > > -- > twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl > > On 13 sep. 2012, at 11:19, Hamza Fawzi Altakroury (Student) < > hamzaf at sabanciuniv.edu> wrote: > > > Hello, > > > > I am tried to run the ft_realtime_selectiveaverage function but I got > the following error: > > (note: the error appears after showing a plot with title: condition 255, > ntrials = 1.) > > > > Could you tell me what is the problem. (exactly what does "connet read > data before the begin of the file"). > > > > Best, > > > > ??? Error using ==> ft_read_data at 243 > > cannot read data before the begin of the file > > > > Error in ==> ft_realtime_selectiveaverage at 94 > > dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', > begsample, 'endsample', endsample, 'chanindx', chanindx, 'checkboundary', > false); > > > > Error in ==> online1 at 48 > > ft_realtime_selectiveaverage(cfg) > > > > Statements: > > > > cfg = []; > > cfg.channel = {'A1'}; > > cfg.dataset = 'buffer://localhost:1972'; > > %cfg.trialfun = 'myfun'; > > cfg.trialdef.eventtype = 'stimulus'; % By placing '?' we > can see the eventtype that we have. > > cfg.trialdef.eventvalue = 255; > > cfg.trialdef.pre = 0; > > cfg.trialdef.post = 1.0; > > cfg = ft_definetrial(cfg); > > ft_realtime_selectiveaverage(cfg) > > > > -- > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabancı University > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Thu Sep 20 14:46:17 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 20 Sep 2012 14:46:17 +0200 Subject: [FieldTrip] Problems plotting TFR with different frequency sacle In-Reply-To: <5059D18D.4070705@donders.ru.nl> References: <5059D18D.4070705@donders.ru.nl> Message-ID: <505B1019.2050904@donders.ru.nl> For those having similar problems, note that FieldTrip (actually Matlab's image function) cannot handle unequal axis, e.g. a data.freq may not be [1 2 3 4 5 10 15 20]. Therefore, ladies and gentlemen, let me introduce bug number 1729: http://bugzilla.fcdonders.nl/show_bug.cgi?id=1729 On 9/19/2012 4:07 PM, "Jörn M. Horschig" wrote: > Hi Haiteng, > > I'm gonna drop by since you are in the office next door ;) > > Best, > Jörn > > On 9/19/2012 3:39 PM, Haiteng Jiang wrote: >> Dear Fieldtripers , >> I try to plot the TFR with Fieldtrip , but I find the frequency >> shift in the plotting when I use different frequency scale. Please >> see the attached two examples (4-30Hz versus 4-100Hz). The TFR >> within 4-30Hz is centered in alpha band while it is switched to beta >> band with the 4-100Hz. scale . Regarding to the TFR, I calculate it >> by using an adaptive sliding time window of four cycles length (?t = >> 4/f) and a Hanning taper for lower frequencies (4--30 Hz), and a >> sliding time window of fixed length (200ms) and three orthogonal >> Slepian tapers resulting in ±10 Hz smoothing (29) for higher >> frequencies (30--100 Hz). >> Any suggestion ? >> All the best, >> Haiteng >> -- >> Haiteng Jiang >> PhD candidate >> Neuronal Oscillations Group >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> >> Visiting address >> Room 2.32 >> Donders Centre for Cognitive Neuroimaging >> Kapittelweg 29 >> 6525 EN Nijmegen >> the Netherlands >> >> Tel.: +31 (0)243668291 >> Web: https://sites.google.com/site/haitengjiang/ >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail:jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web:http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From pgoodin at swin.edu.au Sun Sep 23 15:14:28 2012 From: pgoodin at swin.edu.au (Peter Goodin) Date: Sun, 23 Sep 2012 13:14:28 +0000 Subject: [FieldTrip] Neuromag sensor level stats Message-ID: Hi Fieldtrippers, I'm at a stage where I'd like to do statistical analysis on my ERF neuromag data, but don't really know where to begin. I'd like to do a cluster analysis, but the tutorial material is for a CTF system. I'm using a neuromag 306 channel which complicates matters somewhat due to the different sensor types. I've searched the mailing list but can't find any solid answers / example scripts. The most pressing questions I have are: 1. Despite running the data through maxfilter and entering in the bad channels, occasionally one gets through (not the same one). I've used Fieldtrip's repairchannel function on the data, making sure to replace the channel only with like sensor neighbouring sensors. While I know this is a common method for fixing bad channels in EEG, does the same hold for MEG due to non-existent smearing of the signal? Is it best to keep the fixed channel(s) or just remove them from the stats analysis across all participants? 2. Given the three sensor types on the neuromag system, do I need to run three different cluster analyses (one for mags, one for xgrads, one for ygrads), each time specifying like sensor neighbours? Alternatively, If I'm not interested in the mags data, can I just run one using the data from the combined gradiometers? 3. When examining for group x condition effects, would I use a three row design matrix with row 1 containing group, row 2 containing participants and row 3 conditions? Thanks for any help, Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Sun Sep 23 16:49:02 2012 From: smoratti at psi.ucm.es (smoratti at psi.ucm.es) Date: Sun, 23 Sep 2012 16:49:02 +0200 Subject: [FieldTrip] Neuromag sensor level stats In-Reply-To: References: Message-ID: <2007ABA6-22AA-480F-9DC8-64BFA482CA07@psi.ucm.es> Dear Peter, I would do the stats on Magnetometers and Gradiometers separately. Use cfg.layout = 'neuromag_306mag' for magnetometers. Before using the gradiometers I would use ft_combineplanar and then use the combined planar topographies for the stats (cfg.layout = 'neuromag_306cmb'). Hope that helps, Best, Stephan ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 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 23/09/2012, a las 15:14, Peter Goodin escribió: > Hi Fieldtrippers, > > I'm at a stage where I'd like to do statistical analysis on my ERF neuromag data, but don't really know where to begin. I'd like to do a cluster analysis, but the tutorial material is for a CTF system. I'm using a neuromag 306 channel which complicates matters somewhat due to the different sensor types. I've searched the mailing list but can't find any solid answers / example scripts. > > The most pressing questions I have are: > > 1. Despite running the data through maxfilter and entering in the bad channels, occasionally one gets through (not the same one). I've used Fieldtrip's repairchannel function on the data, making sure to replace the channel only with like sensor neighbouring sensors. While I know this is a common method for fixing bad channels in EEG, does the same hold for MEG due to non-existent smearing of the signal? Is it best to keep the fixed channel(s) or just remove them from the stats analysis across all participants? > > 2. Given the three sensor types on the neuromag system, do I need to run three different cluster analyses (one for mags, one for xgrads, one for ygrads), each time specifying like sensor neighbours? Alternatively, If I'm not interested in the mags data, can I just run one using the data from the combined gradiometers? > > 3. When examining for group x condition effects, would I use a three row design matrix with row 1 containing group, row 2 containing participants and row 3 conditions? > > Thanks for any help, > > Peter > _______________________________________________ > 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 jm.horschig at donders.ru.nl Mon Sep 24 14:15:05 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 24 Sep 2012 14:15:05 +0200 Subject: [FieldTrip] Neuromag sensor level stats In-Reply-To: References: Message-ID: <50604EC9.7050705@donders.ru.nl> Dear Peter, regarding your first question, most people here at the Donders actually repair bad channels. When computing the grandaverage over subjects or doing some statistics across subjects, only those channels which are in common for all datasets are used. Thus, if having different channels damaged/rejected per subjects, you can end up with a fairly low amount of channels. But, in the end it depends pretty much on what channels you reject wrt your hypothesis, e.g. having few occipital channels while being interested in motor regions won't constitute a big problem, so no need to interpolate. I leave the question whether it's a correct thing to do up to you (imho: I wouldn't worry too much about it). Regarding your third question: In FieldTrip you can only compare two conditions directly (at least when doing cluster-based permutation testing). Also, any interaction needs to be setup manually. Best, Jörn On 9/23/2012 3:14 PM, Peter Goodin wrote: > Hi Fieldtrippers, > > I'm at a stage where I'd like to do statistical analysis on my ERF > neuromag data, but don't really know where to begin. I'd like to do a > cluster analysis, but the tutorial material is for a CTF system. I'm > using a neuromag 306 channel which complicates matters somewhat due to > the different sensor types. I've searched the mailing list but can't > find any solid answers / example scripts. > > The most pressing questions I have are: > > 1. Despite running the data through maxfilter and entering in the bad > channels, occasionally one gets through (not the same one). I've used > Fieldtrip's repairchannel function on the data, making sure to replace > the channel only with like sensor neighbouring sensors. While I know > this is a common method for fixing bad channels in EEG, does the same > hold for MEG due to non-existent smearing of the signal? Is it best to > keep the fixed channel(s) or just remove them from the stats analysis > across all participants? > > 2. Given the three sensor types on the neuromag system, do I need to > run three different cluster analyses (one for mags, one for xgrads, > one for ygrads), each time specifying like sensor neighbours? > Alternatively, If I'm not interested in the mags data, can I just run > one using the data from the combined gradiometers? > > 3. When examining for group x condition effects, would I use a three > row design matrix with row 1 containing group, row 2 containing > participants and row 3 conditions? > > Thanks for any help, > > Peter > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From f.roux at bcbl.eu Mon Sep 24 16:29:52 2012 From: f.roux at bcbl.eu (Frederic Roux) Date: Mon, 24 Sep 2012 16:29:52 +0200 (CEST) Subject: [FieldTrip] model order for autoregressive model In-Reply-To: <20f3c578-3f8d-4f9b-8ad6-337627c79057@thalamus_p> Message-ID: Dear all, i am planning to do granger causality on source space time series, and wanted to know if anyone could tell me how to find/chose the right model order when using the ft_mvaranalysis? Any help/advice would be highly appreciated! Best, Fred From sherrykhan78 at gmail.com Mon Sep 24 19:22:01 2012 From: sherrykhan78 at gmail.com (Sheraz Khan) Date: Mon, 24 Sep 2012 13:22:01 -0400 Subject: [FieldTrip] model order for autoregressive model In-Reply-To: References: <20f3c578-3f8d-4f9b-8ad6-337627c79057@thalamus_p> Message-ID: Dear Fred, It is best to use AIC or BIC to determine model. http://en.wikipedia.org/wiki/Akaike_information_criterion Sheraz On Mon, Sep 24, 2012 at 10:29 AM, Frederic Roux wrote: > Dear all, > > i am planning to do granger causality on source space > time series, and wanted to know if anyone could tell me > how to find/chose the right model order when using the > ft_mvaranalysis? > > Any help/advice would be highly appreciated! > > Best, > > Fred > > _______________________________________________ > 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 f.roux at bcbl.eu Mon Sep 24 23:17:52 2012 From: f.roux at bcbl.eu (Frederic Roux) Date: Mon, 24 Sep 2012 23:17:52 +0200 (CEST) Subject: [FieldTrip] model order for autoregressive model In-Reply-To: Message-ID: Dear Sheraz, thank you for your reply and the link. How do you obtain the AIC / BIC from the output of ft_mvaranalyis? Best, Fred ----- Original Message ----- From: "Sheraz Khan" To: "FieldTrip discussion list" Sent: Monday, September 24, 2012 7:22:01 PM Subject: Re: [FieldTrip] model order for autoregressive model Dear Fred, It is best to use AIC or BIC to determine model. http://en.wikipedia.org/wiki/Akaike_information_criterion Sheraz On Mon, Sep 24, 2012 at 10:29 AM, Frederic Roux < f.roux at bcbl.eu > wrote: BeDear all, i am planning to do granger causality on source space time series, and wanted to know if anyone could tell me how to find/chose the right model order when using the ft_mvaranalysis? Any help/advice would be highly appreciated! Best, Fred _______________________________________________ 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 pgoodin at swin.edu.au Tue Sep 25 02:37:14 2012 From: pgoodin at swin.edu.au (Peter Goodin) Date: Tue, 25 Sep 2012 00:37:14 +0000 Subject: [FieldTrip] Neuromag sensor level stats In-Reply-To: <50604EC9.7050705@donders.ru.nl> References: <50604EC9.7050705@donders.ru.nl> Message-ID: Thanks very much for the responses Stephan and Jörn! One last question if possible Jörn. In your opinion, will doing several (at the most 5) cluster based t-tests affect the validity of permutation method testing to control for multiple comparisons? Would being more conservative regarding my alpha (for example a combination of permutation AND Bonferroni) possibly alleviate this? Thanks again for the responses, Peter. From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig" Sent: Monday, 24 September 2012 10:15 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] Neuromag sensor level stats Dear Peter, regarding your first question, most people here at the Donders actually repair bad channels. When computing the grandaverage over subjects or doing some statistics across subjects, only those channels which are in common for all datasets are used. Thus, if having different channels damaged/rejected per subjects, you can end up with a fairly low amount of channels. But, in the end it depends pretty much on what channels you reject wrt your hypothesis, e.g. having few occipital channels while being interested in motor regions won't constitute a big problem, so no need to interpolate. I leave the question whether it's a correct thing to do up to you (imho: I wouldn't worry too much about it). Regarding your third question: In FieldTrip you can only compare two conditions directly (at least when doing cluster-based permutation testing). Also, any interaction needs to be setup manually. Best, Jörn On 9/23/2012 3:14 PM, Peter Goodin wrote: Hi Fieldtrippers, I'm at a stage where I'd like to do statistical analysis on my ERF neuromag data, but don't really know where to begin. I'd like to do a cluster analysis, but the tutorial material is for a CTF system. I'm using a neuromag 306 channel which complicates matters somewhat due to the different sensor types. I've searched the mailing list but can't find any solid answers / example scripts. The most pressing questions I have are: 1. Despite running the data through maxfilter and entering in the bad channels, occasionally one gets through (not the same one). I've used Fieldtrip's repairchannel function on the data, making sure to replace the channel only with like sensor neighbouring sensors. While I know this is a common method for fixing bad channels in EEG, does the same hold for MEG due to non-existent smearing of the signal? Is it best to keep the fixed channel(s) or just remove them from the stats analysis across all participants? 2. Given the three sensor types on the neuromag system, do I need to run three different cluster analyses (one for mags, one for xgrads, one for ygrads), each time specifying like sensor neighbours? Alternatively, If I'm not interested in the mags data, can I just run one using the data from the combined gradiometers? 3. When examining for group x condition effects, would I use a three row design matrix with row 1 containing group, row 2 containing participants and row 3 conditions? Thanks for any help, Peter _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From sherrykhan78 at gmail.com Tue Sep 25 02:56:51 2012 From: sherrykhan78 at gmail.com (Sheraz Khan) Date: Mon, 24 Sep 2012 20:56:51 -0400 Subject: [FieldTrip] model order for autoregressive model In-Reply-To: References: Message-ID: Please look at bsmart tutorial ( http://brain-smart.org/ ) for more detail, It has step by step procedure. fieldtrip also support bsmart based mutivariate model. Sheraz On Mon, Sep 24, 2012 at 5:17 PM, Frederic Roux wrote: > Dear Sheraz, > > thank you for your reply and the link. > > How do you obtain the AIC / BIC from > the output of ft_mvaranalyis? > > Best, > Fred > ----- Original Message ----- > From: "Sheraz Khan" > To: "FieldTrip discussion list" > Sent: Monday, September 24, 2012 7:22:01 PM > Subject: Re: [FieldTrip] model order for autoregressive model > > > Dear Fred, > > > It is best to use AIC or BIC to determine model. > > > http://en.wikipedia.org/wiki/Akaike_information_criterion > > > Sheraz > > > On Mon, Sep 24, 2012 at 10:29 AM, Frederic Roux < f.roux at bcbl.eu > wrote: > > > BeDear all, > > i am planning to do granger causality on source space > time series, and wanted to know if anyone could tell me > how to find/chose the right model order when using the > ft_mvaranalysis? > > Any help/advice would be highly appreciated! > > Best, > > Fred > > _______________________________________________ > 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 eelke.spaak at donders.ru.nl Tue Sep 25 09:21:12 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 25 Sep 2012 09:21:12 +0200 Subject: [FieldTrip] Neuromag sensor level stats In-Reply-To: References: <50604EC9.7050705@donders.ru.nl> Message-ID: Hi Peter, The cluster-based permutation test by itself is fully corrected for multiple comparisons. You mention "cluster based t-tests", but the exact test statistic (in your case, t) is irrelevant for this method. >From your comment I think you already understand this, but I thought it good to point out nonetheless :) Strictly speaking, when doing several cluster-based permutation tests, the cluster-level p-values you get out are uncorrected with respect to the several different tests, so actually I think it would be formally appropriate to correct them (with the number of cluster tests, *not* number of clusters of course), using Bonferroni or Holm-Bonferroni correction or so. I don't think this is commonly done, though. Best, Eelke On 25 September 2012 02:37, Peter Goodin wrote: > Thanks very much for the responses Stephan and Jörn! > > > > One last question if possible Jörn. In your opinion, will doing several (at > the most 5) cluster based t-tests affect the validity of permutation method > testing to control for multiple comparisons? Would being more conservative > regarding my alpha (for example a combination of permutation AND Bonferroni) > possibly alleviate this? > > > Thanks again for the responses, > > > > Peter. > > > > From: fieldtrip-bounces at science.ru.nl > [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig" > Sent: Monday, 24 September 2012 10:15 PM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Neuromag sensor level stats > > > > Dear Peter, > > regarding your first question, most people here at the Donders actually > repair bad channels. When computing the grandaverage over subjects or doing > some statistics across subjects, only those channels which are in common for > all datasets are used. Thus, if having different channels damaged/rejected > per subjects, you can end up with a fairly low amount of channels. But, in > the end it depends pretty much on what channels you reject wrt your > hypothesis, e.g. having few occipital channels while being interested in > motor regions won't constitute a big problem, so no need to interpolate. I > leave the question whether it's a correct thing to do up to you (imho: I > wouldn't worry too much about it). > > Regarding your third question: In FieldTrip you can only compare two > conditions directly (at least when doing cluster-based permutation testing). > Also, any interaction needs to be setup manually. > > Best, > Jörn > > On 9/23/2012 3:14 PM, Peter Goodin wrote: > > Hi Fieldtrippers, > > > > I'm at a stage where I'd like to do statistical analysis on my ERF neuromag > data, but don't really know where to begin. I'd like to do a cluster > analysis, but the tutorial material is for a CTF system. I'm using a > neuromag 306 channel which complicates matters somewhat due to the different > sensor types. I've searched the mailing list but can't find any solid > answers / example scripts. > > > > The most pressing questions I have are: > > > > 1. Despite running the data through maxfilter and entering in the bad > channels, occasionally one gets through (not the same one). I've used > Fieldtrip's repairchannel function on the data, making sure to replace the > channel only with like sensor neighbouring sensors. While I know this is a > common method for fixing bad channels in EEG, does the same hold for MEG due > to non-existent smearing of the signal? Is it best to keep the fixed > channel(s) or just remove them from the stats analysis across all > participants? > > > > 2. Given the three sensor types on the neuromag system, do I need to run > three different cluster analyses (one for mags, one for xgrads, one for > ygrads), each time specifying like sensor neighbours? Alternatively, If I'm > not interested in the mags data, can I just run one using the data from the > combined gradiometers? > > > > 3. When examining for group x condition effects, would I use a three row > design matrix with row 1 containing group, row 2 containing participants and > row 3 conditions? > > > > Thanks for any help, > > > > Peter > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > > Jörn M. Horschig > > PhD Student > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > Neuronal Oscillations Group > > FieldTrip Development Team > > > > P.O. Box 9101 > > NL-6500 HB Nijmegen > > The Netherlands > > > > Contact: > > E-Mail: jm.horschig at donders.ru.nl > > Tel: +31-(0)24-36-68493 > > Web: http://www.ru.nl/donders > > > > Visiting address: > > Trigon, room 2.30 > > Kapittelweg 29 > > NL-6525 EN Nijmegen > > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From g.piantoni at nin.knaw.nl Tue Sep 25 12:21:54 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Tue, 25 Sep 2012 12:21:54 +0200 Subject: [FieldTrip] How to impove dics realfilter solution In-Reply-To: <736231433.1128.1347610993969.JavaMail.root@zimbra> References: <612757646.1088.1347610775726.JavaMail.root@zimbra> <736231433.1128.1347610993969.JavaMail.root@zimbra> Message-ID: Hi Björn, It's not surprising that the results are pretty bad after using real filters. The fourier transform and DICS are intrinsically complex-valued, so using only the real part means throwing away half of the information (and getting meaningless results). The realfilter option was implemented in order to allow to pass the time-domain signal through the complex-value spatial filter and obtain a "virtual electrode". A virtual electrode with complex values is "weird to say the least", see: http://mailman.science.ru.nl/pipermail/fieldtrip/2006-May/000510.html Robert considered it an error in the algorithm and fixed it by providing the realfilter option. However, to me it seems more correct to think that complex spatial filters requires complex input (i.e. frequency-domain signal), so don't use DICS spatial filters on time-domain real-valued MEG recordings to generate time-domain virtual electrodes. If you want time-domain virtual electrodes, use LCMV spatial filters centered at the location of interest. Other smart people might disagree though. I suggest not to use realfilter option at all, but I'd be happy to hear other meaningful applications of this option. Hope this helps, Gio On Fri, Sep 14, 2012 at 10:23 AM, Björn Herrmann wrote: > Dear fieldtrip user, > > I am using the DICS beamformer to localize a 3Hz FFT power topographical distribution (using a neuromag system). The topographies are very clear auditory in single subjects, thus it shouldn't be a problem finding the "right" solution. When I use the beamformer to obtain complex-value spatial filters, the solution looks very good (using NAI). No problem here. However, using cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real values, the localization completely breaks down, sometimes even finding a strong peak in the opposite hemisphere than visible in the sensor topography (the head is centered in the sensor array). > > Does someone have a suggestion how to improve the solution using realfilter = 'yes'. I use the following settings. They are rather standard I guess. > > cfg = []; > cfg.method = 'dics'; > cfg.frequency = 3; > cfg.dics.projectnoise = 'yes'; > cfg.dics.lambda = '5%'; > cfg.dics.keepfilter = 'yes'; > cfg.dics.realfilter = 'yes'; > cfg.dics.fixedori = 'no'; > > > If someone has a suggestion, I would appreciate it. > Thanks in advance, > best, > > Björn > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From landpt at gmail.com Wed Sep 26 20:53:05 2012 From: landpt at gmail.com (Ricardo Jorge) Date: Wed, 26 Sep 2012 19:53:05 +0100 Subject: [FieldTrip] Emotiv and Fieldtrip - filter in the streamer/buffer? Message-ID: Hello there once again, I've contacted you some days ago because I was having troubles reading the data from the Emotiv in the Fieldtrip toolbox, which you replied and solved my trouble. Thanks once again. However, being worked on the data, I've noticed something odd that I cannot understand what exactly is happening: - I did not activate or put any filter (even removed the preprocessing baseline command) and the signals that I get in the fieldtrip have around 4000-5000 of mean and the variance is almost 0.05, something like that. - At the same time, I was running Emotiv Testbench and for some weird reason, the signals that I get in there have exactly the same mean, but its variance is more than 1 (something like between 1 and 1.5). - At the same time, I did run OpenVibe, which was similar to the Testbench. Seeing their plots, there are clearly some variations: Testbench/Openvibe gave much more "peaks" and spread, whereas Fieldtrip (streamer) looks less noisy, as if it was almost-perfect. But I did not apply any filter... Can I have any information about what could be happening here? Does the streamer/buffer apply some filter that I don't know? I've seen that it is not possible to acquire raw data from Emotiv, except using Emotiv SDK, Openvibe or Emokit. Is it related? Thanks in advance. Ricardo Jorge From Jan.Hirschmann at med.uni-duesseldorf.de Thu Sep 27 09:40:46 2012 From: Jan.Hirschmann at med.uni-duesseldorf.de (Jan.Hirschmann at med.uni-duesseldorf.de) Date: Thu, 27 Sep 2012 09:40:46 +0200 Subject: [FieldTrip] How to impove dics realfilter solution In-Reply-To: References: <612757646.1088.1347610775726.JavaMail.root@zimbra><736231433.1128.1347610993969.JavaMail.root@zimbra> Message-ID: <72E993C35FB11743B79FF9286E5B6D8B04772649@Mail2-UKD.VMED.UKD> Hi Gio, What about the application of projecting frequency domain data through a common filter? This is described in the beamformer tutorial on the fieldtrip website and has worked fine for me. After commenting out the realfilter line the group statistical results looked worse in my case (although I also changed lambda on this second try). >From the tutorial: "Then we compute the inverse filter based on both conditions. Note the use of cfg.keepfilter so that the output saves this computed filter. cfg = []; cfg.method = 'dics'; cfg.frequency = 18; cfg.grid = grid; cfg.vol = vol; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.keepfilter = 'yes'; cfg.dics.realfilter = 'yes'; sourceAll = ft_sourceanalysis(cfg, freqAll); By placing this pre-computed filter inside cfg.grid.filter, it can now be applied to each condition separately. cfg.grid.filter = sourceAll.avg.filter; sourcePre_con = ft_sourceanalysis(cfg, freqPre ); sourcePost_con = ft_sourceanalysis(cfg, freqPost);" Best, Jan -----Ursprüngliche Nachricht----- Von: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] Im Auftrag von Gio Piantoni Gesendet: Dienstag, 25. September 2012 12:22 An: FieldTrip discussion list Betreff: Re: [FieldTrip] How to impove dics realfilter solution Hi Björn, It's not surprising that the results are pretty bad after using real filters. The fourier transform and DICS are intrinsically complex-valued, so using only the real part means throwing away half of the information (and getting meaningless results). The realfilter option was implemented in order to allow to pass the time-domain signal through the complex-value spatial filter and obtain a "virtual electrode". A virtual electrode with complex values is "weird to say the least", see: http://mailman.science.ru.nl/pipermail/fieldtrip/2006-May/000510.html Robert considered it an error in the algorithm and fixed it by providing the realfilter option. However, to me it seems more correct to think that complex spatial filters requires complex input (i.e. frequency-domain signal), so don't use DICS spatial filters on time-domain real-valued MEG recordings to generate time-domain virtual electrodes. If you want time-domain virtual electrodes, use LCMV spatial filters centered at the location of interest. Other smart people might disagree though. I suggest not to use realfilter option at all, but I'd be happy to hear other meaningful applications of this option. Hope this helps, Gio On Fri, Sep 14, 2012 at 10:23 AM, Björn Herrmann wrote: > Dear fieldtrip user, > > I am using the DICS beamformer to localize a 3Hz FFT power topographical distribution (using a neuromag system). The topographies are very clear auditory in single subjects, thus it shouldn't be a problem finding the "right" solution. When I use the beamformer to obtain complex-value spatial filters, the solution looks very good (using NAI). No problem here. However, using cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real values, the localization completely breaks down, sometimes even finding a strong peak in the opposite hemisphere than visible in the sensor topography (the head is centered in the sensor array). > > Does someone have a suggestion how to improve the solution using realfilter = 'yes'. I use the following settings. They are rather standard I guess. > > cfg = []; > cfg.method = 'dics'; > cfg.frequency = 3; > cfg.dics.projectnoise = 'yes'; > cfg.dics.lambda = '5%'; > cfg.dics.keepfilter = 'yes'; > cfg.dics.realfilter = 'yes'; > cfg.dics.fixedori = 'no'; > > > If someone has a suggestion, I would appreciate it. > Thanks in advance, > best, > > Björn > > > > _______________________________________________ > 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 b.reuderink at donders.ru.nl Thu Sep 27 11:24:34 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Thu, 27 Sep 2012 11:24:34 +0200 Subject: [FieldTrip] Emotiv and Fieldtrip - filter in the streamer/buffer? In-Reply-To: References: Message-ID: Dear Ricardo, If I understand your remark correctly, there is a scaling difference between other software (OpenVibe & Emotiv Testbench) and FieldTrip's real-time signal from the Emotiv. Would could see if we can find this difference in scaling. But, are there other signal characteristics that are different? You mention 'less noisy' — could that be caused just by scaling, or do you have a clear indication that the signal is filtered? Screenshots would be helpful. There are some places were filtering could take place. The viewer (bufferViewer.exe) has an option to enable a high-pass filter, and the FieldTrip's shared ODM code for streaming can down-sample the signal which also involves filtering, but it should be disabled by default. Can you provide some additional info? Best, Boris PS: emotiv2ft.exe is based on the Emotiv SDK (EDK). -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl On 26 sep. 2012, at 20:53, Ricardo Jorge wrote: > Hello there once again, > > I've contacted you some days ago because I was having troubles reading > the data from the Emotiv in the Fieldtrip toolbox, which you replied > and solved my trouble. Thanks once again. > > However, being worked on the data, I've noticed something odd that I > cannot understand what exactly is happening: > - I did not activate or put any filter (even removed the preprocessing > baseline command) and the signals that I get in the fieldtrip have > around 4000-5000 of mean and the variance is almost 0.05, something > like that. > - At the same time, I was running Emotiv Testbench and for some weird > reason, the signals that I get in there have exactly the same mean, > but its variance is more than 1 (something like between 1 and 1.5). > - At the same time, I did run OpenVibe, which was similar to the Testbench. > > Seeing their plots, there are clearly some variations: > Testbench/Openvibe gave much more "peaks" and spread, whereas > Fieldtrip (streamer) looks less noisy, as if it was almost-perfect. > But I did not apply any filter... > > Can I have any information about what could be happening here? Does > the streamer/buffer apply some filter that I don't know? I've seen > that it is not possible to acquire raw data from Emotiv, except using > Emotiv SDK, Openvibe or Emokit. Is it related? > > Thanks in advance. > > Ricardo Jorge > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Thu Sep 27 13:39:07 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 27 Sep 2012 13:39:07 +0200 Subject: [FieldTrip] How to impove dics realfilter solution In-Reply-To: References: <612757646.1088.1347610775726.JavaMail.root@zimbra> <736231433.1128.1347610993969.JavaMail.root@zimbra> Message-ID: Dear Björn, caro Gio, I don't agree with you, Gio, that one should use complex-valued filters. The reason for this is that they don't make sense from a biophysical point of view. The mixing from sources to channels (as represented in the leadfields) is strictly real-valued, because it is (near-)instantaneous. I think that the unmixing from channels to sources also should be real-valued, for the same argument. When you allow filter coefficients to be complex-valued, this is equivalent to allowing the sensor-level signals to be shifted in time with respect to one another. I consider this a bit odd. In Joachim's seminal paper (on which FieldTrip's initial DICS implementation is based), this was not really explicit in the methods description. However, based on personal communications with said Joachim, I at least distilled that the filters should be real-valued. The complex-valued filters were kept in (as default) for backward compatibilitiy reasons. Although mathematically possible (perhaps even more strictly answering to the minimum variance and unit gain constraints), and sometimes seemingly giving nicer subjective results, I'd advice against using them. Cheers, JM On Sep 25, 2012, at 12:21 PM, Gio Piantoni wrote: > Hi Björn, > > It's not surprising that the results are pretty bad after using real > filters. The fourier transform and DICS are intrinsically > complex-valued, so using only the real part means throwing away half > of the information (and getting meaningless results). > > The realfilter option was implemented in order to allow to pass the > time-domain signal through the complex-value spatial filter and obtain > a "virtual electrode". A virtual electrode with complex values is > "weird to say the least", see: > http://mailman.science.ru.nl/pipermail/fieldtrip/2006-May/000510.html > Robert considered it an error in the algorithm and fixed it by > providing the realfilter option. However, to me it seems more correct > to think that complex spatial filters requires complex input (i.e. > frequency-domain signal), so don't use DICS spatial filters on > time-domain real-valued MEG recordings to generate time-domain virtual > electrodes. If you want time-domain virtual electrodes, use LCMV > spatial filters centered at the location of interest. Other smart > people might disagree though. > > I suggest not to use realfilter option at all, but I'd be happy to > hear other meaningful applications of this option. > > Hope this helps, > > Gio > > On Fri, Sep 14, 2012 at 10:23 AM, Björn Herrmann wrote: >> Dear fieldtrip user, >> >> I am using the DICS beamformer to localize a 3Hz FFT power topographical distribution (using a neuromag system). The topographies are very clear auditory in single subjects, thus it shouldn't be a problem finding the "right" solution. When I use the beamformer to obtain complex-value spatial filters, the solution looks very good (using NAI). No problem here. However, using cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real values, the localization completely breaks down, sometimes even finding a strong peak in the opposite hemisphere than visible in the sensor topography (the head is centered in the sensor array). >> >> Does someone have a suggestion how to improve the solution using realfilter = 'yes'. I use the following settings. They are rather standard I guess. >> >> cfg = []; >> cfg.method = 'dics'; >> cfg.frequency = 3; >> cfg.dics.projectnoise = 'yes'; >> cfg.dics.lambda = '5%'; >> cfg.dics.keepfilter = 'yes'; >> cfg.dics.realfilter = 'yes'; >> cfg.dics.fixedori = 'no'; >> >> >> If someone has a suggestion, I would appreciate it. >> Thanks in advance, >> best, >> >> Björn >> >> >> >> _______________________________________________ >> 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 Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Duncan.Astle at mrc-cbu.cam.ac.uk Thu Sep 27 15:17:08 2012 From: Duncan.Astle at mrc-cbu.cam.ac.uk (Duncan Astle) Date: Thu, 27 Sep 2012 13:17:08 +0000 Subject: [FieldTrip] Transfering SPM TF data into Fieldtrip Message-ID: Dear FieldTrippers, I have some nice time frequency data in SPM8. It is averaged for each subject. I would really like to bring it into fieldtrip to do some stats, but I am struggling. When I use the spm2fieldtrip function it treats my 73 frequencies as 73 different trials. Does anyone have any suggestions about how to get in to fieldtrip? Best, Duncan ________________________________________________ Dr. Duncan Astle, Programme Leader Track, British Academy Research Fellow, MRC Cognition and Brain Sciences Unit, Chaucer Road, Cambridge. Duncan.Astle at mrc-cbu.cam.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Thu Sep 27 15:18:54 2012 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Thu, 27 Sep 2012 14:18:54 +0100 Subject: [FieldTrip] Transfering SPM TF data into Fieldtrip In-Reply-To: References: Message-ID: Dear Duncan, In SPM do: D = spm_eeg_load; ftdata = D.fttimelock; Best, Vladimir On Thu, Sep 27, 2012 at 2:17 PM, Duncan Astle wrote: > Dear FieldTrippers, > > > > I have some nice time frequency data in SPM8. It is averaged for each > subject. I would really like to bring it into fieldtrip to do some stats, > but I am struggling. When I use the spm2fieldtrip function it treats my 73 > frequencies as 73 different trials. > > > > Does anyone have any suggestions about how to get in to fieldtrip? > > > > Best, > > Duncan > > ________________________________________________ > > Dr. Duncan Astle, > > Programme Leader Track, > > British Academy Research Fellow, > > MRC Cognition and Brain Sciences Unit, > > Chaucer Road, > > Cambridge. > > Duncan.Astle at mrc-cbu.cam.ac.uk > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Duncan.Astle at mrc-cbu.cam.ac.uk Thu Sep 27 17:08:55 2012 From: Duncan.Astle at mrc-cbu.cam.ac.uk (Duncan Astle) Date: Thu, 27 Sep 2012 15:08:55 +0000 Subject: [FieldTrip] Update - transfering TF data from SPM Message-ID: Dear all, I keep thinking that I have done it, in that I think that I have recreated all the information that should be needed in a field trip TF object. I did this by bringing in the extra information from D.fttimelock, and creating the cfg field as if I had run it through FT_FREQANALYSIS. The structure has these fields: l5d19 = fsample: 250.0000 label: {68x1 cell} trial: {[68x73 single]} time: {[1x376 double]} trialinfo: 1 cfg: [1x1 struct] powspctrm: [68x73x376 single] freq: [1x73 double] dimord: 'chan_freq_time' However, when I try and use my file in 'FT_FREQGRANDAVERAGE' , it does not recognise this as a TF object, and produces this error message: ??? Error using ==> ft_checkdata at 324 This function requires freq data as input. Error in ==> ft_freqgrandaverage at 66 varargin{i} = ft_checkdata(varargin{i}, 'datatype', 'freq', 'feedback', 'no'); What is it that I am missing?? Best, Duncan ________________________________________________ Dr. Duncan Astle, Programme Leader Track, British Academy Research Fellow, MRC Cognition and Brain Sciences Unit, Chaucer Road, Cambridge. Duncan.Astle at mrc-cbu.cam.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Thu Sep 27 17:32:02 2012 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Thu, 27 Sep 2012 16:32:02 +0100 Subject: [FieldTrip] Update - transfering TF data from SPM In-Reply-To: References: Message-ID: Dear Duncan, You should look in the code how FT differentiates between different structures and what goes wrong. For instance it might be that it is confused by the fsample field that shouldn't be there. It's been a while since I did something like that and FT code has evolved with more stringent checks now. Best, Vladimir On Thu, Sep 27, 2012 at 4:08 PM, Duncan Astle wrote: > Dear all, > > > > I keep thinking that I have done it, in that I think that I have recreated > all the information that should be needed in a field trip TF object. I did > this by bringing in the extra information from D.fttimelock, and creating > the cfg field as if I had run it through FT_FREQANALYSIS. The structure has > these fields: > > > > l5d19 = > > > > fsample: 250.0000 > > label: {68x1 cell} > > trial: {[68x73 single]} > > time: {[1x376 double]} > > trialinfo: 1 > > cfg: [1x1 struct] > > powspctrm: [68x73x376 single] > > freq: [1x73 double] > > dimord: 'chan_freq_time' > > > > However, when I try and use my file in ‘FT_FREQGRANDAVERAGE’ , it does not > recognise this as a TF object, and produces this error message: > > > > ??? Error using ==> ft_checkdata at 324 > > This function requires freq data as input. > > > > Error in ==> ft_freqgrandaverage at 66 > > varargin{i} = ft_checkdata(varargin{i}, 'datatype', 'freq', 'feedback', > 'no'); > > > > What is it that I am missing?? > > > > Best, > > Duncan > > > > ________________________________________________ > > Dr. Duncan Astle, > > Programme Leader Track, > > British Academy Research Fellow, > > MRC Cognition and Brain Sciences Unit, > > Chaucer Road, > > Cambridge. > > Duncan.Astle at mrc-cbu.cam.ac.uk > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Duncan.Astle at mrc-cbu.cam.ac.uk Thu Sep 27 17:55:12 2012 From: Duncan.Astle at mrc-cbu.cam.ac.uk (Duncan Astle) Date: Thu, 27 Sep 2012 15:55:12 +0000 Subject: [FieldTrip] Update - transfering TF data from SPM In-Reply-To: References: Message-ID: Dear Vladimir, Thanks for your help; I worked out what it wanted. Anyone who is interested should contact me and I will take them through it. Best, Duncan ________________________________________________ Dr. Duncan Astle, Programme Leader Track, British Academy Research Fellow, MRC Cognition and Brain Sciences Unit, Chaucer Road, Cambridge. Duncan.Astle at mrc-cbu.cam.ac.uk -----Original Message----- From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Vladimir Litvak Sent: 27 September 2012 16:32 To: FieldTrip discussion list Subject: Re: [FieldTrip] Update - transfering TF data from SPM Dear Duncan, You should look in the code how FT differentiates between different structures and what goes wrong. For instance it might be that it is confused by the fsample field that shouldn't be there. It's been a while since I did something like that and FT code has evolved with more stringent checks now. Best, Vladimir On Thu, Sep 27, 2012 at 4:08 PM, Duncan Astle wrote: > Dear all, > > > > I keep thinking that I have done it, in that I think that I have > recreated all the information that should be needed in a field trip TF > object. I did this by bringing in the extra information from > D.fttimelock, and creating the cfg field as if I had run it through > FT_FREQANALYSIS. The structure has these fields: > > > > l5d19 = > > > > fsample: 250.0000 > > label: {68x1 cell} > > trial: {[68x73 single]} > > time: {[1x376 double]} > > trialinfo: 1 > > cfg: [1x1 struct] > > powspctrm: [68x73x376 single] > > freq: [1x73 double] > > dimord: 'chan_freq_time' > > > > However, when I try and use my file in 'FT_FREQGRANDAVERAGE' , it does > not recognise this as a TF object, and produces this error message: > > > > ??? Error using ==> ft_checkdata at 324 > > This function requires freq data as input. > > > > Error in ==> ft_freqgrandaverage at 66 > > varargin{i} = ft_checkdata(varargin{i}, 'datatype', 'freq', > 'feedback', 'no'); > > > > What is it that I am missing?? > > > > Best, > > Duncan > > > > ________________________________________________ > > Dr. Duncan Astle, > > Programme Leader Track, > > British Academy Research Fellow, > > MRC Cognition and Brain Sciences Unit, > > Chaucer Road, > > Cambridge. > > Duncan.Astle at mrc-cbu.cam.ac.uk > > > > > _______________________________________________ > 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 michael.wibral at web.de Thu Sep 27 20:03:43 2012 From: michael.wibral at web.de (Michael Wibral) Date: Thu, 27 Sep 2012 20:03:43 +0200 Subject: [FieldTrip] Fwd: Re: How to impove dics realfilter solution In-Reply-To: <50649472.3050502@em.uni-frankfurt.de> References: <50649472.3050502@em.uni-frankfurt.de> Message-ID: <506494FF.7070308@web.de> -------- Original Message -------- Subject: Re: [FieldTrip] How to impove dics realfilter solution Date: Thu, 27 Sep 2012 20:01:22 +0200 From: wibral Reply-To: wibral at em.uni-frankfurt.de To: FieldTrip discussion list Dear Filedtrip users, I fully agree with jan Mathijs, in principle when using DICS to reconstruct source power, the nature of the physical processes (forward model) should guarantee that filters are automatically real-valued, because this reflects the quasi-static approximation of maxwell's equations which holds pretty well in MEG. In practice filter coeffcients only deviate from being real because of sensor noise, which is not a desirable effect. Best, Michael On 09/27/2012 01:39 PM, jan-mathijs schoffelen wrote: > Dear Björn, caro Gio, > > I don't agree with you, Gio, that one should use complex-valued > filters. The reason for this is that they don't make sense from a > biophysical point of view. The mixing from sources to channels (as > represented in the leadfields) is strictly real-valued, because it is > (near-)instantaneous. I think that the unmixing from channels to > sources also should be real-valued, for the same argument. When you > allow filter coefficients to be complex-valued, this is equivalent to > allowing the sensor-level signals to be shifted in time with respect > to one another. I consider this a bit odd. In Joachim's seminal paper > (on which FieldTrip's initial DICS implementation is based), this was > not really explicit in the methods description. However, based on > personal communications with said Joachim, I at least distilled that > the filters should be real-valued. The complex-valued filters were > kept in (as default) for backward compatibilitiy reasons. Although > mathematically possible (perhaps even more strictly answering to the > minimum variance and unit gain constraints), and sometimes seemingly > giving nicer subjective results, I'd advice against using them. > > Cheers, > > JM > > > > On Sep 25, 2012, at 12:21 PM, Gio Piantoni wrote: > >> Hi Björn, >> >> It's not surprising that the results are pretty bad after using real >> filters. The fourier transform and DICS are intrinsically >> complex-valued, so using only the real part means throwing away half >> of the information (and getting meaningless results). >> >> The realfilter option was implemented in order to allow to pass the >> time-domain signal through the complex-value spatial filter and obtain >> a "virtual electrode". A virtual electrode with complex values is >> "weird to say the least", see: >> http://mailman.science.ru.nl/pipermail/fieldtrip/2006-May/000510.html >> Robert considered it an error in the algorithm and fixed it by >> providing the realfilter option. However, to me it seems more correct >> to think that complex spatial filters requires complex input (i.e. >> frequency-domain signal), so don't use DICS spatial filters on >> time-domain real-valued MEG recordings to generate time-domain virtual >> electrodes. If you want time-domain virtual electrodes, use LCMV >> spatial filters centered at the location of interest. Other smart >> people might disagree though. >> >> I suggest not to use realfilter option at all, but I'd be happy to >> hear other meaningful applications of this option. >> >> Hope this helps, >> >> Gio >> >> On Fri, Sep 14, 2012 at 10:23 AM, Björn Herrmann >> wrote: >>> Dear fieldtrip user, >>> >>> I am using the DICS beamformer to localize a 3Hz FFT power >>> topographical distribution (using a neuromag system). The >>> topographies are very clear auditory in single subjects, thus it >>> shouldn't be a problem finding the "right" solution. When I use the >>> beamformer to obtain complex-value spatial filters, the solution >>> looks very good (using NAI). No problem here. However, using >>> cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real >>> values, the localization completely breaks down, sometimes even >>> finding a strong peak in the opposite hemisphere than visible in the >>> sensor topography (the head is centered in the sensor array). >>> >>> Does someone have a suggestion how to improve the solution using >>> realfilter = 'yes'. I use the following settings. They are rather >>> standard I guess. >>> >>> cfg = []; >>> cfg.method = 'dics'; >>> cfg.frequency = 3; >>> cfg.dics.projectnoise = 'yes'; >>> cfg.dics.lambda = '5%'; >>> cfg.dics.keepfilter = 'yes'; >>> cfg.dics.realfilter = 'yes'; >>> cfg.dics.fixedori = 'no'; >>> >>> >>> If someone has a suggestion, I would appreciate it. >>> Thanks in advance, >>> best, >>> >>> Björn >>> >>> >>> >>> _______________________________________________ >>> 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 > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > > _______________________________________________ > 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 g.piantoni at nin.knaw.nl Thu Sep 27 21:05:02 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Thu, 27 Sep 2012 21:05:02 +0200 Subject: [FieldTrip] How to impove dics realfilter solution In-Reply-To: References: <612757646.1088.1347610775726.JavaMail.root@zimbra> <736231433.1128.1347610993969.JavaMail.root@zimbra> Message-ID: Well, the people disagreeing with me are indeed very smart! Jan-Mathijs, your argument is very subtle and I agree with you that the imaginary part of the filter contains the non-instantaneous unmixing. However, for frequency-domain data it makes sense to use the non-instantaneous information, for the very reason that frequency-domain data are not instantaneous. If you take the fourier transform of a signal at 10 Hz, you're not computing it at one specific instant but over a period of time. I'd imagine that the imaginary part contains information about the frequency-domain data over that period of time. I see Michael's point as well, but would it be possible for the quasi-static approximation of Maxwell's equations to contain the imaginary part only when applied to frequency-domain data instead of time-domain data? In the end, the complex-value spatial filters are specific to one frequency band over a period of time and maybe the imaginary part accounts for the time-shift (phase-shift) implicit in the frequency-domain representation. Thanks for the interesting discussion! Happy to hear if you have further thoughts on this. Cheers, Gio On Thu, Sep 27, 2012 at 1:39 PM, jan-mathijs schoffelen wrote: > Dear Björn, caro Gio, > > I don't agree with you, Gio, that one should use complex-valued filters. The > reason for this is that they don't make sense from a biophysical point of > view. The mixing from sources to channels (as represented in the leadfields) > is strictly real-valued, because it is (near-)instantaneous. I think that > the unmixing from channels to sources also should be real-valued, for the > same argument. When you allow filter coefficients to be complex-valued, this > is equivalent to allowing the sensor-level signals to be shifted in time > with respect to one another. I consider this a bit odd. In Joachim's seminal > paper (on which FieldTrip's initial DICS implementation is based), this was > not really explicit in the methods description. However, based on personal > communications with said Joachim, I at least distilled that the filters > should be real-valued. The complex-valued filters were kept in (as default) > for backward compatibilitiy reasons. Although mathematically possible > (perhaps even more strictly answering to the minimum variance and unit gain > constraints), and sometimes seemingly giving nicer subjective results, I'd > advice against using them. > > Cheers, > > JM > > > > On Sep 25, 2012, at 12:21 PM, Gio Piantoni wrote: > > Hi Björn, > > It's not surprising that the results are pretty bad after using real > filters. The fourier transform and DICS are intrinsically > complex-valued, so using only the real part means throwing away half > of the information (and getting meaningless results). > > The realfilter option was implemented in order to allow to pass the > time-domain signal through the complex-value spatial filter and obtain > a "virtual electrode". A virtual electrode with complex values is > "weird to say the least", see: > http://mailman.science.ru.nl/pipermail/fieldtrip/2006-May/000510.html > Robert considered it an error in the algorithm and fixed it by > providing the realfilter option. However, to me it seems more correct > to think that complex spatial filters requires complex input (i.e. > frequency-domain signal), so don't use DICS spatial filters on > time-domain real-valued MEG recordings to generate time-domain virtual > electrodes. If you want time-domain virtual electrodes, use LCMV > spatial filters centered at the location of interest. Other smart > people might disagree though. > > I suggest not to use realfilter option at all, but I'd be happy to > hear other meaningful applications of this option. > > Hope this helps, > > Gio > > On Fri, Sep 14, 2012 at 10:23 AM, Björn Herrmann > wrote: > > Dear fieldtrip user, > > > I am using the DICS beamformer to localize a 3Hz FFT power topographical > distribution (using a neuromag system). The topographies are very clear > auditory in single subjects, thus it shouldn't be a problem finding the > "right" solution. When I use the beamformer to obtain complex-value spatial > filters, the solution looks very good (using NAI). No problem here. However, > using cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real > values, the localization completely breaks down, sometimes even finding a > strong peak in the opposite hemisphere than visible in the sensor topography > (the head is centered in the sensor array). > > > Does someone have a suggestion how to improve the solution using realfilter > = 'yes'. I use the following settings. They are rather standard I guess. > > > cfg = []; > > cfg.method = 'dics'; > > cfg.frequency = 3; > > cfg.dics.projectnoise = 'yes'; > > cfg.dics.lambda = '5%'; > > cfg.dics.keepfilter = 'yes'; > > cfg.dics.realfilter = 'yes'; > > cfg.dics.fixedori = 'no'; > > > > If someone has a suggestion, I would appreciate it. > > Thanks in advance, > > best, > > > Björn > > > > > _______________________________________________ > > 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 > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From bherrmann at cbs.mpg.de Thu Sep 27 21:19:06 2012 From: bherrmann at cbs.mpg.de (=?utf-8?Q?Bj=C3=B6rn_Herrmann?=) Date: Thu, 27 Sep 2012 21:19:06 +0200 (CEST) Subject: [FieldTrip] How to impove dics realfilter solution (Michael Wibral) In-Reply-To: Message-ID: <1079339450.6815.1348773546422.JavaMail.root@zimbra> Thank you Gio, Jan and Michael, This is very helpful input. I understand that it makes sense from a biological point of view and also from thinking about leadfields that the filter should be real-valued. What I find surprising though is that just from an application point of view, the localization results really look in my case much better (auditory cortex; for a very clear auditory topography of the FFT to a 3Hz modulated sound) for the complex than the real filter. I used the standard parameters for the localization, maybe something could be impoved there, but this is what really surprises me, also following this interesting discussion here. Just by looking into the struct in fieldtrip and what kind of data goes into the DICS beamformer, then there is mainly the CSD, which is complex, and the power, which is positive real-valued. Thus, thinking of a classical leadfield being generated by a source and which is then compared to the observed topography (i.e. biological meaningful and real-valed), does not completely fit here, at least in my current thinking. Therefore, I was not fully surprised seeing the realfilter producing the more puzzling localization result in my case. Can the DICS beamformer really be thought of in the "classical" way, i.e. that the source produces a real-value leadfield (positive and negative values)? I somehow understood it as localizing a power topography, which is only positive, thus in a way different from a classical leadfield. All the best, BJörn ------ Björn Herrmann Auditory Cognition Group Max Planck Institute for Human Cognitive and Brain Sciences Stephanstrasse 1a, 04103 Leipzig, Germany phone: ++49 (0)341 9940 2606 email: bherrmann at cbs.mpg.de ----- Ursprüngliche Mail ----- Von: fieldtrip-request at science.ru.nl An: fieldtrip at science.ru.nl Gesendet: Donnerstag, 27. September 2012 20:04:01 Betreff: fieldtrip Digest, Vol 22, Issue 47 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: Update - transfering TF data from SPM (Vladimir Litvak) 2. Re: Update - transfering TF data from SPM (Duncan Astle) 3. Fwd: Re: How to impove dics realfilter solution (Michael Wibral) ---------------------------------------------------------------------- Message: 1 Date: Thu, 27 Sep 2012 16:32:02 +0100 From: Vladimir Litvak To: FieldTrip discussion list Subject: Re: [FieldTrip] Update - transfering TF data from SPM Message-ID: Content-Type: text/plain; charset=windows-1252 Dear Duncan, You should look in the code how FT differentiates between different structures and what goes wrong. For instance it might be that it is confused by the fsample field that shouldn't be there. It's been a while since I did something like that and FT code has evolved with more stringent checks now. Best, Vladimir On Thu, Sep 27, 2012 at 4:08 PM, Duncan Astle wrote: > Dear all, > > > > I keep thinking that I have done it, in that I think that I have recreated > all the information that should be needed in a field trip TF object. I did > this by bringing in the extra information from D.fttimelock, and creating > the cfg field as if I had run it through FT_FREQANALYSIS. The structure has > these fields: > > > > l5d19 = > > > > fsample: 250.0000 > > label: {68x1 cell} > > trial: {[68x73 single]} > > time: {[1x376 double]} > > trialinfo: 1 > > cfg: [1x1 struct] > > powspctrm: [68x73x376 single] > > freq: [1x73 double] > > dimord: 'chan_freq_time' > > > > However, when I try and use my file in ?FT_FREQGRANDAVERAGE? , it does not > recognise this as a TF object, and produces this error message: > > > > ??? Error using ==> ft_checkdata at 324 > > This function requires freq data as input. > > > > Error in ==> ft_freqgrandaverage at 66 > > varargin{i} = ft_checkdata(varargin{i}, 'datatype', 'freq', 'feedback', > 'no'); > > > > What is it that I am missing?? > > > > Best, > > Duncan > > > > ________________________________________________ > > Dr. Duncan Astle, > > Programme Leader Track, > > British Academy Research Fellow, > > MRC Cognition and Brain Sciences Unit, > > Chaucer Road, > > Cambridge. > > Duncan.Astle at mrc-cbu.cam.ac.uk > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ------------------------------ Message: 2 Date: Thu, 27 Sep 2012 15:55:12 +0000 From: Duncan Astle To: FieldTrip discussion list Subject: Re: [FieldTrip] Update - transfering TF data from SPM Message-ID: Content-Type: text/plain; charset="us-ascii" Dear Vladimir, Thanks for your help; I worked out what it wanted. Anyone who is interested should contact me and I will take them through it. Best, Duncan ________________________________________________ Dr. Duncan Astle, Programme Leader Track, British Academy Research Fellow, MRC Cognition and Brain Sciences Unit, Chaucer Road, Cambridge. Duncan.Astle at mrc-cbu.cam.ac.uk -----Original Message----- From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Vladimir Litvak Sent: 27 September 2012 16:32 To: FieldTrip discussion list Subject: Re: [FieldTrip] Update - transfering TF data from SPM Dear Duncan, You should look in the code how FT differentiates between different structures and what goes wrong. For instance it might be that it is confused by the fsample field that shouldn't be there. It's been a while since I did something like that and FT code has evolved with more stringent checks now. Best, Vladimir On Thu, Sep 27, 2012 at 4:08 PM, Duncan Astle wrote: > Dear all, > > > > I keep thinking that I have done it, in that I think that I have > recreated all the information that should be needed in a field trip TF > object. I did this by bringing in the extra information from > D.fttimelock, and creating the cfg field as if I had run it through > FT_FREQANALYSIS. The structure has these fields: > > > > l5d19 = > > > > fsample: 250.0000 > > label: {68x1 cell} > > trial: {[68x73 single]} > > time: {[1x376 double]} > > trialinfo: 1 > > cfg: [1x1 struct] > > powspctrm: [68x73x376 single] > > freq: [1x73 double] > > dimord: 'chan_freq_time' > > > > However, when I try and use my file in 'FT_FREQGRANDAVERAGE' , it does > not recognise this as a TF object, and produces this error message: > > > > ??? Error using ==> ft_checkdata at 324 > > This function requires freq data as input. > > > > Error in ==> ft_freqgrandaverage at 66 > > varargin{i} = ft_checkdata(varargin{i}, 'datatype', 'freq', > 'feedback', 'no'); > > > > What is it that I am missing?? > > > > Best, > > Duncan > > > > ________________________________________________ > > Dr. Duncan Astle, > > Programme Leader Track, > > British Academy Research Fellow, > > MRC Cognition and Brain Sciences Unit, > > Chaucer Road, > > Cambridge. > > Duncan.Astle at mrc-cbu.cam.ac.uk > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ------------------------------ Message: 3 Date: Thu, 27 Sep 2012 20:03:43 +0200 From: Michael Wibral To: FieldTrip discussion list Subject: [FieldTrip] Fwd: Re: How to impove dics realfilter solution Message-ID: <506494FF.7070308 at web.de> Content-Type: text/plain; charset="iso-8859-1" -------- Original Message -------- Subject: Re: [FieldTrip] How to impove dics realfilter solution Date: Thu, 27 Sep 2012 20:01:22 +0200 From: wibral Reply-To: wibral at em.uni-frankfurt.de To: FieldTrip discussion list Dear Filedtrip users, I fully agree with jan Mathijs, in principle when using DICS to reconstruct source power, the nature of the physical processes (forward model) should guarantee that filters are automatically real-valued, because this reflects the quasi-static approximation of maxwell's equations which holds pretty well in MEG. In practice filter coeffcients only deviate from being real because of sensor noise, which is not a desirable effect. Best, Michael On 09/27/2012 01:39 PM, jan-mathijs schoffelen wrote: > Dear Bj?rn, caro Gio, > > I don't agree with you, Gio, that one should use complex-valued > filters. The reason for this is that they don't make sense from a > biophysical point of view. The mixing from sources to channels (as > represented in the leadfields) is strictly real-valued, because it is > (near-)instantaneous. I think that the unmixing from channels to > sources also should be real-valued, for the same argument. When you > allow filter coefficients to be complex-valued, this is equivalent to > allowing the sensor-level signals to be shifted in time with respect > to one another. I consider this a bit odd. In Joachim's seminal paper > (on which FieldTrip's initial DICS implementation is based), this was > not really explicit in the methods description. However, based on > personal communications with said Joachim, I at least distilled that > the filters should be real-valued. The complex-valued filters were > kept in (as default) for backward compatibilitiy reasons. Although > mathematically possible (perhaps even more strictly answering to the > minimum variance and unit gain constraints), and sometimes seemingly > giving nicer subjective results, I'd advice against using them. > > Cheers, > > JM > > > > On Sep 25, 2012, at 12:21 PM, Gio Piantoni wrote: > >> Hi Bj?rn, >> >> It's not surprising that the results are pretty bad after using real >> filters. The fourier transform and DICS are intrinsically >> complex-valued, so using only the real part means throwing away half >> of the information (and getting meaningless results). >> >> The realfilter option was implemented in order to allow to pass the >> time-domain signal through the complex-value spatial filter and obtain >> a "virtual electrode". A virtual electrode with complex values is >> "weird to say the least", see: >> http://mailman.science.ru.nl/pipermail/fieldtrip/2006-May/000510.html >> Robert considered it an error in the algorithm and fixed it by >> providing the realfilter option. However, to me it seems more correct >> to think that complex spatial filters requires complex input (i.e. >> frequency-domain signal), so don't use DICS spatial filters on >> time-domain real-valued MEG recordings to generate time-domain virtual >> electrodes. If you want time-domain virtual electrodes, use LCMV >> spatial filters centered at the location of interest. Other smart >> people might disagree though. >> >> I suggest not to use realfilter option at all, but I'd be happy to >> hear other meaningful applications of this option. >> >> Hope this helps, >> >> Gio >> >> On Fri, Sep 14, 2012 at 10:23 AM, Bj?rn Herrmann >> wrote: >>> Dear fieldtrip user, >>> >>> I am using the DICS beamformer to localize a 3Hz FFT power >>> topographical distribution (using a neuromag system). The >>> topographies are very clear auditory in single subjects, thus it >>> shouldn't be a problem finding the "right" solution. When I use the >>> beamformer to obtain complex-value spatial filters, the solution >>> looks very good (using NAI). No problem here. However, using >>> cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real >>> values, the localization completely breaks down, sometimes even >>> finding a strong peak in the opposite hemisphere than visible in the >>> sensor topography (the head is centered in the sensor array). >>> >>> Does someone have a suggestion how to improve the solution using >>> realfilter = 'yes'. I use the following settings. They are rather >>> standard I guess. >>> >>> cfg = []; >>> cfg.method = 'dics'; >>> cfg.frequency = 3; >>> cfg.dics.projectnoise = 'yes'; >>> cfg.dics.lambda = '5%'; >>> cfg.dics.keepfilter = 'yes'; >>> cfg.dics.realfilter = 'yes'; >>> cfg.dics.fixedori = 'no'; >>> >>> >>> If someone has a suggestion, I would appreciate it. >>> Thanks in advance, >>> best, >>> >>> Bj?rn >>> >>> >>> >>> _______________________________________________ >>> 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 > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip End of fieldtrip Digest, Vol 22, Issue 47 ***************************************** From g.piantoni at nin.knaw.nl Fri Sep 28 10:50:35 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Fri, 28 Sep 2012 10:50:35 +0200 Subject: [FieldTrip] Fwd: Re: How to impove dics realfilter solution In-Reply-To: <506494FF.7070308@web.de> References: <50649472.3050502@em.uni-frankfurt.de> <506494FF.7070308@web.de> Message-ID: Hi Michael, Thanks for your suggestion! In fact, the contribution of the imaginary part increases with higher levels of noise (and it's zero when the noise is zero). I tested with a simulation (see code below). The imaginary part derives from the uncorrelated sensor noise and seem to contain no meaningful information, sorry if I had given wrong information before, my intuition tricked me. Thanks for the interesting discussion! Cheers, Gio %-----------------% %-forward model fieldtripdir = '/path/to/fieldtrip/'; elec = ft_read_sens([fieldtripdir 'template/electrode/standard_1020.elc']); load([fieldtripdir 'template/headmodel/standard_bem.mat']); cfg = []; cfg.elec = elec; cfg.vol = vol; cfg.grid.xgrid = -80:10:80; cfg.grid.ygrid = -110:10:80; cfg.grid.zgrid = -70:10:90; cfg.inwardshift = 1; lead = ft_prepare_leadfield(cfg); %-----------------% %-------------------------------------% %-loop over relative noise relnoise = 0:.05:1; realfilter = zeros(size(relnoise)); imagfilter = zeros(size(relnoise)); for i = 1:numel(relnoise) %-----------------% %-create data cfg = []; cfg.dip.pos = [10 30 30]; cfg.dip.mom = [1 0 0]'; cfg.dip.frequency = 10; cfg.vol = vol; cfg.relnoise = relnoise(i); cfg.elec = elec; data = ft_dipolesimulation(cfg); %-----------------% %-----------------% %-fourier freq cfg = []; cfg.method = 'mtmfft'; cfg.output = 'fourier'; cfg.taper = 'hanning'; cfg.foilim = [10 10]; freq = ft_freqanalysis(cfg, data); %-----------------% %-----------------% %-beamformer cfg = []; cfg.method = 'dics'; cfg.frequency = 10; cfg.grid = lead; cfg.vol = vol; cfg.elec = elec; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '1%'; cfg.dics.keepfilter = 'yes'; source = ft_sourceanalysis(cfg, freq); %-take one dipole as example realfilter(i) = sum(abs(real(source.avg.filter{source.inside(100)}(:)))); imagfilter(i) = sum(abs(imag(source.avg.filter{source.inside(100)}(:)))); %-----------------% end plot(relnoise, realfilter) hold on plot(relnoise, imagfilter, 'r') %-------------------------------------% On Thu, Sep 27, 2012 at 8:03 PM, Michael Wibral wrote: > > > > > -------- Original Message -------- > Subject: Re: [FieldTrip] How to impove dics realfilter solution > Date: Thu, 27 Sep 2012 20:01:22 +0200 > From: wibral > Reply-To: wibral at em.uni-frankfurt.de > To: FieldTrip discussion list > > > > Dear Filedtrip users, > > I fully agree with jan Mathijs, > > in principle when using DICS to reconstruct source power, the nature of > the physical processes (forward model) should guarantee that filters are > automatically real-valued, because this reflects the quasi-static > approximation of maxwell's equations which holds pretty well in MEG. In > practice filter coeffcients only deviate from being real because of sensor > noise, which is not a desirable effect. > > Best, > Michael > > > On 09/27/2012 01:39 PM, jan-mathijs schoffelen wrote: > > Dear Björn, caro Gio, > > I don't agree with you, Gio, that one should use complex-valued filters. > The reason for this is that they don't make sense from a biophysical point > of view. The mixing from sources to channels (as represented in the > leadfields) is strictly real-valued, because it is (near-)instantaneous. I > think that the unmixing from channels to sources also should be real-valued, > for the same argument. When you allow filter coefficients to be > complex-valued, this is equivalent to allowing the sensor-level signals to > be shifted in time with respect to one another. I consider this a bit odd. > In Joachim's seminal paper (on which FieldTrip's initial DICS implementation > is based), this was not really explicit in the methods description. However, > based on personal communications with said Joachim, I at least distilled > that the filters should be real-valued. The complex-valued filters were kept > in (as default) for backward compatibilitiy reasons. Although mathematically > possible (perhaps even more strictly answering to the minimum variance and > unit gain constraints), and sometimes seemingly giving nicer subjective > results, I'd advice against using them. > > Cheers, > > JM > > > > On Sep 25, 2012, at 12:21 PM, Gio Piantoni wrote: > > Hi Björn, > > It's not surprising that the results are pretty bad after using real > filters. The fourier transform and DICS are intrinsically > complex-valued, so using only the real part means throwing away half > of the information (and getting meaningless results). > > The realfilter option was implemented in order to allow to pass the > time-domain signal through the complex-value spatial filter and obtain > a "virtual electrode". A virtual electrode with complex values is > "weird to say the least", see: > http://mailman.science.ru.nl/pipermail/fieldtrip/2006-May/000510.html > Robert considered it an error in the algorithm and fixed it by > providing the realfilter option. However, to me it seems more correct > to think that complex spatial filters requires complex input (i.e. > frequency-domain signal), so don't use DICS spatial filters on > time-domain real-valued MEG recordings to generate time-domain virtual > electrodes. If you want time-domain virtual electrodes, use LCMV > spatial filters centered at the location of interest. Other smart > people might disagree though. > > I suggest not to use realfilter option at all, but I'd be happy to > hear other meaningful applications of this option. > > Hope this helps, > > Gio > > On Fri, Sep 14, 2012 at 10:23 AM, Björn Herrmann > wrote: > > Dear fieldtrip user, > > > I am using the DICS beamformer to localize a 3Hz FFT power topographical > distribution (using a neuromag system). The topographies are very clear > auditory in single subjects, thus it shouldn't be a problem finding the > "right" solution. When I use the beamformer to obtain complex-value spatial > filters, the solution looks very good (using NAI). No problem here. However, > using cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real > values, the localization completely breaks down, sometimes even finding a > strong peak in the opposite hemisphere than visible in the sensor topography > (the head is centered in the sensor array). > > > Does someone have a suggestion how to improve the solution using > realfilter = 'yes'. I use the following settings. They are rather standard I > guess. > > > cfg = []; > > cfg.method = 'dics'; > > cfg.frequency = 3; > > cfg.dics.projectnoise = 'yes'; > > cfg.dics.lambda = '5%'; > > cfg.dics.keepfilter = 'yes'; > > cfg.dics.realfilter = 'yes'; > > cfg.dics.fixedori = 'no'; > > > > If someone has a suggestion, I would appreciate it. > > Thanks in advance, > > best, > > > Björn > > > > > _______________________________________________ > > 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 > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > > _______________________________________________ > 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 landpt at gmail.com Fri Sep 28 11:39:58 2012 From: landpt at gmail.com (Ricardo Jorge) Date: Fri, 28 Sep 2012 10:39:58 +0100 Subject: [FieldTrip] Emotiv and Fieldtrip - filter in the streamer/buffer? In-Reply-To: References: Message-ID: Dear Boris, Sorry for the late response, I tried to reply as earliest as possible. Thank for the answer, by the way. I don't think it's a scaling issue: it shouldn't affect the variance that much and Power spectral seem to be different from both ways. Absolutely that I can give you additional information; I am starting with explaining almost everything I've done: 1st: I picked up the function ft_realtime_signalviewer in "fieldtrip-20120904\realtime\example" and adapted it slightly so I could view it in realtime but at the same time, I could see the previous 20 seconds. Besides that, I disabled the ft_preproc_baselinecorrect(data.trial{1}) step in that function and added some steps that allowed me to save the whole record into a file at the same time (is there any function in fieldtrip that does that at the same time as realtime?). I'm not sure if I can send files through this discussion list: tell me if you want to try it. Just for visualization issues, I multiplied the signal in the plot by a factor, so it could be similar to Testbench visually, but it doesn't matter because I'm not changing any data, just the plot. 2nd: I opened Testbench and OpenVibe. In order to compare the results, I saved them into EDF an opened it in matlab. Testbench has an option to set an high-pass filter, but it does not alter the recording, only the visualization in real time. 3rd: I did put the emotiv in the table so it could be at the rest. 4th: I started all 3 of them. They're not be all exactly at the same time because I can't press it all at once (but almost) and so I'll record during a reasonable time so I can get enough samples. Results: 1. There is a weird thing in the testbench/openvibe data, all values in AF3 channel (for instance) are integer numbers, whereas Fieldtrip are not: Fieldtrip: 1.0e+03 * 4.030540530271679 4.030428591191215 4.030553469018260 4.030684982830449 4.030580735490210 4.030495361159973 Testbench: 4029 4030 4031 4031 4032 4032 They're almost the same and it isn't a problem since they didnt start exactly at the same time. However, analyzing their mean/variance, we have: Fieldtrip: Mean: 4.030526515189773e+03 Variance: 0.011920664040352 Offline (Testbench): Mean: 4.030526118470382e+03 Variance:1.641380154961390 Their mean are great but the same cannot be said to their variance: in fact it seems that it spreads way too much while offline. Let's see their min and max through a sample: Fieldtrip: [4.027692307692308e+03 ; 4.032307692307693e+03] Testbench: [4025 ; 4037] I've put a plot in my dropbox folder if you want to check it: https://dl.dropbox.com/u/846911/comparision.jpg I've checked if the signalviewer has any filter, but I can't find any, so I cannot understand exactly what could be happening. Their FFT is similar but not exactly the same as well. What do you think it could be happening? Thanks in advance, Best Regards Ricardo Jorge From b.reuderink at donders.ru.nl Fri Sep 28 13:14:37 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Fri, 28 Sep 2012 13:14:37 +0200 Subject: [FieldTrip] Emotiv and Fieldtrip - filter in the streamer/buffer? In-Reply-To: References: Message-ID: <11DBE635-CEA4-4580-B5B3-19C31E6259F1@donders.ru.nl> Dear Ricardo, No problem, and thank you for your elaborate response :). When I look at your screenshot, the right subplot seems to show a rounding issue; all the values are indeed integers, while on the left a more continuous signal is displayed. So, I would say that the difference between the signals is at least a rounding issue, and I assume that the FieldTrip signal is the more precise one. This might explain the difference in variance. For me this raises the question where this rounding comes from. You say that both OpenVibe and Emotiv's Testbench have these integer valued samples? Could this rounding to integers happen at some other stage (e.g. after importing in MATLAB?). Best, Boris -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl On 28 sep. 2012, at 11:39, Ricardo Jorge wrote: > Dear Boris, > > Sorry for the late response, I tried to reply as earliest as possible. > Thank for the answer, by the way. > > I don't think it's a scaling issue: it shouldn't affect the variance > that much and Power spectral seem to be different from both ways. > Absolutely that I can give you additional information; I am starting > with explaining almost everything I've done: > > 1st: I picked up the function ft_realtime_signalviewer in > "fieldtrip-20120904\realtime\example" and adapted it slightly so I > could view it in realtime but at the same time, I could see the > previous 20 seconds. Besides that, I disabled the > ft_preproc_baselinecorrect(data.trial{1}) step in that function and > added some steps that allowed me to save the whole record into a file > at the same time (is there any function in fieldtrip that does that at > the same time as realtime?). I'm not sure if I can send files through > this discussion list: tell me if you want to try it. Just for > visualization issues, I multiplied the signal in the plot by a factor, > so it could be similar to Testbench visually, but it doesn't matter > because I'm not changing any data, just the plot. > > 2nd: I opened Testbench and OpenVibe. In order to compare the results, > I saved them into EDF an opened it in matlab. Testbench has an option > to set an high-pass filter, but it does not alter the recording, only > the visualization in real time. > > 3rd: I did put the emotiv in the table so it could be at the rest. > > 4th: I started all 3 of them. They're not be all exactly at the same > time because I can't press it all at once (but almost) and so I'll > record during a reasonable time so I can get enough samples. > > Results: > > 1. There is a weird thing in the testbench/openvibe data, all values > in AF3 channel (for instance) are integer numbers, whereas Fieldtrip > are not: > > Fieldtrip: > 1.0e+03 * > > 4.030540530271679 4.030428591191215 4.030553469018260 > 4.030684982830449 4.030580735490210 4.030495361159973 > > Testbench: > 4029 4030 4031 4031 4032 4032 > > They're almost the same and it isn't a problem since they didnt start > exactly at the same time. > However, analyzing their mean/variance, we have: > > Fieldtrip: > > Mean: 4.030526515189773e+03 > Variance: 0.011920664040352 > > Offline (Testbench): > > Mean: 4.030526118470382e+03 > Variance:1.641380154961390 > > Their mean are great but the same cannot be said to their variance: in > fact it seems that it spreads way too much while offline. Let's see > their min and max through a sample: > Fieldtrip: [4.027692307692308e+03 ; 4.032307692307693e+03] > Testbench: [4025 ; 4037] > > I've put a plot in my dropbox folder if you want to check it: > https://dl.dropbox.com/u/846911/comparision.jpg > > > I've checked if the signalviewer has any filter, but I can't find any, > so I cannot understand exactly what could be happening. > > Their FFT is similar but not exactly the same as well. > > What do you think it could be happening? > > Thanks in advance, > > Best Regards > > Ricardo Jorge > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From landpt at gmail.com Fri Sep 28 14:16:10 2012 From: landpt at gmail.com (Ricardo Jorge) Date: Fri, 28 Sep 2012 13:16:10 +0100 Subject: [FieldTrip] Emotiv and Fieldtrip - filter in the streamer/buffer? In-Reply-To: References: Message-ID: Hi again, I'm not sure, to be honest! I would say fieldtrip is the most precise one, but why would it happen - I mean, how could it be better than the testbench? That's what's confusing me: it makes no sense that a signal such as EEG has only integer values indeed. But there are weirder things: In the EDF/CSV files from testbench, the first channel (AF3) has only integer values, the second channel doesn't have only integer values, but have mean 260 around, the third channel goes back to the integer values and 4000 mean again, fourth chan back to ~200 mean, non-integer and it goes on... which makes me thinking that they probably apply something, either the baseline and rounding, or something more. In the EDF files from Openvibe, all numbers are integers as independently of the channel, but variance's different as well. In fact, estimating it right now, it says that it has variance around 3. In the MAT file recorded by Fieldtrip, all numbers are non integer but with an extremely low variance comparing to the others. So, for some reason all methods are different but to be honest I feel that fieldtrip's results are correct and so I'm going to give it a try and use them in my investigation to see if they can confirm what I expect. Thanks once again! Best regards, Ricardo Jorge On Fri, Sep 28, 2012 at 10:39 AM, Ricardo Jorge wrote: > Dear Boris, > > Sorry for the late response, I tried to reply as earliest as possible. > Thank for the answer, by the way. > > I don't think it's a scaling issue: it shouldn't affect the variance > that much and Power spectral seem to be different from both ways. > Absolutely that I can give you additional information; I am starting > with explaining almost everything I've done: > > 1st: I picked up the function ft_realtime_signalviewer in > "fieldtrip-20120904\realtime\example" and adapted it slightly so I > could view it in realtime but at the same time, I could see the > previous 20 seconds. Besides that, I disabled the > ft_preproc_baselinecorrect(data.trial{1}) step in that function and > added some steps that allowed me to save the whole record into a file > at the same time (is there any function in fieldtrip that does that at > the same time as realtime?). I'm not sure if I can send files through > this discussion list: tell me if you want to try it. Just for > visualization issues, I multiplied the signal in the plot by a factor, > so it could be similar to Testbench visually, but it doesn't matter > because I'm not changing any data, just the plot. > > 2nd: I opened Testbench and OpenVibe. In order to compare the results, > I saved them into EDF an opened it in matlab. Testbench has an option > to set an high-pass filter, but it does not alter the recording, only > the visualization in real time. > > 3rd: I did put the emotiv in the table so it could be at the rest. > > 4th: I started all 3 of them. They're not be all exactly at the same > time because I can't press it all at once (but almost) and so I'll > record during a reasonable time so I can get enough samples. > > Results: > > 1. There is a weird thing in the testbench/openvibe data, all values > in AF3 channel (for instance) are integer numbers, whereas Fieldtrip > are not: > > Fieldtrip: > 1.0e+03 * > > 4.030540530271679 4.030428591191215 4.030553469018260 > 4.030684982830449 4.030580735490210 4.030495361159973 > > Testbench: > 4029 4030 4031 4031 4032 4032 > > They're almost the same and it isn't a problem since they didnt start > exactly at the same time. > However, analyzing their mean/variance, we have: > > Fieldtrip: > > Mean: 4.030526515189773e+03 > Variance: 0.011920664040352 > > Offline (Testbench): > > Mean: 4.030526118470382e+03 > Variance:1.641380154961390 > > Their mean are great but the same cannot be said to their variance: in > fact it seems that it spreads way too much while offline. Let's see > their min and max through a sample: > Fieldtrip: [4.027692307692308e+03 ; 4.032307692307693e+03] > Testbench: [4025 ; 4037] > > I've put a plot in my dropbox folder if you want to check it: > https://dl.dropbox.com/u/846911/comparision.jpg > > > I've checked if the signalviewer has any filter, but I can't find any, > so I cannot understand exactly what could be happening. > > Their FFT is similar but not exactly the same as well. > > What do you think it could be happening? > > Thanks in advance, > > Best Regards > > Ricardo Jorge From mark.noordenbos at gmail.com Sun Sep 30 11:30:35 2012 From: mark.noordenbos at gmail.com (Mark Noordenbos) Date: Sun, 30 Sep 2012 11:30:35 +0200 Subject: [FieldTrip] cluster analysis Message-ID: Dear Fieldtrippers, I was wondering how you report the results of the cluster analysis in your papers. I have seen different types of how the results are reported. For example, some report only the p-value of the cluster whereas others report clusters as T(degrees of freedom) = [clusterstat value], p-value. Is T (multivariate t) the correct test statisic for the cluster analysis (like F for anova)? Where can I find (or calculate) the degrees of freedom of the clusterstat value? Thanks Best, Mark -------------- next part -------------- An HTML attachment was scrubbed... URL: From politzerahless at gmail.com Sun Sep 30 15:46:09 2012 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Sun, 30 Sep 2012 08:46:09 -0500 Subject: [FieldTrip] cluster analysis Message-ID: Hi Mark, The Fieldtrip wiki has examples of published papers that report cluster analyses. In what I've seen, usually just the *p* is reported (if even that), along with the latency and topography of the cluster. See e.g. Pijnacker et al. (2011, *Journal of Cognitive Neuroscience*) and Meltzer & Braun (2011, *Frontiers in Human Neuroscience*). There may be others in http://fieldtrip.fcdonders.nl/publications As for your second question, my understanding is that the test statistic doesn't matter (one of the points of the cluster test is that it works no matter which test statistic you use (Maris & Oostenveld, 2007)). Also, to the best of my knowledge, there are no degrees of freedom for the cluster test, since it's non-parametric (it's not based on the distribution of a test statistic, it's based on Monte Carlo estimation). Best, Steve Message: 1 > Date: Sun, 30 Sep 2012 11:30:35 +0200 > From: Mark Noordenbos > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] cluster analysis > Message-ID: > 7qVRZp7goj3AhoE7xaq8tqTPsg at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Fieldtrippers, > > I was wondering how you report the results of the cluster analysis in your > papers. I have seen different types of how the results are reported. > For example, some report only the p-value of the cluster whereas others > report clusters as T(degrees of freedom) = [clusterstat value], p-value. > > Is T (multivariate t) the correct test statisic for the cluster analysis > (like F for anova)? > Where can I find (or calculate) the degrees of freedom of the clusterstat > value? > > Thanks > > Best, > Mark > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120930/fe6908ab/attachment-0001.html > > > > ------------------------------ > -------------- next part -------------- An HTML attachment was scrubbed... URL: From demiral.007 at gmail.com Sat Sep 1 16:29:35 2012 From: demiral.007 at gmail.com (Baris Demiral) Date: Sat, 1 Sep 2012 10:29:35 -0400 Subject: [FieldTrip] CTF data event/reading Message-ID: Hi Nedad, filedtrippers, I have continuous and epoched CTF data as well, and I want to import them into fieldtrip. The event types are previously edited in the early stages. When I looked at the event values with the ft_read_event(cfg.dataset) function, I see that some event values are empty '[ ]'. On the other hand, the initial triggers / event types have integer event values (type: 'front panel trigger', value: 222). Error is in " ft_preprocessing (line 511) ... tim = offset2time(offset, hdr.Fs, size(dat,2)); See below. Can you help me on that? What functions/lines of code shall I call? I followed the instructions on the web tutorials line by line, but nope. Sometimes it says " trialfun is not described." I also download fileio package. I am using the most recent version of FieldTrip. Do you think the event structure has anything to do with the errors, or I had to install some other package as well? Thanks Baris >> cfg.dataset = 'AFLLBCEAXXX_epoched.ds'; % name of CTF dataset data = ft_preprocessing(cfg) readCTFds: You are reading CTF data for use with a software-application tool that is not manufactured by VSM MedTech Ltd. and has not received marketing clearance for clinical applications. If CTF MEG data are processed by this tool, they should not be later employed for clinical and/or diagnostic purposes. undoing the G3BR balancing processing channel { 'UPPT001' 'SCLK01' 'BG1' 'BG2' 'BG3' 'BP1' 'BP2' 'BP3' 'BR1' 'BR2' 'BR3' 'G11' 'G12' 'G13' 'G22' 'G23' 'P11' 'P12' 'P22' 'P23' 'Q11' 'Q12' 'Q13' 'Q22' 'Q23' 'R11' 'R12' 'R13' 'R22' 'R23' 'MLC11' 'MLC12' 'MLC13' 'MLC14' 'MLC15' 'MLC16' 'MLC17' 'MLC21' 'MLC22' 'MLC23' 'MLC24' 'MLC25' 'MLC31' 'MLC32' 'MLC41' 'MLC42' 'MLC51' 'MLC52' 'MLC53' 'MLC54' 'MLC55' 'MLC61' 'MLC62' 'MLC63' 'MLF11' 'MLF12' 'MLF13' 'MLF14' 'MLF21' 'MLF22' 'MLF23' 'MLF24' 'MLF25' 'MLF31' 'MLF32' 'MLF33' 'MLF34' 'MLF35' 'MLF41' 'MLF42' 'MLF43' 'MLF44' 'MLF45' 'MLF46' 'MLF51' 'MLF52' 'MLF53' 'MLF54' 'MLF55' 'MLF56' 'MLF61' 'MLF62' 'MLF63' 'MLF64' 'MLF65' 'MLF66' 'MLF67' 'MLO11' 'MLO12' 'MLO13' 'MLO14' 'MLO21' 'MLO22' 'MLO23' 'MLO24' 'MLO31' 'MLO32' 'MLO33' 'MLO34' 'MLO41' 'MLO42' 'MLO43' 'MLO44' 'MLO51' 'MLO52' 'MLO53' 'MLP11' 'MLP12' 'MLP21' 'MLP22' 'MLP23' 'MLP31' 'MLP32' 'MLP33' 'MLP34' 'MLP35' 'MLP41' 'MLP42' 'MLP43' 'MLP44' 'MLP45' 'MLP51' 'MLP52' 'MLP53' 'MLP54' 'MLP55' 'MLP56' 'MLP57' 'MLT11' 'MLT12' 'MLT13' 'MLT14' 'MLT15' 'MLT16' 'MLT21' 'MLT22' 'MLT23' 'MLT24' 'MLT25' 'MLT26' 'MLT27' 'MLT31' 'MLT32' 'MLT33' 'MLT34' 'MLT35' 'MLT36' 'MLT37' 'MLT41' 'MLT42' 'MLT43' 'MLT44' 'MLT45' 'MLT46' 'MLT47' 'MLT51' 'MLT52' 'MLT53' 'MLT54' 'MLT55' 'MLT56' 'MLT57' 'MRC11' 'MRC12' 'MRC13' 'MRC14' 'MRC15' 'MRC16' 'MRC17' 'MRC21' 'MRC22' 'MRC23' 'MRC24' 'MRC25' 'MRC31' 'MRC32' 'MRC41' 'MRC42' 'MRC51' 'MRC52' 'MRC53' 'MRC54' 'MRC55' 'MRC61' 'MRC62' 'MRC63' 'MRF11' 'MRF12' 'MRF13' 'MRF14' 'MRF21' 'MRF22' 'MRF23' 'MRF24' 'MRF25' 'MRF31' 'MRF32' 'MRF33' 'MRF34' 'MRF35' 'MRF41' 'MRF42' 'MRF44' 'MRF45' 'MRF46' 'MRF51' 'MRF52' 'MRF53' 'MRF54' 'MRF55' 'MRF56' 'MRF61' 'MRF62' 'MRF63' 'MRF64' 'MRF65' 'MRF66' 'MRF67' 'MRO11' 'MRO12' 'MRO14' 'MRO21' 'MRO22' 'MRO23' 'MRO24' 'MRO31' 'MRO32' 'MRO33' 'MRO34' 'MRO41' 'MRO42' 'MRO43' 'MRO44' 'MRO51' 'MRO52' 'MRO53' 'MRP11' 'MRP12' 'MRP21' 'MRP22' 'MRP23' 'MRP31' 'MRP32' 'MRP33' 'MRP34' 'MRP35' 'MRP41' 'MRP42' 'MRP43' 'MRP44' 'MRP45' 'MRP51' 'MRP52' 'MRP53' 'MRP54' 'MRP55' 'MRP56' 'MRP57' 'MRT11' 'MRT12' 'MRT13' 'MRT14' 'MRT15' 'MRT16' 'MRT21' 'MRT22' 'MRT23' 'MRT24' 'MRT25' 'MRT26' 'MRT27' 'MRT31' 'MRT32' 'MRT33' 'MRT34' 'MRT35' 'MRT36' 'MRT37' 'MRT41' 'MRT42' 'MRT43' 'MRT44' 'MRT45' 'MRT46' 'MRT47' 'MRT51' 'MRT52' 'MRT53' 'MRT54' 'MRT55' 'MRT56' 'MRT57' 'MZC01' 'MZC02' 'MZC03' 'MZC04' 'MZF01' 'MZF02' 'MZF03' 'MZO01' 'MZO02' 'MZO03' 'MZP01' 'lip' 'HADC001' 'HADC002' 'HADC003' 'HDAC001' 'HDAC002' 'HDAC003' 'UADC003' 'UADC004' 'UADC016' 'HLC0011' 'HLC0012' 'HLC0013' 'HLC0021' 'HLC0022' 'HLC0023' 'HLC0031' 'HLC0032' 'HLC0033' 'HLC0018' 'HLC0028' 'HLC0038' 'HLC0014' 'HLC0015' 'HLC0016' 'HLC0017' 'HLC0024' 'HLC0025' 'HLC0026' 'HLC0027' 'HLC0034' 'HLC0035' 'HLC0036' 'HLC0037' } reading and preprocessing reading and preprocessing trial 1 from 72 Undefined function 'offset2time' for input arguments of type 'double'. Error in ft_preprocessing (line 511) tim = offset2time(offset, hdr.Fs, size(dat,2)); >> cfg.trialdef.eventtype = '?'; >> cfg = ft_definetrial(cfg); Warning: no trialfun was specified, using ft_trialfun_general > In ft_definetrial at 123 Undefined function 'ft_getuserfun' for input arguments of type 'char'. Error in ft_definetrial (line 140) cfg.trialfun = ft_getuserfun(cfg.trialfun, 'trialfun'); Thanks Baris On Thu, Aug 30, 2012 at 4:33 AM, Nenad Polomac wrote: > Hi, > > I am analyzing data obtained on CTF MEG 275 system. However, 4 sensors are > broken and data ended up with 271 sensor. So, my question is should I > interpolate the missing sensors with FT_CHANNELREPAIR? In the case I leave > data with 271 sensor, will those missing sensors influence neighbors > configuration in the statistic and the source localisation analysis? > > Thank you in advance! > > Kind regards! > > Nenad > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From r.oostenveld at donders.ru.nl Sun Sep 2 12:51:46 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Sun, 2 Sep 2012 12:51:46 +0200 Subject: [FieldTrip] neighbours In-Reply-To: References: Message-ID: <9BF899F9-DD29-482B-B964-CC07CEC56273@donders.ru.nl> Hi Nenad On 30 Aug 2012, at 10:33, Nenad Polomac wrote: > I am analyzing data obtained on CTF MEG 275 system. However, 4 sensors are broken and data ended up with 271 sensor. So, my question is should I interpolate the missing sensors with FT_CHANNELREPAIR? In the case I leave data with 271 sensor, will those missing sensors influence neighbors configuration in the statistic and the source localisation analysis? If the channels are consistently broken in all your subjects, you should better not interpolate them. If the channels are only missing in some, but not all subjects, interpolating will be of use for the channel-level statistics. For source reconstruction you should not interpolate the broken channels. Group statistics on source-level data is also not affected by having slight differences in the working channels over subjects. best regards Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Sun Sep 2 12:53:12 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Sun, 2 Sep 2012 12:53:12 +0200 Subject: [FieldTrip] neighbours In-Reply-To: <50406CB9.7090209@donders.ru.nl> References: <50406CB9.7090209@donders.ru.nl> Message-ID: whoops, I now see that Jorn has already provided a much better and elaborate answer. Better pay attention to what he writes and ignore my quick reply. Robert On 31 Aug 2012, at 9:50, Jörn M. Horschig wrote: > Hi Nenad, > > the question you are asking does not deserve a definite 'yes' or 'no'. In any case, note that when averaging over subjects, missing sensors for one subject will be removed for all other subjects as well. So, if you are talking about different missing sensors per subject, an interpolation will definitely be a wise thing to do. In case you choose for interpolating the missing channels, you can try to check out the new spherical spline interpolation method (see help ft_channelrepair) - theoretically that should result in a quite good reconstruction. But the (standard) nearest neighbour interpolation is fine as well. > > With respect to your second question: missing sensors will influence the neighbour configuration depending on the method you chose for neighbour selection. For the 'distance' and 'template' method, each neighbouring channel of the missing will have one sensor less (i.e. the missing one). The 'triangulation' method will create triangle neighbour no matter how many channels you have, so it will just ignore the whole in space. In any case, I'd propose that you check out how satisfied you personally are with the neighbours by calling ft_neighbourplot. Just last week, I added the new option that if you use cfg.enableedit='yes', you can interactively change the neighbourhood structure within the neighbourplot. If I were you, I would start from the template method. As an additional piece of information: I am currently working on improving the neighbour templates, and will upload them probably next week. > > All that advertised, let me also say that having 4 out of 275 sensors missing won't affect your statistics much. Here, it of course depends on your region if interest, research question etc. E.g. if you are interested in posterior alpha power, but miss four temporal channels, there is no reason to worry. So, without knowing what you are looking for and where the missing channels are, I cannot give you a general advise what to do. As a last remark, the sensitiviy of the statistics will of course be influenced by missing sensors, but I doubt that it will matter much. Btw, I am not quite sure how much the spherical spline interpolation will buy you here, you might give it a try. I bet that it will increase your sensitivity more than the nearest neighbour approach, although both might result in rather low increases. But this is just a general gut feeling rather than anything I empirically validated. > > Best, > Jörn > > On 8/30/2012 10:33 AM, Nenad Polomac wrote: >> Hi, >> >> I am analyzing data obtained on CTF MEG 275 system. However, 4 sensors are broken and data ended up with 271 sensor. So, my question is should I interpolate the missing sensors with FT_CHANNELREPAIR? In the case I leave data with 271 sensor, will those missing sensors influence neighbors configuration in the statistic and the source localisation analysis? >> >> Thank you in advance! >> >> Kind regards! >> >> Nenad >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Sun Sep 2 12:54:22 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Sun, 2 Sep 2012 12:54:22 +0200 Subject: [FieldTrip] CTF data event/reading In-Reply-To: References: Message-ID: Hi Baris, First something in general: This error > Undefined function 'offset2time' for input arguments > of type 'double'. > > Error in ft_preprocessing (line 511) > tim = offset2time(offset, hdr.Fs, size(dat,2)); should not happen with recent versions of FieldTrip (nor with older ones). The offset2time helper function is present in fieldtrip/private and can be found there by ft_preprocessing. Also the error > Undefined function 'ft_getuserfun' for input arguments > of type 'char'. > > Error in ft_definetrial (line 140) > cfg.trialfun = ft_getuserfun(cfg.trialfun, > 'trialfun'); suggests that your fieldtrip installation is broken. Please upgrade to the most recent version, that might resolve some (or all) of your problems. Don't move around the directories in the fieldtrip zip file, or rename them, otherwise ft_defaults is not able to set up the path correctly. See also http://fieldtrip.fcdonders.nl/faq/should_i_add_fieldtrip_with_all_subdirectories_to_my_matlab_path Then on to some other aspects of your question, which may be of interest to other CTF users as well. From the CTF channel naming scheme I can see that you have a CTF275 system. The 151 channel MEG system we started off with at the Donders in 2002 had an electronics rack which was placed such that there was a clear front and back side. Each side of the rack exposed 16 binary inputs (i.e. bits) for connecting external triggers. To the front we connected the button boxes, to the back we connected the stimulus presentation computer. The 16 bits from the front and from the back were combined in the 32 bit STIM channel. Given the connections of the button boxes and stimulus computers, in the analysis the 32 bit STIM channel did not match the users scripts with respect to button box and presentation trigger codes. Therefore the FieldTrip reading software was implemented to split the 32 bits into the 16 frontpanel and the 16 backpanel bits. This also shifts the bits to recover the trigger codes that were used in the presentation software by the users. This situation from early '2000 at the Donders in Nijmegen is still supported by FieldTrip. The “Subject01.ds” tutorial dataset is from that time, so that is why you see it in the tutorials. The front and back panel at other CTF sites with the old electronics rack may be (or have been) connected differently. Furthermore, the present CTF systems have more trigger input options and no front and back side any more, so better don't use those any more in your analyses. In many cases UPPT001 and similarly named channels are the interesting trigger channels. MEG data acquired with the older CTF systems uses the STIM channel. So please be aware that “frontpanel” and “backpanel” are Donders conventions that have ended up in FieldTrip, but may not be of any relevance to you. Another topic is that in Nijmegen (as many other CTF sites) we record the data continuously, and don't use the CTF software for epoching, classification of artifacts and trial marking. However FieldTrip does support the CTF ClassFile and Markerfile in FieldTrip. If you do ft_read_event('dataset.ds') you will see an event structure that combines all information. Some "events" are instantaneous, some "events" have a duration. This is explained in more detail at http://fieldtrip.fcdonders.nl/faq/what_is_the_relation_between_events_such_as_triggers_and_trials best regards, Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: From polomacnenad at gmail.com Sun Sep 2 16:51:31 2012 From: polomacnenad at gmail.com (Nenad Polomac) Date: Sun, 2 Sep 2012 16:51:31 +0200 Subject: [FieldTrip] neighbours Message-ID: Dear Jörn, Thank you very much for the thorough explanation! All the best! Nenad -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sun Sep 2 17:48:43 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sun, 2 Sep 2012 18:48:43 +0300 Subject: [FieldTrip] 'dml' variable Message-ID: Hello, I am trying to classify my data using ft_timelockstatistics function I am using the output of ft_timelockanalysis function and the following options: cfg.layout = 'CTF275.lay'; cfg.method = 'crossvalidate'; cfg.design = [ones(size(class1.trial,1),1); 2*ones(size(class2.trial,1),1)]'; But I got the following error: ??? Undefined variable "dml" or class "dml.standardizer". Error in ==> ft_statistics_crossvalidate at 44 cfg.mva = dml.analysis({ ... Error in ==> statistics_wrapper at 306 [stat] = statmethod(cfg, dat, design); Error in ==> ft_timelockstatistics at 110 [stat, cfg] = statistics_wrapper(cfg, varargin{:}); Did I forgot to add something?! Thanks -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghumana at upmc.edu Mon Sep 3 07:05:37 2012 From: ghumana at upmc.edu (Ghuman, Avniel) Date: Mon, 3 Sep 2012 05:05:37 +0000 Subject: [FieldTrip] A postdoc position in developing methods for MEG with atomic magnetometers In-Reply-To: <20385F716E75B746A7F52BBB3C46A1300226C790@MSXMBXNSPRD03.acct.upmchs.net> References: <20385F716E75B746A7F52BBB3C46A1300226C772@MSXMBXNSPRD03.acct.upmchs.net>, <20385F716E75B746A7F52BBB3C46A1300226C790@MSXMBXNSPRD03.acct.upmchs.net> Message-ID: <20385F716E75B746A7F52BBB3C46A1300226C809@MSXMBXNSPRD03.acct.upmchs.net> Post-doc in MEG with Atomic Magnetometers The Ghuman Lab at the University of Pittsburgh, in collaboration with the Romalis Group at Princeton University and Twinleaf LLC, is recruiting a Post doc to develop methods for atomic magnetometer based MEG and multimodal integration (simultaneous MEG-EEG and MEG-fNIRS). The position is available immediately. Responsibilities: • Develop novel solutions for MEG using atomic magnetometers concerning source localization, noise cancellation and head modeling • Acquire and analyze MEG, MEG-EEG, and MEG-fNIRS data • Develop novel methods for integrating multimodal data • Design and implement novel data analysis tools • Assist with preparation of progress reports • Prepare manuscripts and presentations • Work with Investigators to identify future problems and research opportunities Minimum Qualifications: • Ph.D. in Engineering, Physics, Neuroscience, Computer Science, Math, or related field. • Demonstrated expertise in solving MEG technological issues as shown through publication record, awards, successful patents and/or received applications. • Data analysis expertise includes independent components analysis, Bayesian algorithms, statistical parametric mapping, and MRI image processing. • Proficiency in creating software analysis tools and programs for investigators • MATLAB and Python programming knowledge preferred. Conditions of Employment: • Position available immediately • Salary: according to NIH postdoc salary scale • The University of Pittsburgh has excellent benefits, including health benefits and retirement plans with employer contributions. • The University of Pittsburgh values diversity and is committed to equal opportunity in employment. How to Apply: • E-mail Avniel Ghuman, Ph.D. (ghumana at upmc.edu) or Mike Romalis, Ph.D. (romalis at princeton.edu) From ghumana at upmc.edu Mon Sep 3 07:07:22 2012 From: ghumana at upmc.edu (Ghuman, Avniel) Date: Mon, 3 Sep 2012 05:07:22 +0000 Subject: [FieldTrip] A postdoc position in developing methods for MEG with atomic magnetometers In-Reply-To: <20385F716E75B746A7F52BBB3C46A1300226C790@MSXMBXNSPRD03.acct.upmchs.net> References: <20385F716E75B746A7F52BBB3C46A1300226C772@MSXMBXNSPRD03.acct.upmchs.net>, <20385F716E75B746A7F52BBB3C46A1300226C790@MSXMBXNSPRD03.acct.upmchs.net> Message-ID: <20385F716E75B746A7F52BBB3C46A1300226C827@MSXMBXNSPRD03.acct.upmchs.net> Post-doc in MEG with Atomic Magnetometers The Ghuman Lab at the University of Pittsburgh, in collaboration with the Romalis Group at Princeton University and Twinleaf LLC, is recruiting a Post doc to develop methods for atomic magnetometer based MEG and multimodal integration (simultaneous MEG-EEG and MEG-fNIRS). The position is available immediately. Responsibilities: • Develop novel solutions for MEG using atomic magnetometers concerning source localization, noise cancellation and head modeling • Acquire and analyze MEG, MEG-EEG, and MEG-fNIRS data • Develop novel methods for integrating multimodal data • Design and implement novel data analysis tools • Assist with preparation of progress reports • Prepare manuscripts and presentations • Work with Investigators to identify future problems and research opportunities Minimum Qualifications: • Ph.D. in Engineering, Physics, Neuroscience, Computer Science, Math, or related field. • Demonstrated expertise in solving MEG technological issues as shown through publication record, awards, successful patents and/or received applications. • Data analysis expertise includes independent components analysis, Bayesian algorithms, statistical parametric mapping, and MRI image processing. • Proficiency in creating software analysis tools and programs for investigators • MATLAB and Python programming knowledge preferred. Conditions of Employment: • Position available immediately • Salary: according to NIH postdoc salary scale • The University of Pittsburgh has excellent benefits, including health benefits and retirement plans with employer contributions. • The University of Pittsburgh values diversity and is committed to equal opportunity in employment. How to Apply: • E-mail Avniel Ghuman, Ph.D. (ghumana at upmc.edu) or Mike Romalis, Ph.D. (romalis at princeton.edu) From jm.horschig at donders.ru.nl Mon Sep 3 09:56:40 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 03 Sep 2012 09:56:40 +0200 Subject: [FieldTrip] 'dml' variable In-Reply-To: References: Message-ID: <504462B8.2060508@donders.ru.nl> Dear Hamza, 'crossvalidate' is part of the Donders Machine Learning Toolbox (DMLT). Formerly, it was known under a different name (afair MVA or multivariate toolbox) but recently it became an external toolbox and moved to the external/ folder. FieldTrip supports external toolboxes but takes no initiative in adding them automatically, so you need to it manually: addpath(genpath(fullfile('your_fieldtrip_folder', 'external', 'dmlt'))) See also here: http://fieldtrip.fcdonders.nl/tutorial/multivariateanalysis Since Marcel and others, who are developing this toolbox or have experience with using it, are on this mailinglist, feel free to post further questions concerning DMLT to this list anyhow. Best regards, Jörn On 9/2/2012 5:48 PM, Hamza Fawzi Altakroury (Student) wrote: > Hello, > > I am trying to classify my data using ft_timelockstatistics function > > I am using the output of ft_timelockanalysis function and the > following options: > > cfg.layout = 'CTF275.lay'; > cfg.method = 'crossvalidate'; > cfg.design = [ones(size(class1.trial,1),1); > 2*ones(size(class2.trial,1),1)]'; > > But I got the following error: > > ??? Undefined variable "dml" or class "dml.standardizer". > > Error in ==> ft_statistics_crossvalidate at 44 > cfg.mva = dml.analysis({ ... > > Error in ==> statistics_wrapper at 306 > [stat] = statmethod(cfg, dat, design); > > Error in ==> ft_timelockstatistics at 110 > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > Did I forgot to add something?! > > Thanks > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabanc? University > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From hubert.preissl at uni-tuebingen.de Mon Sep 3 14:08:21 2012 From: hubert.preissl at uni-tuebingen.de (Hubert Preissl) Date: Mon, 03 Sep 2012 14:08:21 +0200 Subject: [FieldTrip] 5th Autumn School Structure the Brain: 9th-11th October 2012, 2nd announcement In-Reply-To: References: Message-ID: <50449DB5.3000501@uni-tuebingen.de> Hello, we are pleased to announce the upcoming “5th Autumn School” in Tübingen organized by the MEG Center. For application and further information on the scientific program please visit our website: http://www.mp.uni-tuebingen.de/mp/index.php?id=400 Confirmed speakers: Christian Gaser, PhD, University of Jena, Germany Volkmar Glauche, MSc, University of Freiburg,Germany Matti Hämäläinen, PhD, Harvard Medical School, Boston, USA Risto Ilmoniemi, PhD, Aalto University, Aalto, Finland Svenja Knappe, PhD, National Institute of Standards and Technology, Boulder, USA Daniela Prayer, MD, University of Vienna, Austria Dana Small, PhD, The John B Pierce Laboratory and Yale University, USA Fabrice Wallois, PhD, University of Picardy,France We look forward meeting you in Tübingen! Best regards, Hubert Preissl -- Dr. Hubert Preissl MEG Center phone: ++49-(0)7071-2987704 Otfried Müller Str 47 fax: ++49-(0)7071-295706 72076 Tübingen, Germany email: hubert.preissl at uni-tuebingen.de From hamzaf at sabanciuniv.edu Mon Sep 3 17:22:02 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Mon, 3 Sep 2012 18:22:02 +0300 Subject: [FieldTrip] 'dml' variable In-Reply-To: <504462B8.2060508@donders.ru.nl> References: <504462B8.2060508@donders.ru.nl> Message-ID: Thank you Jörn, it works. Hamza On Mon, Sep 3, 2012 at 10:56 AM, "Jörn M. Horschig" < jm.horschig at donders.ru.nl> wrote: > Dear Hamza, > > 'crossvalidate' is part of the Donders Machine Learning Toolbox (DMLT). > Formerly, it was known under a different name (afair MVA or multivariate > toolbox) but recently it became an external toolbox and moved to the > external/ folder. FieldTrip supports external toolboxes but takes no > initiative in adding them automatically, so you need to it manually: > addpath(genpath(fullfile('your_fieldtrip_folder', 'external', 'dmlt'))) > > See also here: > http://fieldtrip.fcdonders.nl/tutorial/multivariateanalysis > > Since Marcel and others, who are developing this toolbox or have > experience with using it, are on this mailinglist, feel free to post > further questions concerning DMLT to this list anyhow. > > Best regards, > Jörn > > > On 9/2/2012 5:48 PM, Hamza Fawzi Altakroury (Student) wrote: > > Hello, > > I am trying to classify my data using ft_timelockstatistics function > > I am using the output of ft_timelockanalysis function and the following > options: > > cfg.layout = 'CTF275.lay'; > cfg.method = 'crossvalidate'; > cfg.design = [ones(size(class1.trial,1),1); > 2*ones(size(class2.trial,1),1)]'; > > But I got the following error: > > ??? Undefined variable "dml" or class "dml.standardizer". > > Error in ==> ft_statistics_crossvalidate at 44 > cfg.mva = dml.analysis({ ... > > Error in ==> statistics_wrapper at 306 > [stat] = statmethod(cfg, dat, design); > > Error in ==> ft_timelockstatistics at 110 > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > Did I forgot to add something?! > > Thanks > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From daria.laptinskaya at googlemail.com Mon Sep 3 17:22:58 2012 From: daria.laptinskaya at googlemail.com (Daria Laptinskaya) Date: Mon, 3 Sep 2012 17:22:58 +0200 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? Message-ID: Dear Fieldtrippers, I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip toolbox. The ERPs look perfect. The 'only' problem is, that my signals look to strong. It looks like if I get amplitutes (average) until 70 µV. I think it must be an intern amplifier for the signals. Does anyone know this problem with EGI-data? Or does anyone know, where I can see the amplifier? Greetings, Daria -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Mon Sep 3 19:04:47 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Mon, 3 Sep 2012 20:04:47 +0300 Subject: [FieldTrip] Changing the classifier Message-ID: Hello, I am dealing with ft_timelockstatistics function for classification, as I understand from the tutorail, the default classifier used is the SVM. I want to ask about the ability to change the classifier. Thanks for help. Best, -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Mon Sep 3 22:35:06 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 3 Sep 2012 22:35:06 +0200 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: References: Message-ID: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> Hi Daria, There might indeed be an incompatibility in the gain value applied to the data. If you are able to export the data using the EGI software in another format (e.g. EDF), you could read them both into FieldTrip and compare the timecourse aplitudes to check whether they are different. In case they are, I suggest to involve EGI support. They are aware of the FieldTrip reading functions and will know much more about the internals of their various file formats. best regards Robert On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: > Dear Fieldtrippers, > > I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip toolbox. > The ERPs look perfect. > The 'only' problem is, that my signals look to strong. > It looks like if I get amplitutes (average) until 70 µV. > I think it must be an intern amplifier for the signals. > Does anyone know this problem with EGI-data? > > Or does anyone know, where I can see the amplifier? > > > > > Greetings, > > Daria _______________________________________________ > 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 Mon Sep 3 23:02:21 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 3 Sep 2012 23:02:21 +0200 Subject: [FieldTrip] A postdoc position in developing methods for MEG with atomic magnetometers In-Reply-To: <20385F716E75B746A7F52BBB3C46A1300226C827@MSXMBXNSPRD03.acct.upmchs.net> References: <20385F716E75B746A7F52BBB3C46A1300226C772@MSXMBXNSPRD03.acct.upmchs.net>, <20385F716E75B746A7F52BBB3C46A1300226C790@MSXMBXNSPRD03.acct.upmchs.net> <20385F716E75B746A7F52BBB3C46A1300226C827@MSXMBXNSPRD03.acct.upmchs.net> Message-ID: <9D7A03F8-3318-498E-B2DD-BFE41B461548@donders.ru.nl> Dear Avniel (CC to the FieldTrip list) Thanks for announcing this interesting post doc position. Last week at the Biomag conference I attended the atomic/optical magnetic field sensor symposium and was very impressed with the progress that was presented. With respect to some of the tasks you outline (see below), I think that there is quite some overlap with the methods used in squid based MEG technology. E.g., the volume conduction modelling and forward solutions relate the equivalent current dipole strength in the model head to magnetic field strength outside the head. This is independent of the sensor technology, although the precise sensor geometry is of course different (as it also is between the various MEG systems). See for example http://fieldtrip.fcdonders.nl/faq/how_are_electrodes_magnetometers_or_gradiometers_described. The noise characteristics of the atomic magnetometers themselves will at the moment also be quite different for that of a squid-based system, but once the S/N gets good enough, a large fraction of the noise will be environmental and biological, again resulting in similar methods being applicable to deal with those parts of the noise (especially when compared to the magnetometer channels in some of the presently used MEG systems). I hope that it will be possible to develop methods for atomical magnetometer based MEG in close collaboration with the methods that are used and developed for conventional MEG. Actually it would be cool to implement support for the data formats that are being used by you and in Princeton in the FieldTrip toolbox. I believe that this would facilitate working together, not specifically with the Donders Institute in Nijmegen, but rather with the MEG field as a whole. It would also allow your data to be processed in the other large open source toolboxes (such as SPM and Nutmeg), as these all share the same data access functions and sensor representation. At the moment FieldTrip supports MEG data from about 15 different MEG systems (3x BTi, 2x Neuromag, 4x CTF, 4x Yokogawa, 2x ITAB, ranging from adult MEG to fetal MCG and even rodent MEG) and provides data processing and source reconstruction for all of them. Adding support for your data format and sensor arrangements is something that we could provide assistance with. I hope you will be able to attract a good candidate for the position and that the new atomic sensor technology will soon become available to the whole MEG community. best regards Robert ----------------------------------------------------------- Robert Oostenveld, PhD Senior Researcher & MEG Physicist Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen tel.: +31 (0)24 3619695 e-mail: r.oostenveld at donders.ru.nl web: http://www.ru.nl/neuroimaging skype: r.oostenveld ----------------------------------------------------------- On 3 Sep 2012, at 7:07, Ghuman, Avniel wrote: > Post-doc in MEG with Atomic Magnetometers > > The Ghuman Lab at the University of Pittsburgh, in collaboration with the Romalis Group at Princeton University and Twinleaf LLC, is recruiting a Post doc to develop methods for atomic magnetometer based MEG and multimodal integration (simultaneous MEG-EEG and MEG-fNIRS). The position is available immediately. > Responsibilities: > • Develop novel solutions for MEG using atomic magnetometers concerning source localization, noise cancellation and head modeling > • Acquire and analyze MEG, MEG-EEG, and MEG-fNIRS data > • Develop novel methods for integrating multimodal data > • Design and implement novel data analysis tools > • Assist with preparation of progress reports > • Prepare manuscripts and presentations > • Work with Investigators to identify future problems and research opportunities > > Minimum Qualifications: > • Ph.D. in Engineering, Physics, Neuroscience, Computer Science, Math, or related field. > • Demonstrated expertise in solving MEG technological issues as shown through publication record, awards, successful patents and/or received applications. > • Data analysis expertise includes independent components analysis, Bayesian algorithms, statistical parametric mapping, and MRI image processing. > • Proficiency in creating software analysis tools and programs for investigators > • MATLAB and Python programming knowledge preferred. > > Conditions of Employment: > • Position available immediately > • Salary: according to NIH postdoc salary scale > • The University of Pittsburgh has excellent benefits, including health benefits and retirement plans with employer contributions. > • The University of Pittsburgh values diversity and is committed to equal opportunity in employment. > > How to Apply: > • E-mail Avniel Ghuman, Ph.D. (ghumana at upmc.edu) or Mike Romalis, Ph.D. (romalis at princeton.edu) > > _______________________________________________ > 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 ayelet.landau at gmail.com Tue Sep 4 13:23:21 2012 From: ayelet.landau at gmail.com (Ayelet Landau) Date: Tue, 4 Sep 2012 13:23:21 +0200 Subject: [FieldTrip] problem with ft_rejectartifact Message-ID: Dear FieldTrip experts, I have encountered a strange behavior in ft_rejectartifact script. artifacts are defined in variables that contain two collumns and fed into this function as follows: cfg.artfctdef.eog.artifact =artifact_eog_all; other parameters I use are: cfg.trl=trl; cfg.artfctdef.reject = 'partial'; cfg.artfctdef.minaccepttim = .2; then I run ft_rejectartifact with this cfg (and many more categories of artifacts as exemplified above) and a structure containing my preprocessed data (with a the same trl I give in cfg.trl above). This is an example of what the data structure fed into ft_rejectartifact might looks like hdr: [1x1 struct] fsample: 1200 grad: [1x1 struct] sampleinfo: [50x2 double] trialinfo: [50x4 double] trial: {1x50 cell} time: {1x50 cell} label: {275x1 cell} cfg: [1x1 struct] and here is the error that I get: ??? Subscripted assignment dimension mismatch. Error in ==> ft_redefinetrial at 253 data.trialinfo(iTrl,:) = dataold.trialinfo(iTrlorig,:); Error in ==> ft_rejectartifact at 483 data = ft_redefinetrial(tmpcfg, data); When I run ft_rejectartifact with a cfg.data field calling my *.ds file, I get the following which I could probably use later as an adjusted trl for ft_preprocessing: datafile: 'XX_20120821_05.ds' trl: [79x7 double] artfctdef: [1x1 struct] trackconfig: 'off' checkconfig: 'loose' checksize: 100000 showcallinfo: 'yes' headerfile: 'XX_20120821_05.ds' trlold: [50x7 double] callinfo: [1x1 struct] version: [1x1 struct] Its a bit strange that my original approach stopped working. Any insights most welcome! -- Ayelet N. Landau Postdoctoral Scientist, Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society Deutschordenstr. 46, D-60528 Frankfurt Mobile: +49 (0)16 22733 110 Fax: +49 (0)69 96769 555 -------------- next part -------------- An HTML attachment was scrubbed... URL: From inieuwenhuis at berkeley.edu Tue Sep 4 22:00:03 2012 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Tue, 04 Sep 2012 13:00:03 -0700 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> Message-ID: <50465DC3.7080005@berkeley.edu> Hi Daria, Also, did you try looking at your raw data (so before the ERPs are made) in FieldTrip and in Net Station? So open your .raw data in NetStation. You can just look at a random participant's data, and check if the scale is the same. I'm pretty sure no amplification takes place when reading in the data into FieldTrip, this check can confirm that. Hope this helps, and let us know what you find. Cheers, Ingrid On 9/3/2012 1:35 PM, Robert Oostenveld wrote: > Hi Daria, > > There might indeed be an incompatibility in the gain value applied to > the data. > > If you are able to export the data using the EGI software in another > format (e.g. EDF), you could read them both into FieldTrip and compare > the timecourse aplitudes to check whether they are different. In case > they are, I suggest to involve EGI support. They are aware of the > FieldTrip reading functions and will know much more about the > internals of their various file formats. > > best regards > Robert > > > > > On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: > >> Dear Fieldtrippers, >> >> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip >> toolbox. >> The ERPs look perfect. >> The 'only' problem is, that my signals look to strong. >> It looks like if I get amplitutes (average) until 70 µV. >> I think it must be an intern amplifier for the signals. >> >> Does anyone know this problem with EGI-data? >> >> Or does anyone know, where I can see the amplifier? >> >> >> >> Greetings, >> >> Daria _______________________________________________ >> 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 -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jochem.rieger at uni-oldenburg.de Wed Sep 5 03:24:18 2012 From: jochem.rieger at uni-oldenburg.de (Jochem Rieger) Date: Wed, 05 Sep 2012 03:24:18 +0200 Subject: [FieldTrip] 1 post-doc and 1 PhD position in human auditory and motor neuroscience Message-ID: <5046A9C2.2020704@uni-oldenburg.de> The Department of Applied Neurocognitive Psychology at Oldenburg University, Germany, offers a *Post-doctoral position (E13/TVL, 3 years plus) * and a *PhD position (0.5*E13/TVL, initially 2 years)* The lab focuses on the fields of neural coding of complex movements and neural coding of speech in the human brain with the aim of developing brain-machine-interfaces. To extend our interdisciplinary team we seek for highly motivated candidates with strong quantitative and experimental skills. The post-doctoral position requires a PhD or comparable degree and the PhD position requires a masters or comparable degree. The post-doctoral position is initially limited to three years after with an option for an extension to obtain habilitation (post-doctoral degree, similar to a lecturer qualification). Successful candidates will perform cutting edge research in one of the lab's foci and should have a background in one or more of the following fields: non-invasive or invasive human neurophysiology of the motor or auditory system, statistical learning, brain-machine-interfacing. The positions offer an excellent interdisciplinary working environment with opportunities for international exchange. The lab is involved in the EU-project BRACOG (brain controlled grasping) and we have a close collaboration with UC Berkeley, USA. The University of Oldenburg was recently awarded a Cluster of Excellence in hearing research. The Dept. of Psychology will offer an attractive scientific environment with access to research dedicated state-of-the-art approaches to human neurophysiological techniques (fMRI, NIRS, EEG, ECoG, and MEG). Electronic applications are preferred and can be send to: Professor Dr. Jochem Rieger: Jochem.rieger at uni-oldenburg.de Please send paper applications until September 30^th 2012 to: Margrit Jung Dept. of Applied Neurocognitive Psychology Institute of Psychology Oldenburg University 26111 Oldenburg Germany Applications should include your CV and a list of most recent publications. Applications for the post-doctoral position should include a research statement (max. 3 pages). The University of Oldenburg aims to employ more women in this area and therefore particularly welcomes applications from women. We also welcome applications from disabled persons. -- Prof. Dr. rer. nat. Jochem Rieger Applied Neurocognitive Knight Lab Psychology Helen Wills Neuroscience Institute Faculty V University of California Carl-von-Ossietzky University 132 Barker Hall 26111 Oldenburg Berkeley, CA 94720-3192 Germany USA Phone: +49(0)4417984533 Fax: +49(0)4417983865 -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.piantoni at nin.knaw.nl Wed Sep 5 10:20:41 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Wed, 5 Sep 2012 10:20:41 +0200 Subject: [FieldTrip] freesurfer surfaces Message-ID: Dear Fieldtrip developers, I'd like to run source reconstruction on the cortical sheets obtained from Freesurfer and average them using the "sphere" approach of Freesurfer. I have these steps in mind: 1) create a 3-layer BEM ('outer_skin' 'inner_skull' 'brain' from the bem/watershed folder, which I think might be better than 'outer_skin' 'outer_skull' 'inner_skull' as in http://fieldtrip.fcdonders.nl/development/replicate_functionality_of_mne_software ) 2) create a forward model from a subset of points in "?h.smoothwm" (for computational purposes) 3) do source reconstruction on this subset of dipoles 4) source interpolate to the high resolution of ?h.smoothwm 5) project all the locations onto the ?h.sphere 6) interpolate to the points to the ?h.sphere of fsaverage 7) do 2-D statistics on the values of the ?h.sphere of fsaverage (and plot them using ?h.inflated of fsaverage) I was wondering if anybody has tried something similar and if there are steps I should be careful about. There was a discussion in January/February about doing statistics on cortical sheets: http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004749.html http://mailman.science.ru.nl/pipermail/fieldtrip/2012-February/004766.html Does anybody have suggestions about these steps? I promise I'll make a tutorial out of this, if it works out ;) A practical point I get stuck in is at steps 3) and 4). The interpolation from a subset of 2-D points to another subset of 2-D points gives a bit of nonsensical results. Code: %-get freesurfer surface bnd = ft_read_headshape('lh.smoothwm'); % get it from https://skydrive.live.com/redir?resid=6D9DCA0F726A645C!7000 % or any freesurfer surface you have %-downsample bnd_down = bnd; P.faces = bnd_down.tri; P.vertices = bnd_down.pnt; P = reducepatch(P, 0.05); bnd_down.tri = P.faces; bnd_down.pnt = P.vertices; %-create source source.pos = bnd_down.pnt; source.inside = true(size(source.pos,1),1); source.pow = bnd_down.pnt(:,3); % "fake" source reconstruction figure ft_plot_mesh(bnd_down, 'edgecolor', 'none', 'vertexcolor', source.pow) % the rainbow brain view(90, 0); camlight %-sourceinterpolate cfg = []; cfg.parameter = 'pow'; ana = []; ana.pnt = bnd_down.pnt; ana.orig = bnd; souinterp = ft_sourceinterpolate(cfg, source, ana); figure ft_plot_mesh(souinterp, 'edgecolor', 'none', 'vertexcolor', souinterp.pow) % the Arlecchino brain view(90, 0); camlight Should I file a bugzilla report for this? I haven't done it as I'm not even sure this is the correct input format. Thanks for any suggestion. Best wishes, Gio -- Giovanni Piantoni, MSc Dept. Sleep & Cognition Netherlands Institute for Neuroscience Meibergdreef 47 1105 BA Amsterdam (NL) www.gpiantoni.com From johanna.zumer at donders.ru.nl Wed Sep 5 12:41:38 2012 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Wed, 5 Sep 2012 12:41:38 +0200 Subject: [FieldTrip] FT_SCALPCURRENTDENSITY options and elec units In-Reply-To: References: Message-ID: Hi Akiko, Hopefully someone else can answer your main SCD question (although ft_scalpcurrentdensity provides the citations for the original papers on which these 2 methods are based). But for now, just a quick answer to your units question. The best way to convert the units of a FieldTrip data structure is with ft_convert_units, for example: elec_out = ft_convert_units(elec_in, 'm'). If elec.unit does not already exist in the structure, then either you can set it first if you know the units, or FT will do its best to assume which units the structure is in. Also note that the 'help' of ft_scalpcurrentdensity states that "the spatial distribution still will be correct" even if units do not match, which should explain why the topoplot shows the same results. Cheers, Johanna 2012/8/31 Akiko Ikkai > Hi, > > I'm trying to run plv analysis, first acquiring SCD of my data with > ft_scalcurrentdensity, and am confused about the difference between > cfg.method = 'finite' and 'spline.' Both gave similar results > short-range, but 'spline' gives higher plv at long range plv. I'd love it > if someone could explain or suggest reading on the difference between these > two methods (or is one method preferred over the other in some cases?). > > Also, I'm not sure whether or not I should convert my elec.pnt values, > since the code ft_scalcurrentdensity says that > "Note that the skin conductivity, electrode dimensions and the potential all > have to be expressed in the same SI units." My elec.pnt are in cm, and > I'm using the default conductivity (0.33 S/m). Do I need to do something > like elec.pnt = elec.pnt/100 to convert the unit from cm to m? With or > without conversion, I got the same results (viewed with ft_topoplotTFR), > and I'm a little confused... Thank you in advance for your time! Akiko > > -- > Akiko Ikkai, Ph.D. > Postdoctoral Fellow > Department of Psychological and Brain Sciences > Johns Hopkins University > Ames Hall, 3400 N. Charles St. > Baltimore, MD 21218 > > > > _______________________________________________ > 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 f.roux at bcbl.eu Wed Sep 5 14:47:29 2012 From: f.roux at bcbl.eu (Frederic Roux) Date: Wed, 05 Sep 2012 14:47:29 +0200 (CEST) Subject: [FieldTrip] left to right inversion after source interpolation In-Reply-To: Message-ID: <075a92dd-147e-45e9-a4d1-726999c597b1@thalamus_p> Dear fieldtrip users, I have noticed that after interpolating a dummy source volume with ft_sourceinterpolate, voxels that were located in the left side of the volume, apear to be located in the right side of the volume. The code that I use is as following: dummy is a dummy structure of an lcmv beamformer map with the fields dummy = dim : [15 18 17] time: [1x272662 double] pos: [4590x3 double] inside: [1x2144 double] outside: [1x2446 double] method: 'average' avg: [1x1 struct] voxpos = dummy.pos(dummy.inside,1);% get the coordinates of voxels inside the volume dummy.avg.pow(dummy.inside(sign(voxpos)==1)) = 0; % set activity in the left hemisphere to 0 dummy.avg.pow(dummy.inside(sign(voxpos)==-1)) = 1; % set activity in the left hemisphere to 1 cfg = []; cfg.parameters = 'all'; int_dummy = ft_sourceinterpolate(cfg,dummy,template_MNI_mri); cfg = []; cfg.funparameter = 'avg.pow'; cfg.method = 'ortho'; %plot the non-interpolated volume figure; ft_sourceplot(cfg,dummy); %plot the interpolated volume figure; ft_sourceplot(cfg,int_dummy); As you can see from the figure in the attachement, the voxels that corresponded to the left hemisphere prior to the interpolation, no appear to be located in the rigth hemisphere. This is also something that I have observed in real data. Does anybody have an explanation why this is happening? Am I doing something wrong? Best, Fred -------------- next part -------------- A non-text attachment was scrubbed... Name: non_interp_vs_interp.jpg Type: image/jpeg Size: 25092 bytes Desc: not available URL: From k.muesch at uke.uni-hamburg.de Wed Sep 5 16:30:49 2012 From: k.muesch at uke.uni-hamburg.de (=?iso-8859-1?Q?Kathrin_M=FCsch?=) Date: Wed, 5 Sep 2012 16:30:49 +0200 Subject: [FieldTrip] left to right inversion after source interpolation In-Reply-To: <075a92dd-147e-45e9-a4d1-726999c597b1@thalamus_p> References: <075a92dd-147e-45e9-a4d1-726999c597b1@thalamus_p> Message-ID: <44E1ACF5-2C6D-4BA2-8FA7-B0886FB8AF20@uke.uni-hamburg.de> Dear Fred, I encountered a similar thing a while ago and it was because spm8 seems to plot in radiological convention (i.e. left is plotted right and vice versa - http://mailman.science.ru.nl/pipermail/fieldtrip/2012-May/005229.html) so you're plots should actually be correct. If you use cfg.interactive = 'yes'; and click into the activated side of the brain, the first coordinate should be negative because you are in the left hemisphere. Hope that helps, Kathrin Am 05.09.2012 um 14:47 schrieb Frederic Roux: > Dear fieldtrip users, > > I have noticed that after interpolating a dummy source volume with ft_sourceinterpolate, > voxels that were located in the left side of the volume, apear to be located in the right > side of the volume. > > The code that I use is as following: > > dummy is a dummy structure of an lcmv beamformer map with the fields > > dummy = > dim : [15 18 17] > time: [1x272662 double] > pos: [4590x3 double] > inside: [1x2144 double] > outside: [1x2446 double] > method: 'average' > avg: [1x1 struct] > > voxpos = dummy.pos(dummy.inside,1);% get the coordinates of voxels inside the volume > dummy.avg.pow(dummy.inside(sign(voxpos)==1)) = 0; % set activity in the left hemisphere to 0 > dummy.avg.pow(dummy.inside(sign(voxpos)==-1)) = 1; % set activity in the left hemisphere to 1 > > cfg = []; > cfg.parameters = 'all'; > > int_dummy = ft_sourceinterpolate(cfg,dummy,template_MNI_mri); > > cfg = []; > cfg.funparameter = 'avg.pow'; > cfg.method = 'ortho'; > > %plot the non-interpolated volume > figure; > ft_sourceplot(cfg,dummy); > > %plot the interpolated volume > figure; > ft_sourceplot(cfg,int_dummy); > > As you can see from the figure in the attachement, the voxels that > corresponded to the left hemisphere prior to the interpolation, > no appear to be located in the rigth hemisphere. > > This is also something that I have observed in real data. > > Does anybody have an explanation why this is happening? > Am I doing something wrong? > > Best, > > Fred > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus From jdien07 at mac.com Thu Sep 6 03:17:03 2012 From: jdien07 at mac.com (Joseph Dien) Date: Wed, 05 Sep 2012 21:17:03 -0400 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: <50465DC3.7080005@berkeley.edu> References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> Message-ID: <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> The Simple Binary (.raw) files don't get corrected for gain when imported (I helped write them). I've experienced occasional unpredictable bugs with NetStation export routines where the files are generated with amplitudes many times too large, even with text format files. It's a bit disconcerting to say the least. I could take a look at your files if you'd like confirmation. Joe On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis wrote: > Hi Daria, > > Also, did you try looking at your raw data (so before the ERPs are made) in FieldTrip and in Net Station? So open your .raw data in NetStation. You can just look at a random participant's data, and check if the scale is the same. I'm pretty sure no amplification takes place when reading in the data into FieldTrip, this check can confirm that. Hope this helps, and let us know what you find. > > Cheers, > Ingrid > > > On 9/3/2012 1:35 PM, Robert Oostenveld wrote: >> Hi Daria, >> >> There might indeed be an incompatibility in the gain value applied to the data. >> >> If you are able to export the data using the EGI software in another format (e.g. EDF), you could read them both into FieldTrip and compare the timecourse aplitudes to check whether they are different. In case they are, I suggest to involve EGI support. They are aware of the FieldTrip reading functions and will know much more about the internals of their various file formats. >> >> best regards >> Robert >> >> >> >> >> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: >> >>> Dear Fieldtrippers, >>> >>> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip toolbox. >>> The ERPs look perfect. >>> The 'only' problem is, that my signals look to strong. >>> It looks like if I get amplitutes (average) until 70 µV. >>> I think it must be an intern amplifier for the signals. >>> Does anyone know this problem with EGI-data? >>> >>> Or does anyone know, where I can see the amplifier? >>> >>> >>> >>> >>> Greetings, >>> >>> Daria _______________________________________________ >>> 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 > > -- > Ingrid Nieuwenhuis PhD > Postdoctoral Fellow > Sleep and Neuroimaging Laboratory > Department of Psychology > University of California, Berkeley > California 94720-1650 > Tolman Hall, room 5305 > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07 at mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan.debener at uni-oldenburg.de Thu Sep 6 09:12:09 2012 From: stefan.debener at uni-oldenburg.de (Stefan Debener) Date: Thu, 06 Sep 2012 09:12:09 +0200 Subject: [FieldTrip] 1 post-doc and 1 PhD position in human auditory and motor neuroscience In-Reply-To: <5046A9C2.2020704@uni-oldenburg.de> References: <5046A9C2.2020704@uni-oldenburg.de> Message-ID: <50484CC9.2070601@uni-oldenburg.de> Lieber Jochem, ich habe vo ein paar Tagen Frau Straube gesprochen, die bei Prof. Kauss, Neurochirurgie Hannover, die Forschung leitet. Herr Krauss ist sehr kooperationsfreudig und es ist kein Problem an BG und Dystonie DBS Patienten zu kommen, das machen die wohl ziemlich häufig inzwischen (ca 1/Woche), und Ausleitung mehrere Tage danach ist auch kein Problem. Vielleicht solltest Du den Kontakt suchen, ist zwar nicht ecog, aber immerhin... lg, s Am 9/5/12 3:24 AM, schrieb Jochem Rieger: > The Department of Applied Neurocognitive Psychology at Oldenburg > University, Germany, offers a > > *Post-doctoral position (E13/TVL, 3 years plus) * > > and a > > *PhD position (0.5*E13/TVL, initially 2 years)* > > The lab focuses on the fields of neural coding of complex movements > and neural coding of speech in the human brain with the aim of > developing brain-machine-interfaces. > > To extend our interdisciplinary team we seek for highly motivated > candidates with strong quantitative and experimental skills. The > post-doctoral position requires a PhD or comparable degree and the PhD > position requires a masters or comparable degree. The post-doctoral > position is initially limited to three years after with an option for > an extension to obtain habilitation (post-doctoral degree, similar to > a lecturer qualification). Successful candidates will perform cutting > edge research in one of the lab's foci and should have a background in > one or more of the following fields: non-invasive or invasive human > neurophysiology of the motor or auditory system, statistical learning, > brain-machine-interfacing. The positions offer an excellent > interdisciplinary working environment with opportunities for > international exchange. The lab is involved in the EU-project BRACOG > (brain controlled grasping) and we have a close collaboration with UC > Berkeley, USA. The University of Oldenburg was recently awarded a > Cluster of Excellence in hearing research. The Dept. of Psychology > will offer an attractive scientific environment with access to > research dedicated state-of-the-art approaches to human > neurophysiological techniques (fMRI, NIRS, EEG, ECoG, and MEG). > > Electronic applications are preferred and can be send to: > Professor Dr. Jochem Rieger: Jochem.rieger at uni-oldenburg.de > > > Please send paper applications until September 30^th 2012 to: > > Margrit Jung > > Dept. of Applied Neurocognitive Psychology > > Institute of Psychology > > Oldenburg University > > 26111 Oldenburg > > Germany > > Applications should include your CV and a list of most recent > publications. Applications for the post-doctoral position should > include a research statement (max. 3 pages). The University of > Oldenburg aims to employ more women in this area and therefore > particularly welcomes applications from women. We also welcome > applications from disabled persons. > > > -- > Prof. Dr. rer. nat. Jochem Rieger > > Applied Neurocognitive Knight Lab > Psychology Helen Wills Neuroscience Institute > Faculty V University of California > Carl-von-Ossietzky University 132 Barker Hall > 26111 Oldenburg Berkeley, CA 94720-3192 > Germany USA > > Phone: +49(0)4417984533 > Fax: +49(0)4417983865 > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Prof. Dr. Stefan Debener Neuropsychology Lab Department of Psychology University of Oldenburg D-26111 Oldenburg Germany Office: A7 0-038 Phone: +49-441-798-4271 Fax: +49-441-798-5522 Email: stefan.debener at uni-oldenburg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.piantoni at nin.knaw.nl Thu Sep 6 10:21:58 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Thu, 6 Sep 2012 10:21:58 +0200 Subject: [FieldTrip] freesurfer surfaces In-Reply-To: References: Message-ID: I fixed the "Arlecchino brain" problem and committed the patch (r6433). I'd still appreciate if people had some suggestions about the analysis steps for the group-average. Best, Gio On Wed, Sep 5, 2012 at 10:20 AM, Gio Piantoni wrote: > Dear Fieldtrip developers, > > I'd like to run source reconstruction on the cortical sheets obtained > from Freesurfer and average them using the "sphere" approach of > Freesurfer. I have these steps in mind: > > 1) create a 3-layer BEM ('outer_skin' 'inner_skull' 'brain' from the > bem/watershed folder, which I think might be better than 'outer_skin' > 'outer_skull' 'inner_skull' as in > http://fieldtrip.fcdonders.nl/development/replicate_functionality_of_mne_software > ) > 2) create a forward model from a subset of points in "?h.smoothwm" > (for computational purposes) > 3) do source reconstruction on this subset of dipoles > 4) source interpolate to the high resolution of ?h.smoothwm > 5) project all the locations onto the ?h.sphere > 6) interpolate to the points to the ?h.sphere of fsaverage > 7) do 2-D statistics on the values of the ?h.sphere of fsaverage (and > plot them using ?h.inflated of fsaverage) > > I was wondering if anybody has tried something similar and if there > are steps I should be careful about. There was a discussion in > January/February about doing statistics on cortical sheets: > http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004749.html > http://mailman.science.ru.nl/pipermail/fieldtrip/2012-February/004766.html > > Does anybody have suggestions about these steps? I promise I'll make a > tutorial out of this, if it works out ;) > > A practical point I get stuck in is at steps 3) and 4). The > interpolation from a subset of 2-D points to another subset of 2-D > points gives a bit of nonsensical results. Code: > > %-get freesurfer surface > bnd = ft_read_headshape('lh.smoothwm'); > % get it from https://skydrive.live.com/redir?resid=6D9DCA0F726A645C!7000 > % or any freesurfer surface you have > > %-downsample > bnd_down = bnd; > P.faces = bnd_down.tri; > P.vertices = bnd_down.pnt; > P = reducepatch(P, 0.05); > bnd_down.tri = P.faces; > bnd_down.pnt = P.vertices; > > %-create source > source.pos = bnd_down.pnt; > source.inside = true(size(source.pos,1),1); > source.pow = bnd_down.pnt(:,3); % "fake" source reconstruction > > figure > ft_plot_mesh(bnd_down, 'edgecolor', 'none', 'vertexcolor', source.pow) > % the rainbow brain > view(90, 0); camlight > > %-sourceinterpolate > cfg = []; > cfg.parameter = 'pow'; > ana = []; > ana.pnt = bnd_down.pnt; > ana.orig = bnd; > souinterp = ft_sourceinterpolate(cfg, source, ana); > > figure > ft_plot_mesh(souinterp, 'edgecolor', 'none', 'vertexcolor', > souinterp.pow) % the Arlecchino brain > view(90, 0); camlight > > Should I file a bugzilla report for this? I haven't done it as I'm not > even sure this is the correct input format. > Thanks for any suggestion. > > Best wishes, > > Gio > > -- > Giovanni Piantoni, MSc > Dept. Sleep & Cognition > Netherlands Institute for Neuroscience > Meibergdreef 47 > 1105 BA Amsterdam (NL) > www.gpiantoni.com From stefan.debener at uni-oldenburg.de Thu Sep 6 12:22:46 2012 From: stefan.debener at uni-oldenburg.de (Stefan Debener) Date: Thu, 06 Sep 2012 12:22:46 +0200 Subject: [FieldTrip] 1 post-doc and 1 PhD position in human auditory and motor neuroscience In-Reply-To: <50484CC9.2070601@uni-oldenburg.de> References: <5046A9C2.2020704@uni-oldenburg.de> <50484CC9.2070601@uni-oldenburg.de> Message-ID: <50487976.7040900@uni-oldenburg.de> Apologies to all for spoiling this list with a personal mail, Stefan Am 9/5/12 3:24 AM, schrieb Jochem Rieger: >> The Department of Applied Neurocognitive Psychology at Oldenburg >> University, Germany, offers a >> >> *Post-doctoral position (E13/TVL, 3 years plus) * >> >> and a >> >> *PhD position (0.5*E13/TVL, initially 2 years)* >> >> The lab focuses on the fields of neural coding of complex movements >> and neural coding of speech in the human brain with the aim of >> developing brain-machine-interfaces. >> >> To extend our interdisciplinary team we seek for highly motivated >> candidates with strong quantitative and experimental skills. The >> post-doctoral position requires a PhD or comparable degree and the >> PhD position requires a masters or comparable degree. The >> post-doctoral position is initially limited to three years after with >> an option for an extension to obtain habilitation (post-doctoral >> degree, similar to a lecturer qualification). Successful candidates >> will perform cutting edge research in one of the lab's foci and >> should have a background in one or more of the following fields: >> non-invasive or invasive human neurophysiology of the motor or >> auditory system, statistical learning, brain-machine-interfacing. The >> positions offer an excellent interdisciplinary working environment >> with opportunities for international exchange. The lab is involved in >> the EU-project BRACOG (brain controlled grasping) and we have a close >> collaboration with UC Berkeley, USA. The University of Oldenburg was >> recently awarded a Cluster of Excellence in hearing research. The >> Dept. of Psychology will offer an attractive scientific environment >> with access to research dedicated state-of-the-art approaches to >> human neurophysiological techniques (fMRI, NIRS, EEG, ECoG, and MEG). >> >> Electronic applications are preferred and can be send to: >> Professor Dr. Jochem Rieger: Jochem.rieger at uni-oldenburg.de >> >> >> Please send paper applications until September 30^th 2012 to: >> >> Margrit Jung >> >> Dept. of Applied Neurocognitive Psychology >> >> Institute of Psychology >> >> Oldenburg University >> >> 26111 Oldenburg >> >> Germany >> >> Applications should include your CV and a list of most recent >> publications. Applications for the post-doctoral position should >> include a research statement (max. 3 pages). The University of >> Oldenburg aims to employ more women in this area and therefore >> particularly welcomes applications from women. We also welcome >> applications from disabled persons. >> >> >> -- >> Prof. Dr. rer. nat. Jochem Rieger >> >> Applied Neurocognitive Knight Lab >> Psychology Helen Wills Neuroscience Institute >> Faculty V University of California >> Carl-von-Ossietzky University 132 Barker Hall >> 26111 Oldenburg Berkeley, CA 94720-3192 >> Germany USA >> >> Phone: +49(0)4417984533 >> Fax: +49(0)4417983865 >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Prof. Dr. Stefan Debener > Neuropsychology Lab > Department of Psychology > University of Oldenburg > D-26111 Oldenburg > Germany > > Office: A7 0-038 > Phone: +49-441-798-4271 > Fax: +49-441-798-5522 > Email:stefan.debener at uni-oldenburg.de > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Prof. Dr. Stefan Debener Neuropsychology Lab Department of Psychology University of Oldenburg D-26111 Oldenburg Germany Office: A7 0-038 Phone: +49-441-798-4271 Fax: +49-441-798-5522 Email: stefan.debener at uni-oldenburg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From landpt at gmail.com Thu Sep 6 12:25:47 2012 From: landpt at gmail.com (Ricardo Jorge) Date: Thu, 6 Sep 2012 11:25:47 +0100 Subject: [FieldTrip] Having troubles with Emotiv + Fieldtrip + Matlab Message-ID: Hello there, I'm new to Fieldtrip: I've been assigned to work with signals acquired by Emotiv in Matlab environment, specially in real-time - or at least almost real-time - so I can work and study these signals with my own Matlab's functions. However, here's the bad thing: we did not expect it to be that complicated to extract signals directly to Matlab. While searching for any module, program, anything I could find, to help our problem, I found Fieldtrip. Correct me if I am wrong, but it seems that it is able to stream/buffer from emotiv's sdk to matlab. The problem is that we do not have that much experience with compiling C programs, hence I am having a really hard time to understand what do you mean with: "Compilation We provide a simple Makefile for the MinGW compiler, but you will need the Emotiv SDK. Please go to the realtime/datasource/emotiv directory and type make or mingw32-make. Note that you might need to compile the libbuffer library first." Here's what I did so far: 1. I have installed Matlab r2011b 64-bit and Emotiv SDK Research Edition; 2. I installed MinGW and set the path of the /bin in environmental variables; 3. I downloaded all these files from: http://code.google.com/p/fieldtrip/source/browse/trunk/realtime/datasource/emotiv/?r=1742 4. Then I went cmd and tried to do: mingw32-make -f makefile.gcc SHARED=1 UNICODE=1 BUILD=release which obviously failed: it said it was missing a file "Ftbuffer.h". I assumed it was the libbuffer library, however I can't seem to find it anywhere in the Internet (just some site that would ask me to install Makestuff application, which I did and was unsuccessful. I found a "buffer" folder in fieldtrip release but I dont think it's that. Hence I tried to download the Ftbuffer.h itself from internet and put it in the folder where emotiv2ft was. It worked, but then it started to ask others files.... and more.. and more.. So, obviously I'm stuck right here. Can you help me right here? What should I do? Have I done something wrong? I've read this discussion list and found one thread quite related to this - but his problem was not having research edition, which in fact, I do have it. I'm sorry bothering you with probably authentic beginner questions, but as I said, I only have high experience with Matlab. Best Regards, Ricardo From Lilla.Magyari at mpi.nl Thu Sep 6 14:45:55 2012 From: Lilla.Magyari at mpi.nl (Lilla.Magyari at mpi.nl) Date: Thu, 6 Sep 2012 14:45:55 +0200 (CEST) Subject: [FieldTrip] Having troubles with Emotiv + Fieldtrip + Matlab In-Reply-To: References: Message-ID: <49788.131.174.45.70.1346935555.squirrel@131.174.45.70> Hello Ricardo, I haven't tried to work with Emotiv, but I see an FtBuffer.h file in the latest version of FieldTrip in the realtime/src/buffer/cpp. I hope this helps. (It is also not clear for me if you downloaded only files related to emotive, or also the whole FieldTrip package (this latest is probably useful)). Best, Lilla > Hello there, > > I'm new to Fieldtrip: I've been assigned to work with signals acquired > by Emotiv in Matlab environment, specially in real-time - or at least > almost real-time - so I can work and study these signals with my own > Matlab's functions. However, here's the bad thing: we did not expect > it to be that complicated to extract signals directly to Matlab. > > While searching for any module, program, anything I could find, to > help our problem, I found Fieldtrip. Correct me if I am wrong, but it > seems that it is able to stream/buffer from emotiv's sdk to matlab. > > The problem is that we do not have that much experience with compiling > C programs, hence I am having a really hard time to understand what do > you mean with: > > "Compilation > We provide a simple Makefile for the MinGW compiler, but you will need > the Emotiv SDK. Please go to the realtime/datasource/emotiv directory > and type make or mingw32-make. Note that you might need to compile the > libbuffer library first." > > > Here's what I did so far: > > 1. I have installed Matlab r2011b 64-bit and Emotiv SDK Research Edition; > > 2. I installed MinGW and set the path of the /bin in environmental > variables; > > 3. I downloaded all these files from: > http://code.google.com/p/fieldtrip/source/browse/trunk/realtime/datasource/emotiv/?r=1742 > > 4. Then I went cmd and tried to do: mingw32-make -f makefile.gcc > SHARED=1 UNICODE=1 BUILD=release > which obviously failed: it said it was missing a file "Ftbuffer.h". I > assumed it was the libbuffer library, however I can't seem to find it > anywhere in the Internet (just some site that would ask me to install > Makestuff application, which I did and was unsuccessful. > I found a "buffer" folder in fieldtrip release but I dont think it's that. > Hence I tried to download the Ftbuffer.h itself from internet and put > it in the folder where emotiv2ft was. It worked, but then it started > to ask others files.... and more.. and more.. > > So, obviously I'm stuck right here. > Can you help me right here? What should I do? Have I done something wrong? > I've read this discussion list and found one thread quite related to > this - but his problem was not having research edition, which in fact, > I do have it. > > I'm sorry bothering you with probably authentic beginner questions, > but as I said, I only have high experience with Matlab. > > Best Regards, > Ricardo > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From r.oostenveld at donders.ru.nl Thu Sep 6 15:05:32 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 6 Sep 2012 15:05:32 +0200 Subject: [FieldTrip] Having troubles with Emotiv + Fieldtrip + Matlab In-Reply-To: References: Message-ID: <094D4EED-A39B-4788-BB7B-9C801AF65B78@donders.ru.nl> Dear Ricardo, We provide the full source code for you to investigate, modify and recompile, but we also provide pre-compiled binaries that you shoiuld be able to use to just get it to run. Rather than just grabbing a small section of the fieldtrip code, which you seem to have done, I suggest you get a complete fieldtrip version from http://fieldtrip.fcdonders.nl/download or through SVN (you want the complete trunk). In the fieldtrip/realtime/bin/win32 directory you will find the compiled emotiv2ft.exe program (it is present both in th ezip file from the ftp, as well as in the svn version). The emotiv2ft.exe application copies the data from the emotiv dll into the FT buffer, where you can access it from MATLAB using the methods described here http://fieldtrip.fcdonders.nl/getting_started/realtime for end-users and here http://fieldtrip.fcdonders.nl/development/realtime for developers. Hope this helps, Robert On 6 Sep 2012, at 12:25, Ricardo Jorge wrote: > Hello there, > > I'm new to Fieldtrip: I've been assigned to work with signals acquired > by Emotiv in Matlab environment, specially in real-time - or at least > almost real-time - so I can work and study these signals with my own > Matlab's functions. However, here's the bad thing: we did not expect > it to be that complicated to extract signals directly to Matlab. > > While searching for any module, program, anything I could find, to > help our problem, I found Fieldtrip. Correct me if I am wrong, but it > seems that it is able to stream/buffer from emotiv's sdk to matlab. > > The problem is that we do not have that much experience with compiling > C programs, hence I am having a really hard time to understand what do > you mean with: > > "Compilation > We provide a simple Makefile for the MinGW compiler, but you will need > the Emotiv SDK. Please go to the realtime/datasource/emotiv directory > and type make or mingw32-make. Note that you might need to compile the > libbuffer library first." > > > Here's what I did so far: > > 1. I have installed Matlab r2011b 64-bit and Emotiv SDK Research Edition; > > 2. I installed MinGW and set the path of the /bin in environmental variables; > > 3. I downloaded all these files from: > http://code.google.com/p/fieldtrip/source/browse/trunk/realtime/datasource/emotiv/?r=1742 > > 4. Then I went cmd and tried to do: mingw32-make -f makefile.gcc > SHARED=1 UNICODE=1 BUILD=release > which obviously failed: it said it was missing a file "Ftbuffer.h". I > assumed it was the libbuffer library, however I can't seem to find it > anywhere in the Internet (just some site that would ask me to install > Makestuff application, which I did and was unsuccessful. > I found a "buffer" folder in fieldtrip release but I dont think it's that. > Hence I tried to download the Ftbuffer.h itself from internet and put > it in the folder where emotiv2ft was. It worked, but then it started > to ask others files.... and more.. and more.. > > So, obviously I'm stuck right here. > Can you help me right here? What should I do? Have I done something wrong? > I've read this discussion list and found one thread quite related to > this - but his problem was not having research edition, which in fact, > I do have it. > > I'm sorry bothering you with probably authentic beginner questions, > but as I said, I only have high experience with Matlab. > > Best Regards, > Ricardo > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Jan.Hirschmann at med.uni-duesseldorf.de Thu Sep 6 15:06:02 2012 From: Jan.Hirschmann at med.uni-duesseldorf.de (Jan.Hirschmann at med.uni-duesseldorf.de) Date: Thu, 6 Sep 2012 15:06:02 +0200 Subject: [FieldTrip] phase difference between sources Message-ID: <72E993C35FB11743B79FF9286E5B6D8B04617307@Mail2-UKD.VMED.UKD> Dear fieldtrip experts, I was wondering how to get the mean phase difference between two sources A and B at a particular frequency f (mean across data segments). My idea was to use dics and to say cfg.refdip=A and cfg.keepcsd='yes'. Then I would get C, the cross spectral density between A and B, which is a 3x3 matrix with complex entries. Joachim Gross wrote that one could estimate csd in the dominant direction as the trace of C. So I guess I could get the phase difference by angle(trace(C)). Is this correct? If I wanted to use SVD to estimate the dominant direction instead of the trace, how would I get the phase difference then? And finally, if I wanted to have coherence not with the dipole orientation that maximizes power but with the orientation that maximizes phase difference, how would that work? Thanks for any remarks! Jan -- Jan Hirschmann MSc Neuroscience Institute of Clinical Neuroscience and Medical Psychology Heinrich Heine University Düsseldorf Universitätsstr. 1 40225 Düsseldorf Germany Tel: +49 (0)211 81 18415 Fax: +49 (0)211 81 19033 -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Sep 6 15:10:28 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 6 Sep 2012 15:10:28 +0200 Subject: [FieldTrip] left to right inversion after source interpolation In-Reply-To: <44E1ACF5-2C6D-4BA2-8FA7-B0886FB8AF20@uke.uni-hamburg.de> References: <075a92dd-147e-45e9-a4d1-726999c597b1@thalamus_p> <44E1ACF5-2C6D-4BA2-8FA7-B0886FB8AF20@uke.uni-hamburg.de> Message-ID: <7B18D5B7-9B69-4E09-AFD8-3B6D5B30D6A0@donders.ru.nl> Hi Fred, On http://fieldtrip.fcdonders.nl/faq/why_does_my_anatomical_mri_show_upside-down_when_plotting_it_with_ft_sourceplot there is an explanation to a related question. Also in your case FT_VOLUMERSLICE might be of use. See also http://fieldtrip.fcdonders.nl/faq/what_is_the_plotting_convention_for_anatomical_mris best Robert On 5 Sep 2012, at 16:30, Kathrin Müsch wrote: > Dear Fred, > > I encountered a similar thing a while ago and it was because spm8 seems to plot in radiological convention (i.e. left is plotted right and vice versa - http://mailman.science.ru.nl/pipermail/fieldtrip/2012-May/005229.html) so you're plots should actually be correct. > > If you use cfg.interactive = 'yes'; and click into the activated side of the brain, the first coordinate should be negative because you are in the left hemisphere. > > Hope that helps, > Kathrin > > > Am 05.09.2012 um 14:47 schrieb Frederic Roux: > >> Dear fieldtrip users, >> >> I have noticed that after interpolating a dummy source volume with ft_sourceinterpolate, >> voxels that were located in the left side of the volume, apear to be located in the right >> side of the volume. >> >> The code that I use is as following: >> >> dummy is a dummy structure of an lcmv beamformer map with the fields >> >> dummy = >> dim : [15 18 17] >> time: [1x272662 double] >> pos: [4590x3 double] >> inside: [1x2144 double] >> outside: [1x2446 double] >> method: 'average' >> avg: [1x1 struct] >> >> voxpos = dummy.pos(dummy.inside,1);% get the coordinates of voxels inside the volume >> dummy.avg.pow(dummy.inside(sign(voxpos)==1)) = 0; % set activity in the left hemisphere to 0 >> dummy.avg.pow(dummy.inside(sign(voxpos)==-1)) = 1; % set activity in the left hemisphere to 1 >> >> cfg = []; >> cfg.parameters = 'all'; >> >> int_dummy = ft_sourceinterpolate(cfg,dummy,template_MNI_mri); >> >> cfg = []; >> cfg.funparameter = 'avg.pow'; >> cfg.method = 'ortho'; >> >> %plot the non-interpolated volume >> figure; >> ft_sourceplot(cfg,dummy); >> >> %plot the interpolated volume >> figure; >> ft_sourceplot(cfg,int_dummy); >> >> As you can see from the figure in the attachement, the voxels that >> corresponded to the left hemisphere prior to the interpolation, >> no appear to be located in the rigth hemisphere. >> >> This is also something that I have observed in real data. >> >> Does anybody have an explanation why this is happening? >> Am I doing something wrong? >> >> Best, >> >> Fred >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): > > Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg > > Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From landpt at gmail.com Thu Sep 6 17:48:27 2012 From: landpt at gmail.com (Ricardo Jorge) Date: Thu, 6 Sep 2012 16:48:27 +0100 Subject: [FieldTrip] Having troubles with Emotiv + Fieldtrip + Matlab Message-ID: Hello there, Thanks! I'm a feeling a bit shamed because now they did seem like stupid questions but it really worked now - I had to read the walkthough to understand some definitions, and then I read your replies about the emotiv executable and really worked now! I was not understanding why I would need to compile again if there was an executable - I thought it was related to the fact that EPOC wouldn't allow the redistribution of their dlls or something like that, I don't know. Thanks again. Best, Ricardo Jorge From daria.laptinskaya at googlemail.com Thu Sep 6 18:52:44 2012 From: daria.laptinskaya at googlemail.com (Daria Laptinskaya) Date: Thu, 6 Sep 2012 18:52:44 +0200 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> Message-ID: Thanks you all for the answers! It seems to be a problem with reading the raw.-files. My collegue found a formula, maybe we can use it for microvolt-scaling. @Joe: It would be a great helf, if you could have a look at one of the files. Can I send you a dropbox-link? Best, Daria 2012/9/6 Joseph Dien > The Simple Binary (.raw) files don't get corrected for gain when imported > (I helped write them). I've experienced occasional unpredictable bugs with > NetStation export routines where the files are generated with amplitudes > many times too large, even with text format files. It's a bit > disconcerting to say the least. I could take a look at your files if you'd > like confirmation. > > Joe > > On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis > wrote: > > Hi Daria, > > Also, did you try looking at your raw data (so before the ERPs are made) > in FieldTrip and in Net Station? So open your .raw data in NetStation. You > can just look at a random participant's data, and check if the scale is the > same. I'm pretty sure no amplification takes place when reading in the data > into FieldTrip, this check can confirm that. Hope this helps, and let us > know what you find. > > Cheers, > Ingrid > > > On 9/3/2012 1:35 PM, Robert Oostenveld wrote: > > Hi Daria, > > There might indeed be an incompatibility in the gain value applied to > the data. > > If you are able to export the data using the EGI software in another > format (e.g. EDF), you could read them both into FieldTrip and compare the > timecourse aplitudes to check whether they are different. In case they are, > I suggest to involve EGI support. They are aware of the FieldTrip reading > functions and will know much more about the internals of their various file > formats. > > best regards > Robert > > > > > On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: > > Dear Fieldtrippers, > > I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip > toolbox. > The ERPs look perfect. > The 'only' problem is, that my signals look to strong. > It looks like if I get amplitutes (average) until 70 µV. > I think it must be an intern amplifier for the signals. > > Does anyone know this problem with EGI-data? > > Or does anyone know, where I can see the amplifier? > > > > Greetings, > Daria _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Ingrid Nieuwenhuis PhD > Postdoctoral Fellow > Sleep and Neuroimaging Laboratory > Department of Psychology > University of California, Berkeley > California 94720-1650 > Tolman Hall, room 5305 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mollison at gmail.com Thu Sep 6 19:01:42 2012 From: matt.mollison at gmail.com (Matt Mollison) Date: Thu, 6 Sep 2012 11:01:42 -0600 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> Message-ID: Joe, A few related questions: Does using the "calibrate data" option when exporting to raw (simple binary) correct for gain? Or is there a different solution/recommendation? Does exporting to MFF (Net Station 4.5.x only) or EGIS have this issue? I tend to use EGIS (faster to read than raw) and have no recollection of seeing unusually large voltages. Thanks, Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ On Wed, Sep 5, 2012 at 7:17 PM, Joseph Dien wrote: > The Simple Binary (.raw) files don't get corrected for gain when imported > (I helped write them). I've experienced occasional unpredictable bugs with > NetStation export routines where the files are generated with amplitudes > many times too large, even with text format files. It's a bit > disconcerting to say the least. I could take a look at your files if you'd > like confirmation. > > Joe > > On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis > wrote: > > Hi Daria, > > Also, did you try looking at your raw data (so before the ERPs are made) > in FieldTrip and in Net Station? So open your .raw data in NetStation. You > can just look at a random participant's data, and check if the scale is the > same. I'm pretty sure no amplification takes place when reading in the data > into FieldTrip, this check can confirm that. Hope this helps, and let us > know what you find. > > Cheers, > Ingrid > > > On 9/3/2012 1:35 PM, Robert Oostenveld wrote: > > Hi Daria, > > There might indeed be an incompatibility in the gain value applied to > the data. > > If you are able to export the data using the EGI software in another > format (e.g. EDF), you could read them both into FieldTrip and compare the > timecourse aplitudes to check whether they are different. In case they are, > I suggest to involve EGI support. They are aware of the FieldTrip reading > functions and will know much more about the internals of their various file > formats. > > best regards > Robert > > > > > On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: > > Dear Fieldtrippers, > > I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip > toolbox. > The ERPs look perfect. > The 'only' problem is, that my signals look to strong. > It looks like if I get amplitutes (average) until 70 µV. > I think it must be an intern amplifier for the signals. > > Does anyone know this problem with EGI-data? > > Or does anyone know, where I can see the amplifier? > > > > Greetings, > Daria _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Ingrid Nieuwenhuis PhD > Postdoctoral Fellow > Sleep and Neuroimaging Laboratory > Department of Psychology > University of California, Berkeley > California 94720-1650 > Tolman Hall, room 5305 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jdien07 at mac.com Fri Sep 7 02:58:43 2012 From: jdien07 at mac.com (Joseph Dien) Date: Thu, 06 Sep 2012 20:58:43 -0400 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> Message-ID: <293829E7-6D3C-4ED9-B592-5981F73098F8@mac.com> By all means! Joe On Sep 6, 2012, at 12:52 PM, Daria Laptinskaya wrote: > Thanks you all for the answers! > It seems to be a problem with reading the raw.-files. > My collegue found a formula, maybe we can use it for microvolt-scaling. > > @Joe: It would be a great helf, if you could have a look at one of the files. > Can I send you a dropbox-link? > > Best, > Daria > > > 2012/9/6 Joseph Dien > The Simple Binary (.raw) files don't get corrected for gain when imported (I helped write them). I've experienced occasional unpredictable bugs with NetStation export routines where the files are generated with amplitudes many times too large, even with text format files. It's a bit disconcerting to say the least. I could take a look at your files if you'd like confirmation. > > Joe > > On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis wrote: > >> Hi Daria, >> >> Also, did you try looking at your raw data (so before the ERPs are made) in FieldTrip and in Net Station? So open your .raw data in NetStation. You can just look at a random participant's data, and check if the scale is the same. I'm pretty sure no amplification takes place when reading in the data into FieldTrip, this check can confirm that. Hope this helps, and let us know what you find. >> >> Cheers, >> Ingrid >> >> >> On 9/3/2012 1:35 PM, Robert Oostenveld wrote: >>> Hi Daria, >>> >>> There might indeed be an incompatibility in the gain value applied to the data. >>> >>> If you are able to export the data using the EGI software in another format (e.g. EDF), you could read them both into FieldTrip and compare the timecourse aplitudes to check whether they are different. In case they are, I suggest to involve EGI support. They are aware of the FieldTrip reading functions and will know much more about the internals of their various file formats. >>> >>> best regards >>> Robert >>> >>> >>> >>> >>> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: >>> >>>> Dear Fieldtrippers, >>>> >>>> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip toolbox. >>>> The ERPs look perfect. >>>> The 'only' problem is, that my signals look to strong. >>>> It looks like if I get amplitutes (average) until 70 µV. >>>> I think it must be an intern amplifier for the signals. >>>> Does anyone know this problem with EGI-data? >>>> >>>> Or does anyone know, where I can see the amplifier? >>>> >>>> >>>> >>>> >>>> Greetings, >>>> >>>> Daria _______________________________________________ >>>> 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 >> >> -- >> Ingrid Nieuwenhuis PhD >> Postdoctoral Fellow >> Sleep and Neuroimaging Laboratory >> Department of Psychology >> University of California, Berkeley >> California 94720-1650 >> Tolman Hall, room 5305 >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07 at mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// -------------- next part -------------- An HTML attachment was scrubbed... URL: From jdien07 at mac.com Fri Sep 7 03:07:12 2012 From: jdien07 at mac.com (Joseph Dien) Date: Thu, 06 Sep 2012 21:07:12 -0400 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> Message-ID: <77D46473-6907-4AC1-96E1-F51756C119C0@mac.com> I don't recall ever seeing this problem with EGIS files, which is one of the reasons I prefer using this file format despite EGI's preference for newer Simple Binary format, but it's an unpredictable bug so I can't say it can't happen. I also can't say which versions of NetStation it happens with. It may have been fixed. I'm still trying to test out MFF so can't say anything about it. I had problems with the FieldTrip code for reading segmented MFF files (which is what I'm interested in). I also had trouble with writing them out from NetStation so I don't have a valid segmented test file and I'm still waiting for EGI to make one available so I can work them out. The simple binary file format (this is the original name for the EGI .raw file format and I prefer to use it over ".raw" as the BESA .raw file format is actually the .egis file format so it can get confusing) doesn't actually have separate calibration information for the channels (unlike EGIS), just one single gain value and no zeros values. So basically the simple binary format makes the assumption that calibration corrections have already been performed prior to generating the file. My understanding is that this is indeed what the "calibrate data" option is doing, but you'd have to confirm with EGI. Joe -------------------------------------------------------------------------------- On Sep 6, 2012, at 1:01 PM, Matt Mollison wrote: > Joe, > > A few related questions: > > Does using the "calibrate data" option when exporting to raw (simple binary) correct for gain? Or is there a different solution/recommendation? > Does exporting to MFF (Net Station 4.5.x only) or EGIS have this issue? I tend to use EGIS (faster to read than raw) and have no recollection of seeing unusually large voltages. > > Thanks, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > > On Wed, Sep 5, 2012 at 7:17 PM, Joseph Dien wrote: > The Simple Binary (.raw) files don't get corrected for gain when imported (I helped write them). I've experienced occasional unpredictable bugs with NetStation export routines where the files are generated with amplitudes many times too large, even with text format files. It's a bit disconcerting to say the least. I could take a look at your files if you'd like confirmation. > > Joe > > On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis wrote: > >> Hi Daria, >> >> Also, did you try looking at your raw data (so before the ERPs are made) in FieldTrip and in Net Station? So open your .raw data in NetStation. You can just look at a random participant's data, and check if the scale is the same. I'm pretty sure no amplification takes place when reading in the data into FieldTrip, this check can confirm that. Hope this helps, and let us know what you find. >> >> Cheers, >> Ingrid >> >> >> On 9/3/2012 1:35 PM, Robert Oostenveld wrote: >>> Hi Daria, >>> >>> There might indeed be an incompatibility in the gain value applied to the data. >>> >>> If you are able to export the data using the EGI software in another format (e.g. EDF), you could read them both into FieldTrip and compare the timecourse aplitudes to check whether they are different. In case they are, I suggest to involve EGI support. They are aware of the FieldTrip reading functions and will know much more about the internals of their various file formats. >>> >>> best regards >>> Robert >>> >>> >>> >>> >>> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: >>> >>>> Dear Fieldtrippers, >>>> >>>> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip toolbox. >>>> The ERPs look perfect. >>>> The 'only' problem is, that my signals look to strong. >>>> It looks like if I get amplitutes (average) until 70 µV. >>>> I think it must be an intern amplifier for the signals. >>>> Does anyone know this problem with EGI-data? >>>> >>>> Or does anyone know, where I can see the amplifier? >>>> >>>> >>>> >>>> >>>> Greetings, >>>> >>>> Daria _______________________________________________ >>>> 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 >> >> -- >> Ingrid Nieuwenhuis PhD >> Postdoctoral Fellow >> Sleep and Neuroimaging Laboratory >> Department of Psychology >> University of California, Berkeley >> California 94720-1650 >> Tolman Hall, room 5305 >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07 at mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// -------------- next part -------------- An HTML attachment was scrubbed... URL: From polomacnenad at gmail.com Fri Sep 7 12:36:05 2012 From: polomacnenad at gmail.com (Nenad Polomac) Date: Fri, 7 Sep 2012 12:36:05 +0200 Subject: [FieldTrip] problem with FT_MEGPLANAR Message-ID: Dear all, I would like to apply FT_MEGPLANAR on ERF data obtain from FT_TIMELOCKANALYSIS. According to tutorial that should be possible. This is the error I get: Error using ft_checkdata (line 376) This function requires ctf151, ctf275, bti148, bti248, itab153, yokogawa160 or yokogawa64 data as input, but you are giving ctf275 data. Error in ft_megplanar (line 109) data = ft_checkdata(data, 'datatype', {'raw' 'freq'}, 'feedback', 'yes', 'hassampleinfo', 'yes', 'ismeg', 'yes', 'senstype', {'ctf151', 'ctf275', 'bti148', 'bti248', 'itab153', 'yokogawa160', 'yokoga This is how looks like output form FT_TIMELOCKANALYSIS. On this data I would like to apply FT_MEGPLANAR. average32 = avg: [271x1440 double] var: [271x1440 double] time: [1x1440 double] dof: [271x1440 double] label: {271x1 cell} trial: [75x271x1440 double] dimord: 'rpt_chan_time' trialinfo: [75x1 double] cfg: [1x1 struct] My code: cfg = []; cfg.method = 'template'; cfg.template = 'CTF275_neighb.mat'; neighbours = ft_prepare_neighbours(cfg, grad); cfg=[]; cfg.neighbours=neighbours; cfg.planarmethod = 'orig'; cfg.trials = 'all'; planar32 = ft_megplanar(cfg, average32); *grad is structure obtained earlier with FT_PREPROCESSING Furthermore, I would also like to apply FT_MEGPLANAR on the other data obtained from ft_rejectcomponent (after ICA rejection) and this doesn't work as well. This error is the same as one I mentioned above. Thank you in advance! Nenad -------------- next part -------------- An HTML attachment was scrubbed... URL: From Markus.Butz at uni-duesseldorf.de Fri Sep 7 14:33:22 2012 From: Markus.Butz at uni-duesseldorf.de (Markus Butz) Date: Fri, 07 Sep 2012 13:33:22 +0100 Subject: [FieldTrip] Frontiers in Human Neuroscience - Research Topic: The Functional Role of Gamma Band Activity - Lessons from MEG Message-ID: <7620e04b44e3.5049f7a2@uni-duesseldorf.de> Dear FieldTrip list We are pleased to announce an upcoming Research Topic in Frontiers in Human Neuroscience on “The Functional Role of Gamma Band Activity – Lessons From MEG”. Further information can be found here: http://www.frontiersin.org/human_neuroscience/researchtopics/the_functional_role_of_gamma_b/962 Deadline for abstract submission: 01 Dec 2012 Deadline for full article submission: 01 Feb 2013 We are looking forward to your contributions! Please don’t hesitate to get in contact in case you have any further questions. Thank you very much for your consideration Krish & Markus -------------- next part -------------- An HTML attachment was scrubbed... URL: From tim.curran at Colorado.EDU Fri Sep 7 22:58:59 2012 From: tim.curran at Colorado.EDU (Tim Curran) Date: Fri, 7 Sep 2012 14:58:59 -0600 Subject: [FieldTrip] Colorado Computational Cognition Faculty Position In-Reply-To: References: Message-ID: <59F8E65D-69AE-4FCD-A985-1D0A28659020@colorado.edu> Computational Approaches to Cognition, Institute of Cognitive Science Tenure Track Position The Institute of Cognitive Science at the University of Colorado invites applications for a full-time tenure-track position in computational approaches to cognitive and/or affective processes at the assistant professor level with a starting date of Fall 2013. The Institute is a multidisciplinary unit with representation from the departments of Psychology & Neuroscience, Computer Science, Education, Philosophy, Linguistics, Architecture & Planning, and Speech, Language & Hearing Sciences. We seek applicants with a strong research program in theoretical and technical aspects of computational science. preferably with prior experience or interest in integrating cognitive science with state-of-the-art computational approaches. For example, individuals who utilize machine learning and statistical techniques to understand cognitive processes, such as language or learning, or to analyze high dimensional data from methods, such as functional magnetic resonance imaging, will be competitive for the position. Successful applicants could come from one of several fields, including cognitive science/cognitive neuroscience, computer science, statistics, biostatistics, physics, or other related disciplines. An ability for and commitment to interdisciplinary research is a priority, as is an approach that both exploits existing computational techniques to address questions relevant to cognitive science and advances machine-learning theory. Duties include research, research supervision, service, as well as graduate and undergraduate teaching. Applicants are directed to the CU online job application website: www.jobsatcu.com; Job Posting Number 818695. At this site you will be asked for a curriculum vitae, copies of representative publications, a teaching statement, a research summary, and letter from three referees. For fullest consideration, please apply by September 24th, 2012. Applications will continue to be accepted after this date until the position is filled. Email inquiries may be sent to Donna.Caccamise at colorado.edu. The University of Colorado is an Equal Opportunity Employer committed to building a diverse workforce. We encourage applications from women, racial and ethnic minorities, individuals with disabilities and veterans. Alternative formats of this ad can be provided upon request for individuals with disabilities by contacting the ADA Coordinator at hr-ada at colorado.edu. The University of Colorado Boulder conducts background checks on all final applicants being considered for employment. From jdien07 at mac.com Mon Sep 10 02:44:44 2012 From: jdien07 at mac.com (Joseph Dien) Date: Sun, 09 Sep 2012 20:44:44 -0400 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: <77D46473-6907-4AC1-96E1-F51756C119C0@mac.com> References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> <77D46473-6907-4AC1-96E1-F51756C119C0@mac.com> Message-ID: <3B494ED9-B6C3-46A3-840C-8EEEDAA85E5E@mac.com> Hey Daria, glad you were able to get it worked out! Thank Matt for his reminder (below) about the calibration option. Cheers! Joe > Hi Joe, > > > > I didn’t know that there is a function like this. > > The most of my colleagues use the RAW.-files they get from the file-exporter without problems. > > Not even NetStation-support could give me an answer. > > So I thought, it must be a problem between NetStation and fieldtrip. > > Because of your tip I opened an original datafile and tried to save a copy of the file. > > Doing so NetStation offers a possibility to ‘convert to microvolts’ and create a .ses –datafile. > > The .raw-files I get this way have microvolt as unit. > > I compared the signals I get this way with the signals I get by using the formula (5000 mircovolts / (2^16 bits) I send you. They are almost the same-that’s great!!! > > It seems to work now. > > Thank you very much!!! You were a great help!!! > > > Cheers, > > Daria > On Sep 6, 2012, at 9:07 PM, Joseph Dien wrote: > I don't recall ever seeing this problem with EGIS files, which is one of the reasons I prefer using this file format despite EGI's preference for newer Simple Binary format, but it's an unpredictable bug so I can't say it can't happen. I also can't say which versions of NetStation it happens with. It may have been fixed. I'm still trying to test out MFF so can't say anything about it. I had problems with the FieldTrip code for reading segmented MFF files (which is what I'm interested in). I also had trouble with writing them out from NetStation so I don't have a valid segmented test file and I'm still waiting for EGI to make one available so I can work them out. The simple binary file format (this is the original name for the EGI .raw file format and I prefer to use it over ".raw" as the BESA .raw file format is actually the .egis file format so it can get confusing) doesn't actually have separate calibration information for the channels (unlike EGIS), just one single gain value and no zeros values. So basically the simple binary format makes the assumption that calibration corrections have already been performed prior to generating the file. My understanding is that this is indeed what the "calibrate data" option is doing, but you'd have to confirm with EGI. > > Joe > > > -------------------------------------------------------------------------------- > > On Sep 6, 2012, at 1:01 PM, Matt Mollison wrote: > >> Joe, >> >> A few related questions: >> >> Does using the "calibrate data" option when exporting to raw (simple binary) correct for gain? Or is there a different solution/recommendation? >> Does exporting to MFF (Net Station 4.5.x only) or EGIS have this issue? I tend to use EGIS (faster to read than raw) and have no recollection of seeing unusually large voltages. >> >> Thanks, >> Matt >> >> -- >> Univ. of Colorado at Boulder >> Dept. of Psychology and Neuroscience >> matthew.mollison at colorado.edu >> http://psych.colorado.edu/~mollison/ >> >> On Wed, Sep 5, 2012 at 7:17 PM, Joseph Dien wrote: >> The Simple Binary (.raw) files don't get corrected for gain when imported (I helped write them). I've experienced occasional unpredictable bugs with NetStation export routines where the files are generated with amplitudes many times too large, even with text format files. It's a bit disconcerting to say the least. I could take a look at your files if you'd like confirmation. >> >> Joe >> >> On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis wrote: >> >>> Hi Daria, >>> >>> Also, did you try looking at your raw data (so before the ERPs are made) in FieldTrip and in Net Station? So open your .raw data in NetStation. You can just look at a random participant's data, and check if the scale is the same. I'm pretty sure no amplification takes place when reading in the data into FieldTrip, this check can confirm that. Hope this helps, and let us know what you find. >>> >>> Cheers, >>> Ingrid >>> >>> >>> On 9/3/2012 1:35 PM, Robert Oostenveld wrote: >>>> Hi Daria, >>>> >>>> There might indeed be an incompatibility in the gain value applied to the data. >>>> >>>> If you are able to export the data using the EGI software in another format (e.g. EDF), you could read them both into FieldTrip and compare the timecourse aplitudes to check whether they are different. In case they are, I suggest to involve EGI support. They are aware of the FieldTrip reading functions and will know much more about the internals of their various file formats. >>>> >>>> best regards >>>> Robert >>>> >>>> >>>> >>>> >>>> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: >>>> >>>>> Dear Fieldtrippers, >>>>> >>>>> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip toolbox. >>>>> The ERPs look perfect. >>>>> The 'only' problem is, that my signals look to strong. >>>>> It looks like if I get amplitutes (average) until 70 µV. >>>>> I think it must be an intern amplifier for the signals. >>>>> Does anyone know this problem with EGI-data? >>>>> >>>>> Or does anyone know, where I can see the amplifier? >>>>> >>>>> >>>>> >>>>> >>>>> Greetings, >>>>> >>>>> Daria _______________________________________________ >>>>> 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 >>> >>> -- >>> Ingrid Nieuwenhuis PhD >>> Postdoctoral Fellow >>> Sleep and Neuroimaging Laboratory >>> Department of Psychology >>> University of California, Berkeley >>> California 94720-1650 >>> Tolman Hall, room 5305 >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, >> Senior Research Scientist >> University of Maryland >> >> E-mail: jdien07 at mac.com >> Phone: 301-226-8848 >> Fax: 301-226-8811 >> http://joedien.com// >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07 at mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// -------------- next part -------------- An HTML attachment was scrubbed... URL: From sahand.babapoor at gmail.com Mon Sep 10 02:49:31 2012 From: sahand.babapoor at gmail.com (sahand babapoor) Date: Sun, 9 Sep 2012 20:49:31 -0400 Subject: [FieldTrip] Using WPLI od WPLI-debiased to do the coherence analysis Message-ID: Hi all, I am trying to do coherency analysis between ACC and FEF. I have tried both WPLI and WPLI-debiased methods to do the analysis. When I am using WPLI I find a very nice coherence pattern between ACC and FEF in the frequencies between ~11Hz to 20 Hz. However, when I am using WPLI-debiased method, the previous WPLI coherence pattern disappears and breaks into many sparse clusters across many time points and frequencies. Is there a way to know which method is the best for me. I should note that I am recording using tungsten microelectrodes advanced into the brain. I would appreciate if your help. Best, Sahand -------------- next part -------------- An HTML attachment was scrubbed... URL: From ivano_triggiani at yahoo.it Mon Sep 10 12:27:09 2012 From: ivano_triggiani at yahoo.it (Ivano Triggiani) Date: Mon, 10 Sep 2012 11:27:09 +0100 (BST) Subject: [FieldTrip] about overlap in PSD calculation In-Reply-To: References: Message-ID: <1347272829.31720.YahooMailNeo@web133103.mail.ir2.yahoo.com> Hi all. How can I obtain informations about the kind of overlapping performed by fiedltrip implemented method to obtain a Power Spectral Density ? I need to compare fieldtrip PSD with another spectral density, so I need to be sure of everything. I found docs about tapering, but I don't understand if using a kind of tapering the overlapping is given. Ivano   ------------------------------------------------------------------------ "No man can wear one face to himself and another to the multitude, without finally getting bewildered as to which one is true." Nathaniel Hawthorne ________________________________ Da: "fieldtrip-request at science.ru.nl" A: fieldtrip at science.ru.nl Inviato: Lunedì 10 Settembre 2012 12:00 Oggetto: fieldtrip Digest, Vol 22, Issue 17 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. Using WPLI od WPLI-debiased to do the coherence analysis       (sahand babapoor) ---------------------------------------------------------------------- Message: 1 Date: Sun, 9 Sep 2012 20:49:31 -0400 From: sahand babapoor To: fieldtrip at science.ru.nl Subject: [FieldTrip] Using WPLI od WPLI-debiased to do the coherence     analysis Message-ID:     Content-Type: text/plain; charset="iso-8859-1" Hi all, I am trying to do coherency analysis between ACC and FEF. I have tried both WPLI and WPLI-debiased methods to do the analysis. When I am using WPLI I find a very nice coherence pattern between ACC and FEF in the frequencies between ~11Hz to 20 Hz. However, when I am using WPLI-debiased method, the previous WPLI coherence pattern disappears and  breaks into many sparse clusters across many time points and frequencies. Is there a way to know which method is the best for me. I should note that I am recording using tungsten microelectrodes advanced into the brain. I would appreciate if your help. Best, Sahand -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip End of fieldtrip Digest, Vol 22, Issue 17 ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From bherrmann at cbs.mpg.de Mon Sep 10 13:16:09 2012 From: bherrmann at cbs.mpg.de (=?utf-8?Q?Bj=C3=B6rn_Herrmann?=) Date: Mon, 10 Sep 2012 13:16:09 +0200 (CEST) Subject: [FieldTrip] real-value spatial filter from FFT dipole localization? In-Reply-To: <380027886.2137.1347269068602.JavaMail.root@zimbra> Message-ID: <1396322041.3317.1347275769488.JavaMail.root@zimbra> Dear fieldtrip users, maybe someone can point me in the right direction. I try to obtain a spatial filter from localizing the sources of an auditory 3Hz peak in my FFT spectrum. I would like to apply the filter to my single trial real data, i.e. basically reducing my 204 gradiometer channels (neuromag system) to one or two channels in source space. I was using DICS beamformer and cfg.realfilter = 'yes' but the source localization results (NAI) looked not too well compared to the nice auditory gradiometer topographies. I then used ft_dipolefitting, however, I have trouble understanding the output. This is where I wondered whether someone could help me, in telling whether it is possible to obtain a real-value spatial filter from this: source = label: {204x1 cell} dip: [1x1 struct] Vdata: [204x408 double] Vmodel: [204x408 double] freq: 3 dimord: 'chan_freq' grad: [1x1 struct] cfg: [1x1 struct] source.dip = pos: [2x3 double] mom: [6x408 double] pot: [204x408 double] rv: [1x408 double] pow: 2.7948e+18 csd: [6x6 double] fourier: [6x204 double] I would appreciate helping comments, as I tested the different methods for some time now, but was unable to extract a reasonable real-value spatial filter for my auditory cortex activations. Best regards, Björn From wallisgj at gmail.com Mon Sep 10 14:22:20 2012 From: wallisgj at gmail.com (George Wallis) Date: Mon, 10 Sep 2012 13:22:20 +0100 Subject: [FieldTrip] Appending data.grad, after using D.ftraw(0) Message-ID: Dear fieldtrippers, if anyone can help me with this I'd be very grateful! I have a bunch of preprocessed and epoched data files in SPM format, and I'm converting them to fieldtrip format using the following: D = spm_eeg_load(fn); data = D.ftraw(0); ...which results in... data = fsample: 250 label: {350x1 cell} trial: {1x360 cell} time: {1x360 cell} Comparing this to data structures generated using fieldtrip alone, field like data.grad are missing. I can create something like a grad field by doing: D.sensors('MEG') ans = pnt: [510x3 double] ori: [510x3 double] tra: [306x510 double] unit: 'mm' label: {306x1 cell} If I then append this to the data: data.grad = D.sensors('MEG'); I get an error: --- Error using ft_chantype (line 56) the input that was provided to this function cannot be deciphered Error in ft_datatype_sens (line 128) sens.chantype = ft_chantype(sens); Error in ft_datatype_raw (line 99) data.grad = ft_datatype_sens(data.grad); Error in ft_checkdata (line 177) data = ft_datatype_raw(data, 'hassampleinfo', hassampleinfo); Error in ft_timelockanalysis (line 134) data = ft_checkdata(data, 'datatype', {'raw', 'comp'}, 'feedback', 'yes', 'hassampleinfo', 'yes'); Error in ft_SENS_ERF_grRep (line 82) avdat = ft_timelockanalysis(cfg,raw); --- ...when I try to do timelockanalysis on this data. If I leave the grad field off (i.e. not append it to the output of ftraw(0)) there's no problem, and the analysis runs fine. However, because I want to do spatial neighbour cluster analysis later, I think I need the .grad field, so I might as well get it incorporated at this stage. Going a bit further into the error messages above, the function ft_datatype_sens appears to convert the old format .ori, .pnt into the newer .coilori, .coilpos ... etc. But the next function in the chain, ft_chantype, looks for .pnt and .ori when doing: isgrad = isa(input, 'struct') && isfield(input, 'pnt') && isfield(input, 'ori'); I'm wondering if this could be the problem? Sorry for the long message! I'd be very grateful if anyone can help out. Best wishes, George -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Mon Sep 10 15:55:26 2012 From: smoratti at psi.ucm.es (smoratti at psi.ucm.es) Date: Mon, 10 Sep 2012 15:55:26 +0200 Subject: [FieldTrip] Appending data.grad, after using D.ftraw(0) In-Reply-To: References: Message-ID: <44D6E4E8-E44D-4D08-B012-C3B506F6E935@psi.ucm.es> Dear George, Your approach was right, and it would have worked with older versions of field trip. Now in field trip the grad field contents have changed a little bit. Now it contains balance: [1x1 struct] chanori: [306x3 double] chanpos: [306x3 double] chantype: {306x1 cell} chanunit: {306x1 cell} coilori: [510x3 double] coilpos: [510x3 double] label: {306x1 cell} tra: [306x510 double] unit: 'cm' so the field put would be chanpos, ori would be chanori (or coilpos/ coilori depending on your MEG system). So check this out and you can easily adapt the structure. I think SPM does not go with the últimate field trip version. I hope this helps, best, Stephan ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 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 10/09/2012, a las 14:22, George Wallis escribió: > Dear fieldtrippers, > > if anyone can help me with this I'd be very grateful! > > I have a bunch of preprocessed and epoched data files in SPM format, and I'm converting them to fieldtrip format using the following: > > D = spm_eeg_load(fn); > data = D.ftraw(0); > > ...which results in... > > data = > > fsample: 250 > label: {350x1 cell} > trial: {1x360 cell} > time: {1x360 cell} > > Comparing this to data structures generated using fieldtrip alone, field like data.grad are missing. > > I can create something like a grad field by doing: > > D.sensors('MEG') > > ans = > > pnt: [510x3 double] > ori: [510x3 double] > tra: [306x510 double] > unit: 'mm' > label: {306x1 cell} > > If I then append this to the data: > > data.grad = D.sensors('MEG'); > > I get an error: > > --- > > Error using ft_chantype (line 56) > the input that was provided to this function cannot be deciphered > > Error in ft_datatype_sens (line 128) > sens.chantype = ft_chantype(sens); > > Error in ft_datatype_raw (line 99) > data.grad = ft_datatype_sens(data.grad); > > Error in ft_checkdata (line 177) > data = ft_datatype_raw(data, 'hassampleinfo', hassampleinfo); > > Error in ft_timelockanalysis (line 134) > data = ft_checkdata(data, 'datatype', {'raw', 'comp'}, 'feedback', 'yes', 'hassampleinfo', > 'yes'); > > Error in ft_SENS_ERF_grRep (line 82) > avdat = ft_timelockanalysis(cfg,raw); > > --- > > ...when I try to do timelockanalysis on this data. If I leave the grad field off (i.e. not append it to the output of ftraw(0)) there's no problem, and the analysis runs fine. However, because I want to do spatial neighbour cluster analysis later, I think I need the .grad field, so I might as well get it incorporated at this stage. > > Going a bit further into the error messages above, the function ft_datatype_sens appears to convert the old format .ori, .pnt into the newer .coilori, .coilpos ... etc. But the next function in the chain, ft_chantype, looks for .pnt and .ori when doing: > > isgrad = isa(input, 'struct') && isfield(input, 'pnt') && isfield(input, 'ori'); > > I'm wondering if this could be the problem? > > Sorry for the long message! I'd be very grateful if anyone can help out. > > Best wishes, > George > _______________________________________________ > 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 wallisgj at gmail.com Mon Sep 10 18:21:36 2012 From: wallisgj at gmail.com (George Wallis) Date: Mon, 10 Sep 2012 17:21:36 +0100 Subject: [FieldTrip] Appending data.grad, after using D.ftraw(0) Message-ID: Hi Stephan, Thanks very much for your reply (and sorry for not replying to the thread; I get a digest, and couldn't figure out how to reply to an individual message). So, SPM will produce an outdated .grad format, which can be corrected. There is one thing I don't get, which is why ft_chantype looks for the older fields, viz: *isgrad = isa(input, 'struct') && isfield(input, 'pnt') && isfield(input, 'ori');* It seems like the function ft_chantype is called from, ft_datatype_sens, automatically corrects the old grad format before passing the structure (now called 'sens') to ft_chantype: % sensor description is a MEG sensor-array, containing oriented coils [chanpos, chanori, chanlab] = channelposition(sens, 'channel', 'all'); sens.coilori = sens.ori; sens = rmfield(sens, 'ori'); sens.coilpos = sens.pnt; sens = rmfield(sens, 'pnt'); sens.chanpos = chanpos; sens.chanori = chanori; Did the new format not propagate through? best wishes, George On Mon, Sep 10, 2012 at 2:55 PM, 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. about overlap in PSD calculation (Ivano Triggiani) > 2. real-value spatial filter from FFT dipole localization? > (Bj?rn Herrmann) > 3. Appending data.grad, after using D.ftraw(0) (George Wallis) > 4. Re: Appending data.grad, after using D.ftraw(0) > (smoratti at psi.ucm.es) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 10 Sep 2012 11:27:09 +0100 (BST) > From: Ivano Triggiani > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] about overlap in PSD calculation > Message-ID: > <1347272829.31720.YahooMailNeo at web133103.mail.ir2.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all. > > How can I obtain informations about the kind of overlapping performed by > fiedltrip implemented method to obtain a Power Spectral Density ? > > I need to compare fieldtrip PSD with another spectral density, so I need > to be sure of everything. I found docs about tapering, but I don't > understand if using a kind of tapering the overlapping is given. > Ivano > > ? > ------------------------------------------------------------------------ > > > > > "No man can wear one face to himself > and another to the multitude, > without finally getting bewildered > as to which one is true." > > > Nathaniel Hawthorne > > > ________________________________ > Da: "fieldtrip-request at science.ru.nl" > A: fieldtrip at science.ru.nl > Inviato: Luned? 10 Settembre 2012 12:00 > Oggetto: fieldtrip Digest, Vol 22, Issue 17 > > 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. Using WPLI od WPLI-debiased to do the coherence analysis > ? ? ? (sahand babapoor) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 9 Sep 2012 20:49:31 -0400 > From: sahand babapoor > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Using WPLI od WPLI-debiased to do the coherence > ??? analysis > Message-ID: > ??? > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > > I am trying to do coherency analysis between ACC and FEF. I have tried both > WPLI and WPLI-debiased methods to do the analysis. When I am using WPLI I > find a very nice coherence pattern between ACC and FEF in the frequencies > between ~11Hz to 20 Hz. However, when I am using WPLI-debiased method, the > previous WPLI coherence pattern disappears and? breaks into many sparse > clusters across many time points and frequencies. Is there a way to know > which method is the best for me. I should note that I am recording using > tungsten microelectrodes advanced into the brain. I would appreciate if > your help. > > Best, > Sahand > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120909/2a47bbc7/attachment-0001.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 22, Issue 17 > ***************************************** > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120910/448a5494/attachment-0001.html > > > > ------------------------------ > > Message: 2 > Date: Mon, 10 Sep 2012 13:16:09 +0200 (CEST) > From: Bj?rn Herrmann > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] real-value spatial filter from FFT dipole > localization? > Message-ID: <1396322041.3317.1347275769488.JavaMail.root at zimbra> > Content-Type: text/plain; charset=utf-8 > > Dear fieldtrip users, > > maybe someone can point me in the right direction. I try to obtain a > spatial filter from localizing the sources of an auditory 3Hz peak in my > FFT spectrum. I would like to apply the filter to my single trial real > data, i.e. basically reducing my 204 gradiometer channels (neuromag system) > to one or two channels in source space. > I was using DICS beamformer and cfg.realfilter = 'yes' but the source > localization results (NAI) looked not too well compared to the nice > auditory gradiometer topographies. > I then used ft_dipolefitting, however, I have trouble understanding the > output. This is where I wondered whether someone could help me, in telling > whether it is possible to obtain a real-value spatial filter from this: > > source = > label: {204x1 cell} > dip: [1x1 struct] > Vdata: [204x408 double] > Vmodel: [204x408 double] > freq: 3 > dimord: 'chan_freq' > grad: [1x1 struct] > cfg: [1x1 struct] > > source.dip = > pos: [2x3 double] > mom: [6x408 double] > pot: [204x408 double] > rv: [1x408 double] > pow: 2.7948e+18 > csd: [6x6 double] > fourier: [6x204 double] > > I would appreciate helping comments, as I tested the different methods for > some time now, but was unable to extract a reasonable real-value spatial > filter for my auditory cortex activations. > > Best regards, > > Bj?rn > > > > > > ------------------------------ > > Message: 3 > Date: Mon, 10 Sep 2012 13:22:20 +0100 > From: George Wallis > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Appending data.grad, after using D.ftraw(0) > Message-ID: > < > CADqk8UgZ-wUf-FAjLL9K0hScW6ZTWrOVJKaR0S+PVhvuKx31-w at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear fieldtrippers, > > if anyone can help me with this I'd be very grateful! > > I have a bunch of preprocessed and epoched data files in SPM format, and > I'm converting them to fieldtrip format using the following: > > D = spm_eeg_load(fn); > data = D.ftraw(0); > > ...which results in... > > data = > > fsample: 250 > label: {350x1 cell} > trial: {1x360 cell} > time: {1x360 cell} > > Comparing this to data structures generated using fieldtrip alone, field > like data.grad are missing. > > I can create something like a grad field by doing: > > D.sensors('MEG') > > ans = > > pnt: [510x3 double] > ori: [510x3 double] > tra: [306x510 double] > unit: 'mm' > label: {306x1 cell} > > If I then append this to the data: > > data.grad = D.sensors('MEG'); > > I get an error: > > --- > > Error using ft_chantype (line 56) > the input that was provided to this function cannot be deciphered > > Error in ft_datatype_sens (line 128) > sens.chantype = ft_chantype(sens); > > Error in ft_datatype_raw (line 99) > data.grad = ft_datatype_sens(data.grad); > > Error in ft_checkdata (line 177) > data = ft_datatype_raw(data, 'hassampleinfo', hassampleinfo); > > Error in ft_timelockanalysis (line 134) > data = ft_checkdata(data, 'datatype', {'raw', 'comp'}, 'feedback', 'yes', > 'hassampleinfo', > 'yes'); > > Error in ft_SENS_ERF_grRep (line 82) > avdat = ft_timelockanalysis(cfg,raw); > > --- > > ...when I try to do timelockanalysis on this data. If I leave the grad > field off (i.e. not append it to the output of ftraw(0)) there's no > problem, and the analysis runs fine. However, because I want to do spatial > neighbour cluster analysis later, I think I need the .grad field, so I > might as well get it incorporated at this stage. > > Going a bit further into the error messages above, the function > ft_datatype_sens appears to convert the old format .ori, .pnt into the > newer .coilori, .coilpos ... etc. But the next function in the chain, > ft_chantype, looks for .pnt and .ori when doing: > > isgrad = isa(input, 'struct') && isfield(input, 'pnt') && isfield(input, > 'ori'); > > I'm wondering if this could be the problem? > > Sorry for the long message! I'd be very grateful if anyone can help out. > > Best wishes, > George > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120910/8418e2de/attachment-0001.html > > > > ------------------------------ > > Message: 4 > Date: Mon, 10 Sep 2012 15:55:26 +0200 > From: "smoratti at psi.ucm.es" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Appending data.grad, after using D.ftraw(0) > Message-ID: <44D6E4E8-E44D-4D08-B012-C3B506F6E935 at psi.ucm.es> > Content-Type: text/plain; charset="iso-8859-1" > > Dear George, > > Your approach was right, and it would have worked with older versions of > field trip. Now in field trip the grad field contents have changed a little > bit. > > Now it contains > > balance: [1x1 struct] > chanori: [306x3 double] > chanpos: [306x3 double] > chantype: {306x1 cell} > chanunit: {306x1 cell} > coilori: [510x3 double] > coilpos: [510x3 double] > label: {306x1 cell} > tra: [306x510 double] > unit: 'cm' > > so the field put would be chanpos, ori would be chanori (or coilpos/ > coilori depending on your MEG system). > > So check this out and you can easily adapt the structure. I think SPM does > not go with the ?ltimate field trip version. > > I hope this helps, > > best, > > Stephan > > ________________________________________________________ > Stephan Moratti, PhD > > see also: http://web.me.com/smoratti/ > > Universidad Complutense de Madrid > Facultad de Psicolog?a > Departamento de Psicolog?a B?sica I > Campus de Somosaguas > 28223 Pozuelo de Alarc?n (Madrid) > Spain > > and > > Center for Biomedical Technology > Laboratory for Cognitive and Computational Neuroscience > Parque Cient?fico y Tecnol?gico de la Universidad Politecnica de Madrid > Campus Montegancedo > 28223 Pozuelo de Alarc?n (Madrid) > Spain > > > email: smoratti at psi.ucm.es > Tel.: +34 679219982 > > El 10/09/2012, a las 14:22, George Wallis escribi?: > > > Dear fieldtrippers, > > > > if anyone can help me with this I'd be very grateful! > > > > I have a bunch of preprocessed and epoched data files in SPM format, and > I'm converting them to fieldtrip format using the following: > > > > D = spm_eeg_load(fn); > > data = D.ftraw(0); > > > > ...which results in... > > > > data = > > > > fsample: 250 > > label: {350x1 cell} > > trial: {1x360 cell} > > time: {1x360 cell} > > > > Comparing this to data structures generated using fieldtrip alone, field > like data.grad are missing. > > > > I can create something like a grad field by doing: > > > > D.sensors('MEG') > > > > ans = > > > > pnt: [510x3 double] > > ori: [510x3 double] > > tra: [306x510 double] > > unit: 'mm' > > label: {306x1 cell} > > > > If I then append this to the data: > > > > data.grad = D.sensors('MEG'); > > > > I get an error: > > > > --- > > > > Error using ft_chantype (line 56) > > the input that was provided to this function cannot be deciphered > > > > Error in ft_datatype_sens (line 128) > > sens.chantype = ft_chantype(sens); > > > > Error in ft_datatype_raw (line 99) > > data.grad = ft_datatype_sens(data.grad); > > > > Error in ft_checkdata (line 177) > > data = ft_datatype_raw(data, 'hassampleinfo', hassampleinfo); > > > > Error in ft_timelockanalysis (line 134) > > data = ft_checkdata(data, 'datatype', {'raw', 'comp'}, 'feedback', > 'yes', 'hassampleinfo', > > 'yes'); > > > > Error in ft_SENS_ERF_grRep (line 82) > > avdat = ft_timelockanalysis(cfg,raw); > > > > --- > > > > ...when I try to do timelockanalysis on this data. If I leave the grad > field off (i.e. not append it to the output of ftraw(0)) there's no > problem, and the analysis runs fine. However, because I want to do spatial > neighbour cluster analysis later, I think I need the .grad field, so I > might as well get it incorporated at this stage. > > > > Going a bit further into the error messages above, the function > ft_datatype_sens appears to convert the old format .ori, .pnt into the > newer .coilori, .coilpos ... etc. But the next function in the chain, > ft_chantype, looks for .pnt and .ori when doing: > > > > isgrad = isa(input, 'struct') && isfield(input, 'pnt') && > isfield(input, 'ori'); > > > > I'm wondering if this could be the problem? > > > > Sorry for the long message! I'd be very grateful if anyone can help out. > > > > Best wishes, > > George > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120910/444962f9/attachment.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 22, Issue 18 > ***************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Mon Sep 10 18:36:02 2012 From: litvak.vladimir at gmail.com (litvak.vladimir at gmail.com) Date: Mon, 10 Sep 2012 16:36:02 +0000 Subject: [FieldTrip] Appending data.grad, after using D.ftraw(0) In-Reply-To: References: Message-ID: <1665240477-1347294953-cardhu_decombobulator_blackberry.rim.net-1232560809-@b18.c20.bise7.blackberry> Dear George, Yes, what you describe is still a bug in Fieldtrip because the conversion from the old to new grad format should be automatic. This might be related to a similar bug I reported on Bugzilla last Friday. The problem was specific to Neuromag data. The next SPM8 update will include an updated Fieldtrip version and will work with the new sensor formats. I hope the FT team will look at this soon. Vladimir Sent using BlackBerry® from Orange -----Original Message----- From: George Wallis Sender: fieldtrip-bounces at science.ru.nl Date: Mon, 10 Sep 2012 17:21:36 To: Reply-To: FieldTrip discussion list Subject: [FieldTrip] Appending data.grad, after using D.ftraw(0) _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From martin.maier at student.hu-berlin.de Tue Sep 11 14:06:38 2012 From: martin.maier at student.hu-berlin.de (Martin Maier) Date: Tue, 11 Sep 2012 14:06:38 +0200 Subject: [FieldTrip] example cross-frequency analysis In-Reply-To: References: Message-ID: Hi there, I'm trying to analyse my data for phase-amplitude cross-frequency coupling.The example script (http://fieldtrip.fcdonders.nl/example/crossfreq/phalow_amphigh) still uses ft_freqdescriptives to get the coherence-spectrum, but this has since been implemented in ft_connectivityanalysis. My question concerns the channelcombination when using ft_connectivityanalysis. When calculating the coherence between power and raw, I get the following error message: "??? Error using ==> univariate2bivariate at 25 no channel combinations are specified" I did specify channel combinations, but somehow ft_connectivityanalysis doesn't get them. Does the function need a different format when setting the channels to be combined? Or should I use a different function to calculate the coherence spectra (instead of ft_connectivityanalysis)? Thanks, Martin From member at linkedin.com Wed Sep 12 01:26:18 2012 From: member at linkedin.com (=?UTF-8?Q?Alicia_Gonz=C3=A1lez_Moreno_via_LinkedIn?=) Date: Tue, 11 Sep 2012 23:26:18 +0000 (UTC) Subject: [FieldTrip] Join my network on LinkedIn Message-ID: <1377830396.2855738.1347405978358.JavaMail.app@ela4-app2314.prod> LinkedIn ------------ Alicia González Moreno requested to add you as a connection on LinkedIn: ------------------------------------------ I'd like to add you to my professional network on LinkedIn. Accept invitation from Alicia González Moreno http://www.linkedin.com/e/-deyl8h-h6zmqar3-2j/2ql61bZWrtgNAx4NauUqWbaswiGNhc8KtyoV/blk/I214712724_50/0UcDpKqiRzolZKqiRybmRSrCBvrmRLoORIrmkZt5YCpnlOt3RApnhMpmdzgmhxrSNBszYMdlYQczsOcjsQcj99bTtdszl6sCl4bPsRc3oNcjsMdzwLrCBxbOYWrSlI/eml-comm_invm-b-in_ac-inv28/?hs=false&tok=2DIcL0uIu-Glo1 View profile of Alicia González Moreno http://www.linkedin.com/e/-deyl8h-h6zmqar3-2j/rso/203786050/UX0W/name/51465358_I214712724_50/?hs=false&tok=1RKIB_Kum-Glo1 ------------------------------------------ You are receiving Invitation emails. This email was intended for lin wang. Learn why this is included: http://www.linkedin.com/e/-deyl8h-h6zmqar3-2j/plh/http%3A%2F%2Fhelp%2Elinkedin%2Ecom%2Fapp%2Fanswers%2Fdetail%2Fa_id%2F4788/-GXI/?hs=false&tok=2C0EwII2W-Glo1 (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA. -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.hartmann at th-ht.de Wed Sep 12 14:57:37 2012 From: thomas.hartmann at th-ht.de (Thomas Hartmann) Date: Wed, 12 Sep 2012 14:57:37 +0200 Subject: [FieldTrip] units after beamforming Message-ID: <505086C1.9010004@th-ht.de> hi all, i do lcmv beamforming on meg data and use cfg.method='localspheres' and cfg.singlesphere='yes' as options to call ft_prepare_localspheres. i was wondering about the units of the resulting spatial filter. does anyone know, what those might be? thanks a lot! best, thomas -- Dr. Thomas Hartmann CIMeC - Center for Mind/Brain Sciences Università degli Studi di Trento via delle Regole, 101 38060 Mattarello (TN) ITALY Tel: +39 0461 28 2779 Fax: +39 0461 28 3066 Email: thomas.hartmann at th-ht.de Homepage: http://sites.google.com/site/obobcimec/ "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle) From elizabeth.bock at mcgill.ca Wed Sep 12 20:32:39 2012 From: elizabeth.bock at mcgill.ca (Elizabeth Anne Bock, Ms) Date: Wed, 12 Sep 2012 18:32:39 +0000 Subject: [FieldTrip] realtime buffer does not exit Message-ID: <86D86365C4E767468A79EB52DFBFB46F0510F73C@exmbx2010-8.campus.MCGILL.CA> I am using the realtime buffer and I have found I cannot exit the buffer within the Matlab command window. I am forced to exit Matlab or, more often, must kill the process manually from the windows task manager. I am using Windows XP to host the buffer and Linux to run acqftx. Here is what I am seeing: >> buffer('tcpserver', 'exit', ft_host, ft_port) In main: requesting cancelation of tcpserver thread >> buffer('tcpserver', 'init', ft_host, ft_port) ??? Error using ==> buffer thread is already running Any suggestions? Thanks, Elizabeth ------------------------------------------------------------------------------------------ Elizabeth Bock / MEG System Engineer McConnell Brain Imaging Centre / Montreal Neurological Institute McGill University / 3801 University St. / Montreal, QC H3A 2B4 MEG Lab: 514.398.6056 Mobile: 514.718.6342 From daria.laptinskaya at googlemail.com Thu Sep 13 09:21:00 2012 From: daria.laptinskaya at googlemail.com (Daria Laptinskaya) Date: Thu, 13 Sep 2012 09:21:00 +0200 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: <3B494ED9-B6C3-46A3-840C-8EEEDAA85E5E@mac.com> References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> <77D46473-6907-4AC1-96E1-F51756C119C0@mac.com> <3B494ED9-B6C3-46A3-840C-8EEEDAA85E5E@mac.com> Message-ID: Yes, it works fine now-thank you!!! @Matt: Do you know a calibration-function for existing raw-files? Best, Daria 2012/9/10 Joseph Dien > Hey Daria, > glad you were able to get it worked out! Thank Matt for his reminder > (below) about the calibration option. > > Cheers! > > Joe > > > Hi Joe, > > > I didn’t know that there is a function like this. > > The most of my colleagues use the RAW.-files they get from the > file-exporter without problems. > > Not even NetStation-support could give me an answer. > > So I thought, it must be a problem between NetStation and fieldtrip. > > Because of your tip I opened an original datafile and tried to save a copy > of the file. > > Doing so NetStation offers a possibility to ‘convert to microvolts’ and > create a .ses –datafile. > > The .raw-files I get this way have microvolt as unit. > > I compared the signals I get this way with the signals I get by using the > formula (5000 mircovolts / (2^16 bits) I send you. They are almost the > same-that’s great!!! > > It seems to work now. > > Thank you very much!!! You were a great help!!! > > > Cheers, > > Daria > > On Sep 6, 2012, at 9:07 PM, Joseph Dien wrote: > > I don't recall ever seeing this problem with EGIS files, which is one of > the reasons I prefer using this file format despite EGI's preference for > newer Simple Binary format, but it's an unpredictable bug so I can't say it > can't happen. I also can't say which versions of NetStation it happens > with. It may have been fixed. I'm still trying to test out MFF so can't > say anything about it. I had problems with the FieldTrip code for reading > segmented MFF files (which is what I'm interested in). I also had trouble > with writing them out from NetStation so I don't have a valid segmented > test file and I'm still waiting for EGI to make one available so I can work > them out. The simple binary file format (this is the original name for the > EGI .raw file format and I prefer to use it over ".raw" as the BESA .raw > file format is actually the .egis file format so it can get confusing) > doesn't actually have separate calibration information for the channels > (unlike EGIS), just one single gain value and no zeros values. So > basically the simple binary format makes the assumption that calibration > corrections have already been performed prior to generating the file. My > understanding is that this is indeed what the "calibrate data" option is > doing, but you'd have to confirm with EGI. > > Joe > > > > -------------------------------------------------------------------------------- > > On Sep 6, 2012, at 1:01 PM, Matt Mollison wrote: > > Joe, > > A few related questions: > > Does using the "calibrate data" option when exporting to raw (simple > binary) correct for gain? Or is there a different solution/recommendation? > Does exporting to MFF (Net Station 4.5.x only) or EGIS have this issue? I > tend to use EGIS (faster to read than raw) and have no recollection of > seeing unusually large voltages. > > Thanks, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > > On Wed, Sep 5, 2012 at 7:17 PM, Joseph Dien wrote: > >> The Simple Binary (.raw) files don't get corrected for gain when imported >> (I helped write them). I've experienced occasional unpredictable bugs with >> NetStation export routines where the files are generated with amplitudes >> many times too large, even with text format files. It's a bit >> disconcerting to say the least. I could take a look at your files if you'd >> like confirmation. >> >> Joe >> >> On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis >> wrote: >> >> Hi Daria, >> >> Also, did you try looking at your raw data (so before the ERPs are made) >> in FieldTrip and in Net Station? So open your .raw data in NetStation. You >> can just look at a random participant's data, and check if the scale is the >> same. I'm pretty sure no amplification takes place when reading in the data >> into FieldTrip, this check can confirm that. Hope this helps, and let us >> know what you find. >> >> Cheers, >> Ingrid >> >> >> On 9/3/2012 1:35 PM, Robert Oostenveld wrote: >> >> Hi Daria, >> >> There might indeed be an incompatibility in the gain value applied to >> the data. >> >> If you are able to export the data using the EGI software in another >> format (e.g. EDF), you could read them both into FieldTrip and compare the >> timecourse aplitudes to check whether they are different. In case they are, >> I suggest to involve EGI support. They are aware of the FieldTrip reading >> functions and will know much more about the internals of their various file >> formats. >> >> best regards >> Robert >> >> >> >> >> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: >> >> Dear Fieldtrippers, >> >> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip >> toolbox. >> The ERPs look perfect. >> The 'only' problem is, that my signals look to strong. >> It looks like if I get amplitutes (average) until 70 µV. >> I think it must be an intern amplifier for the signals. >> >> Does anyone know this problem with EGI-data? >> >> Or does anyone know, where I can see the amplifier? >> >> >> >> Greetings, >> Daria _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> _______________________________________________ >> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -- >> Ingrid Nieuwenhuis PhD >> Postdoctoral Fellow >> Sleep and Neuroimaging Laboratory >> Department of Psychology >> University of California, Berkeley >> California 94720-1650 >> Tolman Hall, room 5305 >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, >> Senior Research Scientist >> University of Maryland >> >> E-mail: jdien07 at mac.com >> Phone: 301-226-8848 >> Fax: 301-226-8811 >> http://joedien.com// >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > > > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joscha.schmiedt at esi-frankfurt.de Thu Sep 13 09:46:19 2012 From: joscha.schmiedt at esi-frankfurt.de (Schmiedt, Joscha) Date: Thu, 13 Sep 2012 07:46:19 +0000 Subject: [FieldTrip] Verbosity of fieldtrip functions Message-ID: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> Hi, I was wondering whether there is any option to suppress the printed output of a fieldtrip function or whether there are any plans for implementing a cfg.verbose option. Whenever I'm running some kind of loop I'd be glad to be able to use my own progress feedback without interruption from all the involved functions. Best, Joscha --------------------------- Joscha Schmiedt, MS 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 411 -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu Sep 13 10:03:19 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 13 Sep 2012 10:03:19 +0200 Subject: [FieldTrip] Verbosity of fieldtrip functions In-Reply-To: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> References: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> Message-ID: Hi Joscha, At the moment, we are thinking about implementing a generic logging mechanism in FieldTrip. Such a mechanism would allow you to specify the level of feedback you desire on the console, and also allow people to conveniently store log files for e.g. posting on this list for debugging. But given that (1) our thinking about this is still in its early stages, and (2) it requires a replace of all fprintf() statements in the entire codebase, it could be a while before this is fully implemented. But, to repeat, this is something we plan to do in the (near) future. Best, Eelke On 13 September 2012 09:46, Schmiedt, Joscha wrote: > Hi, > > I was wondering whether there is any option to suppress the printed output > of a fieldtrip function or whether there are any plans for implementing a > cfg.verbose option. Whenever I'm running some kind of loop I'd be glad to be > able to use my own progress feedback without interruption from all the > involved functions. > > Best, > Joscha > > > --------------------------- > Joscha Schmiedt, MS > 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 411 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From eelke.spaak at donders.ru.nl Thu Sep 13 10:03:19 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 13 Sep 2012 10:03:19 +0200 Subject: [FieldTrip] Verbosity of fieldtrip functions In-Reply-To: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> References: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> Message-ID: Hi Joscha, At the moment, we are thinking about implementing a generic logging mechanism in FieldTrip. Such a mechanism would allow you to specify the level of feedback you desire on the console, and also allow people to conveniently store log files for e.g. posting on this list for debugging. But given that (1) our thinking about this is still in its early stages, and (2) it requires a replace of all fprintf() statements in the entire codebase, it could be a while before this is fully implemented. But, to repeat, this is something we plan to do in the (near) future. Best, Eelke On 13 September 2012 09:46, Schmiedt, Joscha wrote: > Hi, > > I was wondering whether there is any option to suppress the printed output > of a fieldtrip function or whether there are any plans for implementing a > cfg.verbose option. Whenever I'm running some kind of loop I'd be glad to be > able to use my own progress feedback without interruption from all the > involved functions. > > Best, > Joscha > > > --------------------------- > Joscha Schmiedt, MS > 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 411 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From g.piantoni at nin.knaw.nl Thu Sep 13 10:28:31 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Thu, 13 Sep 2012 10:28:31 +0200 Subject: [FieldTrip] Verbosity of fieldtrip functions In-Reply-To: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> References: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> Message-ID: Hi Joscha, A quick and dirty solution is evalc: [~, data] = evalc('yourfunction(cfg)'); Cheers, Gio On Thu, Sep 13, 2012 at 9:46 AM, Schmiedt, Joscha wrote: > Hi, > > I was wondering whether there is any option to suppress the printed output > of a fieldtrip function or whether there are any plans for implementing a > cfg.verbose option. Whenever I'm running some kind of loop I'd be glad to be > able to use my own progress feedback without interruption from all the > involved functions. > > Best, > Joscha > > > --------------------------- > Joscha Schmiedt, MS > 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 411 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From smoratti at psi.ucm.es Thu Sep 13 10:36:05 2012 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Thu, 13 Sep 2012 10:36:05 +0200 Subject: [FieldTrip] Verbosity of fieldtrip functions In-Reply-To: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> References: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> Message-ID: <2EF4BF72-E8CE-4134-9DEB-7657B034C167@psi.ucm.es> Hi Joscha, Sometimes you can suppress some outputs with cfg.feedback = 'no'; Best, Stephan El 13/09/2012, a las 09:46, Schmiedt, Joscha escribió: > Hi, > > I was wondering whether there is any option to suppress the printed output of a fieldtrip function or whether there are any plans for implementing a cfg.verbose option. Whenever I'm running some kind of loop I'd be glad to be able to use my own progress feedback without interruption from all the involved functions. > > Best, > Joscha > > > --------------------------- > Joscha Schmiedt, MS > 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 411 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Thu Sep 13 10:36:05 2012 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Thu, 13 Sep 2012 10:36:05 +0200 Subject: [FieldTrip] Verbosity of fieldtrip functions In-Reply-To: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> References: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> Message-ID: <2EF4BF72-E8CE-4134-9DEB-7657B034C167@psi.ucm.es> Hi Joscha, Sometimes you can suppress some outputs with cfg.feedback = 'no'; Best, Stephan El 13/09/2012, a las 09:46, Schmiedt, Joscha escribió: > Hi, > > I was wondering whether there is any option to suppress the printed output of a fieldtrip function or whether there are any plans for implementing a cfg.verbose option. Whenever I'm running some kind of loop I'd be glad to be able to use my own progress feedback without interruption from all the involved functions. > > Best, > Joscha > > > --------------------------- > Joscha Schmiedt, MS > 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 411 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Thu Sep 13 10:55:55 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Thu, 13 Sep 2012 11:55:55 +0300 Subject: [FieldTrip] Making your own trialfun Message-ID: Hello, I tried to run the example in the following page: http://fieldtrip.fcdonders.nl/example/making_your_own_trialfun_for_conditional_trial_definition I did the required modifications so it can be run using biosemi system. But I don't know what to put instead of the variable "trigger" in the following statement: for j = 1:(length(trigger)-1) Could you help me Best, -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu Sep 13 11:02:32 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 13 Sep 2012 11:02:32 +0200 Subject: [FieldTrip] Making your own trialfun In-Reply-To: References: Message-ID: Hi Hamza, This is a bug in the example code; apologies. The "trigger" variable here actually refers to "value", so the vector of trigger values, assigned a few lines earlier. I will update the wiki. Best, Eelke On 13 September 2012 10:55, Hamza Fawzi Altakroury (Student) wrote: > Hello, > > I tried to run the example in the following page: > http://fieldtrip.fcdonders.nl/example/making_your_own_trialfun_for_conditional_trial_definition > > I did the required modifications so it can be run using biosemi system. > > But I don't know what to put instead of the variable "trigger" in the > following statement: > > for j = 1:(length(trigger)-1) > > > Could you help me > > Best, > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From eelke.spaak at donders.ru.nl Thu Sep 13 11:02:32 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 13 Sep 2012 11:02:32 +0200 Subject: [FieldTrip] Making your own trialfun In-Reply-To: References: Message-ID: Hi Hamza, This is a bug in the example code; apologies. The "trigger" variable here actually refers to "value", so the vector of trigger values, assigned a few lines earlier. I will update the wiki. Best, Eelke On 13 September 2012 10:55, Hamza Fawzi Altakroury (Student) wrote: > Hello, > > I tried to run the example in the following page: > http://fieldtrip.fcdonders.nl/example/making_your_own_trialfun_for_conditional_trial_definition > > I did the required modifications so it can be run using biosemi system. > > But I don't know what to put instead of the variable "trigger" in the > following statement: > > for j = 1:(length(trigger)-1) > > > Could you help me > > Best, > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From a.stolk at fcdonders.ru.nl Thu Sep 13 11:05:20 2012 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Thu, 13 Sep 2012 11:05:20 +0200 (CEST) Subject: [FieldTrip] realtime buffer does not exit In-Reply-To: <86D86365C4E767468A79EB52DFBFB46F0510F73C@exmbx2010-8.campus.MCGILL.CA> Message-ID: <3342976.328678.1347527120171.JavaMail.root@sculptor.zimbra.ru.nl> Hi Elizabeth, Could you try and start the buffer from outside matlab using 'demo_buffer.exe' (to be found in the 'realtime/bin/win32' directory)? This application may operate smoother than when starting the buffer from a single matlab thread. Best, Arjen ----- Oorspronkelijk bericht ----- > Van: "Elizabeth Anne Bock, Ms" > Aan: fieldtrip at science.ru.nl > Verzonden: Woensdag 12 september 2012 20:32:39 > Onderwerp: [FieldTrip] realtime buffer does not exit > I am using the realtime buffer and I have found I cannot exit the > buffer within the Matlab command window. I am forced to exit Matlab > or, more often, must kill the process manually from the windows task > manager. I am using Windows XP to host the buffer and Linux to run > acqftx. Here is what I am seeing: > > >> buffer('tcpserver', 'exit', ft_host, ft_port) > In main: requesting cancelation of tcpserver thread > > >> buffer('tcpserver', 'init', ft_host, ft_port) > ??? Error using ==> buffer > thread is already running > > Any suggestions? > Thanks, > Elizabeth > > > ------------------------------------------------------------------------------------------ > > Elizabeth Bock / MEG System Engineer > > McConnell Brain Imaging Centre / Montreal Neurological Institute > > McGill University / 3801 University St. / Montreal, QC H3A 2B4 > > > > MEG Lab: 514.398.6056 > > Mobile: 514.718.6342 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From hamzaf at sabanciuniv.edu Thu Sep 13 11:13:20 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Thu, 13 Sep 2012 12:13:20 +0300 Subject: [FieldTrip] Making your own trialfun In-Reply-To: References: Message-ID: Thank you Eelke, it works now. Best, Hamza On Thu, Sep 13, 2012 at 12:02 PM, Eelke Spaak wrote: > Hi Hamza, > > This is a bug in the example code; apologies. The "trigger" variable > here actually refers to "value", so the vector of trigger values, > assigned a few lines earlier. > > I will update the wiki. > > Best, > Eelke > > On 13 September 2012 10:55, Hamza Fawzi Altakroury (Student) > wrote: > > Hello, > > > > I tried to run the example in the following page: > > > http://fieldtrip.fcdonders.nl/example/making_your_own_trialfun_for_conditional_trial_definition > > > > I did the required modifications so it can be run using biosemi system. > > > > But I don't know what to put instead of the variable "trigger" in the > > following statement: > > > > for j = 1:(length(trigger)-1) > > > > > > Could you help me > > > > Best, > > > > -- > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabancı University > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Thu Sep 13 11:19:37 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Thu, 13 Sep 2012 12:19:37 +0300 Subject: [FieldTrip] ft_realtime_selectiveaverage Message-ID: Hello, I am tried to run the ft_realtime_selectiveaverage function but I got the following error: (note: the error appears after showing a plot with title: condition 255, ntrials = 1.) Could you tell me what is the problem. (exactly what does "connet read data before the begin of the file"). Best, ??? Error using ==> ft_read_data at 243 cannot read data before the begin of the file Error in ==> ft_realtime_selectiveaverage at 94 dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', chanindx, 'checkboundary', false); Error in ==> online1 at 48 ft_realtime_selectiveaverage(cfg) Statements: cfg = []; cfg.channel = {'A1'}; cfg.dataset = 'buffer://localhost:1972'; %cfg.trialfun = 'myfun'; cfg.trialdef.eventtype = 'stimulus'; % By placing '?' we can see the eventtype that we have. cfg.trialdef.eventvalue = 255; cfg.trialdef.pre = 0; cfg.trialdef.post = 1.0; cfg = ft_definetrial(cfg); ft_realtime_selectiveaverage(cfg) -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Sep 13 12:19:26 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 13 Sep 2012 05:19:26 -0500 Subject: [FieldTrip] Verbosity of fieldtrip functions In-Reply-To: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> References: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> Message-ID: <7638A242-2EF9-46AF-AB27-9448413A153E@donders.ru.nl> Hi Joscha There is indeed such a plan, see http://bugzilla.fcdonders.nl/show_bug.cgi?id=1686. If you want, you can provide your comments or ideas there. best Robert On 13 Sep 2012, at 2:46, Schmiedt, Joscha wrote: > Hi, > > I was wondering whether there is any option to suppress the printed output of a fieldtrip function or whether there are any plans for implementing a cfg.verbose option. Whenever I'm running some kind of loop I'd be glad to be able to use my own progress feedback without interruption from all the involved functions. > > Best, > Joscha > > > --------------------------- > Joscha Schmiedt, MS > 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 411 > > _______________________________________________ > 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 Duncan.Astle at mrc-cbu.cam.ac.uk Thu Sep 13 12:46:49 2012 From: Duncan.Astle at mrc-cbu.cam.ac.uk (Duncan Astle) Date: Thu, 13 Sep 2012 10:46:49 +0000 Subject: [FieldTrip] Problem with clustering across electrode neighbours Message-ID: Dear Fieldtrippers, I am rather new to this, but am attempting to do some cluster stats on my ERP sensor level data. It is working well, and I can cluster across time, but I can't get it to cluster across electrode locations. I think it is because of a mistake that I am making in my 'neighbours' file, although it looks fine when I inspect it. This is the error message that I get: ??? Cell contents reference from a non-cell array object. Error in ==> clusterstat>makechanneighbstructmat at 520 [seld] = match_str(cfg.channel, cfg.neighbours{chan}.label); Error in ==> clusterstat at 60 channeighbstructmat = makechanneighbstructmat(cfg); Error in ==> statistics_montecarlo at 322 [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); Error in ==> statistics_wrapper at 285 [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); Error in ==> ft_timelockstatistics at 119 [stat, cfg] = statistics_wrapper(cfg, varargin{:}); Can anyone spot what I am doing wrong? This is how I make my neighbour file: cfg = []; cfg.layout = 'EEG1010.lay'; % try 'distance' as well cfg.feedback = 'yes'; % show a neighbour plot cfg.method = 'template'; cfg.neighbourdist = 'number'; cfg.template = 'EEG1010_neighb.mat' cfg.channel = 'all' cfg.feedback = 'yes'; neighbours = ft_prepare_neighbours(cfg, Load5Hard); % define neighbouring channels This is how I then try the stats: cfg = []; cfg.channel = 'all'; cfg.latency = [0.1 1.3]; cfg.avgovertime = 'no'; cfg.avgoverchannel = 'no'; cfg.parameter = 'individual'; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT' cfg.alpha = 0.05; cfg.correctm = 'cluster'; cfg.correcttail = 'prob'; cfg.numrandomization = 1000; cfg.feedback = 'yes'; % show a neighbour plot cfg.neighbours = neighbours; %cfg.minnbchan = 2; cfg.clusterstatistic = 'maxsum'; cfg.clusterthreshold = 'nonparametric'; cfg.clusteralpha = 0.01; cfg.clustercritval = 0.06; % cfg.clustertail = 0; cfg.tail = 0; Nsub = 19; cfg.design(1,1:2*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub)]; cfg.design(2,1:2*Nsub) = [1:Nsub 1:Nsub]; cfg.ivar = 1; % the 1st row in cfg.design contains the independent variable cfg.uvar = 2; % the 2nd row in cfg.design contains the subject number [stat] = ft_timelockstatistics(cfg, Load3Hard, Load3Easy) Any suggestions very gratefully received. Thanks, Duncan ________________________________________________ Dr. Duncan Astle, Programme Leader Track, British Academy Research Fellow, MRC Cognition and Brain Sciences Unit, Chaucer Road, Cambridge. Duncan.Astle at mrc-cbu.cam.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu Sep 13 12:55:34 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 13 Sep 2012 12:55:34 +0200 Subject: [FieldTrip] Problem with clustering across electrode neighbours In-Reply-To: References: Message-ID: Dear Duncan, Jörn can correct me if I'm wrong, but I think it is sufficient to write cfg = []; cfg.method = 'template'; cfg.template = 'EEG1010_neighb.mat'; neighbours = ft_prepare_neighbours(cfg); if you want to use the neighbourhood structure template. So, specifying all those other options might have confused ft_prepare_neighbours. Best, Eelke On 13 September 2012 12:46, Duncan Astle wrote: > Dear Fieldtrippers, > > > > I am rather new to this, but am attempting to do some cluster stats on my > ERP sensor level data. It is working well, and I can cluster across time, > but I can’t get it to cluster across electrode locations. I think it is > because of a mistake that I am making in my ‘neighbours’ file, although it > looks fine when I inspect it. This is the error message that I get: > > > > ??? Cell contents reference from a non-cell array object. > > > > Error in ==> clusterstat>makechanneighbstructmat at 520 > > [seld] = match_str(cfg.channel, cfg.neighbours{chan}.label); > > > > Error in ==> clusterstat at 60 > > channeighbstructmat = makechanneighbstructmat(cfg); > > > > Error in ==> statistics_montecarlo at 322 > > [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); > > > > Error in ==> statistics_wrapper at 285 > > [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); > > > > Error in ==> ft_timelockstatistics at 119 > > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > > > Can anyone spot what I am doing wrong? > > > > This is how I make my neighbour file: > > > > cfg = []; > > cfg.layout = 'EEG1010.lay'; % try 'distance' as well > > cfg.feedback = 'yes'; % show a neighbour plot > > cfg.method = 'template'; > > cfg.neighbourdist = 'number'; > > cfg.template = 'EEG1010_neighb.mat' > > cfg.channel = 'all' > > cfg.feedback = 'yes'; > > neighbours = ft_prepare_neighbours(cfg, Load5Hard); % define > neighbouring channels > > > > This is how I then try the stats: > > > > cfg = []; > > cfg.channel = 'all'; > > cfg.latency = [0.1 1.3]; > > cfg.avgovertime = 'no'; > > cfg.avgoverchannel = 'no'; > > cfg.parameter = 'individual'; > > cfg.method = 'montecarlo'; > > cfg.statistic = 'depsamplesT' > > cfg.alpha = 0.05; > > cfg.correctm = 'cluster'; > > cfg.correcttail = 'prob'; > > cfg.numrandomization = 1000; > > cfg.feedback = 'yes'; % show a neighbour plot > > cfg.neighbours = neighbours; > > %cfg.minnbchan = 2; > > cfg.clusterstatistic = 'maxsum'; > > cfg.clusterthreshold = 'nonparametric'; > > cfg.clusteralpha = 0.01; > > cfg.clustercritval = 0.06; > > % cfg.clustertail = 0; > > cfg.tail = 0; > > Nsub = 19; > > cfg.design(1,1:2*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub)]; > > cfg.design(2,1:2*Nsub) = [1:Nsub 1:Nsub]; > > cfg.ivar = 1; % the 1st row in cfg.design contains the > independent variable > > cfg.uvar = 2; % the 2nd row in cfg.design contains the > subject number > > > > > > [stat] = ft_timelockstatistics(cfg, Load3Hard, Load3Easy) > > > > Any suggestions very gratefully received. > > > > Thanks, > > Duncan > > ________________________________________________ > > Dr. Duncan Astle, > > Programme Leader Track, > > British Academy Research Fellow, > > MRC Cognition and Brain Sciences Unit, > > Chaucer Road, > > Cambridge. > > Duncan.Astle at mrc-cbu.cam.ac.uk > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Thu Sep 13 13:11:15 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 13 Sep 2012 13:11:15 +0200 Subject: [FieldTrip] Problem with clustering across electrode neighbours In-Reply-To: References: Message-ID: <5051BF53.5030606@donders.ru.nl> Hey Duncan, it looks pretty much like you are using an old FieldTrip version with a new neighbourhood-structure. Could you check the with the most recent version again? Some months (about a year?) ago we changed the neighbour definition from cell arrays to structure arrays, so any attempt to access cfg.neighbours{i} will fail, cause it has to be cfg.neighbours(i) instead. But as I already said, this has been changed quite some time back in the past :) Essentially, your code is fine, but some note that cfg.neighbourdist should be a scalar, not the string 'number', but only if cfg.method='distance'. If you choose cfg.method = 'template' then cfg.neighbourdist is not used, cause a template is loaded. Best, Jörn On 9/13/2012 12:46 PM, Duncan Astle wrote: > > Dear Fieldtrippers, > > I am rather new to this, but am attempting to do some cluster stats on > my ERP sensor level data. It is working well, and I can cluster across > time, but I can't get it to cluster across electrode locations. I > think it is because of a mistake that I am making in my 'neighbours' > file, although it looks fine when I inspect it. This is the error > message that I get: > > ??? Cell contents reference from a non-cell array object. > > Error in ==> clusterstat>makechanneighbstructmat at 520 > > [seld] = match_str(cfg.channel, cfg.neighbours{chan}.label); > > Error in ==> clusterstat at 60 > > channeighbstructmat = makechanneighbstructmat(cfg); > > Error in ==> statistics_montecarlo at 322 > > [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); > > Error in ==> statistics_wrapper at 285 > > [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); > > Error in ==> ft_timelockstatistics at 119 > > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > Can anyone spot what I am doing wrong? > > This is how I make my neighbour file: > > cfg = []; > > cfg.layout = 'EEG1010.lay'; % try 'distance' as well > > cfg.feedback = 'yes'; % show a neighbour plot > > cfg.method = 'template'; > > cfg.neighbourdist = 'number'; > > cfg.template = 'EEG1010_neighb.mat' > > cfg.channel = 'all' > > cfg.feedback = 'yes'; > > neighbours = ft_prepare_neighbours(cfg, Load5Hard); % define > neighbouring channels > > This is how I then try the stats: > > cfg = []; > > cfg.channel = 'all'; > > cfg.latency = [0.1 1.3]; > > cfg.avgovertime = 'no'; > > cfg.avgoverchannel = 'no'; > > cfg.parameter = 'individual'; > > cfg.method = 'montecarlo'; > > cfg.statistic = 'depsamplesT' > > cfg.alpha = 0.05; > > cfg.correctm = 'cluster'; > > cfg.correcttail = 'prob'; > > cfg.numrandomization = 1000; > > cfg.feedback = 'yes'; % show a neighbour plot > > cfg.neighbours = neighbours; > > %cfg.minnbchan = 2; > > cfg.clusterstatistic = 'maxsum'; > > cfg.clusterthreshold = 'nonparametric'; > > cfg.clusteralpha = 0.01; > > cfg.clustercritval = 0.06; > > % cfg.clustertail = 0; > > cfg.tail = 0; > > Nsub = 19; > > cfg.design(1,1:2*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub)]; > > cfg.design(2,1:2*Nsub) = [1:Nsub 1:Nsub]; > > cfg.ivar = 1; % the 1st row in cfg.design contains > the independent variable > > cfg.uvar = 2; % the 2nd row in cfg.design contains > the subject number > > [stat] = ft_timelockstatistics(cfg, Load3Hard, Load3Easy) > > Any suggestions very gratefully received. > > Thanks, > > Duncan > > ________________________________________________ > > Dr. Duncan Astle, > > Programme Leader Track, > > British Academy Research Fellow, > > MRC Cognition and Brain Sciences Unit, > > Chaucer Road, > > Cambridge. > > Duncan.Astle at mrc-cbu.cam.ac.uk > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From elizabeth.bock at mcgill.ca Thu Sep 13 14:51:42 2012 From: elizabeth.bock at mcgill.ca (Elizabeth Anne Bock, Ms) Date: Thu, 13 Sep 2012 12:51:42 +0000 Subject: [FieldTrip] realtime buffer does not exit In-Reply-To: <3342976.328678.1347527120171.JavaMail.root@sculptor.zimbra.ru.nl> References: <86D86365C4E767468A79EB52DFBFB46F0510F73C@exmbx2010-8.campus.MCGILL.CA>, <3342976.328678.1347527120171.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <86D86365C4E767468A79EB52DFBFB46F05110836@exmbx2010-8.campus.MCGILL.CA> Thanks for the feedback. However, I would like to read the header and the data from the buffer into Matlab (I am doing realtime processing of the data). Is this possible to run the buffer in the windows environment and then read from it in Matlab? hdr = buffer('get_hdr', [], ft_host, ft_port) ??? Error using ==> buffer ERROR: failed to create socket (1) Thanks, Beth ------------------------------------------------------------------------------------------ Elizabeth Bock / MEG System Engineer McConnell Brain Imaging Centre / Montreal Neurological Institute McGill University / 3801 University St. / Montreal, QC H3A 2B4 MEG Lab: 514.398.6056 Mobile: 514.718.6342 ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Stolk, A. [a.stolk at fcdonders.ru.nl] Sent: Thursday, September 13, 2012 5:05 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] realtime buffer does not exit Hi Elizabeth, Could you try and start the buffer from outside matlab using 'demo_buffer.exe' (to be found in the 'realtime/bin/win32' directory)? This application may operate smoother than when starting the buffer from a single matlab thread. Best, Arjen ----- Oorspronkelijk bericht ----- > Van: "Elizabeth Anne Bock, Ms" > Aan: fieldtrip at science.ru.nl > Verzonden: Woensdag 12 september 2012 20:32:39 > Onderwerp: [FieldTrip] realtime buffer does not exit > I am using the realtime buffer and I have found I cannot exit the > buffer within the Matlab command window. I am forced to exit Matlab > or, more often, must kill the process manually from the windows task > manager. I am using Windows XP to host the buffer and Linux to run > acqftx. Here is what I am seeing: > > >> buffer('tcpserver', 'exit', ft_host, ft_port) > In main: requesting cancelation of tcpserver thread > > >> buffer('tcpserver', 'init', ft_host, ft_port) > ??? Error using ==> buffer > thread is already running > > Any suggestions? > Thanks, > Elizabeth > > > ------------------------------------------------------------------------------------------ > > Elizabeth Bock / MEG System Engineer > > McConnell Brain Imaging Centre / Montreal Neurological Institute > > McGill University / 3801 University St. / Montreal, QC H3A 2B4 > > > > MEG Lab: 514.398.6056 > > Mobile: 514.718.6342 > > _______________________________________________ > 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 wallisgj at gmail.com Thu Sep 13 15:26:55 2012 From: wallisgj at gmail.com (George Wallis) Date: Thu, 13 Sep 2012 14:26:55 +0100 Subject: [FieldTrip] Dimension mismatch in .grad struct for neuromag data Message-ID: Dear fieldtrippers, With neuromag306 data, after the old style of .grad gets converted to the new style, the field have dimensions as follows: data.grad: ans = unit: 'mm' label: {306x1 cell} coilori: [510x3 double] coilpos: [510x3 double] lab: {102x3 cell} chanpos: [102x3 double] chanori: [102x3 double] balance: [1x1 struct] Because there are three sensors in each location, there are 1/3 as many elements in chanpos as in coilpos. However, in ft_combineplanar, where the function remakes the .grad field to match the new list of channels (where the gradiometers have been combined), is uses a list of channel indices 'sel' which is concatenated vertically: sel = [sel_comb(:);sel_other(:)]; ...and indexes into newgrad.chanpos. As above, newgrad.chanpos is 102x3, but sel is 204x1: 102 combined gradiometers ('sel_comb') plus 102 magnetometers ('sel_other'). There is therefore a dimension mismatch, because the different channel types are 'overlaid' in 'chanpos' but not in 'sel'. Have I set up my .chanpos, .chanori incorrectly? Thanks for any tips, George -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mollison at gmail.com Thu Sep 13 16:50:58 2012 From: matt.mollison at gmail.com (Matt Mollison) Date: Thu, 13 Sep 2012 08:50:58 -0600 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> <77D46473-6907-4AC1-96E1-F51756C119C0@mac.com> <3B494ED9-B6C3-46A3-840C-8EEEDAA85E5E@mac.com> Message-ID: Daria, I do not know any calibration function for raw files that were exported without calibration, but maybe it is a simple formula? You might want to contact EGI. Let us know if you find anything out. Best, Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ On Thu, Sep 13, 2012 at 1:21 AM, Daria Laptinskaya < daria.laptinskaya at googlemail.com> wrote: > Yes, it works fine now-thank you!!! > > @Matt: Do you know a calibration-function for existing raw-files? > > > > Best, > > Daria > > > 2012/9/10 Joseph Dien > >> Hey Daria, >> glad you were able to get it worked out! Thank Matt for his reminder >> (below) about the calibration option. >> >> Cheers! >> >> Joe >> >> >> Hi Joe, >> >> >> I didn’t know that there is a function like this. >> >> The most of my colleagues use the RAW.-files they get from the >> file-exporter without problems. >> >> Not even NetStation-support could give me an answer. >> >> So I thought, it must be a problem between NetStation and fieldtrip. >> >> Because of your tip I opened an original datafile and tried to save a >> copy of the file. >> >> Doing so NetStation offers a possibility to ‘convert to microvolts’ and >> create a .ses –datafile. >> >> The .raw-files I get this way have microvolt as unit. >> >> I compared the signals I get this way with the signals I get by using the >> formula (5000 mircovolts / (2^16 bits) I send you. They are almost the >> same-that’s great!!! >> >> It seems to work now. >> >> Thank you very much!!! You were a great help!!! >> >> >> Cheers, >> >> Daria >> >> On Sep 6, 2012, at 9:07 PM, Joseph Dien wrote: >> >> I don't recall ever seeing this problem with EGIS files, which is one of >> the reasons I prefer using this file format despite EGI's preference for >> newer Simple Binary format, but it's an unpredictable bug so I can't say it >> can't happen. I also can't say which versions of NetStation it happens >> with. It may have been fixed. I'm still trying to test out MFF so can't >> say anything about it. I had problems with the FieldTrip code for reading >> segmented MFF files (which is what I'm interested in). I also had trouble >> with writing them out from NetStation so I don't have a valid segmented >> test file and I'm still waiting for EGI to make one available so I can work >> them out. The simple binary file format (this is the original name for the >> EGI .raw file format and I prefer to use it over ".raw" as the BESA .raw >> file format is actually the .egis file format so it can get confusing) >> doesn't actually have separate calibration information for the channels >> (unlike EGIS), just one single gain value and no zeros values. So >> basically the simple binary format makes the assumption that calibration >> corrections have already been performed prior to generating the file. My >> understanding is that this is indeed what the "calibrate data" option is >> doing, but you'd have to confirm with EGI. >> >> Joe >> >> >> >> -------------------------------------------------------------------------------- >> >> On Sep 6, 2012, at 1:01 PM, Matt Mollison >> wrote: >> >> Joe, >> >> A few related questions: >> >> Does using the "calibrate data" option when exporting to raw (simple >> binary) correct for gain? Or is there a different solution/recommendation? >> Does exporting to MFF (Net Station 4.5.x only) or EGIS have this issue? I >> tend to use EGIS (faster to read than raw) and have no recollection of >> seeing unusually large voltages. >> >> Thanks, >> Matt >> >> On Wed, Sep 5, 2012 at 7:17 PM, Joseph Dien wrote: >> >>> The Simple Binary (.raw) files don't get corrected for gain when >>> imported (I helped write them). I've experienced occasional unpredictable >>> bugs with NetStation export routines where the files are generated with >>> amplitudes many times too large, even with text format files. It's a bit >>> disconcerting to say the least. I could take a look at your files if you'd >>> like confirmation. >>> >>> Joe >>> >>> On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis < >>> inieuwenhuis at BERKELEY.EDU> wrote: >>> >>> Hi Daria, >>> >>> Also, did you try looking at your raw data (so before the ERPs are made) >>> in FieldTrip and in Net Station? So open your .raw data in NetStation. You >>> can just look at a random participant's data, and check if the scale is the >>> same. I'm pretty sure no amplification takes place when reading in the data >>> into FieldTrip, this check can confirm that. Hope this helps, and let us >>> know what you find. >>> >>> Cheers, >>> Ingrid >>> >>> >>> On 9/3/2012 1:35 PM, Robert Oostenveld wrote: >>> >>> Hi Daria, >>> >>> There might indeed be an incompatibility in the gain value applied to >>> the data. >>> >>> If you are able to export the data using the EGI software in another >>> format (e.g. EDF), you could read them both into FieldTrip and compare the >>> timecourse aplitudes to check whether they are different. In case they are, >>> I suggest to involve EGI support. They are aware of the FieldTrip reading >>> functions and will know much more about the internals of their various file >>> formats. >>> >>> best regards >>> Robert >>> >>> >>> >>> >>> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: >>> >>> Dear Fieldtrippers, >>> >>> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip >>> toolbox. >>> The ERPs look perfect. >>> The 'only' problem is, that my signals look to strong. >>> It looks like if I get amplitutes (average) until 70 µV. >>> I think it must be an intern amplifier for the signals. >>> >>> Does anyone know this problem with EGI-data? >>> >>> Or does anyone know, where I can see the amplifier? >>> >>> >>> >>> Greetings, >>> Daria _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> -- >>> Ingrid Nieuwenhuis PhD >>> Postdoctoral Fellow >>> Sleep and Neuroimaging Laboratory >>> Department of Psychology >>> University of California, Berkeley >>> California 94720-1650 >>> Tolman Hall, room 5305 >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> Joseph Dien, >>> Senior Research Scientist >>> University of Maryland >>> >>> E-mail: jdien07 at mac.com >>> Phone: 301-226-8848 >>> Fax: 301-226-8811 >>> http://joedien.com// >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, >> Senior Research Scientist >> University of Maryland >> >> E-mail: jdien07 at mac.com >> Phone: 301-226-8848 >> Fax: 301-226-8811 >> http://joedien.com// >> >> >> >> >> >> >> >> >> >> >> >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, >> Senior Research Scientist >> University of Maryland >> >> E-mail: jdien07 at mac.com >> Phone: 301-226-8848 >> Fax: 301-226-8811 >> http://joedien.com// >> >> >> >> >> >> >> >> >> >> >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From daria.laptinskaya at googlemail.com Thu Sep 13 17:14:37 2012 From: daria.laptinskaya at googlemail.com (Daria Laptinskaya) Date: Thu, 13 Sep 2012 17:14:37 +0200 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> <77D46473-6907-4AC1-96E1-F51756C119C0@mac.com> <3B494ED9-B6C3-46A3-840C-8EEEDAA85E5E@mac.com> Message-ID: There is a formula in the NetStation-manual: (5000 mircovolts / (2^16 bits). You can convert bits to microvolts by multiplicating all signals with the factor 0,076293945 in fieldtrip. This solution isn't perfect, because it doesn't consider gains. We asked EGI for an other formula, but didn't yet get an answer. I compare the two methods and for little N the gains don't make a great difference. Best, Daria 2012/9/13 Matt Mollison > Daria, > > I do not know any calibration function for raw files that were exported > without calibration, but maybe it is a simple formula? You might want to > contact EGI. Let us know if you find anything out. > > Best, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > > On Thu, Sep 13, 2012 at 1:21 AM, Daria Laptinskaya < > daria.laptinskaya at googlemail.com> wrote: > >> Yes, it works fine now-thank you!!! >> >> @Matt: Do you know a calibration-function for existing raw-files? >> >> >> >> Best, >> >> Daria >> >> >> 2012/9/10 Joseph Dien >> >>> Hey Daria, >>> glad you were able to get it worked out! Thank Matt for his reminder >>> (below) about the calibration option. >>> >>> Cheers! >>> >>> Joe >>> >>> >>> Hi Joe, >>> >>> >>> I didn’t know that there is a function like this. >>> >>> The most of my colleagues use the RAW.-files they get from the >>> file-exporter without problems. >>> >>> Not even NetStation-support could give me an answer. >>> >>> So I thought, it must be a problem between NetStation and fieldtrip. >>> >>> Because of your tip I opened an original datafile and tried to save a >>> copy of the file. >>> >>> Doing so NetStation offers a possibility to ‘convert to microvolts’ and >>> create a .ses –datafile. >>> >>> The .raw-files I get this way have microvolt as unit. >>> >>> I compared the signals I get this way with the signals I get by using >>> the formula (5000 mircovolts / (2^16 bits) I send you. They are almost the >>> same-that’s great!!! >>> >>> It seems to work now. >>> >>> Thank you very much!!! You were a great help!!! >>> >>> >>> Cheers, >>> >>> Daria >>> >>> On Sep 6, 2012, at 9:07 PM, Joseph Dien wrote: >>> >>> I don't recall ever seeing this problem with EGIS files, which is one of >>> the reasons I prefer using this file format despite EGI's preference for >>> newer Simple Binary format, but it's an unpredictable bug so I can't say it >>> can't happen. I also can't say which versions of NetStation it happens >>> with. It may have been fixed. I'm still trying to test out MFF so can't >>> say anything about it. I had problems with the FieldTrip code for reading >>> segmented MFF files (which is what I'm interested in). I also had trouble >>> with writing them out from NetStation so I don't have a valid segmented >>> test file and I'm still waiting for EGI to make one available so I can work >>> them out. The simple binary file format (this is the original name for the >>> EGI .raw file format and I prefer to use it over ".raw" as the BESA .raw >>> file format is actually the .egis file format so it can get confusing) >>> doesn't actually have separate calibration information for the channels >>> (unlike EGIS), just one single gain value and no zeros values. So >>> basically the simple binary format makes the assumption that calibration >>> corrections have already been performed prior to generating the file. My >>> understanding is that this is indeed what the "calibrate data" option is >>> doing, but you'd have to confirm with EGI. >>> >>> Joe >>> >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> On Sep 6, 2012, at 1:01 PM, Matt Mollison >>> wrote: >>> >>> Joe, >>> >>> A few related questions: >>> >>> Does using the "calibrate data" option when exporting to raw (simple >>> binary) correct for gain? Or is there a different solution/recommendation? >>> Does exporting to MFF (Net Station 4.5.x only) or EGIS have this issue? >>> I tend to use EGIS (faster to read than raw) and have no recollection of >>> seeing unusually large voltages. >>> >>> Thanks, >>> Matt >>> >>> On Wed, Sep 5, 2012 at 7:17 PM, Joseph Dien wrote: >>> >>>> The Simple Binary (.raw) files don't get corrected for gain when >>>> imported (I helped write them). I've experienced occasional unpredictable >>>> bugs with NetStation export routines where the files are generated with >>>> amplitudes many times too large, even with text format files. It's a bit >>>> disconcerting to say the least. I could take a look at your files if you'd >>>> like confirmation. >>>> >>>> Joe >>>> >>>> On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis < >>>> inieuwenhuis at BERKELEY.EDU> wrote: >>>> >>>> Hi Daria, >>>> >>>> Also, did you try looking at your raw data (so before the ERPs are >>>> made) in FieldTrip and in Net Station? So open your .raw data in >>>> NetStation. You can just look at a random participant's data, and check if >>>> the scale is the same. I'm pretty sure no amplification takes place when >>>> reading in the data into FieldTrip, this check can confirm that. Hope this >>>> helps, and let us know what you find. >>>> >>>> Cheers, >>>> Ingrid >>>> >>>> >>>> On 9/3/2012 1:35 PM, Robert Oostenveld wrote: >>>> >>>> Hi Daria, >>>> >>>> There might indeed be an incompatibility in the gain value applied >>>> to the data. >>>> >>>> If you are able to export the data using the EGI software in another >>>> format (e.g. EDF), you could read them both into FieldTrip and compare the >>>> timecourse aplitudes to check whether they are different. In case they are, >>>> I suggest to involve EGI support. They are aware of the FieldTrip reading >>>> functions and will know much more about the internals of their various file >>>> formats. >>>> >>>> best regards >>>> Robert >>>> >>>> >>>> >>>> >>>> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: >>>> >>>> Dear Fieldtrippers, >>>> >>>> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip >>>> toolbox. >>>> The ERPs look perfect. >>>> The 'only' problem is, that my signals look to strong. >>>> It looks like if I get amplitutes (average) until 70 µV. >>>> I think it must be an intern amplifier for the signals. >>>> >>>> Does anyone know this problem with EGI-data? >>>> >>>> Or does anyone know, where I can see the amplifier? >>>> >>>> >>>> >>>> Greetings, >>>> Daria _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> >>>> -- >>>> Ingrid Nieuwenhuis PhD >>>> Postdoctoral Fellow >>>> Sleep and Neuroimaging Laboratory >>>> Department of Psychology >>>> University of California, Berkeley >>>> California 94720-1650 >>>> Tolman Hall, room 5305 >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> >>>> >>>> >>>> -------------------------------------------------------------------------------- >>>> >>>> Joseph Dien, >>>> Senior Research Scientist >>>> University of Maryland >>>> >>>> E-mail: jdien07 at mac.com >>>> Phone: 301-226-8848 >>>> Fax: 301-226-8811 >>>> http://joedien.com// >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> Joseph Dien, >>> Senior Research Scientist >>> University of Maryland >>> >>> E-mail: jdien07 at mac.com >>> Phone: 301-226-8848 >>> Fax: 301-226-8811 >>> http://joedien.com// >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> Joseph Dien, >>> Senior Research Scientist >>> University of Maryland >>> >>> E-mail: jdien07 at mac.com >>> Phone: 301-226-8848 >>> Fax: 301-226-8811 >>> http://joedien.com// >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bherrmann at cbs.mpg.de Fri Sep 14 10:23:14 2012 From: bherrmann at cbs.mpg.de (=?utf-8?Q?Bj=C3=B6rn_Herrmann?=) Date: Fri, 14 Sep 2012 10:23:14 +0200 (CEST) Subject: [FieldTrip] How to impove dics realfilter solution In-Reply-To: <612757646.1088.1347610775726.JavaMail.root@zimbra> Message-ID: <736231433.1128.1347610993969.JavaMail.root@zimbra> Dear fieldtrip user, I am using the DICS beamformer to localize a 3Hz FFT power topographical distribution (using a neuromag system). The topographies are very clear auditory in single subjects, thus it shouldn't be a problem finding the "right" solution. When I use the beamformer to obtain complex-value spatial filters, the solution looks very good (using NAI). No problem here. However, using cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real values, the localization completely breaks down, sometimes even finding a strong peak in the opposite hemisphere than visible in the sensor topography (the head is centered in the sensor array). Does someone have a suggestion how to improve the solution using realfilter = 'yes'. I use the following settings. They are rather standard I guess. cfg = []; cfg.method = 'dics'; cfg.frequency = 3; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.keepfilter = 'yes'; cfg.dics.realfilter = 'yes'; cfg.dics.fixedori = 'no'; If someone has a suggestion, I would appreciate it. Thanks in advance, best, Björn From r.oostenveld at donders.ru.nl Fri Sep 14 11:25:54 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 14 Sep 2012 04:25:54 -0500 Subject: [FieldTrip] fieldtrip wiki website unstable In-Reply-To: References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> <77D46473-6907-4AC1-96E1-F51756C119C0@mac.com> <3B494ED9-B6C3-46A3-840C-8EEEDAA85E5E@mac.com> Message-ID: <8FD34ABA-CEDF-4E8C-B024-9F175E1CD573@donders.ru.nl> Dear FieldTrip users, As you may have noticed, we have some issues with the FieldTrip wiki. The underlying cause is that the file server hosting the webserver, bugzilla, svn and the ftp server is acting weird, causing temporary failures of the online services. Our ICT group is working on it. So if you notice that either the FieldTrip wiki or one of the related servers is not doing what you expect, please try again later. best regards Robert From b.reuderink at donders.ru.nl Fri Sep 14 12:21:52 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Fri, 14 Sep 2012 12:21:52 +0200 Subject: [FieldTrip] realtime buffer does not exit In-Reply-To: <86D86365C4E767468A79EB52DFBFB46F05110836@exmbx2010-8.campus.MCGILL.CA> References: <86D86365C4E767468A79EB52DFBFB46F0510F73C@exmbx2010-8.campus.MCGILL.CA>, <3342976.328678.1347527120171.JavaMail.root@sculptor.zimbra.ru.nl> <86D86365C4E767468A79EB52DFBFB46F05110836@exmbx2010-8.campus.MCGILL.CA> Message-ID: <81D26A77-1088-4A8A-89FF-AA9B199F0320@donders.ru.nl> Dear Elizabeth, It is indeed possible (perhaps preferable) to run the FieldTrip buffer outside of the MATLAB environment. Basically, the 'demo_buffer.exe' functions as a stand-alone server that holds the neuro data. Then, you would need a client, that reads from your acquisition hardware and writes new samples and events to the server. FieldTrip has programs for many different acquisition systems, see [1]. Your MATLAB program can then act as another client and read form the buffer. The advantage of this setup is that you can restart your MATLAB session without disrupting the FieldTrip real-time buffer. You can even run the serving buffer and your MATLAB code on different computers in you lab. Without additional details I can only guess why you got the error message you described. Perhaps the ft_host and ft_port are not set correctly? For ft_host you could try 'localhost' or '127.0.0.1', and for ft_port the default is 1972. These settings tell FieldTrip to connect to a buffer (=server) on the same computer. If you can't get it to work, please don't hesitate to ask. BTW, some background information on real-time signal processing with FieldTrip can be found on [2] — perhaps that is useful. Best regards, Boris Reuderink [1] http://fieldtrip.fcdonders.nl/development/realtime/implementation [2] http://fieldtrip.fcdonders.nl/development/realtime/buffer_overview -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl On 13 sep. 2012, at 14:51, "Elizabeth Anne Bock, Ms" wrote: > Thanks for the feedback. However, I would like to read the header and the data from the buffer into Matlab (I am doing realtime processing of the data). Is this possible to run the buffer in the windows environment and then read from it in Matlab? > > hdr = buffer('get_hdr', [], ft_host, ft_port) > ??? Error using ==> buffer > ERROR: failed to create socket (1) > > Thanks, > Beth > > ------------------------------------------------------------------------------------------ > > Elizabeth Bock / MEG System Engineer > > McConnell Brain Imaging Centre / Montreal Neurological Institute > > McGill University / 3801 University St. / Montreal, QC H3A 2B4 > > > > MEG Lab: 514.398.6056 > > Mobile: 514.718.6342 > > ________________________________________ > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Stolk, A. [a.stolk at fcdonders.ru.nl] > Sent: Thursday, September 13, 2012 5:05 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] realtime buffer does not exit > > Hi Elizabeth, > > Could you try and start the buffer from outside matlab using 'demo_buffer.exe' (to be found in the 'realtime/bin/win32' directory)? This application may operate smoother than when starting the buffer from a single matlab thread. > > Best, > Arjen > > ----- Oorspronkelijk bericht ----- >> Van: "Elizabeth Anne Bock, Ms" >> Aan: fieldtrip at science.ru.nl >> Verzonden: Woensdag 12 september 2012 20:32:39 >> Onderwerp: [FieldTrip] realtime buffer does not exit >> I am using the realtime buffer and I have found I cannot exit the >> buffer within the Matlab command window. I am forced to exit Matlab >> or, more often, must kill the process manually from the windows task >> manager. I am using Windows XP to host the buffer and Linux to run >> acqftx. Here is what I am seeing: >> >>>> buffer('tcpserver', 'exit', ft_host, ft_port) >> In main: requesting cancelation of tcpserver thread >> >>>> buffer('tcpserver', 'init', ft_host, ft_port) >> ??? Error using ==> buffer >> thread is already running >> >> Any suggestions? >> Thanks, >> Elizabeth >> >> >> ------------------------------------------------------------------------------------------ >> >> Elizabeth Bock / MEG System Engineer >> >> McConnell Brain Imaging Centre / Montreal Neurological Institute >> >> McGill University / 3801 University St. / Montreal, QC H3A 2B4 >> >> >> >> MEG Lab: 514.398.6056 >> >> Mobile: 514.718.6342 >> >> _______________________________________________ >> 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 andrea.brovelli at univ-amu.fr Fri Sep 14 12:27:59 2012 From: andrea.brovelli at univ-amu.fr (andrea brovelli) Date: Fri, 14 Sep 2012 12:27:59 +0200 Subject: [FieldTrip] Data prewhitening Message-ID: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> Dear all, I was wondering whether we can whiten the data using the cfg options in the ft_preprocessing function. Does anyone know ? Or does anyone have some code for prewhitening raw data ? Thanks a lot Andrea From jan.schoffelen at donders.ru.nl Fri Sep 14 12:41:41 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 14 Sep 2012 12:41:41 +0200 Subject: [FieldTrip] Data prewhitening In-Reply-To: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> References: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> Message-ID: Caro Andrea, I think you could achieve this with ft_componentanalysis (but have never tried it myself): try: cfg = []; cfg.method = 'fastica'; cfg.fastica.only = 'white'; data2 = ft_componentanalysis(cfg, data); the fastica toolbox is in fieldtrip/external/ Check out the documentation in fastica.m Ciao, JM On Sep 14, 2012, at 12:27 PM, andrea brovelli wrote: > Dear all, > > I was wondering whether we can whiten the data using the cfg options in the ft_preprocessing function. Does anyone know ? > > Or does anyone have some code for prewhitening raw data ? > > Thanks a lot > > Andrea > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.vandermeij at donders.ru.nl Fri Sep 14 13:03:32 2012 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Fri, 14 Sep 2012 13:03:32 +0200 Subject: [FieldTrip] Data prewhitening In-Reply-To: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> References: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> Message-ID: Hi Andrea, Are you referring to pre-whitening by removing the first parameter of an auto-regressive model, thereby removing most (if not all) of the 1/f shape in the spectrum? If so, this can be done by taking the first temporal derivative of the raw-data, effectively setting the first AR parameter to 0. This is implemented by setting cfg.derivative = 'yes' in preprocessing. I don't know of any good references for this trick though, so if anybody else can help out, that'd be great. Best, Roemer On Fri, Sep 14, 2012 at 12:27 PM, andrea brovelli < andrea.brovelli at univ-amu.fr> wrote: > Dear all, > > I was wondering whether we can whiten the data using the cfg options in > the ft_preprocessing function. Does anyone know ? > > Or does anyone have some code for prewhitening raw data ? > > Thanks a lot > > Andrea > > > ______________________________**_________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip > -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri Sep 14 13:52:43 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 14 Sep 2012 13:52:43 +0200 Subject: [FieldTrip] Data prewhitening In-Reply-To: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> References: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> Message-ID: <55DE5D38-8A8E-4452-AE65-1326CE686A97@donders.ru.nl> Hi Andrea, As a follow up to my previous mail. There even seems to be a cfg.method = 'white' in ft_componentanalysis. As an addition to Roemers suggestion: if you want to spectrally whiten your data, his approach can be used. I interpreted your question as that you want to achieve spatial whitening. Best, JM On Sep 14, 2012, at 12:27 PM, andrea brovelli wrote: > Dear all, > > I was wondering whether we can whiten the data using the cfg options in the ft_preprocessing function. Does anyone know ? > > Or does anyone have some code for prewhitening raw data ? > > Thanks a lot > > Andrea > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrea.brovelli at univ-amu.fr Fri Sep 14 14:09:43 2012 From: andrea.brovelli at univ-amu.fr (andrea brovelli) Date: Fri, 14 Sep 2012 14:09:43 +0200 Subject: [FieldTrip] Data prewhitening In-Reply-To: References: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> Message-ID: <20120914140943.11107al822gjc39c@wmelperso1.univmed.fr> Thank you all for these suggestions, I'll try them out. bye Andrea ----- Message de r.vandermeij at donders.ru.nl --------- Date : Fri, 14 Sep 2012 13:03:32 +0200 De : Roemer van der Meij Répondre à : FieldTrip discussion list Objet : Re: [FieldTrip] Data prewhitening À : FieldTrip discussion list > Hi Andrea, > > Are you referring to pre-whitening by removing the first parameter of > an auto-regressive model, thereby removing most (if not all) of the 1/f > shape in the spectrum? If so, this can be done by taking the first > temporal derivative of the raw-data, effectively setting the first AR > parameter to 0. This is implemented by setting cfg.derivative = 'yes' in > preprocessing. > I don't know of any good references for this trick though, so if anybody > else can help out, that'd be great. > > Best, > Roemer > > > On Fri, Sep 14, 2012 at 12:27 PM, andrea brovelli < > andrea.brovelli at univ-amu.fr> wrote: > >> Dear all, >> >> I was wondering whether we can whiten the data using the cfg options in >> the ft_preprocessing function. Does anyone know ? >> >> Or does anyone have some code for prewhitening raw data ? >> >> Thanks a lot >> >> Andrea >> >> >> ______________________________**_________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip >> > > > > -- > Roemer van der Meij M.Sc. > PhD student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > Tel: +31(0)24 3655932 > E-mail: r.vandermeij at donders.ru.nl > ----- Fin du message de r.vandermeij at donders.ru.nl ----- -- NEW EMAIL: andrea.brovelli at univ-amu.fr From eelke.spaak at donders.ru.nl Fri Sep 14 14:27:54 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Fri, 14 Sep 2012 14:27:54 +0200 Subject: [FieldTrip] Data prewhitening In-Reply-To: <20120914140943.11107al822gjc39c@wmelperso1.univmed.fr> References: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> <20120914140943.11107al822gjc39c@wmelperso1.univmed.fr> Message-ID: Hi Andrea, To add to Roemer's suggestion: it's not exactly a reference perhaps, but Robert posted on the list a while ago some explanation behind using the temporal derivative to remove 1/f power (=whitening). See http://mailman.science.ru.nl/pipermail/fieldtrip/2011-October/004390.html Best, Eelke On 14 September 2012 14:09, andrea brovelli wrote: > Thank you all for these suggestions, I'll try them out. > > bye > > Andrea > > > ----- Message de r.vandermeij at donders.ru.nl --------- > Date : Fri, 14 Sep 2012 13:03:32 +0200 > De : Roemer van der Meij > Répondre à : FieldTrip discussion list > Objet : Re: [FieldTrip] Data prewhitening > À : FieldTrip discussion list > > >> Hi Andrea, >> >> Are you referring to pre-whitening by removing the first parameter of >> an auto-regressive model, thereby removing most (if not all) of the 1/f >> shape in the spectrum? If so, this can be done by taking the first >> temporal derivative of the raw-data, effectively setting the first AR >> parameter to 0. This is implemented by setting cfg.derivative = 'yes' in >> preprocessing. >> I don't know of any good references for this trick though, so if anybody >> else can help out, that'd be great. >> >> Best, >> Roemer >> >> >> On Fri, Sep 14, 2012 at 12:27 PM, andrea brovelli < >> andrea.brovelli at univ-amu.fr> wrote: >> >>> Dear all, >>> >>> I was wondering whether we can whiten the data using the cfg options in >>> the ft_preprocessing function. Does anyone know ? >>> >>> Or does anyone have some code for prewhitening raw data ? >>> >>> Thanks a lot >>> >>> Andrea >>> >>> >>> ______________________________**_________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> >>> http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> Roemer van der Meij M.Sc. >> PhD student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognition >> P.O. Box 9104 >> 6500 HE Nijmegen >> The Netherlands >> Tel: +31(0)24 3655932 >> E-mail: r.vandermeij at donders.ru.nl >> > > > ----- Fin du message de r.vandermeij at donders.ru.nl ----- > > > > -- > > NEW EMAIL: andrea.brovelli at univ-amu.fr > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Fri Sep 14 14:42:10 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 14 Sep 2012 14:42:10 +0200 Subject: [FieldTrip] improved edge behavior for cfg.boxcar in ft_preprocessing Message-ID: Dear all, I just pushed an improved version of boxcar smoothing to the svn-repository (will be available for download as of tonight). I just want to mention it, because it behaves slightly different from what you are used to (provided you actually ever use the option cfg.boxcar in ft_preprocessing). In a nutshell, the old implementation did an implicit zero-padding when performing the boxcar convolution. This could sometimes lead to ugly edges, if the local mean of the data (close to the edge) significantly deviated from 0. Therefore I implemented an explicit padding with the local mean value. You can read the code in ft_preproc_smooth. Since I think this change entails a significant improvement, and the old implementation was far from ideal, I decided to not support backward compatibility in this case. This means that you will not be able to reproduce the bad edge behavior of FT's boxcar functionality on your data anymore. Too bad. Happy computing and with best wishes, Jan-Mathijs Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.m.groppe at gmail.com Fri Sep 14 14:54:23 2012 From: david.m.groppe at gmail.com (David Groppe) Date: Fri, 14 Sep 2012 08:54:23 -0400 Subject: [FieldTrip] Data prewhitening In-Reply-To: References: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> <20120914140943.11107al822gjc39c@wmelperso1.univmed.fr> Message-ID: Here's a reference for whitening: Applications of spectral methods in functional brain imaging. D. Kleinfeld and P. P. Mitra. In Imaging: A Laboratory Manual (Book 1) R. Yuste, editor and series editor, 2011, Cold Spring Harbor Laboratory Press, NY, Chapter 12, 143-158. http://physics.ucsd.edu/neurophysics/publications/12_08_IMG.pdf And thanks to Robert Oostenveld for that original email response to my question about removing 1/f power trends. -David On Fri, Sep 14, 2012 at 8:27 AM, Eelke Spaak wrote: > Hi Andrea, > > To add to Roemer's suggestion: it's not exactly a reference perhaps, > but Robert posted on the list a while ago some explanation behind > using the temporal derivative to remove 1/f power (=whitening). See > http://mailman.science.ru.nl/pipermail/fieldtrip/2011-October/004390.html > > Best, > Eelke > > On 14 September 2012 14:09, andrea brovelli wrote: >> Thank you all for these suggestions, I'll try them out. >> >> bye >> >> Andrea >> >> >> ----- Message de r.vandermeij at donders.ru.nl --------- >> Date : Fri, 14 Sep 2012 13:03:32 +0200 >> De : Roemer van der Meij >> Répondre à : FieldTrip discussion list >> Objet : Re: [FieldTrip] Data prewhitening >> À : FieldTrip discussion list >> >> >>> Hi Andrea, >>> >>> Are you referring to pre-whitening by removing the first parameter of >>> an auto-regressive model, thereby removing most (if not all) of the 1/f >>> shape in the spectrum? If so, this can be done by taking the first >>> temporal derivative of the raw-data, effectively setting the first AR >>> parameter to 0. This is implemented by setting cfg.derivative = 'yes' in >>> preprocessing. >>> I don't know of any good references for this trick though, so if anybody >>> else can help out, that'd be great. >>> >>> Best, >>> Roemer >>> >>> >>> On Fri, Sep 14, 2012 at 12:27 PM, andrea brovelli < >>> andrea.brovelli at univ-amu.fr> wrote: >>> >>>> Dear all, >>>> >>>> I was wondering whether we can whiten the data using the cfg options in >>>> the ft_preprocessing function. Does anyone know ? >>>> >>>> Or does anyone have some code for prewhitening raw data ? >>>> >>>> Thanks a lot >>>> >>>> Andrea >>>> >>>> >>>> ______________________________**_________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> >>>> http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip >>>> >>> >>> >>> >>> -- >>> Roemer van der Meij M.Sc. >>> PhD student >>> Donders Institute for Brain, Cognition and Behaviour >>> Centre for Cognition >>> P.O. Box 9104 >>> 6500 HE Nijmegen >>> The Netherlands >>> Tel: +31(0)24 3655932 >>> E-mail: r.vandermeij at donders.ru.nl >>> >> >> >> ----- Fin du message de r.vandermeij at donders.ru.nl ----- >> >> >> >> -- >> >> NEW EMAIL: andrea.brovelli at univ-amu.fr >> >> >> _______________________________________________ >> 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 -- David Groppe, Ph.D. Postdoctoral Researcher North Shore LIJ Health System New Hyde Park, New York http://www.cogsci.ucsd.edu/~dgroppe/ From elizabeth.bock at mcgill.ca Fri Sep 14 16:23:51 2012 From: elizabeth.bock at mcgill.ca (Elizabeth Anne Bock, Ms) Date: Fri, 14 Sep 2012 14:23:51 +0000 Subject: [FieldTrip] realtime buffer does not exit In-Reply-To: <81D26A77-1088-4A8A-89FF-AA9B199F0320@donders.ru.nl> References: <86D86365C4E767468A79EB52DFBFB46F0510F73C@exmbx2010-8.campus.MCGILL.CA>, <3342976.328678.1347527120171.JavaMail.root@sculptor.zimbra.ru.nl> <86D86365C4E767468A79EB52DFBFB46F05110836@exmbx2010-8.campus.MCGILL.CA>, <81D26A77-1088-4A8A-89FF-AA9B199F0320@donders.ru.nl> Message-ID: <86D86365C4E767468A79EB52DFBFB46F05110DDE@exmbx2010-8.campus.MCGILL.CA> Thanks! This works great. Elizabeth ------------------------------------------------------------------------------------------ Elizabeth Bock / MEG System Engineer McConnell Brain Imaging Centre / Montreal Neurological Institute McGill University / 3801 University St. / Montreal, QC H3A 2B4 MEG Lab: 514.398.6056 Mobile: 514.718.6342 ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Boris Reuderink [b.reuderink at donders.ru.nl] Sent: Friday, September 14, 2012 6:21 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] realtime buffer does not exit Dear Elizabeth, It is indeed possible (perhaps preferable) to run the FieldTrip buffer outside of the MATLAB environment. Basically, the 'demo_buffer.exe' functions as a stand-alone server that holds the neuro data. Then, you would need a client, that reads from your acquisition hardware and writes new samples and events to the server. FieldTrip has programs for many different acquisition systems, see [1]. Your MATLAB program can then act as another client and read form the buffer. The advantage of this setup is that you can restart your MATLAB session without disrupting the FieldTrip real-time buffer. You can even run the serving buffer and your MATLAB code on different computers in you lab. Without additional details I can only guess why you got the error message you described. Perhaps the ft_host and ft_port are not set correctly? For ft_host you could try 'localhost' or '127.0.0.1', and for ft_port the default is 1972. These settings tell FieldTrip to connect to a buffer (=server) on the same computer. If you can't get it to work, please don't hesitate to ask. BTW, some background information on real-time signal processing with FieldTrip can be found on [2] — perhaps that is useful. Best regards, Boris Reuderink [1] http://fieldtrip.fcdonders.nl/development/realtime/implementation [2] http://fieldtrip.fcdonders.nl/development/realtime/buffer_overview -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl On 13 sep. 2012, at 14:51, "Elizabeth Anne Bock, Ms" wrote: > Thanks for the feedback. However, I would like to read the header and the data from the buffer into Matlab (I am doing realtime processing of the data). Is this possible to run the buffer in the windows environment and then read from it in Matlab? > > hdr = buffer('get_hdr', [], ft_host, ft_port) > ??? Error using ==> buffer > ERROR: failed to create socket (1) > > Thanks, > Beth > > ------------------------------------------------------------------------------------------ > > Elizabeth Bock / MEG System Engineer > > McConnell Brain Imaging Centre / Montreal Neurological Institute > > McGill University / 3801 University St. / Montreal, QC H3A 2B4 > > > > MEG Lab: 514.398.6056 > > Mobile: 514.718.6342 > > ________________________________________ > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Stolk, A. [a.stolk at fcdonders.ru.nl] > Sent: Thursday, September 13, 2012 5:05 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] realtime buffer does not exit > > Hi Elizabeth, > > Could you try and start the buffer from outside matlab using 'demo_buffer.exe' (to be found in the 'realtime/bin/win32' directory)? This application may operate smoother than when starting the buffer from a single matlab thread. > > Best, > Arjen > > ----- Oorspronkelijk bericht ----- >> Van: "Elizabeth Anne Bock, Ms" >> Aan: fieldtrip at science.ru.nl >> Verzonden: Woensdag 12 september 2012 20:32:39 >> Onderwerp: [FieldTrip] realtime buffer does not exit >> I am using the realtime buffer and I have found I cannot exit the >> buffer within the Matlab command window. I am forced to exit Matlab >> or, more often, must kill the process manually from the windows task >> manager. I am using Windows XP to host the buffer and Linux to run >> acqftx. Here is what I am seeing: >> >>>> buffer('tcpserver', 'exit', ft_host, ft_port) >> In main: requesting cancelation of tcpserver thread >> >>>> buffer('tcpserver', 'init', ft_host, ft_port) >> ??? Error using ==> buffer >> thread is already running >> >> Any suggestions? >> Thanks, >> Elizabeth >> >> >> ------------------------------------------------------------------------------------------ >> >> Elizabeth Bock / MEG System Engineer >> >> McConnell Brain Imaging Centre / Montreal Neurological Institute >> >> McGill University / 3801 University St. / Montreal, QC H3A 2B4 >> >> >> >> MEG Lab: 514.398.6056 >> >> Mobile: 514.718.6342 >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Duncan.Astle at mrc-cbu.cam.ac.uk Fri Sep 14 16:58:26 2012 From: Duncan.Astle at mrc-cbu.cam.ac.uk (Duncan Astle) Date: Fri, 14 Sep 2012 14:58:26 +0000 Subject: [FieldTrip] Problem with clustering across electrode neighbours In-Reply-To: <5051BF53.5030606@donders.ru.nl> References: <5051BF53.5030606@donders.ru.nl> Message-ID: Thanks for your help. You were spot on; now the version is updated it runs perfectly. Thanks, Duncan ________________________________________________ Dr. Duncan Astle, Programme Leader Track, British Academy Research Fellow, MRC Cognition and Brain Sciences Unit, Chaucer Road, Cambridge. Duncan.Astle at mrc-cbu.cam.ac.uk From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig" Sent: 13 September 2012 12:11 To: FieldTrip discussion list Subject: Re: [FieldTrip] Problem with clustering across electrode neighbours Hey Duncan, it looks pretty much like you are using an old FieldTrip version with a new neighbourhood-structure. Could you check the with the most recent version again? Some months (about a year?) ago we changed the neighbour definition from cell arrays to structure arrays, so any attempt to access cfg.neighbours{i} will fail, cause it has to be cfg.neighbours(i) instead. But as I already said, this has been changed quite some time back in the past :) Essentially, your code is fine, but some note that cfg.neighbourdist should be a scalar, not the string 'number', but only if cfg.method='distance'. If you choose cfg.method = 'template' then cfg.neighbourdist is not used, cause a template is loaded. Best, Jörn On 9/13/2012 12:46 PM, Duncan Astle wrote: Dear Fieldtrippers, I am rather new to this, but am attempting to do some cluster stats on my ERP sensor level data. It is working well, and I can cluster across time, but I can't get it to cluster across electrode locations. I think it is because of a mistake that I am making in my 'neighbours' file, although it looks fine when I inspect it. This is the error message that I get: ??? Cell contents reference from a non-cell array object. Error in ==> clusterstat>makechanneighbstructmat at 520 [seld] = match_str(cfg.channel, cfg.neighbours{chan}.label); Error in ==> clusterstat at 60 channeighbstructmat = makechanneighbstructmat(cfg); Error in ==> statistics_montecarlo at 322 [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); Error in ==> statistics_wrapper at 285 [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); Error in ==> ft_timelockstatistics at 119 [stat, cfg] = statistics_wrapper(cfg, varargin{:}); Can anyone spot what I am doing wrong? This is how I make my neighbour file: cfg = []; cfg.layout = 'EEG1010.lay'; % try 'distance' as well cfg.feedback = 'yes'; % show a neighbour plot cfg.method = 'template'; cfg.neighbourdist = 'number'; cfg.template = 'EEG1010_neighb.mat' cfg.channel = 'all' cfg.feedback = 'yes'; neighbours = ft_prepare_neighbours(cfg, Load5Hard); % define neighbouring channels This is how I then try the stats: cfg = []; cfg.channel = 'all'; cfg.latency = [0.1 1.3]; cfg.avgovertime = 'no'; cfg.avgoverchannel = 'no'; cfg.parameter = 'individual'; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT' cfg.alpha = 0.05; cfg.correctm = 'cluster'; cfg.correcttail = 'prob'; cfg.numrandomization = 1000; cfg.feedback = 'yes'; % show a neighbour plot cfg.neighbours = neighbours; %cfg.minnbchan = 2; cfg.clusterstatistic = 'maxsum'; cfg.clusterthreshold = 'nonparametric'; cfg.clusteralpha = 0.01; cfg.clustercritval = 0.06; % cfg.clustertail = 0; cfg.tail = 0; Nsub = 19; cfg.design(1,1:2*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub)]; cfg.design(2,1:2*Nsub) = [1:Nsub 1:Nsub]; cfg.ivar = 1; % the 1st row in cfg.design contains the independent variable cfg.uvar = 2; % the 2nd row in cfg.design contains the subject number [stat] = ft_timelockstatistics(cfg, Load3Hard, Load3Easy) Any suggestions very gratefully received. Thanks, Duncan ________________________________________________ Dr. Duncan Astle, Programme Leader Track, British Academy Research Fellow, MRC Cognition and Brain Sciences Unit, Chaucer Road, Cambridge. Duncan.Astle at mrc-cbu.cam.ac.uk _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sat Sep 15 07:49:07 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sat, 15 Sep 2012 08:49:07 +0300 Subject: [FieldTrip] example: ft_realtime_selectiveaverage Message-ID: Hello, Did any of you dealt before with ft_realtime_selectiveaverage function. If so, could I have a simple code so I can see how it is run? Best, -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From dmitri89 at ut.ee Tue Sep 18 10:00:35 2012 From: dmitri89 at ut.ee (Dmitri Filimonov) Date: Tue, 18 Sep 2012 11:00:35 +0300 Subject: [FieldTrip] channel repair script Message-ID: <259e43dd8af0ecf135e3965765705a76.squirrel@mailhost.ut.ee> Dear Sir/Madam, My name is Dmitri Filimonov, I am a master student in University of Tartu (Estonia), using fieldtrip for EEG data analysis. I would like to ask some assistance with fieldtrip script. The task is to repair some EEG channels, so need to use ft_channelrepair. And I tried to do that after artifact rejection, so I could first see, which channels are noisy or disabled. I tried multiple combinations, yet there are still problems with the script. It looks like: >> channels_to_repair={'Fp1', 'Fp2'}; layout_file=('C:\ fieldtrip-20120703\template\layout\EEG1010.lay'); cfg=[]; cfg.layout = 'EEG1010.lay'; data.elec = ft_prepare_layout(cfg); neighbours = ft_prepare_neighbours(cfg, good_data) cfg = ft_checkconfig(cfg, 'required', {'method'}); cfg.method = 'distance'; (or ‘nearest’) cfg.badchannel=channels_to_repair; cfg.neighbours = ft_prepare_neighbours (cfg, good_data); G_data = ft_channelrepair(cfg, dood_data); (Good_data –is a processed and filtered data, yet containing channels, which have to be repaired.) After processing the program gives me several errors: reading layout from file EEG1010.lay the call to "ft_prepare_layout" took 0 seconds and an estimated NaN MB ??? Error using ==> ft_checkconfig at 151 The field cfg.method is required Error in ==> ft_prepare_neighbours at 77 cfg = ft_checkconfig(cfg, 'required', {'method'}); Other combinations emerge similar errors, or Error in ==> ft_neighbourselection at 30 neighbours = ft_prepare_neighbours(varargin{:}); Can you give me some help, what kind of ‘method’ exactly program wants me to mention (type)? Yours sincerely, Dmitri From Joachim.Gross at glasgow.ac.uk Tue Sep 18 11:00:34 2012 From: Joachim.Gross at glasgow.ac.uk (Joachim Gross) Date: Tue, 18 Sep 2012 10:00:34 +0100 Subject: [FieldTrip] Five PostDoc Positions in Glasgow Message-ID: Research Associate (5 posts available) University of Glasgow - Institute of Neuroscience and Psychology You will contribute to Wellcome Trust funded research entitled "Natural and modulated neural communication: State-dependent decoding and driving of human Brain Oscillations" (Joint Investigators: Gregor Thut, Joachim Gross). This is one of 5 simultaneously filled 5-year Research Associate positions covering different aspects of the above project. The job requires working in an interdisciplinary team of researchers on longstanding questions of how brain oscillations orchestrate brain functions, or relate to brain dysfunction. Depending on the position within the team, this will involve the development and/or application of new analysis methods to eavesdrop on brain communication and decode some of the information coded in brain oscillations (MEG/EEG), or using this knowledge for controlled intervention into brain oscillations by transcranial stimulation to modulate brain function (combined TMS/tACS-EEG). For more information on the position and environment please write to Joachim.Gross at glasgow.ac.uk, or Gregor.Thut at glasgow.ac.uk This post has funding available until 31 December 2017 Ref: 002653 Please apply here: http://www.gla.ac.uk/about/jobs/ Salary: Grade 7, £31,948 - £35,938 per annum Closing date: 15 October 2012 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Tue Sep 18 12:34:01 2012 From: jm.horschig at donders.ru.nl (=?UTF-8?B?IkrDtnJuIE0uIEhvcnNjaGlnIg==?=) Date: Tue, 18 Sep 2012 12:34:01 +0200 Subject: [FieldTrip] channel repair script In-Reply-To: <259e43dd8af0ecf135e3965765705a76.squirrel@mailhost.ut.ee> References: <259e43dd8af0ecf135e3965765705a76.squirrel@mailhost.ut.ee> Message-ID: <50584E19.3090300@donders.ru.nl> Dear Dmitri, I think you are confusing things here. Note that you are calling two FieldTrip functions subsequently. The error message you are receiving results from ft_prepare_neighbours. ft_prepare_neighbours needs a different cfg than ft_channelrepair. The call you are making, does however not make much sense, because you already called that function a few lines before. So just drop that cfg.neighbours = ft_prepare_neighbours(...) line and replace it by cfg.neighbours = neighbours. Thereby, you are removing the function call that results in an error (and you already did that call), and I guess everything will work fine. Best, Jörn On 9/18/2012 10:00 AM, Dmitri Filimonov wrote: > Dear Sir/Madam, > > My name is Dmitri Filimonov, I am a master student in University of Tartu > (Estonia), using fieldtrip for EEG data analysis. I would like to ask some > assistance with fieldtrip script. > The task is to repair some EEG channels, so need to use ft_channelrepair. > And I tried to do that after artifact rejection, so I could first see, > which channels are noisy or disabled. I tried multiple combinations, yet > there are still problems with the script. > It looks like: > >>> channels_to_repair={'Fp1', 'Fp2'}; > layout_file=('C:\ fieldtrip-20120703\template\layout\EEG1010.lay'); > > cfg=[]; > cfg.layout = 'EEG1010.lay'; > data.elec = ft_prepare_layout(cfg); > neighbours = ft_prepare_neighbours(cfg, good_data) > cfg = ft_checkconfig(cfg, 'required', {'method'}); > cfg.method = 'distance'; (or ‘nearest’) > cfg.badchannel=channels_to_repair; > cfg.neighbours = ft_prepare_neighbours (cfg, good_data); > G_data = ft_channelrepair(cfg, dood_data); > (Good_data –is a processed and filtered data, yet containing channels, > which have to be repaired.) > After processing the program gives me several errors: > > reading layout from file EEG1010.lay > the call to "ft_prepare_layout" took 0 seconds and an estimated NaN MB > ??? Error using ==> ft_checkconfig at 151 > The field cfg.method is required > Error in ==> ft_prepare_neighbours at 77 > cfg = ft_checkconfig(cfg, 'required', {'method'}); > > Other combinations emerge similar errors, or > > Error in ==> ft_neighbourselection at 30 > neighbours = ft_prepare_neighbours(varargin{:}); > > Can you give me some help, what kind of ‘method’ exactly program wants me > to mention (type)? > > Yours sincerely, > Dmitri > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From r.vandermeij at donders.ru.nl Wed Sep 19 11:20:12 2012 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Wed, 19 Sep 2012 11:20:12 +0200 Subject: [FieldTrip] Question of implementing Fieldtrip In-Reply-To: <201209190328.q8J3SNa4008385@melipona.ucdavis.edu> References: <201209190328.q8J3SNa4008385@melipona.ucdavis.edu> Message-ID: Hi Jinghao, I forwarded your question to the Fieldtrip mailing list. I don't entirely understand what you mean only saving clusters with psychological meaning. Given the parameters that you chose, you get a certain number of clusters, all of which are significant as a whole. In analogy, this means that the whole 'mountain range' is significant or not, not the 'individual peaks'. You could of course focus on a few of those clusters in your report, as long as you mention the other clusters. You could also try to set your parameters a little more stringent (i.e. a lower cfg.clusteralpha), this would 'reduce the number of peaks in your mountain range', as some peaks would then fall below the threshold. Hopefully, your clusters with 'psychological meaning' would still show up, albeit a little smaller/shorter. Hope this helps, Roemer > Well in fact I'm doing an intracranial EEG project currently where the data > should be analyzed statistically. The permutation analysis seems a good > choice and first I ran it with sample-specific independent t-test to get a > rough idea of the data in different conditions. > > I'm wondering how to apply cluster-based permutation in single sensor > analysis where I would like to save only the time clusters with > psychological meaning. I could not find the guidance of how to do this in > Fieldtrip. Could you please share with me the approach? That'll be really > helpful. > > Best Regards, > Jinghao Lu > > > Dept. of Physics > Zhejiang University > 866 Yuhangtang Road > Hangzhou > 310058 ZHEJIANG > CHINA > > Temporary Affiliate > Dynamic Memory Lab > UC Davis > > > Jinghao Lu > > > Dept. of Physics > Zhejiang University > 866 Yuhangtang Road > Hangzhou > 310058 ZHEJIANG > CHINA > > Temporary Affiliate > Dynamic Memory Lab > UC Davis > -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From politzerahless at gmail.com Wed Sep 19 13:46:19 2012 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Wed, 19 Sep 2012 06:46:19 -0500 Subject: [FieldTrip] Question of implementing Fieldtrip Message-ID: Hi Jinghao, You can use cfg.latency to limit the time period in which the test will look for clusters (for example, if you expect a difference to show up in a particular small time window and you are only interested in that difference, and don't want to test earlier or later differences); the tutorial has some more information. The choice of time window should be made based on predictions you had before the experiment, not based on inspection of the data. But like Roemer points out, it's not possible to save "only clusters with psychological meaning", as the statistical test doesn't know whether or not clusters have psychological meaning. Best, Steve > Message: 2 > Date: Wed, 19 Sep 2012 11:20:12 +0200 > From: Roemer van der Meij > To: Email discussion list for the FieldTrip project > > Cc: Jinghao Lu > Subject: Re: [FieldTrip] Question of implementing Fieldtrip > Message-ID: > < > CA+WpQ37dfrEoQV4gLuVTHWbMrBKexo8HFRprSJ9d5t8w45ZvYg at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Jinghao, > > I forwarded your question to the Fieldtrip mailing list. I don't entirely > understand what you mean only saving clusters with psychological meaning. > Given the parameters that you chose, you get a certain number of clusters, > all of which are significant as a whole. In analogy, this means that the > whole 'mountain range' is significant or not, not the 'individual peaks'. > You could of course focus on a few of those clusters in your report, as > long as you mention the other clusters. You could also try to set your > parameters a little more stringent (i.e. a lower cfg.clusteralpha), this > would 'reduce the number of peaks in your mountain range', as some peaks > would then fall below the threshold. Hopefully, your clusters with > 'psychological meaning' would still show up, albeit a little > smaller/shorter. > > Hope this helps, > Roemer > > > > > > Well in fact I'm doing an intracranial EEG project currently where the > data > > should be analyzed statistically. The permutation analysis seems a good > > choice and first I ran it with sample-specific independent t-test to get > a > > rough idea of the data in different conditions. > > > > I'm wondering how to apply cluster-based permutation in single sensor > > analysis where I would like to save only the time clusters with > > psychological meaning. I could not find the guidance of how to do this in > > Fieldtrip. Could you please share with me the approach? That'll be really > > helpful. > > > > Best Regards, > > Jinghao Lu > > > > > > Dept. of Physics > > Zhejiang University > > 866 Yuhangtang Road > > Hangzhou > > 310058 ZHEJIANG > > CHINA > > > > Temporary Affiliate > > Dynamic Memory Lab > > UC Davis > > > > > > Jinghao Lu > > > > > > Dept. of Physics > > Zhejiang University > > 866 Yuhangtang Road > > Hangzhou > > 310058 ZHEJIANG > > CHINA > > > > Temporary Affiliate > > Dynamic Memory Lab > > UC Davis > > > > > > -- > Roemer van der Meij M.Sc. > PhD student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > Tel: +31(0)24 3655932 > E-mail: r.vandermeij at donders.ru.nl > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120919/bc3080b9/attachment-0001.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 22, Issue 35 > ***************************************** > -- Stephen Politzer-Ahles University of Kansas Linguistics Department http://www.linguistics.ku.edu/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From haiteng.jiang at gmail.com Wed Sep 19 15:39:15 2012 From: haiteng.jiang at gmail.com (Haiteng Jiang) Date: Wed, 19 Sep 2012 15:39:15 +0200 Subject: [FieldTrip] Problems plotting TFR with different frequency sacle Message-ID: Dear Fieldtripers , I try to plot the TFR with Fieldtrip , but I find the frequency shift in the plotting when I use different frequency scale. Please see the attached two examples (4-30Hz versus 4-100Hz). The TFR within 4-30Hz is centered in alpha band while it is switched to beta band with the 4-100Hz. scale . Regarding to the TFR, I calculate it by using an adaptive sliding time window of four cycles length (Δt = 4/f) and a Hanning taper for lower frequencies (4–30 Hz), and a sliding time window of fixed length (200ms) and three orthogonal Slepian tapers resulting in ±10 Hz smoothing (29) for higher frequencies (30–100 Hz). Any suggestion ? All the best, Haiteng -- Haiteng Jiang PhD candidate Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Visiting address Room 2.32 Donders Centre for Cognitive Neuroimaging Kapittelweg 29 6525 EN Nijmegen the Netherlands Tel.: +31 (0)243668291 Web: https://sites.google.com/site/haitengjiang/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TFR_4-30.jpg Type: image/jpeg Size: 84855 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TFR_4-100.jpg Type: image/jpeg Size: 76534 bytes Desc: not available URL: From r.vandermeij at donders.ru.nl Wed Sep 19 16:04:19 2012 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Wed, 19 Sep 2012 16:04:19 +0200 Subject: [FieldTrip] Question of implementing Fieldtrip In-Reply-To: <201209191150.q8JBoQsp022660@phaenicia.ucdavis.edu> References: <201209191150.q8JBoQsp022660@phaenicia.ucdavis.edu> Message-ID: Hi Jinghao, If you are talking about only looking at a single channel and using those for analyses, you can use cfg.channel for this purpose. It might be a good idea as well to run through the respective tutorial, which can be found at: http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock. My previous suggestion will also aid in reducing small clusters popping up. Best, Roemer On Wed, Sep 19, 2012 at 1:50 PM, Jinghao Lu wrote: > > > As for my question, what I mean is that I want to apply the cluster-based > permutation on the data from a single intracranial electrode just like what > Maris did in his paper 'Nonparametric statistical testing of EEG- and MEG- > data'. In this way, the scattered clusters will reduce to only several. > Some discrete sample with significant difference may disappear as well. > > In Fieldtrip, if I choose cfg.correctm = 'cluster', then a neighborhood is > required. However, I only have one electrode and want to apply it on > time(or further frequency). How can I set cfg? > > -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Wed Sep 19 16:07:09 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 19 Sep 2012 16:07:09 +0200 Subject: [FieldTrip] Problems plotting TFR with different frequency sacle In-Reply-To: References: Message-ID: <5059D18D.4070705@donders.ru.nl> Hi Haiteng, I'm gonna drop by since you are in the office next door ;) Best, Jörn On 9/19/2012 3:39 PM, Haiteng Jiang wrote: > Dear Fieldtripers , > I try to plot the TFR with Fieldtrip , but I find the frequency > shift in the plotting when I use different frequency scale. Please > see the attached two examples (4-30Hz versus 4-100Hz). The TFR within > 4-30Hz is centered in alpha band while it is switched to beta band > with the 4-100Hz. scale . Regarding to the TFR, I calculate it by > using an adaptive sliding time window of four cycles length (?t = 4/f) > and a Hanning taper for lower frequencies (4--30 Hz), and a sliding > time window of fixed length (200ms) and three orthogonal Slepian > tapers resulting in ±10 Hz smoothing (29) for higher frequencies > (30--100 Hz). > Any suggestion ? > All the best, > Haiteng > -- > Haiteng Jiang > PhD candidate > Neuronal Oscillations Group > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > > Visiting address > Room 2.32 > Donders Centre for Cognitive Neuroimaging > Kapittelweg 29 > 6525 EN Nijmegen > the Netherlands > > Tel.: +31 (0)243668291 > Web: https://sites.google.com/site/haitengjiang/ > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From Markus.Butz at uni-duesseldorf.de Wed Sep 19 16:25:33 2012 From: Markus.Butz at uni-duesseldorf.de (Markus Butz) Date: Wed, 19 Sep 2012 15:25:33 +0100 Subject: [FieldTrip] ft_checkcoordsys outdated? Message-ID: <7630d250a5f1.5059e3ed@uni-duesseldorf.de> Dear list the headmodel tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the function ft_checkcoordsys. This function is also explained here http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. However, as far as I can see it is not existent in the fieldtrip version I am using right now, ie 20111101. How come? Is it outdated or do I miss something here? Best wishes Markus -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at donders.ru.nl Wed Sep 19 18:17:43 2012 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Wed, 19 Sep 2012 18:17:43 +0200 Subject: [FieldTrip] ft_checkcoordsys outdated? In-Reply-To: <7630d250a5f1.5059e3ed@uni-duesseldorf.de> References: <7630d250a5f1.5059e3ed@uni-duesseldorf.de> Message-ID: Hi Markus, Indeed it is outdated. It has been renamed to ft_determine_coordsys and moved to utilities: http://code.google.com/p/fieldtrip/source/detail?spec=svn3219&r=3219 Thanks for spotting that on the tutorial, as it should be updated. Cheers, Johanna 2012/9/19 Markus Butz > Dear list > > the headmodel tutorial ( > http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the > function ft_checkcoordsys. > This function is also explained here > http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. > However, as far as I can see it is not existent in the fieldtrip version I > am using right now, ie 20111101. > How come? Is it outdated or do I miss something here? > > Best wishes > Markus > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Sep 19 19:06:12 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 19 Sep 2012 19:06:12 +0200 Subject: [FieldTrip] ft_checkcoordsys outdated? In-Reply-To: References: <7630d250a5f1.5059e3ed@uni-duesseldorf.de> Message-ID: ...and the good thing about a wiki is: anybody can update it! ;-) Best, Jan-Mathijs On Sep 19, 2012, at 6:17 PM, Johanna Zumer wrote: > Hi Markus, > > Indeed it is outdated. It has been renamed to ft_determine_coordsys and moved to utilities: http://code.google.com/p/fieldtrip/source/detail?spec=svn3219&r=3219 > Thanks for spotting that on the tutorial, as it should be updated. > > Cheers, > Johanna > > 2012/9/19 Markus Butz > Dear list > > the headmodel tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the function ft_checkcoordsys. > This function is also explained here http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. > However, as far as I can see it is not existent in the fieldtrip version I am using right now, ie 20111101. > How come? Is it outdated or do I miss something here? > > Best wishes > Markus > > > > > > _______________________________________________ > 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 Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jhlu at ucdavis.edu Thu Sep 20 00:29:25 2012 From: jhlu at ucdavis.edu (Jinghao Lu) Date: Wed, 19 Sep 2012 15:29:25 -0700 (PDT) Subject: [FieldTrip] problem of implementing fieldtrip Message-ID: <201209192229.q8JMTPtA023532@syrphus.ucdavis.edu> Hi Roemer, the more exact problem may be like this: 1. I used eeglab to do all the erps and time-frequency and then used 'eeglab2fieldtrip(preprocessing, which seems the only way)' 2. then ran ft_timelockanalysis to generate erps, with cfg.channel = {'naLeft1'}(only one channel) 3. ran permutation with cfg.correctm = 'cluster' and subsequent cfg settings. However, an error message came out saying: "Error using ==> statistics_wrapper at 249 You need to specify a neighbourstructure" Which part did I set wrong? Best, Jinghao > 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: Question of implementing Fieldtrip (Roemer van der Meij) > 2. Re: Problems plotting TFR with different frequency sacle > (J?rn M. Horschig) > 3. ft_checkcoordsys outdated? (Markus Butz) > 4. Re: ft_checkcoordsys outdated? (Johanna Zumer) > 5. Re: ft_checkcoordsys outdated? (jan-mathijs schoffelen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 19 Sep 2012 16:04:19 +0200 > From: Roemer van der Meij > To: Email discussion list for the FieldTrip project > > Subject: Re: [FieldTrip] Question of implementing Fieldtrip > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Jinghao, > > If you are talking about only looking at a single channel and using those > for analyses, you can use cfg.channel for this purpose. It might be a > good > idea as well to run through the respective tutorial, which can be found > at: http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock. > My previous suggestion will also aid in reducing small clusters popping > up. > > Best, > Roemer > > > > On Wed, Sep 19, 2012 at 1:50 PM, Jinghao Lu wrote: > > > > > > > As for my question, what I mean is that I want to apply the > cluster-based > > permutation on the data from a single intracranial electrode just like > what > > Maris did in his paper 'Nonparametric statistical testing of EEG- and > MEG- > > data'. In this way, the scattered clusters will reduce to only several. > > Some discrete sample with significant difference may disappear as well. > > > > In Fieldtrip, if I choose cfg.correctm = 'cluster', then a neighborhood > is > > required. However, I only have one electrode and want to apply it on > > time(or further frequency). How can I set cfg? > > > > > -- > Roemer van der Meij M.Sc. > PhD student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > Tel: +31(0)24 3655932 > E-mail: r.vandermeij at donders.ru.nl > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Message: 2 > Date: Wed, 19 Sep 2012 16:07:09 +0200 > From: "J?rn M. Horschig" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Problems plotting TFR with different > frequency sacle > Message-ID: <5059D18D.4070705 at donders.ru.nl> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hi Haiteng, > > I'm gonna drop by since you are in the office next door ;) > > Best, > J?rn > > On 9/19/2012 3:39 PM, Haiteng Jiang wrote: > > Dear Fieldtripers , > > I try to plot the TFR with Fieldtrip , but I find the frequency > > shift in the plotting when I use different frequency scale. Please > > see the attached two examples (4-30Hz versus 4-100Hz). The TFR within > > 4-30Hz is centered in alpha band while it is switched to beta band > > with the 4-100Hz. scale . Regarding to the TFR, I calculate it by > > using an adaptive sliding time window of four cycles length (?t = 4/f) > > and a Hanning taper for lower frequencies (4--30 Hz), and a sliding > > time window of fixed length (200ms) and three orthogonal Slepian > > tapers resulting in ?10 Hz smoothing (29) for higher frequencies > > (30--100 Hz). > > Any suggestion ? > > All the best, > > Haiteng > > -- > > Haiteng Jiang > > PhD candidate > > Neuronal Oscillations Group > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > > > Visiting address > > Room 2.32 > > Donders Centre for Cognitive Neuroimaging > > Kapittelweg 29 > > 6525 EN Nijmegen > > the Netherlands > > > > Tel.: +31 (0)243668291 > > Web: https://sites.google.com/site/haitengjiang/ > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > J?rn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Message: 3 > Date: Wed, 19 Sep 2012 15:25:33 +0100 > From: Markus Butz > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] ft_checkcoordsys outdated? > Message-ID: <7630d250a5f1.5059e3ed at uni-duesseldorf.de> > Content-Type: text/plain; charset="us-ascii" > > Dear list > > the headmodel tutorial > (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the > function ft_checkcoordsys. > This function is also explained here > http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. > However, as far as I can see it is not existent in the fieldtrip version I > am using right now, ie 20111101. > How come? Is it outdated or do I miss something here? > > Best wishes > Markus > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Message: 4 > Date: Wed, 19 Sep 2012 18:17:43 +0200 > From: Johanna Zumer > To: Markus.Butz at uni-duesseldorf.de, FieldTrip discussion list > > Subject: Re: [FieldTrip] ft_checkcoordsys outdated? > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Markus, > > Indeed it is outdated. It has been renamed to ft_determine_coordsys and > moved to utilities: > http://code.google.com/p/fieldtrip/source/detail?spec=svn3219&r=3219 > Thanks for spotting that on the tutorial, as it should be updated. > > Cheers, > Johanna > > 2012/9/19 Markus Butz > > > Dear list > > > > the headmodel tutorial ( > > http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the > > function ft_checkcoordsys. > > This function is also explained here > > http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. > > However, as far as I can see it is not existent in the fieldtrip version > I > > am using right now, ie 20111101. > > How come? Is it outdated or do I miss something here? > > > > Best wishes > > Markus > > > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Message: 5 > Date: Wed, 19 Sep 2012 19:06:12 +0200 > From: jan-mathijs schoffelen > To: FieldTrip discussion list > Subject: Re: [FieldTrip] ft_checkcoordsys outdated? > Message-ID: > Content-Type: text/plain; charset="us-ascii" > > ...and the good thing about a wiki is: anybody can update it! ;-) > > Best, > Jan-Mathijs > > > On Sep 19, 2012, at 6:17 PM, Johanna Zumer wrote: > > > Hi Markus, > > > > Indeed it is outdated. It has been renamed to ft_determine_coordsys and > moved to utilities: > http://code.google.com/p/fieldtrip/source/detail?spec=svn3219&r=3219 > > Thanks for spotting that on the tutorial, as it should be updated. > > > > Cheers, > > Johanna > > > > 2012/9/19 Markus Butz > > Dear list > > > > the headmodel tutorial > (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the > function ft_checkcoordsys. > > This function is also explained here > http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. > > However, as far as I can see it is not existent in the fieldtrip version > I am using right now, ie 20111101. > > How come? Is it outdated or do I miss something here? > > > > Best wishes > > Markus > > > > > > > > > > > > _______________________________________________ > > 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 > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 22, Issue 37 > ***************************************** > Jinghao Lu Dept. of Physics Zhejiang University 866 Yuhangtang Road Hangzhou 310058 ZHEJIANG CHINA Temporary Affiliate Dynamic Memory Lab UC Davis From dmitri89 at ut.ee Thu Sep 20 09:54:59 2012 From: dmitri89 at ut.ee (Dmitri Filimonov) Date: Thu, 20 Sep 2012 10:54:59 +0300 Subject: [FieldTrip] channel repair script In-Reply-To: <50584E19.3090300@donders.ru.nl> References: <259e43dd8af0ecf135e3965765705a76.squirrel@mailhost.ut.ee> <50584E19.3090300@donders.ru.nl> Message-ID: Dear Jörn, Thank you for answering, but unfortunately it doesn't work anyway. I tried that also. It always gives "The field cfg.method is required" I've put several possible cfg.methods = *(like cfg.method = 'mtmfft' (in case if program wants me to set spectra calculating parameters); or 'nearest' (in case of neighbour selection method). Non of this works, yet I am trying to deal with it now. Best wishes, Dmitri > Dear Dmitri, > > I think you are confusing things here. > Note that you are calling two FieldTrip functions subsequently. The > error message you are receiving results from ft_prepare_neighbours. > ft_prepare_neighbours needs a different cfg than ft_channelrepair. The > call you are making, does however not make much sense, because you > already called that function a few lines before. So just drop that > cfg.neighbours = ft_prepare_neighbours(...) line and replace it by > cfg.neighbours = neighbours. Thereby, you are removing the function call > that results in an error (and you already did that call), and I guess > everything will work fine. > > Best, > Jörn > > On 9/18/2012 10:00 AM, Dmitri Filimonov wrote: >> Dear Sir/Madam, >> >> My name is Dmitri Filimonov, I am a master student in University of >> Tartu >> (Estonia), using fieldtrip for EEG data analysis. I would like to ask >> some >> assistance with fieldtrip script. >> The task is to repair some EEG channels, so need to use >> ft_channelrepair. >> And I tried to do that after artifact rejection, so I could first see, >> which channels are noisy or disabled. I tried multiple combinations, yet >> there are still problems with the script. >> It looks like: >> >>>> channels_to_repair={'Fp1', 'Fp2'}; >> layout_file=('C:\ fieldtrip-20120703\template\layout\EEG1010.lay'); >> >> cfg=[]; >> cfg.layout = 'EEG1010.lay'; >> data.elec = ft_prepare_layout(cfg); >> neighbours = ft_prepare_neighbours(cfg, good_data) >> cfg = ft_checkconfig(cfg, 'required', {'method'}); >> cfg.method = 'distance'; (or ‘nearest’) >> cfg.badchannel=channels_to_repair; >> cfg.neighbours = ft_prepare_neighbours (cfg, good_data); >> G_data = ft_channelrepair(cfg, dood_data); >> (Good_data –is a processed and filtered data, yet containing channels, >> which have to be repaired.) >> After processing the program gives me several errors: >> >> reading layout from file EEG1010.lay >> the call to "ft_prepare_layout" took 0 seconds and an estimated NaN MB >> ??? Error using ==> ft_checkconfig at 151 >> The field cfg.method is required >> Error in ==> ft_prepare_neighbours at 77 >> cfg = ft_checkconfig(cfg, 'required', {'method'}); >> >> Other combinations emerge similar errors, or >> >> Error in ==> ft_neighbourselection at 30 >> neighbours = ft_prepare_neighbours(varargin{:}); >> >> Can you give me some help, what kind of ‘method’ exactly program wants >> me >> to mention (type)? >> >> Yours sincerely, >> Dmitri >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Thu Sep 20 09:59:27 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 20 Sep 2012 09:59:27 +0200 Subject: [FieldTrip] problem of implementing fieldtrip In-Reply-To: <201209192229.q8JMTPtA023532@syrphus.ucdavis.edu> References: <201209192229.q8JMTPtA023532@syrphus.ucdavis.edu> Message-ID: <505ACCDF.6020100@donders.ru.nl> Dear Jinghao, you need to specify cfg.avgoverchan='yes' prior to calling ft_timelockstatistics to tell fieldtrip that no clustering in space is needed. It should work fine then. Best, Jörn On 9/20/2012 12:29 AM, Jinghao Lu wrote: > Hi Roemer, > > the more exact problem may be like this: > > 1. I used eeglab to do all the erps and time-frequency and then used > 'eeglab2fieldtrip(preprocessing, which seems the only way)' > > 2. then ran ft_timelockanalysis to generate erps, with cfg.channel = > {'naLeft1'}(only one channel) > > 3. ran permutation with cfg.correctm = 'cluster' and subsequent cfg > settings. However, an error message came out saying: > > > "Error using ==> statistics_wrapper at 249 > You need to specify a neighbourstructure" > > Which part did I set wrong? > > Best, > Jinghao > > > > > >> 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: Question of implementing Fieldtrip (Roemer van der Meij) >> 2. Re: Problems plotting TFR with different frequency sacle >> (J?rn M. Horschig) >> 3. ft_checkcoordsys outdated? (Markus Butz) >> 4. Re: ft_checkcoordsys outdated? (Johanna Zumer) >> 5. Re: ft_checkcoordsys outdated? (jan-mathijs schoffelen) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Wed, 19 Sep 2012 16:04:19 +0200 >> From: Roemer van der Meij >> To: Email discussion list for the FieldTrip project >> >> Subject: Re: [FieldTrip] Question of implementing Fieldtrip >> Message-ID: >> XXYb5Wb0vcyG_j=8g at mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi Jinghao, >> >> If you are talking about only looking at a single channel and using those >> for analyses, you can use cfg.channel for this purpose. It might be a >> good >> idea as well to run through the respective tutorial, which can be found >> at: http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock. >> My previous suggestion will also aid in reducing small clusters popping >> up. >> >> Best, >> Roemer >> >> >> >> On Wed, Sep 19, 2012 at 1:50 PM, Jinghao Lu wrote: >> >>> >>> As for my question, what I mean is that I want to apply the >> cluster-based >>> permutation on the data from a single intracranial electrode just like >> what >>> Maris did in his paper 'Nonparametric statistical testing of EEG- and >> MEG- >>> data'. In this way, the scattered clusters will reduce to only several. >>> Some discrete sample with significant difference may disappear as well. >>> >>> In Fieldtrip, if I choose cfg.correctm = 'cluster', then a neighborhood >> is >>> required. However, I only have one electrode and want to apply it on >>> time(or further frequency). How can I set cfg? >>> >>> >> -- >> Roemer van der Meij M.Sc. >> PhD student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognition >> P.O. Box 9104 >> 6500 HE Nijmegen >> The Netherlands >> Tel: +31(0)24 3655932 >> E-mail: r.vandermeij at donders.ru.nl >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> > 56cf/attachment-0001.html> >> ------------------------------ >> >> Message: 2 >> Date: Wed, 19 Sep 2012 16:07:09 +0200 >> From: "J?rn M. Horschig" >> To: FieldTrip discussion list >> Subject: Re: [FieldTrip] Problems plotting TFR with different >> frequency sacle >> Message-ID: <5059D18D.4070705 at donders.ru.nl> >> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" >> >> Hi Haiteng, >> >> I'm gonna drop by since you are in the office next door ;) >> >> Best, >> J?rn >> >> On 9/19/2012 3:39 PM, Haiteng Jiang wrote: >>> Dear Fieldtripers , >>> I try to plot the TFR with Fieldtrip , but I find the frequency >>> shift in the plotting when I use different frequency scale. Please >>> see the attached two examples (4-30Hz versus 4-100Hz). The TFR within >>> 4-30Hz is centered in alpha band while it is switched to beta band >>> with the 4-100Hz. scale . Regarding to the TFR, I calculate it by >>> using an adaptive sliding time window of four cycles length (?t = 4/f) >>> and a Hanning taper for lower frequencies (4--30 Hz), and a sliding >>> time window of fixed length (200ms) and three orthogonal Slepian >>> tapers resulting in ?10 Hz smoothing (29) for higher frequencies >>> (30--100 Hz). >>> Any suggestion ? >>> All the best, >>> Haiteng >>> -- >>> Haiteng Jiang >>> PhD candidate >>> Neuronal Oscillations Group >>> Donders Institute for Brain, Cognition and Behaviour >>> Centre for Cognitive Neuroimaging >>> Radboud University Nijmegen >>> >>> Visiting address >>> Room 2.32 >>> Donders Centre for Cognitive Neuroimaging >>> Kapittelweg 29 >>> 6525 EN Nijmegen >>> the Netherlands >>> >>> Tel.: +31 (0)243668291 >>> Web: https://sites.google.com/site/haitengjiang/ >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> -- >> J?rn M. Horschig >> PhD Student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> Neuronal Oscillations Group >> FieldTrip Development Team >> >> P.O. Box 9101 >> NL-6500 HB Nijmegen >> The Netherlands >> >> Contact: >> E-Mail: jm.horschig at donders.ru.nl >> Tel: +31-(0)24-36-68493 >> Web: http://www.ru.nl/donders >> >> Visiting address: >> Trigon, room 2.30 >> Kapittelweg 29 >> NL-6525 EN Nijmegen >> The Netherlands >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> > dfd7/attachment-0001.html> >> ------------------------------ >> >> Message: 3 >> Date: Wed, 19 Sep 2012 15:25:33 +0100 >> From: Markus Butz >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] ft_checkcoordsys outdated? >> Message-ID: <7630d250a5f1.5059e3ed at uni-duesseldorf.de> >> Content-Type: text/plain; charset="us-ascii" >> >> Dear list >> >> the headmodel tutorial >> (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the >> function ft_checkcoordsys. >> This function is also explained here >> http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. >> However, as far as I can see it is not existent in the fieldtrip version > I >> am using right now, ie 20111101. >> How come? Is it outdated or do I miss something here? >> >> Best wishes >> Markus >> >> >> >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> > 9565/attachment-0001.html> >> ------------------------------ >> >> Message: 4 >> Date: Wed, 19 Sep 2012 18:17:43 +0200 >> From: Johanna Zumer >> To: Markus.Butz at uni-duesseldorf.de, FieldTrip discussion list >> >> Subject: Re: [FieldTrip] ft_checkcoordsys outdated? >> Message-ID: >> 8FHxUvcAhG0Or35B=Ow at mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi Markus, >> >> Indeed it is outdated. It has been renamed to ft_determine_coordsys and >> moved to utilities: >> http://code.google.com/p/fieldtrip/source/detail?spec=svn3219&r=3219 >> Thanks for spotting that on the tutorial, as it should be updated. >> >> Cheers, >> Johanna >> >> 2012/9/19 Markus Butz >> >>> Dear list >>> >>> the headmodel tutorial ( >>> http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the >>> function ft_checkcoordsys. >>> This function is also explained here >>> http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. >>> However, as far as I can see it is not existent in the fieldtrip > version >> I >>> am using right now, ie 20111101. >>> How come? Is it outdated or do I miss something here? >>> >>> Best wishes >>> Markus >>> >>> >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> > 1c05/attachment-0001.html> >> ------------------------------ >> >> Message: 5 >> Date: Wed, 19 Sep 2012 19:06:12 +0200 >> From: jan-mathijs schoffelen >> To: FieldTrip discussion list >> Subject: Re: [FieldTrip] ft_checkcoordsys outdated? >> Message-ID: >> Content-Type: text/plain; charset="us-ascii" >> >> ...and the good thing about a wiki is: anybody can update it! ;-) >> >> Best, >> Jan-Mathijs >> >> >> On Sep 19, 2012, at 6:17 PM, Johanna Zumer wrote: >> >>> Hi Markus, >>> >>> Indeed it is outdated. It has been renamed to ft_determine_coordsys > and >> moved to utilities: >> http://code.google.com/p/fieldtrip/source/detail?spec=svn3219&r=3219 >>> Thanks for spotting that on the tutorial, as it should be updated. >>> >>> Cheers, >>> Johanna >>> >>> 2012/9/19 Markus Butz >>> Dear list >>> >>> the headmodel tutorial >> (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the >> function ft_checkcoordsys. >>> This function is also explained here >> http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. >>> However, as far as I can see it is not existent in the fieldtrip > version >> I am using right now, ie 20111101. >>> How come? Is it outdated or do I miss something here? >>> >>> Best wishes >>> Markus >>> >>> >>> >>> >>> >>> _______________________________________________ >>> 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 >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> > 674f/attachment.html> >> ------------------------------ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> End of fieldtrip Digest, Vol 22, Issue 37 >> ***************************************** >> > Jinghao Lu > > > Dept. of Physics > Zhejiang University > 866 Yuhangtang Road > Hangzhou > 310058 ZHEJIANG > CHINA > > Temporary Affiliate > Dynamic Memory Lab > UC Davis > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From jm.horschig at donders.ru.nl Thu Sep 20 10:09:53 2012 From: jm.horschig at donders.ru.nl (=?UTF-8?B?IkrDtnJuIE0uIEhvcnNjaGlnIg==?=) Date: Thu, 20 Sep 2012 10:09:53 +0200 Subject: [FieldTrip] channel repair script In-Reply-To: References: <259e43dd8af0ecf135e3965765705a76.squirrel@mailhost.ut.ee> <50584E19.3090300@donders.ru.nl> Message-ID: <505ACF51.4040706@donders.ru.nl> Hi Dmitri, looking at your script it seems that the error occurs even right at the start. You said you are doing this (the very first lines that you pasted) cfg=[]; cfg.layout = 'EEG1010.lay'; data.elec = ft_prepare_layout(cfg); neighbours = ft_prepare_neighbours(cfg, good_data) which means that you call ft_prepare_neighbours with a configuration structure which only has cfg.layout and nothing else. However, you did not specify a method how neighbours should be defined. If you look up the help from ft_prepare_neighbours, you will see what methods are available. Note that these are distinct from cfg.method for other functions. Every function has it's own cfg-settings, which are mostly independent from those of other functions. For example 'nearest' is not an method for ft_prepare_neighbours but for ft_channelrepair. Likewise, 'mtmfft' is a method for ft_freqanalysis, but not for any other method. I would strongly advise you to start with FieldTrip by going through our tutorials: http://fieldtrip.fcdonders.nl/tutorial This is the easiest way to get acquainted and used to the way FieldTrip works with cfg-and data-structures. And then check our frequently asked questions: http://fieldtrip.fcdonders.nl/faq In your case, especially http://fieldtrip.fcdonders.nl/faq/how_can_i_define_neighbouring_sensors http://fieldtrip.fcdonders.nl/faq/how_does_ft_prepare_neighbours_work Should you need any more assistance, feel free to ask. Best, Jörn On 9/20/2012 9:54 AM, Dmitri Filimonov wrote: > Dear Jörn, > > Thank you for answering, but unfortunately it doesn't work anyway. I tried > that also. It always gives > > "The field cfg.method is required" > > I've put several possible cfg.methods = *(like cfg.method = 'mtmfft' (in > case if program wants me to set spectra calculating parameters); or > 'nearest' (in case of neighbour selection method). Non of this works, yet > I am trying to deal with it now. > > Best wishes, > Dmitri > > > > >> Dear Dmitri, >> >> I think you are confusing things here. >> Note that you are calling two FieldTrip functions subsequently. The >> error message you are receiving results from ft_prepare_neighbours. >> ft_prepare_neighbours needs a different cfg than ft_channelrepair. The >> call you are making, does however not make much sense, because you >> already called that function a few lines before. So just drop that >> cfg.neighbours = ft_prepare_neighbours(...) line and replace it by >> cfg.neighbours = neighbours. Thereby, you are removing the function call >> that results in an error (and you already did that call), and I guess >> everything will work fine. >> >> Best, >> Jörn >> >> On 9/18/2012 10:00 AM, Dmitri Filimonov wrote: >>> Dear Sir/Madam, >>> >>> My name is Dmitri Filimonov, I am a master student in University of >>> Tartu >>> (Estonia), using fieldtrip for EEG data analysis. I would like to ask >>> some >>> assistance with fieldtrip script. >>> The task is to repair some EEG channels, so need to use >>> ft_channelrepair. >>> And I tried to do that after artifact rejection, so I could first see, >>> which channels are noisy or disabled. I tried multiple combinations, yet >>> there are still problems with the script. >>> It looks like: >>> >>>>> channels_to_repair={'Fp1', 'Fp2'}; >>> layout_file=('C:\ fieldtrip-20120703\template\layout\EEG1010.lay'); >>> >>> cfg=[]; >>> cfg.layout = 'EEG1010.lay'; >>> data.elec = ft_prepare_layout(cfg); >>> neighbours = ft_prepare_neighbours(cfg, good_data) >>> cfg = ft_checkconfig(cfg, 'required', {'method'}); >>> cfg.method = 'distance'; (or ‘nearest’) >>> cfg.badchannel=channels_to_repair; >>> cfg.neighbours = ft_prepare_neighbours (cfg, good_data); >>> G_data = ft_channelrepair(cfg, dood_data); >>> (Good_data –is a processed and filtered data, yet containing channels, >>> which have to be repaired.) >>> After processing the program gives me several errors: >>> >>> reading layout from file EEG1010.lay >>> the call to "ft_prepare_layout" took 0 seconds and an estimated NaN MB >>> ??? Error using ==> ft_checkconfig at 151 >>> The field cfg.method is required >>> Error in ==> ft_prepare_neighbours at 77 >>> cfg = ft_checkconfig(cfg, 'required', {'method'}); >>> >>> Other combinations emerge similar errors, or >>> >>> Error in ==> ft_neighbourselection at 30 >>> neighbours = ft_prepare_neighbours(varargin{:}); >>> >>> Can you give me some help, what kind of ‘method’ exactly program wants >>> me >>> to mention (type)? >>> >>> Yours sincerely, >>> Dmitri >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> -- >> Jörn M. Horschig >> PhD Student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> Neuronal Oscillations Group >> FieldTrip Development Team >> >> P.O. Box 9101 >> NL-6500 HB Nijmegen >> The Netherlands >> >> Contact: >> E-Mail: jm.horschig at donders.ru.nl >> Tel: +31-(0)24-36-68493 >> Web: http://www.ru.nl/donders >> >> Visiting address: >> Trigon, room 2.30 >> Kapittelweg 29 >> NL-6525 EN Nijmegen >> The Netherlands >> >> _______________________________________________ >> 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 -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From b.reuderink at donders.ru.nl Thu Sep 20 11:16:27 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Thu, 20 Sep 2012 11:16:27 +0200 Subject: [FieldTrip] ft_realtime_selectiveaverage In-Reply-To: References: Message-ID: Dear Hamza, I guess that the function is trying to samples form the FieldTrip buffer form the period before it was started, i.e. samples with negative indices. This might be related to the triggers you have and your trial fun. Your best bet is to start the MATLAB debugger, and just step through the code until the error occurs. Inspection of variables might give a clue on what is happening. In the mean-time, I'll try to update the examples with some extra information on how to call these functions. Best regards, Boris -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl On 13 sep. 2012, at 11:19, Hamza Fawzi Altakroury (Student) wrote: > Hello, > > I am tried to run the ft_realtime_selectiveaverage function but I got the following error: > (note: the error appears after showing a plot with title: condition 255, ntrials = 1.) > > Could you tell me what is the problem. (exactly what does "connet read data before the begin of the file"). > > Best, > > ??? Error using ==> ft_read_data at 243 > cannot read data before the begin of the file > > Error in ==> ft_realtime_selectiveaverage at 94 > dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', chanindx, 'checkboundary', false); > > Error in ==> online1 at 48 > ft_realtime_selectiveaverage(cfg) > > Statements: > > cfg = []; > cfg.channel = {'A1'}; > cfg.dataset = 'buffer://localhost:1972'; > %cfg.trialfun = 'myfun'; > cfg.trialdef.eventtype = 'stimulus'; % By placing '?' we can see the eventtype that we have. > cfg.trialdef.eventvalue = 255; > cfg.trialdef.pre = 0; > cfg.trialdef.post = 1.0; > cfg = ft_definetrial(cfg); > ft_realtime_selectiveaverage(cfg) > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From hamzaf at sabanciuniv.edu Thu Sep 20 11:29:48 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Thu, 20 Sep 2012 12:29:48 +0300 Subject: [FieldTrip] ft_realtime_selectiveaverage In-Reply-To: References: Message-ID: Thank you Boris Best, Hamza On Thu, Sep 20, 2012 at 12:16 PM, Boris Reuderink wrote: > Dear Hamza, > > I guess that the function is trying to samples form the FieldTrip buffer > form the period before it was started, i.e. samples with negative indices. > This might be related to the triggers you have and your trial fun. > > Your best bet is to start the MATLAB debugger, and just step through the > code until the error occurs. Inspection of variables might give a clue on > what is happening. > > In the mean-time, I'll try to update the examples with some extra > information on how to call these functions. > > Best regards, > > Boris > > -- > twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl > > On 13 sep. 2012, at 11:19, Hamza Fawzi Altakroury (Student) < > hamzaf at sabanciuniv.edu> wrote: > > > Hello, > > > > I am tried to run the ft_realtime_selectiveaverage function but I got > the following error: > > (note: the error appears after showing a plot with title: condition 255, > ntrials = 1.) > > > > Could you tell me what is the problem. (exactly what does "connet read > data before the begin of the file"). > > > > Best, > > > > ??? Error using ==> ft_read_data at 243 > > cannot read data before the begin of the file > > > > Error in ==> ft_realtime_selectiveaverage at 94 > > dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', > begsample, 'endsample', endsample, 'chanindx', chanindx, 'checkboundary', > false); > > > > Error in ==> online1 at 48 > > ft_realtime_selectiveaverage(cfg) > > > > Statements: > > > > cfg = []; > > cfg.channel = {'A1'}; > > cfg.dataset = 'buffer://localhost:1972'; > > %cfg.trialfun = 'myfun'; > > cfg.trialdef.eventtype = 'stimulus'; % By placing '?' we > can see the eventtype that we have. > > cfg.trialdef.eventvalue = 255; > > cfg.trialdef.pre = 0; > > cfg.trialdef.post = 1.0; > > cfg = ft_definetrial(cfg); > > ft_realtime_selectiveaverage(cfg) > > > > -- > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabancı University > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Thu Sep 20 14:46:17 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 20 Sep 2012 14:46:17 +0200 Subject: [FieldTrip] Problems plotting TFR with different frequency sacle In-Reply-To: <5059D18D.4070705@donders.ru.nl> References: <5059D18D.4070705@donders.ru.nl> Message-ID: <505B1019.2050904@donders.ru.nl> For those having similar problems, note that FieldTrip (actually Matlab's image function) cannot handle unequal axis, e.g. a data.freq may not be [1 2 3 4 5 10 15 20]. Therefore, ladies and gentlemen, let me introduce bug number 1729: http://bugzilla.fcdonders.nl/show_bug.cgi?id=1729 On 9/19/2012 4:07 PM, "Jörn M. Horschig" wrote: > Hi Haiteng, > > I'm gonna drop by since you are in the office next door ;) > > Best, > Jörn > > On 9/19/2012 3:39 PM, Haiteng Jiang wrote: >> Dear Fieldtripers , >> I try to plot the TFR with Fieldtrip , but I find the frequency >> shift in the plotting when I use different frequency scale. Please >> see the attached two examples (4-30Hz versus 4-100Hz). The TFR >> within 4-30Hz is centered in alpha band while it is switched to beta >> band with the 4-100Hz. scale . Regarding to the TFR, I calculate it >> by using an adaptive sliding time window of four cycles length (?t = >> 4/f) and a Hanning taper for lower frequencies (4--30 Hz), and a >> sliding time window of fixed length (200ms) and three orthogonal >> Slepian tapers resulting in ±10 Hz smoothing (29) for higher >> frequencies (30--100 Hz). >> Any suggestion ? >> All the best, >> Haiteng >> -- >> Haiteng Jiang >> PhD candidate >> Neuronal Oscillations Group >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> >> Visiting address >> Room 2.32 >> Donders Centre for Cognitive Neuroimaging >> Kapittelweg 29 >> 6525 EN Nijmegen >> the Netherlands >> >> Tel.: +31 (0)243668291 >> Web: https://sites.google.com/site/haitengjiang/ >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail:jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web:http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From pgoodin at swin.edu.au Sun Sep 23 15:14:28 2012 From: pgoodin at swin.edu.au (Peter Goodin) Date: Sun, 23 Sep 2012 13:14:28 +0000 Subject: [FieldTrip] Neuromag sensor level stats Message-ID: Hi Fieldtrippers, I'm at a stage where I'd like to do statistical analysis on my ERF neuromag data, but don't really know where to begin. I'd like to do a cluster analysis, but the tutorial material is for a CTF system. I'm using a neuromag 306 channel which complicates matters somewhat due to the different sensor types. I've searched the mailing list but can't find any solid answers / example scripts. The most pressing questions I have are: 1. Despite running the data through maxfilter and entering in the bad channels, occasionally one gets through (not the same one). I've used Fieldtrip's repairchannel function on the data, making sure to replace the channel only with like sensor neighbouring sensors. While I know this is a common method for fixing bad channels in EEG, does the same hold for MEG due to non-existent smearing of the signal? Is it best to keep the fixed channel(s) or just remove them from the stats analysis across all participants? 2. Given the three sensor types on the neuromag system, do I need to run three different cluster analyses (one for mags, one for xgrads, one for ygrads), each time specifying like sensor neighbours? Alternatively, If I'm not interested in the mags data, can I just run one using the data from the combined gradiometers? 3. When examining for group x condition effects, would I use a three row design matrix with row 1 containing group, row 2 containing participants and row 3 conditions? Thanks for any help, Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Sun Sep 23 16:49:02 2012 From: smoratti at psi.ucm.es (smoratti at psi.ucm.es) Date: Sun, 23 Sep 2012 16:49:02 +0200 Subject: [FieldTrip] Neuromag sensor level stats In-Reply-To: References: Message-ID: <2007ABA6-22AA-480F-9DC8-64BFA482CA07@psi.ucm.es> Dear Peter, I would do the stats on Magnetometers and Gradiometers separately. Use cfg.layout = 'neuromag_306mag' for magnetometers. Before using the gradiometers I would use ft_combineplanar and then use the combined planar topographies for the stats (cfg.layout = 'neuromag_306cmb'). Hope that helps, Best, Stephan ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 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 23/09/2012, a las 15:14, Peter Goodin escribió: > Hi Fieldtrippers, > > I'm at a stage where I'd like to do statistical analysis on my ERF neuromag data, but don't really know where to begin. I'd like to do a cluster analysis, but the tutorial material is for a CTF system. I'm using a neuromag 306 channel which complicates matters somewhat due to the different sensor types. I've searched the mailing list but can't find any solid answers / example scripts. > > The most pressing questions I have are: > > 1. Despite running the data through maxfilter and entering in the bad channels, occasionally one gets through (not the same one). I've used Fieldtrip's repairchannel function on the data, making sure to replace the channel only with like sensor neighbouring sensors. While I know this is a common method for fixing bad channels in EEG, does the same hold for MEG due to non-existent smearing of the signal? Is it best to keep the fixed channel(s) or just remove them from the stats analysis across all participants? > > 2. Given the three sensor types on the neuromag system, do I need to run three different cluster analyses (one for mags, one for xgrads, one for ygrads), each time specifying like sensor neighbours? Alternatively, If I'm not interested in the mags data, can I just run one using the data from the combined gradiometers? > > 3. When examining for group x condition effects, would I use a three row design matrix with row 1 containing group, row 2 containing participants and row 3 conditions? > > Thanks for any help, > > Peter > _______________________________________________ > 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 jm.horschig at donders.ru.nl Mon Sep 24 14:15:05 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 24 Sep 2012 14:15:05 +0200 Subject: [FieldTrip] Neuromag sensor level stats In-Reply-To: References: Message-ID: <50604EC9.7050705@donders.ru.nl> Dear Peter, regarding your first question, most people here at the Donders actually repair bad channels. When computing the grandaverage over subjects or doing some statistics across subjects, only those channels which are in common for all datasets are used. Thus, if having different channels damaged/rejected per subjects, you can end up with a fairly low amount of channels. But, in the end it depends pretty much on what channels you reject wrt your hypothesis, e.g. having few occipital channels while being interested in motor regions won't constitute a big problem, so no need to interpolate. I leave the question whether it's a correct thing to do up to you (imho: I wouldn't worry too much about it). Regarding your third question: In FieldTrip you can only compare two conditions directly (at least when doing cluster-based permutation testing). Also, any interaction needs to be setup manually. Best, Jörn On 9/23/2012 3:14 PM, Peter Goodin wrote: > Hi Fieldtrippers, > > I'm at a stage where I'd like to do statistical analysis on my ERF > neuromag data, but don't really know where to begin. I'd like to do a > cluster analysis, but the tutorial material is for a CTF system. I'm > using a neuromag 306 channel which complicates matters somewhat due to > the different sensor types. I've searched the mailing list but can't > find any solid answers / example scripts. > > The most pressing questions I have are: > > 1. Despite running the data through maxfilter and entering in the bad > channels, occasionally one gets through (not the same one). I've used > Fieldtrip's repairchannel function on the data, making sure to replace > the channel only with like sensor neighbouring sensors. While I know > this is a common method for fixing bad channels in EEG, does the same > hold for MEG due to non-existent smearing of the signal? Is it best to > keep the fixed channel(s) or just remove them from the stats analysis > across all participants? > > 2. Given the three sensor types on the neuromag system, do I need to > run three different cluster analyses (one for mags, one for xgrads, > one for ygrads), each time specifying like sensor neighbours? > Alternatively, If I'm not interested in the mags data, can I just run > one using the data from the combined gradiometers? > > 3. When examining for group x condition effects, would I use a three > row design matrix with row 1 containing group, row 2 containing > participants and row 3 conditions? > > Thanks for any help, > > Peter > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From f.roux at bcbl.eu Mon Sep 24 16:29:52 2012 From: f.roux at bcbl.eu (Frederic Roux) Date: Mon, 24 Sep 2012 16:29:52 +0200 (CEST) Subject: [FieldTrip] model order for autoregressive model In-Reply-To: <20f3c578-3f8d-4f9b-8ad6-337627c79057@thalamus_p> Message-ID: Dear all, i am planning to do granger causality on source space time series, and wanted to know if anyone could tell me how to find/chose the right model order when using the ft_mvaranalysis? Any help/advice would be highly appreciated! Best, Fred From sherrykhan78 at gmail.com Mon Sep 24 19:22:01 2012 From: sherrykhan78 at gmail.com (Sheraz Khan) Date: Mon, 24 Sep 2012 13:22:01 -0400 Subject: [FieldTrip] model order for autoregressive model In-Reply-To: References: <20f3c578-3f8d-4f9b-8ad6-337627c79057@thalamus_p> Message-ID: Dear Fred, It is best to use AIC or BIC to determine model. http://en.wikipedia.org/wiki/Akaike_information_criterion Sheraz On Mon, Sep 24, 2012 at 10:29 AM, Frederic Roux wrote: > Dear all, > > i am planning to do granger causality on source space > time series, and wanted to know if anyone could tell me > how to find/chose the right model order when using the > ft_mvaranalysis? > > Any help/advice would be highly appreciated! > > Best, > > Fred > > _______________________________________________ > 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 f.roux at bcbl.eu Mon Sep 24 23:17:52 2012 From: f.roux at bcbl.eu (Frederic Roux) Date: Mon, 24 Sep 2012 23:17:52 +0200 (CEST) Subject: [FieldTrip] model order for autoregressive model In-Reply-To: Message-ID: Dear Sheraz, thank you for your reply and the link. How do you obtain the AIC / BIC from the output of ft_mvaranalyis? Best, Fred ----- Original Message ----- From: "Sheraz Khan" To: "FieldTrip discussion list" Sent: Monday, September 24, 2012 7:22:01 PM Subject: Re: [FieldTrip] model order for autoregressive model Dear Fred, It is best to use AIC or BIC to determine model. http://en.wikipedia.org/wiki/Akaike_information_criterion Sheraz On Mon, Sep 24, 2012 at 10:29 AM, Frederic Roux < f.roux at bcbl.eu > wrote: BeDear all, i am planning to do granger causality on source space time series, and wanted to know if anyone could tell me how to find/chose the right model order when using the ft_mvaranalysis? Any help/advice would be highly appreciated! Best, Fred _______________________________________________ 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 pgoodin at swin.edu.au Tue Sep 25 02:37:14 2012 From: pgoodin at swin.edu.au (Peter Goodin) Date: Tue, 25 Sep 2012 00:37:14 +0000 Subject: [FieldTrip] Neuromag sensor level stats In-Reply-To: <50604EC9.7050705@donders.ru.nl> References: <50604EC9.7050705@donders.ru.nl> Message-ID: Thanks very much for the responses Stephan and Jörn! One last question if possible Jörn. In your opinion, will doing several (at the most 5) cluster based t-tests affect the validity of permutation method testing to control for multiple comparisons? Would being more conservative regarding my alpha (for example a combination of permutation AND Bonferroni) possibly alleviate this? Thanks again for the responses, Peter. From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig" Sent: Monday, 24 September 2012 10:15 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] Neuromag sensor level stats Dear Peter, regarding your first question, most people here at the Donders actually repair bad channels. When computing the grandaverage over subjects or doing some statistics across subjects, only those channels which are in common for all datasets are used. Thus, if having different channels damaged/rejected per subjects, you can end up with a fairly low amount of channels. But, in the end it depends pretty much on what channels you reject wrt your hypothesis, e.g. having few occipital channels while being interested in motor regions won't constitute a big problem, so no need to interpolate. I leave the question whether it's a correct thing to do up to you (imho: I wouldn't worry too much about it). Regarding your third question: In FieldTrip you can only compare two conditions directly (at least when doing cluster-based permutation testing). Also, any interaction needs to be setup manually. Best, Jörn On 9/23/2012 3:14 PM, Peter Goodin wrote: Hi Fieldtrippers, I'm at a stage where I'd like to do statistical analysis on my ERF neuromag data, but don't really know where to begin. I'd like to do a cluster analysis, but the tutorial material is for a CTF system. I'm using a neuromag 306 channel which complicates matters somewhat due to the different sensor types. I've searched the mailing list but can't find any solid answers / example scripts. The most pressing questions I have are: 1. Despite running the data through maxfilter and entering in the bad channels, occasionally one gets through (not the same one). I've used Fieldtrip's repairchannel function on the data, making sure to replace the channel only with like sensor neighbouring sensors. While I know this is a common method for fixing bad channels in EEG, does the same hold for MEG due to non-existent smearing of the signal? Is it best to keep the fixed channel(s) or just remove them from the stats analysis across all participants? 2. Given the three sensor types on the neuromag system, do I need to run three different cluster analyses (one for mags, one for xgrads, one for ygrads), each time specifying like sensor neighbours? Alternatively, If I'm not interested in the mags data, can I just run one using the data from the combined gradiometers? 3. When examining for group x condition effects, would I use a three row design matrix with row 1 containing group, row 2 containing participants and row 3 conditions? Thanks for any help, Peter _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From sherrykhan78 at gmail.com Tue Sep 25 02:56:51 2012 From: sherrykhan78 at gmail.com (Sheraz Khan) Date: Mon, 24 Sep 2012 20:56:51 -0400 Subject: [FieldTrip] model order for autoregressive model In-Reply-To: References: Message-ID: Please look at bsmart tutorial ( http://brain-smart.org/ ) for more detail, It has step by step procedure. fieldtrip also support bsmart based mutivariate model. Sheraz On Mon, Sep 24, 2012 at 5:17 PM, Frederic Roux wrote: > Dear Sheraz, > > thank you for your reply and the link. > > How do you obtain the AIC / BIC from > the output of ft_mvaranalyis? > > Best, > Fred > ----- Original Message ----- > From: "Sheraz Khan" > To: "FieldTrip discussion list" > Sent: Monday, September 24, 2012 7:22:01 PM > Subject: Re: [FieldTrip] model order for autoregressive model > > > Dear Fred, > > > It is best to use AIC or BIC to determine model. > > > http://en.wikipedia.org/wiki/Akaike_information_criterion > > > Sheraz > > > On Mon, Sep 24, 2012 at 10:29 AM, Frederic Roux < f.roux at bcbl.eu > wrote: > > > BeDear all, > > i am planning to do granger causality on source space > time series, and wanted to know if anyone could tell me > how to find/chose the right model order when using the > ft_mvaranalysis? > > Any help/advice would be highly appreciated! > > Best, > > Fred > > _______________________________________________ > 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 eelke.spaak at donders.ru.nl Tue Sep 25 09:21:12 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 25 Sep 2012 09:21:12 +0200 Subject: [FieldTrip] Neuromag sensor level stats In-Reply-To: References: <50604EC9.7050705@donders.ru.nl> Message-ID: Hi Peter, The cluster-based permutation test by itself is fully corrected for multiple comparisons. You mention "cluster based t-tests", but the exact test statistic (in your case, t) is irrelevant for this method. >From your comment I think you already understand this, but I thought it good to point out nonetheless :) Strictly speaking, when doing several cluster-based permutation tests, the cluster-level p-values you get out are uncorrected with respect to the several different tests, so actually I think it would be formally appropriate to correct them (with the number of cluster tests, *not* number of clusters of course), using Bonferroni or Holm-Bonferroni correction or so. I don't think this is commonly done, though. Best, Eelke On 25 September 2012 02:37, Peter Goodin wrote: > Thanks very much for the responses Stephan and Jörn! > > > > One last question if possible Jörn. In your opinion, will doing several (at > the most 5) cluster based t-tests affect the validity of permutation method > testing to control for multiple comparisons? Would being more conservative > regarding my alpha (for example a combination of permutation AND Bonferroni) > possibly alleviate this? > > > Thanks again for the responses, > > > > Peter. > > > > From: fieldtrip-bounces at science.ru.nl > [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig" > Sent: Monday, 24 September 2012 10:15 PM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Neuromag sensor level stats > > > > Dear Peter, > > regarding your first question, most people here at the Donders actually > repair bad channels. When computing the grandaverage over subjects or doing > some statistics across subjects, only those channels which are in common for > all datasets are used. Thus, if having different channels damaged/rejected > per subjects, you can end up with a fairly low amount of channels. But, in > the end it depends pretty much on what channels you reject wrt your > hypothesis, e.g. having few occipital channels while being interested in > motor regions won't constitute a big problem, so no need to interpolate. I > leave the question whether it's a correct thing to do up to you (imho: I > wouldn't worry too much about it). > > Regarding your third question: In FieldTrip you can only compare two > conditions directly (at least when doing cluster-based permutation testing). > Also, any interaction needs to be setup manually. > > Best, > Jörn > > On 9/23/2012 3:14 PM, Peter Goodin wrote: > > Hi Fieldtrippers, > > > > I'm at a stage where I'd like to do statistical analysis on my ERF neuromag > data, but don't really know where to begin. I'd like to do a cluster > analysis, but the tutorial material is for a CTF system. I'm using a > neuromag 306 channel which complicates matters somewhat due to the different > sensor types. I've searched the mailing list but can't find any solid > answers / example scripts. > > > > The most pressing questions I have are: > > > > 1. Despite running the data through maxfilter and entering in the bad > channels, occasionally one gets through (not the same one). I've used > Fieldtrip's repairchannel function on the data, making sure to replace the > channel only with like sensor neighbouring sensors. While I know this is a > common method for fixing bad channels in EEG, does the same hold for MEG due > to non-existent smearing of the signal? Is it best to keep the fixed > channel(s) or just remove them from the stats analysis across all > participants? > > > > 2. Given the three sensor types on the neuromag system, do I need to run > three different cluster analyses (one for mags, one for xgrads, one for > ygrads), each time specifying like sensor neighbours? Alternatively, If I'm > not interested in the mags data, can I just run one using the data from the > combined gradiometers? > > > > 3. When examining for group x condition effects, would I use a three row > design matrix with row 1 containing group, row 2 containing participants and > row 3 conditions? > > > > Thanks for any help, > > > > Peter > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > > Jörn M. Horschig > > PhD Student > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > Neuronal Oscillations Group > > FieldTrip Development Team > > > > P.O. Box 9101 > > NL-6500 HB Nijmegen > > The Netherlands > > > > Contact: > > E-Mail: jm.horschig at donders.ru.nl > > Tel: +31-(0)24-36-68493 > > Web: http://www.ru.nl/donders > > > > Visiting address: > > Trigon, room 2.30 > > Kapittelweg 29 > > NL-6525 EN Nijmegen > > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From g.piantoni at nin.knaw.nl Tue Sep 25 12:21:54 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Tue, 25 Sep 2012 12:21:54 +0200 Subject: [FieldTrip] How to impove dics realfilter solution In-Reply-To: <736231433.1128.1347610993969.JavaMail.root@zimbra> References: <612757646.1088.1347610775726.JavaMail.root@zimbra> <736231433.1128.1347610993969.JavaMail.root@zimbra> Message-ID: Hi Björn, It's not surprising that the results are pretty bad after using real filters. The fourier transform and DICS are intrinsically complex-valued, so using only the real part means throwing away half of the information (and getting meaningless results). The realfilter option was implemented in order to allow to pass the time-domain signal through the complex-value spatial filter and obtain a "virtual electrode". A virtual electrode with complex values is "weird to say the least", see: http://mailman.science.ru.nl/pipermail/fieldtrip/2006-May/000510.html Robert considered it an error in the algorithm and fixed it by providing the realfilter option. However, to me it seems more correct to think that complex spatial filters requires complex input (i.e. frequency-domain signal), so don't use DICS spatial filters on time-domain real-valued MEG recordings to generate time-domain virtual electrodes. If you want time-domain virtual electrodes, use LCMV spatial filters centered at the location of interest. Other smart people might disagree though. I suggest not to use realfilter option at all, but I'd be happy to hear other meaningful applications of this option. Hope this helps, Gio On Fri, Sep 14, 2012 at 10:23 AM, Björn Herrmann wrote: > Dear fieldtrip user, > > I am using the DICS beamformer to localize a 3Hz FFT power topographical distribution (using a neuromag system). The topographies are very clear auditory in single subjects, thus it shouldn't be a problem finding the "right" solution. When I use the beamformer to obtain complex-value spatial filters, the solution looks very good (using NAI). No problem here. However, using cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real values, the localization completely breaks down, sometimes even finding a strong peak in the opposite hemisphere than visible in the sensor topography (the head is centered in the sensor array). > > Does someone have a suggestion how to improve the solution using realfilter = 'yes'. I use the following settings. They are rather standard I guess. > > cfg = []; > cfg.method = 'dics'; > cfg.frequency = 3; > cfg.dics.projectnoise = 'yes'; > cfg.dics.lambda = '5%'; > cfg.dics.keepfilter = 'yes'; > cfg.dics.realfilter = 'yes'; > cfg.dics.fixedori = 'no'; > > > If someone has a suggestion, I would appreciate it. > Thanks in advance, > best, > > Björn > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From landpt at gmail.com Wed Sep 26 20:53:05 2012 From: landpt at gmail.com (Ricardo Jorge) Date: Wed, 26 Sep 2012 19:53:05 +0100 Subject: [FieldTrip] Emotiv and Fieldtrip - filter in the streamer/buffer? Message-ID: Hello there once again, I've contacted you some days ago because I was having troubles reading the data from the Emotiv in the Fieldtrip toolbox, which you replied and solved my trouble. Thanks once again. However, being worked on the data, I've noticed something odd that I cannot understand what exactly is happening: - I did not activate or put any filter (even removed the preprocessing baseline command) and the signals that I get in the fieldtrip have around 4000-5000 of mean and the variance is almost 0.05, something like that. - At the same time, I was running Emotiv Testbench and for some weird reason, the signals that I get in there have exactly the same mean, but its variance is more than 1 (something like between 1 and 1.5). - At the same time, I did run OpenVibe, which was similar to the Testbench. Seeing their plots, there are clearly some variations: Testbench/Openvibe gave much more "peaks" and spread, whereas Fieldtrip (streamer) looks less noisy, as if it was almost-perfect. But I did not apply any filter... Can I have any information about what could be happening here? Does the streamer/buffer apply some filter that I don't know? I've seen that it is not possible to acquire raw data from Emotiv, except using Emotiv SDK, Openvibe or Emokit. Is it related? Thanks in advance. Ricardo Jorge From Jan.Hirschmann at med.uni-duesseldorf.de Thu Sep 27 09:40:46 2012 From: Jan.Hirschmann at med.uni-duesseldorf.de (Jan.Hirschmann at med.uni-duesseldorf.de) Date: Thu, 27 Sep 2012 09:40:46 +0200 Subject: [FieldTrip] How to impove dics realfilter solution In-Reply-To: References: <612757646.1088.1347610775726.JavaMail.root@zimbra><736231433.1128.1347610993969.JavaMail.root@zimbra> Message-ID: <72E993C35FB11743B79FF9286E5B6D8B04772649@Mail2-UKD.VMED.UKD> Hi Gio, What about the application of projecting frequency domain data through a common filter? This is described in the beamformer tutorial on the fieldtrip website and has worked fine for me. After commenting out the realfilter line the group statistical results looked worse in my case (although I also changed lambda on this second try). >From the tutorial: "Then we compute the inverse filter based on both conditions. Note the use of cfg.keepfilter so that the output saves this computed filter. cfg = []; cfg.method = 'dics'; cfg.frequency = 18; cfg.grid = grid; cfg.vol = vol; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.keepfilter = 'yes'; cfg.dics.realfilter = 'yes'; sourceAll = ft_sourceanalysis(cfg, freqAll); By placing this pre-computed filter inside cfg.grid.filter, it can now be applied to each condition separately. cfg.grid.filter = sourceAll.avg.filter; sourcePre_con = ft_sourceanalysis(cfg, freqPre ); sourcePost_con = ft_sourceanalysis(cfg, freqPost);" Best, Jan -----Ursprüngliche Nachricht----- Von: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] Im Auftrag von Gio Piantoni Gesendet: Dienstag, 25. September 2012 12:22 An: FieldTrip discussion list Betreff: Re: [FieldTrip] How to impove dics realfilter solution Hi Björn, It's not surprising that the results are pretty bad after using real filters. The fourier transform and DICS are intrinsically complex-valued, so using only the real part means throwing away half of the information (and getting meaningless results). The realfilter option was implemented in order to allow to pass the time-domain signal through the complex-value spatial filter and obtain a "virtual electrode". A virtual electrode with complex values is "weird to say the least", see: http://mailman.science.ru.nl/pipermail/fieldtrip/2006-May/000510.html Robert considered it an error in the algorithm and fixed it by providing the realfilter option. However, to me it seems more correct to think that complex spatial filters requires complex input (i.e. frequency-domain signal), so don't use DICS spatial filters on time-domain real-valued MEG recordings to generate time-domain virtual electrodes. If you want time-domain virtual electrodes, use LCMV spatial filters centered at the location of interest. Other smart people might disagree though. I suggest not to use realfilter option at all, but I'd be happy to hear other meaningful applications of this option. Hope this helps, Gio On Fri, Sep 14, 2012 at 10:23 AM, Björn Herrmann wrote: > Dear fieldtrip user, > > I am using the DICS beamformer to localize a 3Hz FFT power topographical distribution (using a neuromag system). The topographies are very clear auditory in single subjects, thus it shouldn't be a problem finding the "right" solution. When I use the beamformer to obtain complex-value spatial filters, the solution looks very good (using NAI). No problem here. However, using cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real values, the localization completely breaks down, sometimes even finding a strong peak in the opposite hemisphere than visible in the sensor topography (the head is centered in the sensor array). > > Does someone have a suggestion how to improve the solution using realfilter = 'yes'. I use the following settings. They are rather standard I guess. > > cfg = []; > cfg.method = 'dics'; > cfg.frequency = 3; > cfg.dics.projectnoise = 'yes'; > cfg.dics.lambda = '5%'; > cfg.dics.keepfilter = 'yes'; > cfg.dics.realfilter = 'yes'; > cfg.dics.fixedori = 'no'; > > > If someone has a suggestion, I would appreciate it. > Thanks in advance, > best, > > Björn > > > > _______________________________________________ > 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 b.reuderink at donders.ru.nl Thu Sep 27 11:24:34 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Thu, 27 Sep 2012 11:24:34 +0200 Subject: [FieldTrip] Emotiv and Fieldtrip - filter in the streamer/buffer? In-Reply-To: References: Message-ID: Dear Ricardo, If I understand your remark correctly, there is a scaling difference between other software (OpenVibe & Emotiv Testbench) and FieldTrip's real-time signal from the Emotiv. Would could see if we can find this difference in scaling. But, are there other signal characteristics that are different? You mention 'less noisy' — could that be caused just by scaling, or do you have a clear indication that the signal is filtered? Screenshots would be helpful. There are some places were filtering could take place. The viewer (bufferViewer.exe) has an option to enable a high-pass filter, and the FieldTrip's shared ODM code for streaming can down-sample the signal which also involves filtering, but it should be disabled by default. Can you provide some additional info? Best, Boris PS: emotiv2ft.exe is based on the Emotiv SDK (EDK). -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl On 26 sep. 2012, at 20:53, Ricardo Jorge wrote: > Hello there once again, > > I've contacted you some days ago because I was having troubles reading > the data from the Emotiv in the Fieldtrip toolbox, which you replied > and solved my trouble. Thanks once again. > > However, being worked on the data, I've noticed something odd that I > cannot understand what exactly is happening: > - I did not activate or put any filter (even removed the preprocessing > baseline command) and the signals that I get in the fieldtrip have > around 4000-5000 of mean and the variance is almost 0.05, something > like that. > - At the same time, I was running Emotiv Testbench and for some weird > reason, the signals that I get in there have exactly the same mean, > but its variance is more than 1 (something like between 1 and 1.5). > - At the same time, I did run OpenVibe, which was similar to the Testbench. > > Seeing their plots, there are clearly some variations: > Testbench/Openvibe gave much more "peaks" and spread, whereas > Fieldtrip (streamer) looks less noisy, as if it was almost-perfect. > But I did not apply any filter... > > Can I have any information about what could be happening here? Does > the streamer/buffer apply some filter that I don't know? I've seen > that it is not possible to acquire raw data from Emotiv, except using > Emotiv SDK, Openvibe or Emokit. Is it related? > > Thanks in advance. > > Ricardo Jorge > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Thu Sep 27 13:39:07 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 27 Sep 2012 13:39:07 +0200 Subject: [FieldTrip] How to impove dics realfilter solution In-Reply-To: References: <612757646.1088.1347610775726.JavaMail.root@zimbra> <736231433.1128.1347610993969.JavaMail.root@zimbra> Message-ID: Dear Björn, caro Gio, I don't agree with you, Gio, that one should use complex-valued filters. The reason for this is that they don't make sense from a biophysical point of view. The mixing from sources to channels (as represented in the leadfields) is strictly real-valued, because it is (near-)instantaneous. I think that the unmixing from channels to sources also should be real-valued, for the same argument. When you allow filter coefficients to be complex-valued, this is equivalent to allowing the sensor-level signals to be shifted in time with respect to one another. I consider this a bit odd. In Joachim's seminal paper (on which FieldTrip's initial DICS implementation is based), this was not really explicit in the methods description. However, based on personal communications with said Joachim, I at least distilled that the filters should be real-valued. The complex-valued filters were kept in (as default) for backward compatibilitiy reasons. Although mathematically possible (perhaps even more strictly answering to the minimum variance and unit gain constraints), and sometimes seemingly giving nicer subjective results, I'd advice against using them. Cheers, JM On Sep 25, 2012, at 12:21 PM, Gio Piantoni wrote: > Hi Björn, > > It's not surprising that the results are pretty bad after using real > filters. The fourier transform and DICS are intrinsically > complex-valued, so using only the real part means throwing away half > of the information (and getting meaningless results). > > The realfilter option was implemented in order to allow to pass the > time-domain signal through the complex-value spatial filter and obtain > a "virtual electrode". A virtual electrode with complex values is > "weird to say the least", see: > http://mailman.science.ru.nl/pipermail/fieldtrip/2006-May/000510.html > Robert considered it an error in the algorithm and fixed it by > providing the realfilter option. However, to me it seems more correct > to think that complex spatial filters requires complex input (i.e. > frequency-domain signal), so don't use DICS spatial filters on > time-domain real-valued MEG recordings to generate time-domain virtual > electrodes. If you want time-domain virtual electrodes, use LCMV > spatial filters centered at the location of interest. Other smart > people might disagree though. > > I suggest not to use realfilter option at all, but I'd be happy to > hear other meaningful applications of this option. > > Hope this helps, > > Gio > > On Fri, Sep 14, 2012 at 10:23 AM, Björn Herrmann wrote: >> Dear fieldtrip user, >> >> I am using the DICS beamformer to localize a 3Hz FFT power topographical distribution (using a neuromag system). The topographies are very clear auditory in single subjects, thus it shouldn't be a problem finding the "right" solution. When I use the beamformer to obtain complex-value spatial filters, the solution looks very good (using NAI). No problem here. However, using cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real values, the localization completely breaks down, sometimes even finding a strong peak in the opposite hemisphere than visible in the sensor topography (the head is centered in the sensor array). >> >> Does someone have a suggestion how to improve the solution using realfilter = 'yes'. I use the following settings. They are rather standard I guess. >> >> cfg = []; >> cfg.method = 'dics'; >> cfg.frequency = 3; >> cfg.dics.projectnoise = 'yes'; >> cfg.dics.lambda = '5%'; >> cfg.dics.keepfilter = 'yes'; >> cfg.dics.realfilter = 'yes'; >> cfg.dics.fixedori = 'no'; >> >> >> If someone has a suggestion, I would appreciate it. >> Thanks in advance, >> best, >> >> Björn >> >> >> >> _______________________________________________ >> 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 Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Duncan.Astle at mrc-cbu.cam.ac.uk Thu Sep 27 15:17:08 2012 From: Duncan.Astle at mrc-cbu.cam.ac.uk (Duncan Astle) Date: Thu, 27 Sep 2012 13:17:08 +0000 Subject: [FieldTrip] Transfering SPM TF data into Fieldtrip Message-ID: Dear FieldTrippers, I have some nice time frequency data in SPM8. It is averaged for each subject. I would really like to bring it into fieldtrip to do some stats, but I am struggling. When I use the spm2fieldtrip function it treats my 73 frequencies as 73 different trials. Does anyone have any suggestions about how to get in to fieldtrip? Best, Duncan ________________________________________________ Dr. Duncan Astle, Programme Leader Track, British Academy Research Fellow, MRC Cognition and Brain Sciences Unit, Chaucer Road, Cambridge. Duncan.Astle at mrc-cbu.cam.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Thu Sep 27 15:18:54 2012 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Thu, 27 Sep 2012 14:18:54 +0100 Subject: [FieldTrip] Transfering SPM TF data into Fieldtrip In-Reply-To: References: Message-ID: Dear Duncan, In SPM do: D = spm_eeg_load; ftdata = D.fttimelock; Best, Vladimir On Thu, Sep 27, 2012 at 2:17 PM, Duncan Astle wrote: > Dear FieldTrippers, > > > > I have some nice time frequency data in SPM8. It is averaged for each > subject. I would really like to bring it into fieldtrip to do some stats, > but I am struggling. When I use the spm2fieldtrip function it treats my 73 > frequencies as 73 different trials. > > > > Does anyone have any suggestions about how to get in to fieldtrip? > > > > Best, > > Duncan > > ________________________________________________ > > Dr. Duncan Astle, > > Programme Leader Track, > > British Academy Research Fellow, > > MRC Cognition and Brain Sciences Unit, > > Chaucer Road, > > Cambridge. > > Duncan.Astle at mrc-cbu.cam.ac.uk > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Duncan.Astle at mrc-cbu.cam.ac.uk Thu Sep 27 17:08:55 2012 From: Duncan.Astle at mrc-cbu.cam.ac.uk (Duncan Astle) Date: Thu, 27 Sep 2012 15:08:55 +0000 Subject: [FieldTrip] Update - transfering TF data from SPM Message-ID: Dear all, I keep thinking that I have done it, in that I think that I have recreated all the information that should be needed in a field trip TF object. I did this by bringing in the extra information from D.fttimelock, and creating the cfg field as if I had run it through FT_FREQANALYSIS. The structure has these fields: l5d19 = fsample: 250.0000 label: {68x1 cell} trial: {[68x73 single]} time: {[1x376 double]} trialinfo: 1 cfg: [1x1 struct] powspctrm: [68x73x376 single] freq: [1x73 double] dimord: 'chan_freq_time' However, when I try and use my file in 'FT_FREQGRANDAVERAGE' , it does not recognise this as a TF object, and produces this error message: ??? Error using ==> ft_checkdata at 324 This function requires freq data as input. Error in ==> ft_freqgrandaverage at 66 varargin{i} = ft_checkdata(varargin{i}, 'datatype', 'freq', 'feedback', 'no'); What is it that I am missing?? Best, Duncan ________________________________________________ Dr. Duncan Astle, Programme Leader Track, British Academy Research Fellow, MRC Cognition and Brain Sciences Unit, Chaucer Road, Cambridge. Duncan.Astle at mrc-cbu.cam.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Thu Sep 27 17:32:02 2012 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Thu, 27 Sep 2012 16:32:02 +0100 Subject: [FieldTrip] Update - transfering TF data from SPM In-Reply-To: References: Message-ID: Dear Duncan, You should look in the code how FT differentiates between different structures and what goes wrong. For instance it might be that it is confused by the fsample field that shouldn't be there. It's been a while since I did something like that and FT code has evolved with more stringent checks now. Best, Vladimir On Thu, Sep 27, 2012 at 4:08 PM, Duncan Astle wrote: > Dear all, > > > > I keep thinking that I have done it, in that I think that I have recreated > all the information that should be needed in a field trip TF object. I did > this by bringing in the extra information from D.fttimelock, and creating > the cfg field as if I had run it through FT_FREQANALYSIS. The structure has > these fields: > > > > l5d19 = > > > > fsample: 250.0000 > > label: {68x1 cell} > > trial: {[68x73 single]} > > time: {[1x376 double]} > > trialinfo: 1 > > cfg: [1x1 struct] > > powspctrm: [68x73x376 single] > > freq: [1x73 double] > > dimord: 'chan_freq_time' > > > > However, when I try and use my file in ‘FT_FREQGRANDAVERAGE’ , it does not > recognise this as a TF object, and produces this error message: > > > > ??? Error using ==> ft_checkdata at 324 > > This function requires freq data as input. > > > > Error in ==> ft_freqgrandaverage at 66 > > varargin{i} = ft_checkdata(varargin{i}, 'datatype', 'freq', 'feedback', > 'no'); > > > > What is it that I am missing?? > > > > Best, > > Duncan > > > > ________________________________________________ > > Dr. Duncan Astle, > > Programme Leader Track, > > British Academy Research Fellow, > > MRC Cognition and Brain Sciences Unit, > > Chaucer Road, > > Cambridge. > > Duncan.Astle at mrc-cbu.cam.ac.uk > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Duncan.Astle at mrc-cbu.cam.ac.uk Thu Sep 27 17:55:12 2012 From: Duncan.Astle at mrc-cbu.cam.ac.uk (Duncan Astle) Date: Thu, 27 Sep 2012 15:55:12 +0000 Subject: [FieldTrip] Update - transfering TF data from SPM In-Reply-To: References: Message-ID: Dear Vladimir, Thanks for your help; I worked out what it wanted. Anyone who is interested should contact me and I will take them through it. Best, Duncan ________________________________________________ Dr. Duncan Astle, Programme Leader Track, British Academy Research Fellow, MRC Cognition and Brain Sciences Unit, Chaucer Road, Cambridge. Duncan.Astle at mrc-cbu.cam.ac.uk -----Original Message----- From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Vladimir Litvak Sent: 27 September 2012 16:32 To: FieldTrip discussion list Subject: Re: [FieldTrip] Update - transfering TF data from SPM Dear Duncan, You should look in the code how FT differentiates between different structures and what goes wrong. For instance it might be that it is confused by the fsample field that shouldn't be there. It's been a while since I did something like that and FT code has evolved with more stringent checks now. Best, Vladimir On Thu, Sep 27, 2012 at 4:08 PM, Duncan Astle wrote: > Dear all, > > > > I keep thinking that I have done it, in that I think that I have > recreated all the information that should be needed in a field trip TF > object. I did this by bringing in the extra information from > D.fttimelock, and creating the cfg field as if I had run it through > FT_FREQANALYSIS. The structure has these fields: > > > > l5d19 = > > > > fsample: 250.0000 > > label: {68x1 cell} > > trial: {[68x73 single]} > > time: {[1x376 double]} > > trialinfo: 1 > > cfg: [1x1 struct] > > powspctrm: [68x73x376 single] > > freq: [1x73 double] > > dimord: 'chan_freq_time' > > > > However, when I try and use my file in 'FT_FREQGRANDAVERAGE' , it does > not recognise this as a TF object, and produces this error message: > > > > ??? Error using ==> ft_checkdata at 324 > > This function requires freq data as input. > > > > Error in ==> ft_freqgrandaverage at 66 > > varargin{i} = ft_checkdata(varargin{i}, 'datatype', 'freq', > 'feedback', 'no'); > > > > What is it that I am missing?? > > > > Best, > > Duncan > > > > ________________________________________________ > > Dr. Duncan Astle, > > Programme Leader Track, > > British Academy Research Fellow, > > MRC Cognition and Brain Sciences Unit, > > Chaucer Road, > > Cambridge. > > Duncan.Astle at mrc-cbu.cam.ac.uk > > > > > _______________________________________________ > 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 michael.wibral at web.de Thu Sep 27 20:03:43 2012 From: michael.wibral at web.de (Michael Wibral) Date: Thu, 27 Sep 2012 20:03:43 +0200 Subject: [FieldTrip] Fwd: Re: How to impove dics realfilter solution In-Reply-To: <50649472.3050502@em.uni-frankfurt.de> References: <50649472.3050502@em.uni-frankfurt.de> Message-ID: <506494FF.7070308@web.de> -------- Original Message -------- Subject: Re: [FieldTrip] How to impove dics realfilter solution Date: Thu, 27 Sep 2012 20:01:22 +0200 From: wibral Reply-To: wibral at em.uni-frankfurt.de To: FieldTrip discussion list Dear Filedtrip users, I fully agree with jan Mathijs, in principle when using DICS to reconstruct source power, the nature of the physical processes (forward model) should guarantee that filters are automatically real-valued, because this reflects the quasi-static approximation of maxwell's equations which holds pretty well in MEG. In practice filter coeffcients only deviate from being real because of sensor noise, which is not a desirable effect. Best, Michael On 09/27/2012 01:39 PM, jan-mathijs schoffelen wrote: > Dear Björn, caro Gio, > > I don't agree with you, Gio, that one should use complex-valued > filters. The reason for this is that they don't make sense from a > biophysical point of view. The mixing from sources to channels (as > represented in the leadfields) is strictly real-valued, because it is > (near-)instantaneous. I think that the unmixing from channels to > sources also should be real-valued, for the same argument. When you > allow filter coefficients to be complex-valued, this is equivalent to > allowing the sensor-level signals to be shifted in time with respect > to one another. I consider this a bit odd. In Joachim's seminal paper > (on which FieldTrip's initial DICS implementation is based), this was > not really explicit in the methods description. However, based on > personal communications with said Joachim, I at least distilled that > the filters should be real-valued. The complex-valued filters were > kept in (as default) for backward compatibilitiy reasons. Although > mathematically possible (perhaps even more strictly answering to the > minimum variance and unit gain constraints), and sometimes seemingly > giving nicer subjective results, I'd advice against using them. > > Cheers, > > JM > > > > On Sep 25, 2012, at 12:21 PM, Gio Piantoni wrote: > >> Hi Björn, >> >> It's not surprising that the results are pretty bad after using real >> filters. The fourier transform and DICS are intrinsically >> complex-valued, so using only the real part means throwing away half >> of the information (and getting meaningless results). >> >> The realfilter option was implemented in order to allow to pass the >> time-domain signal through the complex-value spatial filter and obtain >> a "virtual electrode". A virtual electrode with complex values is >> "weird to say the least", see: >> http://mailman.science.ru.nl/pipermail/fieldtrip/2006-May/000510.html >> Robert considered it an error in the algorithm and fixed it by >> providing the realfilter option. However, to me it seems more correct >> to think that complex spatial filters requires complex input (i.e. >> frequency-domain signal), so don't use DICS spatial filters on >> time-domain real-valued MEG recordings to generate time-domain virtual >> electrodes. If you want time-domain virtual electrodes, use LCMV >> spatial filters centered at the location of interest. Other smart >> people might disagree though. >> >> I suggest not to use realfilter option at all, but I'd be happy to >> hear other meaningful applications of this option. >> >> Hope this helps, >> >> Gio >> >> On Fri, Sep 14, 2012 at 10:23 AM, Björn Herrmann >> wrote: >>> Dear fieldtrip user, >>> >>> I am using the DICS beamformer to localize a 3Hz FFT power >>> topographical distribution (using a neuromag system). The >>> topographies are very clear auditory in single subjects, thus it >>> shouldn't be a problem finding the "right" solution. When I use the >>> beamformer to obtain complex-value spatial filters, the solution >>> looks very good (using NAI). No problem here. However, using >>> cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real >>> values, the localization completely breaks down, sometimes even >>> finding a strong peak in the opposite hemisphere than visible in the >>> sensor topography (the head is centered in the sensor array). >>> >>> Does someone have a suggestion how to improve the solution using >>> realfilter = 'yes'. I use the following settings. They are rather >>> standard I guess. >>> >>> cfg = []; >>> cfg.method = 'dics'; >>> cfg.frequency = 3; >>> cfg.dics.projectnoise = 'yes'; >>> cfg.dics.lambda = '5%'; >>> cfg.dics.keepfilter = 'yes'; >>> cfg.dics.realfilter = 'yes'; >>> cfg.dics.fixedori = 'no'; >>> >>> >>> If someone has a suggestion, I would appreciate it. >>> Thanks in advance, >>> best, >>> >>> Björn >>> >>> >>> >>> _______________________________________________ >>> 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 > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > > _______________________________________________ > 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 g.piantoni at nin.knaw.nl Thu Sep 27 21:05:02 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Thu, 27 Sep 2012 21:05:02 +0200 Subject: [FieldTrip] How to impove dics realfilter solution In-Reply-To: References: <612757646.1088.1347610775726.JavaMail.root@zimbra> <736231433.1128.1347610993969.JavaMail.root@zimbra> Message-ID: Well, the people disagreeing with me are indeed very smart! Jan-Mathijs, your argument is very subtle and I agree with you that the imaginary part of the filter contains the non-instantaneous unmixing. However, for frequency-domain data it makes sense to use the non-instantaneous information, for the very reason that frequency-domain data are not instantaneous. If you take the fourier transform of a signal at 10 Hz, you're not computing it at one specific instant but over a period of time. I'd imagine that the imaginary part contains information about the frequency-domain data over that period of time. I see Michael's point as well, but would it be possible for the quasi-static approximation of Maxwell's equations to contain the imaginary part only when applied to frequency-domain data instead of time-domain data? In the end, the complex-value spatial filters are specific to one frequency band over a period of time and maybe the imaginary part accounts for the time-shift (phase-shift) implicit in the frequency-domain representation. Thanks for the interesting discussion! Happy to hear if you have further thoughts on this. Cheers, Gio On Thu, Sep 27, 2012 at 1:39 PM, jan-mathijs schoffelen wrote: > Dear Björn, caro Gio, > > I don't agree with you, Gio, that one should use complex-valued filters. The > reason for this is that they don't make sense from a biophysical point of > view. The mixing from sources to channels (as represented in the leadfields) > is strictly real-valued, because it is (near-)instantaneous. I think that > the unmixing from channels to sources also should be real-valued, for the > same argument. When you allow filter coefficients to be complex-valued, this > is equivalent to allowing the sensor-level signals to be shifted in time > with respect to one another. I consider this a bit odd. In Joachim's seminal > paper (on which FieldTrip's initial DICS implementation is based), this was > not really explicit in the methods description. However, based on personal > communications with said Joachim, I at least distilled that the filters > should be real-valued. The complex-valued filters were kept in (as default) > for backward compatibilitiy reasons. Although mathematically possible > (perhaps even more strictly answering to the minimum variance and unit gain > constraints), and sometimes seemingly giving nicer subjective results, I'd > advice against using them. > > Cheers, > > JM > > > > On Sep 25, 2012, at 12:21 PM, Gio Piantoni wrote: > > Hi Björn, > > It's not surprising that the results are pretty bad after using real > filters. The fourier transform and DICS are intrinsically > complex-valued, so using only the real part means throwing away half > of the information (and getting meaningless results). > > The realfilter option was implemented in order to allow to pass the > time-domain signal through the complex-value spatial filter and obtain > a "virtual electrode". A virtual electrode with complex values is > "weird to say the least", see: > http://mailman.science.ru.nl/pipermail/fieldtrip/2006-May/000510.html > Robert considered it an error in the algorithm and fixed it by > providing the realfilter option. However, to me it seems more correct > to think that complex spatial filters requires complex input (i.e. > frequency-domain signal), so don't use DICS spatial filters on > time-domain real-valued MEG recordings to generate time-domain virtual > electrodes. If you want time-domain virtual electrodes, use LCMV > spatial filters centered at the location of interest. Other smart > people might disagree though. > > I suggest not to use realfilter option at all, but I'd be happy to > hear other meaningful applications of this option. > > Hope this helps, > > Gio > > On Fri, Sep 14, 2012 at 10:23 AM, Björn Herrmann > wrote: > > Dear fieldtrip user, > > > I am using the DICS beamformer to localize a 3Hz FFT power topographical > distribution (using a neuromag system). The topographies are very clear > auditory in single subjects, thus it shouldn't be a problem finding the > "right" solution. When I use the beamformer to obtain complex-value spatial > filters, the solution looks very good (using NAI). No problem here. However, > using cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real > values, the localization completely breaks down, sometimes even finding a > strong peak in the opposite hemisphere than visible in the sensor topography > (the head is centered in the sensor array). > > > Does someone have a suggestion how to improve the solution using realfilter > = 'yes'. I use the following settings. They are rather standard I guess. > > > cfg = []; > > cfg.method = 'dics'; > > cfg.frequency = 3; > > cfg.dics.projectnoise = 'yes'; > > cfg.dics.lambda = '5%'; > > cfg.dics.keepfilter = 'yes'; > > cfg.dics.realfilter = 'yes'; > > cfg.dics.fixedori = 'no'; > > > > If someone has a suggestion, I would appreciate it. > > Thanks in advance, > > best, > > > Björn > > > > > _______________________________________________ > > 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 > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From bherrmann at cbs.mpg.de Thu Sep 27 21:19:06 2012 From: bherrmann at cbs.mpg.de (=?utf-8?Q?Bj=C3=B6rn_Herrmann?=) Date: Thu, 27 Sep 2012 21:19:06 +0200 (CEST) Subject: [FieldTrip] How to impove dics realfilter solution (Michael Wibral) In-Reply-To: Message-ID: <1079339450.6815.1348773546422.JavaMail.root@zimbra> Thank you Gio, Jan and Michael, This is very helpful input. I understand that it makes sense from a biological point of view and also from thinking about leadfields that the filter should be real-valued. What I find surprising though is that just from an application point of view, the localization results really look in my case much better (auditory cortex; for a very clear auditory topography of the FFT to a 3Hz modulated sound) for the complex than the real filter. I used the standard parameters for the localization, maybe something could be impoved there, but this is what really surprises me, also following this interesting discussion here. Just by looking into the struct in fieldtrip and what kind of data goes into the DICS beamformer, then there is mainly the CSD, which is complex, and the power, which is positive real-valued. Thus, thinking of a classical leadfield being generated by a source and which is then compared to the observed topography (i.e. biological meaningful and real-valed), does not completely fit here, at least in my current thinking. Therefore, I was not fully surprised seeing the realfilter producing the more puzzling localization result in my case. Can the DICS beamformer really be thought of in the "classical" way, i.e. that the source produces a real-value leadfield (positive and negative values)? I somehow understood it as localizing a power topography, which is only positive, thus in a way different from a classical leadfield. All the best, BJörn ------ Björn Herrmann Auditory Cognition Group Max Planck Institute for Human Cognitive and Brain Sciences Stephanstrasse 1a, 04103 Leipzig, Germany phone: ++49 (0)341 9940 2606 email: bherrmann at cbs.mpg.de ----- Ursprüngliche Mail ----- Von: fieldtrip-request at science.ru.nl An: fieldtrip at science.ru.nl Gesendet: Donnerstag, 27. September 2012 20:04:01 Betreff: fieldtrip Digest, Vol 22, Issue 47 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: Update - transfering TF data from SPM (Vladimir Litvak) 2. Re: Update - transfering TF data from SPM (Duncan Astle) 3. Fwd: Re: How to impove dics realfilter solution (Michael Wibral) ---------------------------------------------------------------------- Message: 1 Date: Thu, 27 Sep 2012 16:32:02 +0100 From: Vladimir Litvak To: FieldTrip discussion list Subject: Re: [FieldTrip] Update - transfering TF data from SPM Message-ID: Content-Type: text/plain; charset=windows-1252 Dear Duncan, You should look in the code how FT differentiates between different structures and what goes wrong. For instance it might be that it is confused by the fsample field that shouldn't be there. It's been a while since I did something like that and FT code has evolved with more stringent checks now. Best, Vladimir On Thu, Sep 27, 2012 at 4:08 PM, Duncan Astle wrote: > Dear all, > > > > I keep thinking that I have done it, in that I think that I have recreated > all the information that should be needed in a field trip TF object. I did > this by bringing in the extra information from D.fttimelock, and creating > the cfg field as if I had run it through FT_FREQANALYSIS. The structure has > these fields: > > > > l5d19 = > > > > fsample: 250.0000 > > label: {68x1 cell} > > trial: {[68x73 single]} > > time: {[1x376 double]} > > trialinfo: 1 > > cfg: [1x1 struct] > > powspctrm: [68x73x376 single] > > freq: [1x73 double] > > dimord: 'chan_freq_time' > > > > However, when I try and use my file in ?FT_FREQGRANDAVERAGE? , it does not > recognise this as a TF object, and produces this error message: > > > > ??? Error using ==> ft_checkdata at 324 > > This function requires freq data as input. > > > > Error in ==> ft_freqgrandaverage at 66 > > varargin{i} = ft_checkdata(varargin{i}, 'datatype', 'freq', 'feedback', > 'no'); > > > > What is it that I am missing?? > > > > Best, > > Duncan > > > > ________________________________________________ > > Dr. Duncan Astle, > > Programme Leader Track, > > British Academy Research Fellow, > > MRC Cognition and Brain Sciences Unit, > > Chaucer Road, > > Cambridge. > > Duncan.Astle at mrc-cbu.cam.ac.uk > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ------------------------------ Message: 2 Date: Thu, 27 Sep 2012 15:55:12 +0000 From: Duncan Astle To: FieldTrip discussion list Subject: Re: [FieldTrip] Update - transfering TF data from SPM Message-ID: Content-Type: text/plain; charset="us-ascii" Dear Vladimir, Thanks for your help; I worked out what it wanted. Anyone who is interested should contact me and I will take them through it. Best, Duncan ________________________________________________ Dr. Duncan Astle, Programme Leader Track, British Academy Research Fellow, MRC Cognition and Brain Sciences Unit, Chaucer Road, Cambridge. Duncan.Astle at mrc-cbu.cam.ac.uk -----Original Message----- From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Vladimir Litvak Sent: 27 September 2012 16:32 To: FieldTrip discussion list Subject: Re: [FieldTrip] Update - transfering TF data from SPM Dear Duncan, You should look in the code how FT differentiates between different structures and what goes wrong. For instance it might be that it is confused by the fsample field that shouldn't be there. It's been a while since I did something like that and FT code has evolved with more stringent checks now. Best, Vladimir On Thu, Sep 27, 2012 at 4:08 PM, Duncan Astle wrote: > Dear all, > > > > I keep thinking that I have done it, in that I think that I have > recreated all the information that should be needed in a field trip TF > object. I did this by bringing in the extra information from > D.fttimelock, and creating the cfg field as if I had run it through > FT_FREQANALYSIS. The structure has these fields: > > > > l5d19 = > > > > fsample: 250.0000 > > label: {68x1 cell} > > trial: {[68x73 single]} > > time: {[1x376 double]} > > trialinfo: 1 > > cfg: [1x1 struct] > > powspctrm: [68x73x376 single] > > freq: [1x73 double] > > dimord: 'chan_freq_time' > > > > However, when I try and use my file in 'FT_FREQGRANDAVERAGE' , it does > not recognise this as a TF object, and produces this error message: > > > > ??? Error using ==> ft_checkdata at 324 > > This function requires freq data as input. > > > > Error in ==> ft_freqgrandaverage at 66 > > varargin{i} = ft_checkdata(varargin{i}, 'datatype', 'freq', > 'feedback', 'no'); > > > > What is it that I am missing?? > > > > Best, > > Duncan > > > > ________________________________________________ > > Dr. Duncan Astle, > > Programme Leader Track, > > British Academy Research Fellow, > > MRC Cognition and Brain Sciences Unit, > > Chaucer Road, > > Cambridge. > > Duncan.Astle at mrc-cbu.cam.ac.uk > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ------------------------------ Message: 3 Date: Thu, 27 Sep 2012 20:03:43 +0200 From: Michael Wibral To: FieldTrip discussion list Subject: [FieldTrip] Fwd: Re: How to impove dics realfilter solution Message-ID: <506494FF.7070308 at web.de> Content-Type: text/plain; charset="iso-8859-1" -------- Original Message -------- Subject: Re: [FieldTrip] How to impove dics realfilter solution Date: Thu, 27 Sep 2012 20:01:22 +0200 From: wibral Reply-To: wibral at em.uni-frankfurt.de To: FieldTrip discussion list Dear Filedtrip users, I fully agree with jan Mathijs, in principle when using DICS to reconstruct source power, the nature of the physical processes (forward model) should guarantee that filters are automatically real-valued, because this reflects the quasi-static approximation of maxwell's equations which holds pretty well in MEG. In practice filter coeffcients only deviate from being real because of sensor noise, which is not a desirable effect. Best, Michael On 09/27/2012 01:39 PM, jan-mathijs schoffelen wrote: > Dear Bj?rn, caro Gio, > > I don't agree with you, Gio, that one should use complex-valued > filters. The reason for this is that they don't make sense from a > biophysical point of view. The mixing from sources to channels (as > represented in the leadfields) is strictly real-valued, because it is > (near-)instantaneous. I think that the unmixing from channels to > sources also should be real-valued, for the same argument. When you > allow filter coefficients to be complex-valued, this is equivalent to > allowing the sensor-level signals to be shifted in time with respect > to one another. I consider this a bit odd. In Joachim's seminal paper > (on which FieldTrip's initial DICS implementation is based), this was > not really explicit in the methods description. However, based on > personal communications with said Joachim, I at least distilled that > the filters should be real-valued. The complex-valued filters were > kept in (as default) for backward compatibilitiy reasons. Although > mathematically possible (perhaps even more strictly answering to the > minimum variance and unit gain constraints), and sometimes seemingly > giving nicer subjective results, I'd advice against using them. > > Cheers, > > JM > > > > On Sep 25, 2012, at 12:21 PM, Gio Piantoni wrote: > >> Hi Bj?rn, >> >> It's not surprising that the results are pretty bad after using real >> filters. The fourier transform and DICS are intrinsically >> complex-valued, so using only the real part means throwing away half >> of the information (and getting meaningless results). >> >> The realfilter option was implemented in order to allow to pass the >> time-domain signal through the complex-value spatial filter and obtain >> a "virtual electrode". A virtual electrode with complex values is >> "weird to say the least", see: >> http://mailman.science.ru.nl/pipermail/fieldtrip/2006-May/000510.html >> Robert considered it an error in the algorithm and fixed it by >> providing the realfilter option. However, to me it seems more correct >> to think that complex spatial filters requires complex input (i.e. >> frequency-domain signal), so don't use DICS spatial filters on >> time-domain real-valued MEG recordings to generate time-domain virtual >> electrodes. If you want time-domain virtual electrodes, use LCMV >> spatial filters centered at the location of interest. Other smart >> people might disagree though. >> >> I suggest not to use realfilter option at all, but I'd be happy to >> hear other meaningful applications of this option. >> >> Hope this helps, >> >> Gio >> >> On Fri, Sep 14, 2012 at 10:23 AM, Bj?rn Herrmann >> wrote: >>> Dear fieldtrip user, >>> >>> I am using the DICS beamformer to localize a 3Hz FFT power >>> topographical distribution (using a neuromag system). The >>> topographies are very clear auditory in single subjects, thus it >>> shouldn't be a problem finding the "right" solution. When I use the >>> beamformer to obtain complex-value spatial filters, the solution >>> looks very good (using NAI). No problem here. However, using >>> cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real >>> values, the localization completely breaks down, sometimes even >>> finding a strong peak in the opposite hemisphere than visible in the >>> sensor topography (the head is centered in the sensor array). >>> >>> Does someone have a suggestion how to improve the solution using >>> realfilter = 'yes'. I use the following settings. They are rather >>> standard I guess. >>> >>> cfg = []; >>> cfg.method = 'dics'; >>> cfg.frequency = 3; >>> cfg.dics.projectnoise = 'yes'; >>> cfg.dics.lambda = '5%'; >>> cfg.dics.keepfilter = 'yes'; >>> cfg.dics.realfilter = 'yes'; >>> cfg.dics.fixedori = 'no'; >>> >>> >>> If someone has a suggestion, I would appreciate it. >>> Thanks in advance, >>> best, >>> >>> Bj?rn >>> >>> >>> >>> _______________________________________________ >>> 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 > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip End of fieldtrip Digest, Vol 22, Issue 47 ***************************************** From g.piantoni at nin.knaw.nl Fri Sep 28 10:50:35 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Fri, 28 Sep 2012 10:50:35 +0200 Subject: [FieldTrip] Fwd: Re: How to impove dics realfilter solution In-Reply-To: <506494FF.7070308@web.de> References: <50649472.3050502@em.uni-frankfurt.de> <506494FF.7070308@web.de> Message-ID: Hi Michael, Thanks for your suggestion! In fact, the contribution of the imaginary part increases with higher levels of noise (and it's zero when the noise is zero). I tested with a simulation (see code below). The imaginary part derives from the uncorrelated sensor noise and seem to contain no meaningful information, sorry if I had given wrong information before, my intuition tricked me. Thanks for the interesting discussion! Cheers, Gio %-----------------% %-forward model fieldtripdir = '/path/to/fieldtrip/'; elec = ft_read_sens([fieldtripdir 'template/electrode/standard_1020.elc']); load([fieldtripdir 'template/headmodel/standard_bem.mat']); cfg = []; cfg.elec = elec; cfg.vol = vol; cfg.grid.xgrid = -80:10:80; cfg.grid.ygrid = -110:10:80; cfg.grid.zgrid = -70:10:90; cfg.inwardshift = 1; lead = ft_prepare_leadfield(cfg); %-----------------% %-------------------------------------% %-loop over relative noise relnoise = 0:.05:1; realfilter = zeros(size(relnoise)); imagfilter = zeros(size(relnoise)); for i = 1:numel(relnoise) %-----------------% %-create data cfg = []; cfg.dip.pos = [10 30 30]; cfg.dip.mom = [1 0 0]'; cfg.dip.frequency = 10; cfg.vol = vol; cfg.relnoise = relnoise(i); cfg.elec = elec; data = ft_dipolesimulation(cfg); %-----------------% %-----------------% %-fourier freq cfg = []; cfg.method = 'mtmfft'; cfg.output = 'fourier'; cfg.taper = 'hanning'; cfg.foilim = [10 10]; freq = ft_freqanalysis(cfg, data); %-----------------% %-----------------% %-beamformer cfg = []; cfg.method = 'dics'; cfg.frequency = 10; cfg.grid = lead; cfg.vol = vol; cfg.elec = elec; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '1%'; cfg.dics.keepfilter = 'yes'; source = ft_sourceanalysis(cfg, freq); %-take one dipole as example realfilter(i) = sum(abs(real(source.avg.filter{source.inside(100)}(:)))); imagfilter(i) = sum(abs(imag(source.avg.filter{source.inside(100)}(:)))); %-----------------% end plot(relnoise, realfilter) hold on plot(relnoise, imagfilter, 'r') %-------------------------------------% On Thu, Sep 27, 2012 at 8:03 PM, Michael Wibral wrote: > > > > > -------- Original Message -------- > Subject: Re: [FieldTrip] How to impove dics realfilter solution > Date: Thu, 27 Sep 2012 20:01:22 +0200 > From: wibral > Reply-To: wibral at em.uni-frankfurt.de > To: FieldTrip discussion list > > > > Dear Filedtrip users, > > I fully agree with jan Mathijs, > > in principle when using DICS to reconstruct source power, the nature of > the physical processes (forward model) should guarantee that filters are > automatically real-valued, because this reflects the quasi-static > approximation of maxwell's equations which holds pretty well in MEG. In > practice filter coeffcients only deviate from being real because of sensor > noise, which is not a desirable effect. > > Best, > Michael > > > On 09/27/2012 01:39 PM, jan-mathijs schoffelen wrote: > > Dear Björn, caro Gio, > > I don't agree with you, Gio, that one should use complex-valued filters. > The reason for this is that they don't make sense from a biophysical point > of view. The mixing from sources to channels (as represented in the > leadfields) is strictly real-valued, because it is (near-)instantaneous. I > think that the unmixing from channels to sources also should be real-valued, > for the same argument. When you allow filter coefficients to be > complex-valued, this is equivalent to allowing the sensor-level signals to > be shifted in time with respect to one another. I consider this a bit odd. > In Joachim's seminal paper (on which FieldTrip's initial DICS implementation > is based), this was not really explicit in the methods description. However, > based on personal communications with said Joachim, I at least distilled > that the filters should be real-valued. The complex-valued filters were kept > in (as default) for backward compatibilitiy reasons. Although mathematically > possible (perhaps even more strictly answering to the minimum variance and > unit gain constraints), and sometimes seemingly giving nicer subjective > results, I'd advice against using them. > > Cheers, > > JM > > > > On Sep 25, 2012, at 12:21 PM, Gio Piantoni wrote: > > Hi Björn, > > It's not surprising that the results are pretty bad after using real > filters. The fourier transform and DICS are intrinsically > complex-valued, so using only the real part means throwing away half > of the information (and getting meaningless results). > > The realfilter option was implemented in order to allow to pass the > time-domain signal through the complex-value spatial filter and obtain > a "virtual electrode". A virtual electrode with complex values is > "weird to say the least", see: > http://mailman.science.ru.nl/pipermail/fieldtrip/2006-May/000510.html > Robert considered it an error in the algorithm and fixed it by > providing the realfilter option. However, to me it seems more correct > to think that complex spatial filters requires complex input (i.e. > frequency-domain signal), so don't use DICS spatial filters on > time-domain real-valued MEG recordings to generate time-domain virtual > electrodes. If you want time-domain virtual electrodes, use LCMV > spatial filters centered at the location of interest. Other smart > people might disagree though. > > I suggest not to use realfilter option at all, but I'd be happy to > hear other meaningful applications of this option. > > Hope this helps, > > Gio > > On Fri, Sep 14, 2012 at 10:23 AM, Björn Herrmann > wrote: > > Dear fieldtrip user, > > > I am using the DICS beamformer to localize a 3Hz FFT power topographical > distribution (using a neuromag system). The topographies are very clear > auditory in single subjects, thus it shouldn't be a problem finding the > "right" solution. When I use the beamformer to obtain complex-value spatial > filters, the solution looks very good (using NAI). No problem here. However, > using cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real > values, the localization completely breaks down, sometimes even finding a > strong peak in the opposite hemisphere than visible in the sensor topography > (the head is centered in the sensor array). > > > Does someone have a suggestion how to improve the solution using > realfilter = 'yes'. I use the following settings. They are rather standard I > guess. > > > cfg = []; > > cfg.method = 'dics'; > > cfg.frequency = 3; > > cfg.dics.projectnoise = 'yes'; > > cfg.dics.lambda = '5%'; > > cfg.dics.keepfilter = 'yes'; > > cfg.dics.realfilter = 'yes'; > > cfg.dics.fixedori = 'no'; > > > > If someone has a suggestion, I would appreciate it. > > Thanks in advance, > > best, > > > Björn > > > > > _______________________________________________ > > 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 > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > > _______________________________________________ > 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 landpt at gmail.com Fri Sep 28 11:39:58 2012 From: landpt at gmail.com (Ricardo Jorge) Date: Fri, 28 Sep 2012 10:39:58 +0100 Subject: [FieldTrip] Emotiv and Fieldtrip - filter in the streamer/buffer? In-Reply-To: References: Message-ID: Dear Boris, Sorry for the late response, I tried to reply as earliest as possible. Thank for the answer, by the way. I don't think it's a scaling issue: it shouldn't affect the variance that much and Power spectral seem to be different from both ways. Absolutely that I can give you additional information; I am starting with explaining almost everything I've done: 1st: I picked up the function ft_realtime_signalviewer in "fieldtrip-20120904\realtime\example" and adapted it slightly so I could view it in realtime but at the same time, I could see the previous 20 seconds. Besides that, I disabled the ft_preproc_baselinecorrect(data.trial{1}) step in that function and added some steps that allowed me to save the whole record into a file at the same time (is there any function in fieldtrip that does that at the same time as realtime?). I'm not sure if I can send files through this discussion list: tell me if you want to try it. Just for visualization issues, I multiplied the signal in the plot by a factor, so it could be similar to Testbench visually, but it doesn't matter because I'm not changing any data, just the plot. 2nd: I opened Testbench and OpenVibe. In order to compare the results, I saved them into EDF an opened it in matlab. Testbench has an option to set an high-pass filter, but it does not alter the recording, only the visualization in real time. 3rd: I did put the emotiv in the table so it could be at the rest. 4th: I started all 3 of them. They're not be all exactly at the same time because I can't press it all at once (but almost) and so I'll record during a reasonable time so I can get enough samples. Results: 1. There is a weird thing in the testbench/openvibe data, all values in AF3 channel (for instance) are integer numbers, whereas Fieldtrip are not: Fieldtrip: 1.0e+03 * 4.030540530271679 4.030428591191215 4.030553469018260 4.030684982830449 4.030580735490210 4.030495361159973 Testbench: 4029 4030 4031 4031 4032 4032 They're almost the same and it isn't a problem since they didnt start exactly at the same time. However, analyzing their mean/variance, we have: Fieldtrip: Mean: 4.030526515189773e+03 Variance: 0.011920664040352 Offline (Testbench): Mean: 4.030526118470382e+03 Variance:1.641380154961390 Their mean are great but the same cannot be said to their variance: in fact it seems that it spreads way too much while offline. Let's see their min and max through a sample: Fieldtrip: [4.027692307692308e+03 ; 4.032307692307693e+03] Testbench: [4025 ; 4037] I've put a plot in my dropbox folder if you want to check it: https://dl.dropbox.com/u/846911/comparision.jpg I've checked if the signalviewer has any filter, but I can't find any, so I cannot understand exactly what could be happening. Their FFT is similar but not exactly the same as well. What do you think it could be happening? Thanks in advance, Best Regards Ricardo Jorge From b.reuderink at donders.ru.nl Fri Sep 28 13:14:37 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Fri, 28 Sep 2012 13:14:37 +0200 Subject: [FieldTrip] Emotiv and Fieldtrip - filter in the streamer/buffer? In-Reply-To: References: Message-ID: <11DBE635-CEA4-4580-B5B3-19C31E6259F1@donders.ru.nl> Dear Ricardo, No problem, and thank you for your elaborate response :). When I look at your screenshot, the right subplot seems to show a rounding issue; all the values are indeed integers, while on the left a more continuous signal is displayed. So, I would say that the difference between the signals is at least a rounding issue, and I assume that the FieldTrip signal is the more precise one. This might explain the difference in variance. For me this raises the question where this rounding comes from. You say that both OpenVibe and Emotiv's Testbench have these integer valued samples? Could this rounding to integers happen at some other stage (e.g. after importing in MATLAB?). Best, Boris -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl On 28 sep. 2012, at 11:39, Ricardo Jorge wrote: > Dear Boris, > > Sorry for the late response, I tried to reply as earliest as possible. > Thank for the answer, by the way. > > I don't think it's a scaling issue: it shouldn't affect the variance > that much and Power spectral seem to be different from both ways. > Absolutely that I can give you additional information; I am starting > with explaining almost everything I've done: > > 1st: I picked up the function ft_realtime_signalviewer in > "fieldtrip-20120904\realtime\example" and adapted it slightly so I > could view it in realtime but at the same time, I could see the > previous 20 seconds. Besides that, I disabled the > ft_preproc_baselinecorrect(data.trial{1}) step in that function and > added some steps that allowed me to save the whole record into a file > at the same time (is there any function in fieldtrip that does that at > the same time as realtime?). I'm not sure if I can send files through > this discussion list: tell me if you want to try it. Just for > visualization issues, I multiplied the signal in the plot by a factor, > so it could be similar to Testbench visually, but it doesn't matter > because I'm not changing any data, just the plot. > > 2nd: I opened Testbench and OpenVibe. In order to compare the results, > I saved them into EDF an opened it in matlab. Testbench has an option > to set an high-pass filter, but it does not alter the recording, only > the visualization in real time. > > 3rd: I did put the emotiv in the table so it could be at the rest. > > 4th: I started all 3 of them. They're not be all exactly at the same > time because I can't press it all at once (but almost) and so I'll > record during a reasonable time so I can get enough samples. > > Results: > > 1. There is a weird thing in the testbench/openvibe data, all values > in AF3 channel (for instance) are integer numbers, whereas Fieldtrip > are not: > > Fieldtrip: > 1.0e+03 * > > 4.030540530271679 4.030428591191215 4.030553469018260 > 4.030684982830449 4.030580735490210 4.030495361159973 > > Testbench: > 4029 4030 4031 4031 4032 4032 > > They're almost the same and it isn't a problem since they didnt start > exactly at the same time. > However, analyzing their mean/variance, we have: > > Fieldtrip: > > Mean: 4.030526515189773e+03 > Variance: 0.011920664040352 > > Offline (Testbench): > > Mean: 4.030526118470382e+03 > Variance:1.641380154961390 > > Their mean are great but the same cannot be said to their variance: in > fact it seems that it spreads way too much while offline. Let's see > their min and max through a sample: > Fieldtrip: [4.027692307692308e+03 ; 4.032307692307693e+03] > Testbench: [4025 ; 4037] > > I've put a plot in my dropbox folder if you want to check it: > https://dl.dropbox.com/u/846911/comparision.jpg > > > I've checked if the signalviewer has any filter, but I can't find any, > so I cannot understand exactly what could be happening. > > Their FFT is similar but not exactly the same as well. > > What do you think it could be happening? > > Thanks in advance, > > Best Regards > > Ricardo Jorge > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From landpt at gmail.com Fri Sep 28 14:16:10 2012 From: landpt at gmail.com (Ricardo Jorge) Date: Fri, 28 Sep 2012 13:16:10 +0100 Subject: [FieldTrip] Emotiv and Fieldtrip - filter in the streamer/buffer? In-Reply-To: References: Message-ID: Hi again, I'm not sure, to be honest! I would say fieldtrip is the most precise one, but why would it happen - I mean, how could it be better than the testbench? That's what's confusing me: it makes no sense that a signal such as EEG has only integer values indeed. But there are weirder things: In the EDF/CSV files from testbench, the first channel (AF3) has only integer values, the second channel doesn't have only integer values, but have mean 260 around, the third channel goes back to the integer values and 4000 mean again, fourth chan back to ~200 mean, non-integer and it goes on... which makes me thinking that they probably apply something, either the baseline and rounding, or something more. In the EDF files from Openvibe, all numbers are integers as independently of the channel, but variance's different as well. In fact, estimating it right now, it says that it has variance around 3. In the MAT file recorded by Fieldtrip, all numbers are non integer but with an extremely low variance comparing to the others. So, for some reason all methods are different but to be honest I feel that fieldtrip's results are correct and so I'm going to give it a try and use them in my investigation to see if they can confirm what I expect. Thanks once again! Best regards, Ricardo Jorge On Fri, Sep 28, 2012 at 10:39 AM, Ricardo Jorge wrote: > Dear Boris, > > Sorry for the late response, I tried to reply as earliest as possible. > Thank for the answer, by the way. > > I don't think it's a scaling issue: it shouldn't affect the variance > that much and Power spectral seem to be different from both ways. > Absolutely that I can give you additional information; I am starting > with explaining almost everything I've done: > > 1st: I picked up the function ft_realtime_signalviewer in > "fieldtrip-20120904\realtime\example" and adapted it slightly so I > could view it in realtime but at the same time, I could see the > previous 20 seconds. Besides that, I disabled the > ft_preproc_baselinecorrect(data.trial{1}) step in that function and > added some steps that allowed me to save the whole record into a file > at the same time (is there any function in fieldtrip that does that at > the same time as realtime?). I'm not sure if I can send files through > this discussion list: tell me if you want to try it. Just for > visualization issues, I multiplied the signal in the plot by a factor, > so it could be similar to Testbench visually, but it doesn't matter > because I'm not changing any data, just the plot. > > 2nd: I opened Testbench and OpenVibe. In order to compare the results, > I saved them into EDF an opened it in matlab. Testbench has an option > to set an high-pass filter, but it does not alter the recording, only > the visualization in real time. > > 3rd: I did put the emotiv in the table so it could be at the rest. > > 4th: I started all 3 of them. They're not be all exactly at the same > time because I can't press it all at once (but almost) and so I'll > record during a reasonable time so I can get enough samples. > > Results: > > 1. There is a weird thing in the testbench/openvibe data, all values > in AF3 channel (for instance) are integer numbers, whereas Fieldtrip > are not: > > Fieldtrip: > 1.0e+03 * > > 4.030540530271679 4.030428591191215 4.030553469018260 > 4.030684982830449 4.030580735490210 4.030495361159973 > > Testbench: > 4029 4030 4031 4031 4032 4032 > > They're almost the same and it isn't a problem since they didnt start > exactly at the same time. > However, analyzing their mean/variance, we have: > > Fieldtrip: > > Mean: 4.030526515189773e+03 > Variance: 0.011920664040352 > > Offline (Testbench): > > Mean: 4.030526118470382e+03 > Variance:1.641380154961390 > > Their mean are great but the same cannot be said to their variance: in > fact it seems that it spreads way too much while offline. Let's see > their min and max through a sample: > Fieldtrip: [4.027692307692308e+03 ; 4.032307692307693e+03] > Testbench: [4025 ; 4037] > > I've put a plot in my dropbox folder if you want to check it: > https://dl.dropbox.com/u/846911/comparision.jpg > > > I've checked if the signalviewer has any filter, but I can't find any, > so I cannot understand exactly what could be happening. > > Their FFT is similar but not exactly the same as well. > > What do you think it could be happening? > > Thanks in advance, > > Best Regards > > Ricardo Jorge From mark.noordenbos at gmail.com Sun Sep 30 11:30:35 2012 From: mark.noordenbos at gmail.com (Mark Noordenbos) Date: Sun, 30 Sep 2012 11:30:35 +0200 Subject: [FieldTrip] cluster analysis Message-ID: Dear Fieldtrippers, I was wondering how you report the results of the cluster analysis in your papers. I have seen different types of how the results are reported. For example, some report only the p-value of the cluster whereas others report clusters as T(degrees of freedom) = [clusterstat value], p-value. Is T (multivariate t) the correct test statisic for the cluster analysis (like F for anova)? Where can I find (or calculate) the degrees of freedom of the clusterstat value? Thanks Best, Mark -------------- next part -------------- An HTML attachment was scrubbed... URL: From politzerahless at gmail.com Sun Sep 30 15:46:09 2012 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Sun, 30 Sep 2012 08:46:09 -0500 Subject: [FieldTrip] cluster analysis Message-ID: Hi Mark, The Fieldtrip wiki has examples of published papers that report cluster analyses. In what I've seen, usually just the *p* is reported (if even that), along with the latency and topography of the cluster. See e.g. Pijnacker et al. (2011, *Journal of Cognitive Neuroscience*) and Meltzer & Braun (2011, *Frontiers in Human Neuroscience*). There may be others in http://fieldtrip.fcdonders.nl/publications As for your second question, my understanding is that the test statistic doesn't matter (one of the points of the cluster test is that it works no matter which test statistic you use (Maris & Oostenveld, 2007)). Also, to the best of my knowledge, there are no degrees of freedom for the cluster test, since it's non-parametric (it's not based on the distribution of a test statistic, it's based on Monte Carlo estimation). Best, Steve Message: 1 > Date: Sun, 30 Sep 2012 11:30:35 +0200 > From: Mark Noordenbos > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] cluster analysis > Message-ID: > 7qVRZp7goj3AhoE7xaq8tqTPsg at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Fieldtrippers, > > I was wondering how you report the results of the cluster analysis in your > papers. I have seen different types of how the results are reported. > For example, some report only the p-value of the cluster whereas others > report clusters as T(degrees of freedom) = [clusterstat value], p-value. > > Is T (multivariate t) the correct test statisic for the cluster analysis > (like F for anova)? > Where can I find (or calculate) the degrees of freedom of the clusterstat > value? > > Thanks > > Best, > Mark > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120930/fe6908ab/attachment-0001.html > > > > ------------------------------ > -------------- next part -------------- An HTML attachment was scrubbed... URL: From demiral.007 at gmail.com Sat Sep 1 16:29:35 2012 From: demiral.007 at gmail.com (Baris Demiral) Date: Sat, 1 Sep 2012 10:29:35 -0400 Subject: [FieldTrip] CTF data event/reading Message-ID: Hi Nedad, filedtrippers, I have continuous and epoched CTF data as well, and I want to import them into fieldtrip. The event types are previously edited in the early stages. When I looked at the event values with the ft_read_event(cfg.dataset) function, I see that some event values are empty '[ ]'. On the other hand, the initial triggers / event types have integer event values (type: 'front panel trigger', value: 222). Error is in " ft_preprocessing (line 511) ... tim = offset2time(offset, hdr.Fs, size(dat,2)); See below. Can you help me on that? What functions/lines of code shall I call? I followed the instructions on the web tutorials line by line, but nope. Sometimes it says " trialfun is not described." I also download fileio package. I am using the most recent version of FieldTrip. Do you think the event structure has anything to do with the errors, or I had to install some other package as well? Thanks Baris >> cfg.dataset = 'AFLLBCEAXXX_epoched.ds'; % name of CTF dataset data = ft_preprocessing(cfg) readCTFds: You are reading CTF data for use with a software-application tool that is not manufactured by VSM MedTech Ltd. and has not received marketing clearance for clinical applications. If CTF MEG data are processed by this tool, they should not be later employed for clinical and/or diagnostic purposes. undoing the G3BR balancing processing channel { 'UPPT001' 'SCLK01' 'BG1' 'BG2' 'BG3' 'BP1' 'BP2' 'BP3' 'BR1' 'BR2' 'BR3' 'G11' 'G12' 'G13' 'G22' 'G23' 'P11' 'P12' 'P22' 'P23' 'Q11' 'Q12' 'Q13' 'Q22' 'Q23' 'R11' 'R12' 'R13' 'R22' 'R23' 'MLC11' 'MLC12' 'MLC13' 'MLC14' 'MLC15' 'MLC16' 'MLC17' 'MLC21' 'MLC22' 'MLC23' 'MLC24' 'MLC25' 'MLC31' 'MLC32' 'MLC41' 'MLC42' 'MLC51' 'MLC52' 'MLC53' 'MLC54' 'MLC55' 'MLC61' 'MLC62' 'MLC63' 'MLF11' 'MLF12' 'MLF13' 'MLF14' 'MLF21' 'MLF22' 'MLF23' 'MLF24' 'MLF25' 'MLF31' 'MLF32' 'MLF33' 'MLF34' 'MLF35' 'MLF41' 'MLF42' 'MLF43' 'MLF44' 'MLF45' 'MLF46' 'MLF51' 'MLF52' 'MLF53' 'MLF54' 'MLF55' 'MLF56' 'MLF61' 'MLF62' 'MLF63' 'MLF64' 'MLF65' 'MLF66' 'MLF67' 'MLO11' 'MLO12' 'MLO13' 'MLO14' 'MLO21' 'MLO22' 'MLO23' 'MLO24' 'MLO31' 'MLO32' 'MLO33' 'MLO34' 'MLO41' 'MLO42' 'MLO43' 'MLO44' 'MLO51' 'MLO52' 'MLO53' 'MLP11' 'MLP12' 'MLP21' 'MLP22' 'MLP23' 'MLP31' 'MLP32' 'MLP33' 'MLP34' 'MLP35' 'MLP41' 'MLP42' 'MLP43' 'MLP44' 'MLP45' 'MLP51' 'MLP52' 'MLP53' 'MLP54' 'MLP55' 'MLP56' 'MLP57' 'MLT11' 'MLT12' 'MLT13' 'MLT14' 'MLT15' 'MLT16' 'MLT21' 'MLT22' 'MLT23' 'MLT24' 'MLT25' 'MLT26' 'MLT27' 'MLT31' 'MLT32' 'MLT33' 'MLT34' 'MLT35' 'MLT36' 'MLT37' 'MLT41' 'MLT42' 'MLT43' 'MLT44' 'MLT45' 'MLT46' 'MLT47' 'MLT51' 'MLT52' 'MLT53' 'MLT54' 'MLT55' 'MLT56' 'MLT57' 'MRC11' 'MRC12' 'MRC13' 'MRC14' 'MRC15' 'MRC16' 'MRC17' 'MRC21' 'MRC22' 'MRC23' 'MRC24' 'MRC25' 'MRC31' 'MRC32' 'MRC41' 'MRC42' 'MRC51' 'MRC52' 'MRC53' 'MRC54' 'MRC55' 'MRC61' 'MRC62' 'MRC63' 'MRF11' 'MRF12' 'MRF13' 'MRF14' 'MRF21' 'MRF22' 'MRF23' 'MRF24' 'MRF25' 'MRF31' 'MRF32' 'MRF33' 'MRF34' 'MRF35' 'MRF41' 'MRF42' 'MRF44' 'MRF45' 'MRF46' 'MRF51' 'MRF52' 'MRF53' 'MRF54' 'MRF55' 'MRF56' 'MRF61' 'MRF62' 'MRF63' 'MRF64' 'MRF65' 'MRF66' 'MRF67' 'MRO11' 'MRO12' 'MRO14' 'MRO21' 'MRO22' 'MRO23' 'MRO24' 'MRO31' 'MRO32' 'MRO33' 'MRO34' 'MRO41' 'MRO42' 'MRO43' 'MRO44' 'MRO51' 'MRO52' 'MRO53' 'MRP11' 'MRP12' 'MRP21' 'MRP22' 'MRP23' 'MRP31' 'MRP32' 'MRP33' 'MRP34' 'MRP35' 'MRP41' 'MRP42' 'MRP43' 'MRP44' 'MRP45' 'MRP51' 'MRP52' 'MRP53' 'MRP54' 'MRP55' 'MRP56' 'MRP57' 'MRT11' 'MRT12' 'MRT13' 'MRT14' 'MRT15' 'MRT16' 'MRT21' 'MRT22' 'MRT23' 'MRT24' 'MRT25' 'MRT26' 'MRT27' 'MRT31' 'MRT32' 'MRT33' 'MRT34' 'MRT35' 'MRT36' 'MRT37' 'MRT41' 'MRT42' 'MRT43' 'MRT44' 'MRT45' 'MRT46' 'MRT47' 'MRT51' 'MRT52' 'MRT53' 'MRT54' 'MRT55' 'MRT56' 'MRT57' 'MZC01' 'MZC02' 'MZC03' 'MZC04' 'MZF01' 'MZF02' 'MZF03' 'MZO01' 'MZO02' 'MZO03' 'MZP01' 'lip' 'HADC001' 'HADC002' 'HADC003' 'HDAC001' 'HDAC002' 'HDAC003' 'UADC003' 'UADC004' 'UADC016' 'HLC0011' 'HLC0012' 'HLC0013' 'HLC0021' 'HLC0022' 'HLC0023' 'HLC0031' 'HLC0032' 'HLC0033' 'HLC0018' 'HLC0028' 'HLC0038' 'HLC0014' 'HLC0015' 'HLC0016' 'HLC0017' 'HLC0024' 'HLC0025' 'HLC0026' 'HLC0027' 'HLC0034' 'HLC0035' 'HLC0036' 'HLC0037' } reading and preprocessing reading and preprocessing trial 1 from 72 Undefined function 'offset2time' for input arguments of type 'double'. Error in ft_preprocessing (line 511) tim = offset2time(offset, hdr.Fs, size(dat,2)); >> cfg.trialdef.eventtype = '?'; >> cfg = ft_definetrial(cfg); Warning: no trialfun was specified, using ft_trialfun_general > In ft_definetrial at 123 Undefined function 'ft_getuserfun' for input arguments of type 'char'. Error in ft_definetrial (line 140) cfg.trialfun = ft_getuserfun(cfg.trialfun, 'trialfun'); Thanks Baris On Thu, Aug 30, 2012 at 4:33 AM, Nenad Polomac wrote: > Hi, > > I am analyzing data obtained on CTF MEG 275 system. However, 4 sensors are > broken and data ended up with 271 sensor. So, my question is should I > interpolate the missing sensors with FT_CHANNELREPAIR? In the case I leave > data with 271 sensor, will those missing sensors influence neighbors > configuration in the statistic and the source localisation analysis? > > Thank you in advance! > > Kind regards! > > Nenad > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From r.oostenveld at donders.ru.nl Sun Sep 2 12:51:46 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Sun, 2 Sep 2012 12:51:46 +0200 Subject: [FieldTrip] neighbours In-Reply-To: References: Message-ID: <9BF899F9-DD29-482B-B964-CC07CEC56273@donders.ru.nl> Hi Nenad On 30 Aug 2012, at 10:33, Nenad Polomac wrote: > I am analyzing data obtained on CTF MEG 275 system. However, 4 sensors are broken and data ended up with 271 sensor. So, my question is should I interpolate the missing sensors with FT_CHANNELREPAIR? In the case I leave data with 271 sensor, will those missing sensors influence neighbors configuration in the statistic and the source localisation analysis? If the channels are consistently broken in all your subjects, you should better not interpolate them. If the channels are only missing in some, but not all subjects, interpolating will be of use for the channel-level statistics. For source reconstruction you should not interpolate the broken channels. Group statistics on source-level data is also not affected by having slight differences in the working channels over subjects. best regards Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Sun Sep 2 12:53:12 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Sun, 2 Sep 2012 12:53:12 +0200 Subject: [FieldTrip] neighbours In-Reply-To: <50406CB9.7090209@donders.ru.nl> References: <50406CB9.7090209@donders.ru.nl> Message-ID: whoops, I now see that Jorn has already provided a much better and elaborate answer. Better pay attention to what he writes and ignore my quick reply. Robert On 31 Aug 2012, at 9:50, Jörn M. Horschig wrote: > Hi Nenad, > > the question you are asking does not deserve a definite 'yes' or 'no'. In any case, note that when averaging over subjects, missing sensors for one subject will be removed for all other subjects as well. So, if you are talking about different missing sensors per subject, an interpolation will definitely be a wise thing to do. In case you choose for interpolating the missing channels, you can try to check out the new spherical spline interpolation method (see help ft_channelrepair) - theoretically that should result in a quite good reconstruction. But the (standard) nearest neighbour interpolation is fine as well. > > With respect to your second question: missing sensors will influence the neighbour configuration depending on the method you chose for neighbour selection. For the 'distance' and 'template' method, each neighbouring channel of the missing will have one sensor less (i.e. the missing one). The 'triangulation' method will create triangle neighbour no matter how many channels you have, so it will just ignore the whole in space. In any case, I'd propose that you check out how satisfied you personally are with the neighbours by calling ft_neighbourplot. Just last week, I added the new option that if you use cfg.enableedit='yes', you can interactively change the neighbourhood structure within the neighbourplot. If I were you, I would start from the template method. As an additional piece of information: I am currently working on improving the neighbour templates, and will upload them probably next week. > > All that advertised, let me also say that having 4 out of 275 sensors missing won't affect your statistics much. Here, it of course depends on your region if interest, research question etc. E.g. if you are interested in posterior alpha power, but miss four temporal channels, there is no reason to worry. So, without knowing what you are looking for and where the missing channels are, I cannot give you a general advise what to do. As a last remark, the sensitiviy of the statistics will of course be influenced by missing sensors, but I doubt that it will matter much. Btw, I am not quite sure how much the spherical spline interpolation will buy you here, you might give it a try. I bet that it will increase your sensitivity more than the nearest neighbour approach, although both might result in rather low increases. But this is just a general gut feeling rather than anything I empirically validated. > > Best, > Jörn > > On 8/30/2012 10:33 AM, Nenad Polomac wrote: >> Hi, >> >> I am analyzing data obtained on CTF MEG 275 system. However, 4 sensors are broken and data ended up with 271 sensor. So, my question is should I interpolate the missing sensors with FT_CHANNELREPAIR? In the case I leave data with 271 sensor, will those missing sensors influence neighbors configuration in the statistic and the source localisation analysis? >> >> Thank you in advance! >> >> Kind regards! >> >> Nenad >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Sun Sep 2 12:54:22 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Sun, 2 Sep 2012 12:54:22 +0200 Subject: [FieldTrip] CTF data event/reading In-Reply-To: References: Message-ID: Hi Baris, First something in general: This error > Undefined function 'offset2time' for input arguments > of type 'double'. > > Error in ft_preprocessing (line 511) > tim = offset2time(offset, hdr.Fs, size(dat,2)); should not happen with recent versions of FieldTrip (nor with older ones). The offset2time helper function is present in fieldtrip/private and can be found there by ft_preprocessing. Also the error > Undefined function 'ft_getuserfun' for input arguments > of type 'char'. > > Error in ft_definetrial (line 140) > cfg.trialfun = ft_getuserfun(cfg.trialfun, > 'trialfun'); suggests that your fieldtrip installation is broken. Please upgrade to the most recent version, that might resolve some (or all) of your problems. Don't move around the directories in the fieldtrip zip file, or rename them, otherwise ft_defaults is not able to set up the path correctly. See also http://fieldtrip.fcdonders.nl/faq/should_i_add_fieldtrip_with_all_subdirectories_to_my_matlab_path Then on to some other aspects of your question, which may be of interest to other CTF users as well. From the CTF channel naming scheme I can see that you have a CTF275 system. The 151 channel MEG system we started off with at the Donders in 2002 had an electronics rack which was placed such that there was a clear front and back side. Each side of the rack exposed 16 binary inputs (i.e. bits) for connecting external triggers. To the front we connected the button boxes, to the back we connected the stimulus presentation computer. The 16 bits from the front and from the back were combined in the 32 bit STIM channel. Given the connections of the button boxes and stimulus computers, in the analysis the 32 bit STIM channel did not match the users scripts with respect to button box and presentation trigger codes. Therefore the FieldTrip reading software was implemented to split the 32 bits into the 16 frontpanel and the 16 backpanel bits. This also shifts the bits to recover the trigger codes that were used in the presentation software by the users. This situation from early '2000 at the Donders in Nijmegen is still supported by FieldTrip. The “Subject01.ds” tutorial dataset is from that time, so that is why you see it in the tutorials. The front and back panel at other CTF sites with the old electronics rack may be (or have been) connected differently. Furthermore, the present CTF systems have more trigger input options and no front and back side any more, so better don't use those any more in your analyses. In many cases UPPT001 and similarly named channels are the interesting trigger channels. MEG data acquired with the older CTF systems uses the STIM channel. So please be aware that “frontpanel” and “backpanel” are Donders conventions that have ended up in FieldTrip, but may not be of any relevance to you. Another topic is that in Nijmegen (as many other CTF sites) we record the data continuously, and don't use the CTF software for epoching, classification of artifacts and trial marking. However FieldTrip does support the CTF ClassFile and Markerfile in FieldTrip. If you do ft_read_event('dataset.ds') you will see an event structure that combines all information. Some "events" are instantaneous, some "events" have a duration. This is explained in more detail at http://fieldtrip.fcdonders.nl/faq/what_is_the_relation_between_events_such_as_triggers_and_trials best regards, Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: From polomacnenad at gmail.com Sun Sep 2 16:51:31 2012 From: polomacnenad at gmail.com (Nenad Polomac) Date: Sun, 2 Sep 2012 16:51:31 +0200 Subject: [FieldTrip] neighbours Message-ID: Dear Jörn, Thank you very much for the thorough explanation! All the best! Nenad -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sun Sep 2 17:48:43 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sun, 2 Sep 2012 18:48:43 +0300 Subject: [FieldTrip] 'dml' variable Message-ID: Hello, I am trying to classify my data using ft_timelockstatistics function I am using the output of ft_timelockanalysis function and the following options: cfg.layout = 'CTF275.lay'; cfg.method = 'crossvalidate'; cfg.design = [ones(size(class1.trial,1),1); 2*ones(size(class2.trial,1),1)]'; But I got the following error: ??? Undefined variable "dml" or class "dml.standardizer". Error in ==> ft_statistics_crossvalidate at 44 cfg.mva = dml.analysis({ ... Error in ==> statistics_wrapper at 306 [stat] = statmethod(cfg, dat, design); Error in ==> ft_timelockstatistics at 110 [stat, cfg] = statistics_wrapper(cfg, varargin{:}); Did I forgot to add something?! Thanks -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghumana at upmc.edu Mon Sep 3 07:05:37 2012 From: ghumana at upmc.edu (Ghuman, Avniel) Date: Mon, 3 Sep 2012 05:05:37 +0000 Subject: [FieldTrip] A postdoc position in developing methods for MEG with atomic magnetometers In-Reply-To: <20385F716E75B746A7F52BBB3C46A1300226C790@MSXMBXNSPRD03.acct.upmchs.net> References: <20385F716E75B746A7F52BBB3C46A1300226C772@MSXMBXNSPRD03.acct.upmchs.net>, <20385F716E75B746A7F52BBB3C46A1300226C790@MSXMBXNSPRD03.acct.upmchs.net> Message-ID: <20385F716E75B746A7F52BBB3C46A1300226C809@MSXMBXNSPRD03.acct.upmchs.net> Post-doc in MEG with Atomic Magnetometers The Ghuman Lab at the University of Pittsburgh, in collaboration with the Romalis Group at Princeton University and Twinleaf LLC, is recruiting a Post doc to develop methods for atomic magnetometer based MEG and multimodal integration (simultaneous MEG-EEG and MEG-fNIRS). The position is available immediately. Responsibilities: • Develop novel solutions for MEG using atomic magnetometers concerning source localization, noise cancellation and head modeling • Acquire and analyze MEG, MEG-EEG, and MEG-fNIRS data • Develop novel methods for integrating multimodal data • Design and implement novel data analysis tools • Assist with preparation of progress reports • Prepare manuscripts and presentations • Work with Investigators to identify future problems and research opportunities Minimum Qualifications: • Ph.D. in Engineering, Physics, Neuroscience, Computer Science, Math, or related field. • Demonstrated expertise in solving MEG technological issues as shown through publication record, awards, successful patents and/or received applications. • Data analysis expertise includes independent components analysis, Bayesian algorithms, statistical parametric mapping, and MRI image processing. • Proficiency in creating software analysis tools and programs for investigators • MATLAB and Python programming knowledge preferred. Conditions of Employment: • Position available immediately • Salary: according to NIH postdoc salary scale • The University of Pittsburgh has excellent benefits, including health benefits and retirement plans with employer contributions. • The University of Pittsburgh values diversity and is committed to equal opportunity in employment. How to Apply: • E-mail Avniel Ghuman, Ph.D. (ghumana at upmc.edu) or Mike Romalis, Ph.D. (romalis at princeton.edu) From ghumana at upmc.edu Mon Sep 3 07:07:22 2012 From: ghumana at upmc.edu (Ghuman, Avniel) Date: Mon, 3 Sep 2012 05:07:22 +0000 Subject: [FieldTrip] A postdoc position in developing methods for MEG with atomic magnetometers In-Reply-To: <20385F716E75B746A7F52BBB3C46A1300226C790@MSXMBXNSPRD03.acct.upmchs.net> References: <20385F716E75B746A7F52BBB3C46A1300226C772@MSXMBXNSPRD03.acct.upmchs.net>, <20385F716E75B746A7F52BBB3C46A1300226C790@MSXMBXNSPRD03.acct.upmchs.net> Message-ID: <20385F716E75B746A7F52BBB3C46A1300226C827@MSXMBXNSPRD03.acct.upmchs.net> Post-doc in MEG with Atomic Magnetometers The Ghuman Lab at the University of Pittsburgh, in collaboration with the Romalis Group at Princeton University and Twinleaf LLC, is recruiting a Post doc to develop methods for atomic magnetometer based MEG and multimodal integration (simultaneous MEG-EEG and MEG-fNIRS). The position is available immediately. Responsibilities: • Develop novel solutions for MEG using atomic magnetometers concerning source localization, noise cancellation and head modeling • Acquire and analyze MEG, MEG-EEG, and MEG-fNIRS data • Develop novel methods for integrating multimodal data • Design and implement novel data analysis tools • Assist with preparation of progress reports • Prepare manuscripts and presentations • Work with Investigators to identify future problems and research opportunities Minimum Qualifications: • Ph.D. in Engineering, Physics, Neuroscience, Computer Science, Math, or related field. • Demonstrated expertise in solving MEG technological issues as shown through publication record, awards, successful patents and/or received applications. • Data analysis expertise includes independent components analysis, Bayesian algorithms, statistical parametric mapping, and MRI image processing. • Proficiency in creating software analysis tools and programs for investigators • MATLAB and Python programming knowledge preferred. Conditions of Employment: • Position available immediately • Salary: according to NIH postdoc salary scale • The University of Pittsburgh has excellent benefits, including health benefits and retirement plans with employer contributions. • The University of Pittsburgh values diversity and is committed to equal opportunity in employment. How to Apply: • E-mail Avniel Ghuman, Ph.D. (ghumana at upmc.edu) or Mike Romalis, Ph.D. (romalis at princeton.edu) From jm.horschig at donders.ru.nl Mon Sep 3 09:56:40 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 03 Sep 2012 09:56:40 +0200 Subject: [FieldTrip] 'dml' variable In-Reply-To: References: Message-ID: <504462B8.2060508@donders.ru.nl> Dear Hamza, 'crossvalidate' is part of the Donders Machine Learning Toolbox (DMLT). Formerly, it was known under a different name (afair MVA or multivariate toolbox) but recently it became an external toolbox and moved to the external/ folder. FieldTrip supports external toolboxes but takes no initiative in adding them automatically, so you need to it manually: addpath(genpath(fullfile('your_fieldtrip_folder', 'external', 'dmlt'))) See also here: http://fieldtrip.fcdonders.nl/tutorial/multivariateanalysis Since Marcel and others, who are developing this toolbox or have experience with using it, are on this mailinglist, feel free to post further questions concerning DMLT to this list anyhow. Best regards, Jörn On 9/2/2012 5:48 PM, Hamza Fawzi Altakroury (Student) wrote: > Hello, > > I am trying to classify my data using ft_timelockstatistics function > > I am using the output of ft_timelockanalysis function and the > following options: > > cfg.layout = 'CTF275.lay'; > cfg.method = 'crossvalidate'; > cfg.design = [ones(size(class1.trial,1),1); > 2*ones(size(class2.trial,1),1)]'; > > But I got the following error: > > ??? Undefined variable "dml" or class "dml.standardizer". > > Error in ==> ft_statistics_crossvalidate at 44 > cfg.mva = dml.analysis({ ... > > Error in ==> statistics_wrapper at 306 > [stat] = statmethod(cfg, dat, design); > > Error in ==> ft_timelockstatistics at 110 > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > Did I forgot to add something?! > > Thanks > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabanc? University > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From hubert.preissl at uni-tuebingen.de Mon Sep 3 14:08:21 2012 From: hubert.preissl at uni-tuebingen.de (Hubert Preissl) Date: Mon, 03 Sep 2012 14:08:21 +0200 Subject: [FieldTrip] 5th Autumn School Structure the Brain: 9th-11th October 2012, 2nd announcement In-Reply-To: References: Message-ID: <50449DB5.3000501@uni-tuebingen.de> Hello, we are pleased to announce the upcoming “5th Autumn School” in Tübingen organized by the MEG Center. For application and further information on the scientific program please visit our website: http://www.mp.uni-tuebingen.de/mp/index.php?id=400 Confirmed speakers: Christian Gaser, PhD, University of Jena, Germany Volkmar Glauche, MSc, University of Freiburg,Germany Matti Hämäläinen, PhD, Harvard Medical School, Boston, USA Risto Ilmoniemi, PhD, Aalto University, Aalto, Finland Svenja Knappe, PhD, National Institute of Standards and Technology, Boulder, USA Daniela Prayer, MD, University of Vienna, Austria Dana Small, PhD, The John B Pierce Laboratory and Yale University, USA Fabrice Wallois, PhD, University of Picardy,France We look forward meeting you in Tübingen! Best regards, Hubert Preissl -- Dr. Hubert Preissl MEG Center phone: ++49-(0)7071-2987704 Otfried Müller Str 47 fax: ++49-(0)7071-295706 72076 Tübingen, Germany email: hubert.preissl at uni-tuebingen.de From hamzaf at sabanciuniv.edu Mon Sep 3 17:22:02 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Mon, 3 Sep 2012 18:22:02 +0300 Subject: [FieldTrip] 'dml' variable In-Reply-To: <504462B8.2060508@donders.ru.nl> References: <504462B8.2060508@donders.ru.nl> Message-ID: Thank you Jörn, it works. Hamza On Mon, Sep 3, 2012 at 10:56 AM, "Jörn M. Horschig" < jm.horschig at donders.ru.nl> wrote: > Dear Hamza, > > 'crossvalidate' is part of the Donders Machine Learning Toolbox (DMLT). > Formerly, it was known under a different name (afair MVA or multivariate > toolbox) but recently it became an external toolbox and moved to the > external/ folder. FieldTrip supports external toolboxes but takes no > initiative in adding them automatically, so you need to it manually: > addpath(genpath(fullfile('your_fieldtrip_folder', 'external', 'dmlt'))) > > See also here: > http://fieldtrip.fcdonders.nl/tutorial/multivariateanalysis > > Since Marcel and others, who are developing this toolbox or have > experience with using it, are on this mailinglist, feel free to post > further questions concerning DMLT to this list anyhow. > > Best regards, > Jörn > > > On 9/2/2012 5:48 PM, Hamza Fawzi Altakroury (Student) wrote: > > Hello, > > I am trying to classify my data using ft_timelockstatistics function > > I am using the output of ft_timelockanalysis function and the following > options: > > cfg.layout = 'CTF275.lay'; > cfg.method = 'crossvalidate'; > cfg.design = [ones(size(class1.trial,1),1); > 2*ones(size(class2.trial,1),1)]'; > > But I got the following error: > > ??? Undefined variable "dml" or class "dml.standardizer". > > Error in ==> ft_statistics_crossvalidate at 44 > cfg.mva = dml.analysis({ ... > > Error in ==> statistics_wrapper at 306 > [stat] = statmethod(cfg, dat, design); > > Error in ==> ft_timelockstatistics at 110 > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > Did I forgot to add something?! > > Thanks > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From daria.laptinskaya at googlemail.com Mon Sep 3 17:22:58 2012 From: daria.laptinskaya at googlemail.com (Daria Laptinskaya) Date: Mon, 3 Sep 2012 17:22:58 +0200 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? Message-ID: Dear Fieldtrippers, I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip toolbox. The ERPs look perfect. The 'only' problem is, that my signals look to strong. It looks like if I get amplitutes (average) until 70 µV. I think it must be an intern amplifier for the signals. Does anyone know this problem with EGI-data? Or does anyone know, where I can see the amplifier? Greetings, Daria -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Mon Sep 3 19:04:47 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Mon, 3 Sep 2012 20:04:47 +0300 Subject: [FieldTrip] Changing the classifier Message-ID: Hello, I am dealing with ft_timelockstatistics function for classification, as I understand from the tutorail, the default classifier used is the SVM. I want to ask about the ability to change the classifier. Thanks for help. Best, -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Mon Sep 3 22:35:06 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 3 Sep 2012 22:35:06 +0200 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: References: Message-ID: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> Hi Daria, There might indeed be an incompatibility in the gain value applied to the data. If you are able to export the data using the EGI software in another format (e.g. EDF), you could read them both into FieldTrip and compare the timecourse aplitudes to check whether they are different. In case they are, I suggest to involve EGI support. They are aware of the FieldTrip reading functions and will know much more about the internals of their various file formats. best regards Robert On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: > Dear Fieldtrippers, > > I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip toolbox. > The ERPs look perfect. > The 'only' problem is, that my signals look to strong. > It looks like if I get amplitutes (average) until 70 µV. > I think it must be an intern amplifier for the signals. > Does anyone know this problem with EGI-data? > > Or does anyone know, where I can see the amplifier? > > > > > Greetings, > > Daria _______________________________________________ > 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 Mon Sep 3 23:02:21 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 3 Sep 2012 23:02:21 +0200 Subject: [FieldTrip] A postdoc position in developing methods for MEG with atomic magnetometers In-Reply-To: <20385F716E75B746A7F52BBB3C46A1300226C827@MSXMBXNSPRD03.acct.upmchs.net> References: <20385F716E75B746A7F52BBB3C46A1300226C772@MSXMBXNSPRD03.acct.upmchs.net>, <20385F716E75B746A7F52BBB3C46A1300226C790@MSXMBXNSPRD03.acct.upmchs.net> <20385F716E75B746A7F52BBB3C46A1300226C827@MSXMBXNSPRD03.acct.upmchs.net> Message-ID: <9D7A03F8-3318-498E-B2DD-BFE41B461548@donders.ru.nl> Dear Avniel (CC to the FieldTrip list) Thanks for announcing this interesting post doc position. Last week at the Biomag conference I attended the atomic/optical magnetic field sensor symposium and was very impressed with the progress that was presented. With respect to some of the tasks you outline (see below), I think that there is quite some overlap with the methods used in squid based MEG technology. E.g., the volume conduction modelling and forward solutions relate the equivalent current dipole strength in the model head to magnetic field strength outside the head. This is independent of the sensor technology, although the precise sensor geometry is of course different (as it also is between the various MEG systems). See for example http://fieldtrip.fcdonders.nl/faq/how_are_electrodes_magnetometers_or_gradiometers_described. The noise characteristics of the atomic magnetometers themselves will at the moment also be quite different for that of a squid-based system, but once the S/N gets good enough, a large fraction of the noise will be environmental and biological, again resulting in similar methods being applicable to deal with those parts of the noise (especially when compared to the magnetometer channels in some of the presently used MEG systems). I hope that it will be possible to develop methods for atomical magnetometer based MEG in close collaboration with the methods that are used and developed for conventional MEG. Actually it would be cool to implement support for the data formats that are being used by you and in Princeton in the FieldTrip toolbox. I believe that this would facilitate working together, not specifically with the Donders Institute in Nijmegen, but rather with the MEG field as a whole. It would also allow your data to be processed in the other large open source toolboxes (such as SPM and Nutmeg), as these all share the same data access functions and sensor representation. At the moment FieldTrip supports MEG data from about 15 different MEG systems (3x BTi, 2x Neuromag, 4x CTF, 4x Yokogawa, 2x ITAB, ranging from adult MEG to fetal MCG and even rodent MEG) and provides data processing and source reconstruction for all of them. Adding support for your data format and sensor arrangements is something that we could provide assistance with. I hope you will be able to attract a good candidate for the position and that the new atomic sensor technology will soon become available to the whole MEG community. best regards Robert ----------------------------------------------------------- Robert Oostenveld, PhD Senior Researcher & MEG Physicist Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen tel.: +31 (0)24 3619695 e-mail: r.oostenveld at donders.ru.nl web: http://www.ru.nl/neuroimaging skype: r.oostenveld ----------------------------------------------------------- On 3 Sep 2012, at 7:07, Ghuman, Avniel wrote: > Post-doc in MEG with Atomic Magnetometers > > The Ghuman Lab at the University of Pittsburgh, in collaboration with the Romalis Group at Princeton University and Twinleaf LLC, is recruiting a Post doc to develop methods for atomic magnetometer based MEG and multimodal integration (simultaneous MEG-EEG and MEG-fNIRS). The position is available immediately. > Responsibilities: > • Develop novel solutions for MEG using atomic magnetometers concerning source localization, noise cancellation and head modeling > • Acquire and analyze MEG, MEG-EEG, and MEG-fNIRS data > • Develop novel methods for integrating multimodal data > • Design and implement novel data analysis tools > • Assist with preparation of progress reports > • Prepare manuscripts and presentations > • Work with Investigators to identify future problems and research opportunities > > Minimum Qualifications: > • Ph.D. in Engineering, Physics, Neuroscience, Computer Science, Math, or related field. > • Demonstrated expertise in solving MEG technological issues as shown through publication record, awards, successful patents and/or received applications. > • Data analysis expertise includes independent components analysis, Bayesian algorithms, statistical parametric mapping, and MRI image processing. > • Proficiency in creating software analysis tools and programs for investigators > • MATLAB and Python programming knowledge preferred. > > Conditions of Employment: > • Position available immediately > • Salary: according to NIH postdoc salary scale > • The University of Pittsburgh has excellent benefits, including health benefits and retirement plans with employer contributions. > • The University of Pittsburgh values diversity and is committed to equal opportunity in employment. > > How to Apply: > • E-mail Avniel Ghuman, Ph.D. (ghumana at upmc.edu) or Mike Romalis, Ph.D. (romalis at princeton.edu) > > _______________________________________________ > 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 ayelet.landau at gmail.com Tue Sep 4 13:23:21 2012 From: ayelet.landau at gmail.com (Ayelet Landau) Date: Tue, 4 Sep 2012 13:23:21 +0200 Subject: [FieldTrip] problem with ft_rejectartifact Message-ID: Dear FieldTrip experts, I have encountered a strange behavior in ft_rejectartifact script. artifacts are defined in variables that contain two collumns and fed into this function as follows: cfg.artfctdef.eog.artifact =artifact_eog_all; other parameters I use are: cfg.trl=trl; cfg.artfctdef.reject = 'partial'; cfg.artfctdef.minaccepttim = .2; then I run ft_rejectartifact with this cfg (and many more categories of artifacts as exemplified above) and a structure containing my preprocessed data (with a the same trl I give in cfg.trl above). This is an example of what the data structure fed into ft_rejectartifact might looks like hdr: [1x1 struct] fsample: 1200 grad: [1x1 struct] sampleinfo: [50x2 double] trialinfo: [50x4 double] trial: {1x50 cell} time: {1x50 cell} label: {275x1 cell} cfg: [1x1 struct] and here is the error that I get: ??? Subscripted assignment dimension mismatch. Error in ==> ft_redefinetrial at 253 data.trialinfo(iTrl,:) = dataold.trialinfo(iTrlorig,:); Error in ==> ft_rejectartifact at 483 data = ft_redefinetrial(tmpcfg, data); When I run ft_rejectartifact with a cfg.data field calling my *.ds file, I get the following which I could probably use later as an adjusted trl for ft_preprocessing: datafile: 'XX_20120821_05.ds' trl: [79x7 double] artfctdef: [1x1 struct] trackconfig: 'off' checkconfig: 'loose' checksize: 100000 showcallinfo: 'yes' headerfile: 'XX_20120821_05.ds' trlold: [50x7 double] callinfo: [1x1 struct] version: [1x1 struct] Its a bit strange that my original approach stopped working. Any insights most welcome! -- Ayelet N. Landau Postdoctoral Scientist, Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society Deutschordenstr. 46, D-60528 Frankfurt Mobile: +49 (0)16 22733 110 Fax: +49 (0)69 96769 555 -------------- next part -------------- An HTML attachment was scrubbed... URL: From inieuwenhuis at berkeley.edu Tue Sep 4 22:00:03 2012 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Tue, 04 Sep 2012 13:00:03 -0700 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> Message-ID: <50465DC3.7080005@berkeley.edu> Hi Daria, Also, did you try looking at your raw data (so before the ERPs are made) in FieldTrip and in Net Station? So open your .raw data in NetStation. You can just look at a random participant's data, and check if the scale is the same. I'm pretty sure no amplification takes place when reading in the data into FieldTrip, this check can confirm that. Hope this helps, and let us know what you find. Cheers, Ingrid On 9/3/2012 1:35 PM, Robert Oostenveld wrote: > Hi Daria, > > There might indeed be an incompatibility in the gain value applied to > the data. > > If you are able to export the data using the EGI software in another > format (e.g. EDF), you could read them both into FieldTrip and compare > the timecourse aplitudes to check whether they are different. In case > they are, I suggest to involve EGI support. They are aware of the > FieldTrip reading functions and will know much more about the > internals of their various file formats. > > best regards > Robert > > > > > On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: > >> Dear Fieldtrippers, >> >> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip >> toolbox. >> The ERPs look perfect. >> The 'only' problem is, that my signals look to strong. >> It looks like if I get amplitutes (average) until 70 µV. >> I think it must be an intern amplifier for the signals. >> >> Does anyone know this problem with EGI-data? >> >> Or does anyone know, where I can see the amplifier? >> >> >> >> Greetings, >> >> Daria _______________________________________________ >> 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 -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jochem.rieger at uni-oldenburg.de Wed Sep 5 03:24:18 2012 From: jochem.rieger at uni-oldenburg.de (Jochem Rieger) Date: Wed, 05 Sep 2012 03:24:18 +0200 Subject: [FieldTrip] 1 post-doc and 1 PhD position in human auditory and motor neuroscience Message-ID: <5046A9C2.2020704@uni-oldenburg.de> The Department of Applied Neurocognitive Psychology at Oldenburg University, Germany, offers a *Post-doctoral position (E13/TVL, 3 years plus) * and a *PhD position (0.5*E13/TVL, initially 2 years)* The lab focuses on the fields of neural coding of complex movements and neural coding of speech in the human brain with the aim of developing brain-machine-interfaces. To extend our interdisciplinary team we seek for highly motivated candidates with strong quantitative and experimental skills. The post-doctoral position requires a PhD or comparable degree and the PhD position requires a masters or comparable degree. The post-doctoral position is initially limited to three years after with an option for an extension to obtain habilitation (post-doctoral degree, similar to a lecturer qualification). Successful candidates will perform cutting edge research in one of the lab's foci and should have a background in one or more of the following fields: non-invasive or invasive human neurophysiology of the motor or auditory system, statistical learning, brain-machine-interfacing. The positions offer an excellent interdisciplinary working environment with opportunities for international exchange. The lab is involved in the EU-project BRACOG (brain controlled grasping) and we have a close collaboration with UC Berkeley, USA. The University of Oldenburg was recently awarded a Cluster of Excellence in hearing research. The Dept. of Psychology will offer an attractive scientific environment with access to research dedicated state-of-the-art approaches to human neurophysiological techniques (fMRI, NIRS, EEG, ECoG, and MEG). Electronic applications are preferred and can be send to: Professor Dr. Jochem Rieger: Jochem.rieger at uni-oldenburg.de Please send paper applications until September 30^th 2012 to: Margrit Jung Dept. of Applied Neurocognitive Psychology Institute of Psychology Oldenburg University 26111 Oldenburg Germany Applications should include your CV and a list of most recent publications. Applications for the post-doctoral position should include a research statement (max. 3 pages). The University of Oldenburg aims to employ more women in this area and therefore particularly welcomes applications from women. We also welcome applications from disabled persons. -- Prof. Dr. rer. nat. Jochem Rieger Applied Neurocognitive Knight Lab Psychology Helen Wills Neuroscience Institute Faculty V University of California Carl-von-Ossietzky University 132 Barker Hall 26111 Oldenburg Berkeley, CA 94720-3192 Germany USA Phone: +49(0)4417984533 Fax: +49(0)4417983865 -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.piantoni at nin.knaw.nl Wed Sep 5 10:20:41 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Wed, 5 Sep 2012 10:20:41 +0200 Subject: [FieldTrip] freesurfer surfaces Message-ID: Dear Fieldtrip developers, I'd like to run source reconstruction on the cortical sheets obtained from Freesurfer and average them using the "sphere" approach of Freesurfer. I have these steps in mind: 1) create a 3-layer BEM ('outer_skin' 'inner_skull' 'brain' from the bem/watershed folder, which I think might be better than 'outer_skin' 'outer_skull' 'inner_skull' as in http://fieldtrip.fcdonders.nl/development/replicate_functionality_of_mne_software ) 2) create a forward model from a subset of points in "?h.smoothwm" (for computational purposes) 3) do source reconstruction on this subset of dipoles 4) source interpolate to the high resolution of ?h.smoothwm 5) project all the locations onto the ?h.sphere 6) interpolate to the points to the ?h.sphere of fsaverage 7) do 2-D statistics on the values of the ?h.sphere of fsaverage (and plot them using ?h.inflated of fsaverage) I was wondering if anybody has tried something similar and if there are steps I should be careful about. There was a discussion in January/February about doing statistics on cortical sheets: http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004749.html http://mailman.science.ru.nl/pipermail/fieldtrip/2012-February/004766.html Does anybody have suggestions about these steps? I promise I'll make a tutorial out of this, if it works out ;) A practical point I get stuck in is at steps 3) and 4). The interpolation from a subset of 2-D points to another subset of 2-D points gives a bit of nonsensical results. Code: %-get freesurfer surface bnd = ft_read_headshape('lh.smoothwm'); % get it from https://skydrive.live.com/redir?resid=6D9DCA0F726A645C!7000 % or any freesurfer surface you have %-downsample bnd_down = bnd; P.faces = bnd_down.tri; P.vertices = bnd_down.pnt; P = reducepatch(P, 0.05); bnd_down.tri = P.faces; bnd_down.pnt = P.vertices; %-create source source.pos = bnd_down.pnt; source.inside = true(size(source.pos,1),1); source.pow = bnd_down.pnt(:,3); % "fake" source reconstruction figure ft_plot_mesh(bnd_down, 'edgecolor', 'none', 'vertexcolor', source.pow) % the rainbow brain view(90, 0); camlight %-sourceinterpolate cfg = []; cfg.parameter = 'pow'; ana = []; ana.pnt = bnd_down.pnt; ana.orig = bnd; souinterp = ft_sourceinterpolate(cfg, source, ana); figure ft_plot_mesh(souinterp, 'edgecolor', 'none', 'vertexcolor', souinterp.pow) % the Arlecchino brain view(90, 0); camlight Should I file a bugzilla report for this? I haven't done it as I'm not even sure this is the correct input format. Thanks for any suggestion. Best wishes, Gio -- Giovanni Piantoni, MSc Dept. Sleep & Cognition Netherlands Institute for Neuroscience Meibergdreef 47 1105 BA Amsterdam (NL) www.gpiantoni.com From johanna.zumer at donders.ru.nl Wed Sep 5 12:41:38 2012 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Wed, 5 Sep 2012 12:41:38 +0200 Subject: [FieldTrip] FT_SCALPCURRENTDENSITY options and elec units In-Reply-To: References: Message-ID: Hi Akiko, Hopefully someone else can answer your main SCD question (although ft_scalpcurrentdensity provides the citations for the original papers on which these 2 methods are based). But for now, just a quick answer to your units question. The best way to convert the units of a FieldTrip data structure is with ft_convert_units, for example: elec_out = ft_convert_units(elec_in, 'm'). If elec.unit does not already exist in the structure, then either you can set it first if you know the units, or FT will do its best to assume which units the structure is in. Also note that the 'help' of ft_scalpcurrentdensity states that "the spatial distribution still will be correct" even if units do not match, which should explain why the topoplot shows the same results. Cheers, Johanna 2012/8/31 Akiko Ikkai > Hi, > > I'm trying to run plv analysis, first acquiring SCD of my data with > ft_scalcurrentdensity, and am confused about the difference between > cfg.method = 'finite' and 'spline.' Both gave similar results > short-range, but 'spline' gives higher plv at long range plv. I'd love it > if someone could explain or suggest reading on the difference between these > two methods (or is one method preferred over the other in some cases?). > > Also, I'm not sure whether or not I should convert my elec.pnt values, > since the code ft_scalcurrentdensity says that > "Note that the skin conductivity, electrode dimensions and the potential all > have to be expressed in the same SI units." My elec.pnt are in cm, and > I'm using the default conductivity (0.33 S/m). Do I need to do something > like elec.pnt = elec.pnt/100 to convert the unit from cm to m? With or > without conversion, I got the same results (viewed with ft_topoplotTFR), > and I'm a little confused... Thank you in advance for your time! Akiko > > -- > Akiko Ikkai, Ph.D. > Postdoctoral Fellow > Department of Psychological and Brain Sciences > Johns Hopkins University > Ames Hall, 3400 N. Charles St. > Baltimore, MD 21218 > > > > _______________________________________________ > 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 f.roux at bcbl.eu Wed Sep 5 14:47:29 2012 From: f.roux at bcbl.eu (Frederic Roux) Date: Wed, 05 Sep 2012 14:47:29 +0200 (CEST) Subject: [FieldTrip] left to right inversion after source interpolation In-Reply-To: Message-ID: <075a92dd-147e-45e9-a4d1-726999c597b1@thalamus_p> Dear fieldtrip users, I have noticed that after interpolating a dummy source volume with ft_sourceinterpolate, voxels that were located in the left side of the volume, apear to be located in the right side of the volume. The code that I use is as following: dummy is a dummy structure of an lcmv beamformer map with the fields dummy = dim : [15 18 17] time: [1x272662 double] pos: [4590x3 double] inside: [1x2144 double] outside: [1x2446 double] method: 'average' avg: [1x1 struct] voxpos = dummy.pos(dummy.inside,1);% get the coordinates of voxels inside the volume dummy.avg.pow(dummy.inside(sign(voxpos)==1)) = 0; % set activity in the left hemisphere to 0 dummy.avg.pow(dummy.inside(sign(voxpos)==-1)) = 1; % set activity in the left hemisphere to 1 cfg = []; cfg.parameters = 'all'; int_dummy = ft_sourceinterpolate(cfg,dummy,template_MNI_mri); cfg = []; cfg.funparameter = 'avg.pow'; cfg.method = 'ortho'; %plot the non-interpolated volume figure; ft_sourceplot(cfg,dummy); %plot the interpolated volume figure; ft_sourceplot(cfg,int_dummy); As you can see from the figure in the attachement, the voxels that corresponded to the left hemisphere prior to the interpolation, no appear to be located in the rigth hemisphere. This is also something that I have observed in real data. Does anybody have an explanation why this is happening? Am I doing something wrong? Best, Fred -------------- next part -------------- A non-text attachment was scrubbed... Name: non_interp_vs_interp.jpg Type: image/jpeg Size: 25092 bytes Desc: not available URL: From k.muesch at uke.uni-hamburg.de Wed Sep 5 16:30:49 2012 From: k.muesch at uke.uni-hamburg.de (=?iso-8859-1?Q?Kathrin_M=FCsch?=) Date: Wed, 5 Sep 2012 16:30:49 +0200 Subject: [FieldTrip] left to right inversion after source interpolation In-Reply-To: <075a92dd-147e-45e9-a4d1-726999c597b1@thalamus_p> References: <075a92dd-147e-45e9-a4d1-726999c597b1@thalamus_p> Message-ID: <44E1ACF5-2C6D-4BA2-8FA7-B0886FB8AF20@uke.uni-hamburg.de> Dear Fred, I encountered a similar thing a while ago and it was because spm8 seems to plot in radiological convention (i.e. left is plotted right and vice versa - http://mailman.science.ru.nl/pipermail/fieldtrip/2012-May/005229.html) so you're plots should actually be correct. If you use cfg.interactive = 'yes'; and click into the activated side of the brain, the first coordinate should be negative because you are in the left hemisphere. Hope that helps, Kathrin Am 05.09.2012 um 14:47 schrieb Frederic Roux: > Dear fieldtrip users, > > I have noticed that after interpolating a dummy source volume with ft_sourceinterpolate, > voxels that were located in the left side of the volume, apear to be located in the right > side of the volume. > > The code that I use is as following: > > dummy is a dummy structure of an lcmv beamformer map with the fields > > dummy = > dim : [15 18 17] > time: [1x272662 double] > pos: [4590x3 double] > inside: [1x2144 double] > outside: [1x2446 double] > method: 'average' > avg: [1x1 struct] > > voxpos = dummy.pos(dummy.inside,1);% get the coordinates of voxels inside the volume > dummy.avg.pow(dummy.inside(sign(voxpos)==1)) = 0; % set activity in the left hemisphere to 0 > dummy.avg.pow(dummy.inside(sign(voxpos)==-1)) = 1; % set activity in the left hemisphere to 1 > > cfg = []; > cfg.parameters = 'all'; > > int_dummy = ft_sourceinterpolate(cfg,dummy,template_MNI_mri); > > cfg = []; > cfg.funparameter = 'avg.pow'; > cfg.method = 'ortho'; > > %plot the non-interpolated volume > figure; > ft_sourceplot(cfg,dummy); > > %plot the interpolated volume > figure; > ft_sourceplot(cfg,int_dummy); > > As you can see from the figure in the attachement, the voxels that > corresponded to the left hemisphere prior to the interpolation, > no appear to be located in the rigth hemisphere. > > This is also something that I have observed in real data. > > Does anybody have an explanation why this is happening? > Am I doing something wrong? > > Best, > > Fred > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus From jdien07 at mac.com Thu Sep 6 03:17:03 2012 From: jdien07 at mac.com (Joseph Dien) Date: Wed, 05 Sep 2012 21:17:03 -0400 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: <50465DC3.7080005@berkeley.edu> References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> Message-ID: <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> The Simple Binary (.raw) files don't get corrected for gain when imported (I helped write them). I've experienced occasional unpredictable bugs with NetStation export routines where the files are generated with amplitudes many times too large, even with text format files. It's a bit disconcerting to say the least. I could take a look at your files if you'd like confirmation. Joe On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis wrote: > Hi Daria, > > Also, did you try looking at your raw data (so before the ERPs are made) in FieldTrip and in Net Station? So open your .raw data in NetStation. You can just look at a random participant's data, and check if the scale is the same. I'm pretty sure no amplification takes place when reading in the data into FieldTrip, this check can confirm that. Hope this helps, and let us know what you find. > > Cheers, > Ingrid > > > On 9/3/2012 1:35 PM, Robert Oostenveld wrote: >> Hi Daria, >> >> There might indeed be an incompatibility in the gain value applied to the data. >> >> If you are able to export the data using the EGI software in another format (e.g. EDF), you could read them both into FieldTrip and compare the timecourse aplitudes to check whether they are different. In case they are, I suggest to involve EGI support. They are aware of the FieldTrip reading functions and will know much more about the internals of their various file formats. >> >> best regards >> Robert >> >> >> >> >> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: >> >>> Dear Fieldtrippers, >>> >>> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip toolbox. >>> The ERPs look perfect. >>> The 'only' problem is, that my signals look to strong. >>> It looks like if I get amplitutes (average) until 70 µV. >>> I think it must be an intern amplifier for the signals. >>> Does anyone know this problem with EGI-data? >>> >>> Or does anyone know, where I can see the amplifier? >>> >>> >>> >>> >>> Greetings, >>> >>> Daria _______________________________________________ >>> 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 > > -- > Ingrid Nieuwenhuis PhD > Postdoctoral Fellow > Sleep and Neuroimaging Laboratory > Department of Psychology > University of California, Berkeley > California 94720-1650 > Tolman Hall, room 5305 > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07 at mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan.debener at uni-oldenburg.de Thu Sep 6 09:12:09 2012 From: stefan.debener at uni-oldenburg.de (Stefan Debener) Date: Thu, 06 Sep 2012 09:12:09 +0200 Subject: [FieldTrip] 1 post-doc and 1 PhD position in human auditory and motor neuroscience In-Reply-To: <5046A9C2.2020704@uni-oldenburg.de> References: <5046A9C2.2020704@uni-oldenburg.de> Message-ID: <50484CC9.2070601@uni-oldenburg.de> Lieber Jochem, ich habe vo ein paar Tagen Frau Straube gesprochen, die bei Prof. Kauss, Neurochirurgie Hannover, die Forschung leitet. Herr Krauss ist sehr kooperationsfreudig und es ist kein Problem an BG und Dystonie DBS Patienten zu kommen, das machen die wohl ziemlich häufig inzwischen (ca 1/Woche), und Ausleitung mehrere Tage danach ist auch kein Problem. Vielleicht solltest Du den Kontakt suchen, ist zwar nicht ecog, aber immerhin... lg, s Am 9/5/12 3:24 AM, schrieb Jochem Rieger: > The Department of Applied Neurocognitive Psychology at Oldenburg > University, Germany, offers a > > *Post-doctoral position (E13/TVL, 3 years plus) * > > and a > > *PhD position (0.5*E13/TVL, initially 2 years)* > > The lab focuses on the fields of neural coding of complex movements > and neural coding of speech in the human brain with the aim of > developing brain-machine-interfaces. > > To extend our interdisciplinary team we seek for highly motivated > candidates with strong quantitative and experimental skills. The > post-doctoral position requires a PhD or comparable degree and the PhD > position requires a masters or comparable degree. The post-doctoral > position is initially limited to three years after with an option for > an extension to obtain habilitation (post-doctoral degree, similar to > a lecturer qualification). Successful candidates will perform cutting > edge research in one of the lab's foci and should have a background in > one or more of the following fields: non-invasive or invasive human > neurophysiology of the motor or auditory system, statistical learning, > brain-machine-interfacing. The positions offer an excellent > interdisciplinary working environment with opportunities for > international exchange. The lab is involved in the EU-project BRACOG > (brain controlled grasping) and we have a close collaboration with UC > Berkeley, USA. The University of Oldenburg was recently awarded a > Cluster of Excellence in hearing research. The Dept. of Psychology > will offer an attractive scientific environment with access to > research dedicated state-of-the-art approaches to human > neurophysiological techniques (fMRI, NIRS, EEG, ECoG, and MEG). > > Electronic applications are preferred and can be send to: > Professor Dr. Jochem Rieger: Jochem.rieger at uni-oldenburg.de > > > Please send paper applications until September 30^th 2012 to: > > Margrit Jung > > Dept. of Applied Neurocognitive Psychology > > Institute of Psychology > > Oldenburg University > > 26111 Oldenburg > > Germany > > Applications should include your CV and a list of most recent > publications. Applications for the post-doctoral position should > include a research statement (max. 3 pages). The University of > Oldenburg aims to employ more women in this area and therefore > particularly welcomes applications from women. We also welcome > applications from disabled persons. > > > -- > Prof. Dr. rer. nat. Jochem Rieger > > Applied Neurocognitive Knight Lab > Psychology Helen Wills Neuroscience Institute > Faculty V University of California > Carl-von-Ossietzky University 132 Barker Hall > 26111 Oldenburg Berkeley, CA 94720-3192 > Germany USA > > Phone: +49(0)4417984533 > Fax: +49(0)4417983865 > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Prof. Dr. Stefan Debener Neuropsychology Lab Department of Psychology University of Oldenburg D-26111 Oldenburg Germany Office: A7 0-038 Phone: +49-441-798-4271 Fax: +49-441-798-5522 Email: stefan.debener at uni-oldenburg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.piantoni at nin.knaw.nl Thu Sep 6 10:21:58 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Thu, 6 Sep 2012 10:21:58 +0200 Subject: [FieldTrip] freesurfer surfaces In-Reply-To: References: Message-ID: I fixed the "Arlecchino brain" problem and committed the patch (r6433). I'd still appreciate if people had some suggestions about the analysis steps for the group-average. Best, Gio On Wed, Sep 5, 2012 at 10:20 AM, Gio Piantoni wrote: > Dear Fieldtrip developers, > > I'd like to run source reconstruction on the cortical sheets obtained > from Freesurfer and average them using the "sphere" approach of > Freesurfer. I have these steps in mind: > > 1) create a 3-layer BEM ('outer_skin' 'inner_skull' 'brain' from the > bem/watershed folder, which I think might be better than 'outer_skin' > 'outer_skull' 'inner_skull' as in > http://fieldtrip.fcdonders.nl/development/replicate_functionality_of_mne_software > ) > 2) create a forward model from a subset of points in "?h.smoothwm" > (for computational purposes) > 3) do source reconstruction on this subset of dipoles > 4) source interpolate to the high resolution of ?h.smoothwm > 5) project all the locations onto the ?h.sphere > 6) interpolate to the points to the ?h.sphere of fsaverage > 7) do 2-D statistics on the values of the ?h.sphere of fsaverage (and > plot them using ?h.inflated of fsaverage) > > I was wondering if anybody has tried something similar and if there > are steps I should be careful about. There was a discussion in > January/February about doing statistics on cortical sheets: > http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004749.html > http://mailman.science.ru.nl/pipermail/fieldtrip/2012-February/004766.html > > Does anybody have suggestions about these steps? I promise I'll make a > tutorial out of this, if it works out ;) > > A practical point I get stuck in is at steps 3) and 4). The > interpolation from a subset of 2-D points to another subset of 2-D > points gives a bit of nonsensical results. Code: > > %-get freesurfer surface > bnd = ft_read_headshape('lh.smoothwm'); > % get it from https://skydrive.live.com/redir?resid=6D9DCA0F726A645C!7000 > % or any freesurfer surface you have > > %-downsample > bnd_down = bnd; > P.faces = bnd_down.tri; > P.vertices = bnd_down.pnt; > P = reducepatch(P, 0.05); > bnd_down.tri = P.faces; > bnd_down.pnt = P.vertices; > > %-create source > source.pos = bnd_down.pnt; > source.inside = true(size(source.pos,1),1); > source.pow = bnd_down.pnt(:,3); % "fake" source reconstruction > > figure > ft_plot_mesh(bnd_down, 'edgecolor', 'none', 'vertexcolor', source.pow) > % the rainbow brain > view(90, 0); camlight > > %-sourceinterpolate > cfg = []; > cfg.parameter = 'pow'; > ana = []; > ana.pnt = bnd_down.pnt; > ana.orig = bnd; > souinterp = ft_sourceinterpolate(cfg, source, ana); > > figure > ft_plot_mesh(souinterp, 'edgecolor', 'none', 'vertexcolor', > souinterp.pow) % the Arlecchino brain > view(90, 0); camlight > > Should I file a bugzilla report for this? I haven't done it as I'm not > even sure this is the correct input format. > Thanks for any suggestion. > > Best wishes, > > Gio > > -- > Giovanni Piantoni, MSc > Dept. Sleep & Cognition > Netherlands Institute for Neuroscience > Meibergdreef 47 > 1105 BA Amsterdam (NL) > www.gpiantoni.com From stefan.debener at uni-oldenburg.de Thu Sep 6 12:22:46 2012 From: stefan.debener at uni-oldenburg.de (Stefan Debener) Date: Thu, 06 Sep 2012 12:22:46 +0200 Subject: [FieldTrip] 1 post-doc and 1 PhD position in human auditory and motor neuroscience In-Reply-To: <50484CC9.2070601@uni-oldenburg.de> References: <5046A9C2.2020704@uni-oldenburg.de> <50484CC9.2070601@uni-oldenburg.de> Message-ID: <50487976.7040900@uni-oldenburg.de> Apologies to all for spoiling this list with a personal mail, Stefan Am 9/5/12 3:24 AM, schrieb Jochem Rieger: >> The Department of Applied Neurocognitive Psychology at Oldenburg >> University, Germany, offers a >> >> *Post-doctoral position (E13/TVL, 3 years plus) * >> >> and a >> >> *PhD position (0.5*E13/TVL, initially 2 years)* >> >> The lab focuses on the fields of neural coding of complex movements >> and neural coding of speech in the human brain with the aim of >> developing brain-machine-interfaces. >> >> To extend our interdisciplinary team we seek for highly motivated >> candidates with strong quantitative and experimental skills. The >> post-doctoral position requires a PhD or comparable degree and the >> PhD position requires a masters or comparable degree. The >> post-doctoral position is initially limited to three years after with >> an option for an extension to obtain habilitation (post-doctoral >> degree, similar to a lecturer qualification). Successful candidates >> will perform cutting edge research in one of the lab's foci and >> should have a background in one or more of the following fields: >> non-invasive or invasive human neurophysiology of the motor or >> auditory system, statistical learning, brain-machine-interfacing. The >> positions offer an excellent interdisciplinary working environment >> with opportunities for international exchange. The lab is involved in >> the EU-project BRACOG (brain controlled grasping) and we have a close >> collaboration with UC Berkeley, USA. The University of Oldenburg was >> recently awarded a Cluster of Excellence in hearing research. The >> Dept. of Psychology will offer an attractive scientific environment >> with access to research dedicated state-of-the-art approaches to >> human neurophysiological techniques (fMRI, NIRS, EEG, ECoG, and MEG). >> >> Electronic applications are preferred and can be send to: >> Professor Dr. Jochem Rieger: Jochem.rieger at uni-oldenburg.de >> >> >> Please send paper applications until September 30^th 2012 to: >> >> Margrit Jung >> >> Dept. of Applied Neurocognitive Psychology >> >> Institute of Psychology >> >> Oldenburg University >> >> 26111 Oldenburg >> >> Germany >> >> Applications should include your CV and a list of most recent >> publications. Applications for the post-doctoral position should >> include a research statement (max. 3 pages). The University of >> Oldenburg aims to employ more women in this area and therefore >> particularly welcomes applications from women. We also welcome >> applications from disabled persons. >> >> >> -- >> Prof. Dr. rer. nat. Jochem Rieger >> >> Applied Neurocognitive Knight Lab >> Psychology Helen Wills Neuroscience Institute >> Faculty V University of California >> Carl-von-Ossietzky University 132 Barker Hall >> 26111 Oldenburg Berkeley, CA 94720-3192 >> Germany USA >> >> Phone: +49(0)4417984533 >> Fax: +49(0)4417983865 >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Prof. Dr. Stefan Debener > Neuropsychology Lab > Department of Psychology > University of Oldenburg > D-26111 Oldenburg > Germany > > Office: A7 0-038 > Phone: +49-441-798-4271 > Fax: +49-441-798-5522 > Email:stefan.debener at uni-oldenburg.de > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Prof. Dr. Stefan Debener Neuropsychology Lab Department of Psychology University of Oldenburg D-26111 Oldenburg Germany Office: A7 0-038 Phone: +49-441-798-4271 Fax: +49-441-798-5522 Email: stefan.debener at uni-oldenburg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From landpt at gmail.com Thu Sep 6 12:25:47 2012 From: landpt at gmail.com (Ricardo Jorge) Date: Thu, 6 Sep 2012 11:25:47 +0100 Subject: [FieldTrip] Having troubles with Emotiv + Fieldtrip + Matlab Message-ID: Hello there, I'm new to Fieldtrip: I've been assigned to work with signals acquired by Emotiv in Matlab environment, specially in real-time - or at least almost real-time - so I can work and study these signals with my own Matlab's functions. However, here's the bad thing: we did not expect it to be that complicated to extract signals directly to Matlab. While searching for any module, program, anything I could find, to help our problem, I found Fieldtrip. Correct me if I am wrong, but it seems that it is able to stream/buffer from emotiv's sdk to matlab. The problem is that we do not have that much experience with compiling C programs, hence I am having a really hard time to understand what do you mean with: "Compilation We provide a simple Makefile for the MinGW compiler, but you will need the Emotiv SDK. Please go to the realtime/datasource/emotiv directory and type make or mingw32-make. Note that you might need to compile the libbuffer library first." Here's what I did so far: 1. I have installed Matlab r2011b 64-bit and Emotiv SDK Research Edition; 2. I installed MinGW and set the path of the /bin in environmental variables; 3. I downloaded all these files from: http://code.google.com/p/fieldtrip/source/browse/trunk/realtime/datasource/emotiv/?r=1742 4. Then I went cmd and tried to do: mingw32-make -f makefile.gcc SHARED=1 UNICODE=1 BUILD=release which obviously failed: it said it was missing a file "Ftbuffer.h". I assumed it was the libbuffer library, however I can't seem to find it anywhere in the Internet (just some site that would ask me to install Makestuff application, which I did and was unsuccessful. I found a "buffer" folder in fieldtrip release but I dont think it's that. Hence I tried to download the Ftbuffer.h itself from internet and put it in the folder where emotiv2ft was. It worked, but then it started to ask others files.... and more.. and more.. So, obviously I'm stuck right here. Can you help me right here? What should I do? Have I done something wrong? I've read this discussion list and found one thread quite related to this - but his problem was not having research edition, which in fact, I do have it. I'm sorry bothering you with probably authentic beginner questions, but as I said, I only have high experience with Matlab. Best Regards, Ricardo From Lilla.Magyari at mpi.nl Thu Sep 6 14:45:55 2012 From: Lilla.Magyari at mpi.nl (Lilla.Magyari at mpi.nl) Date: Thu, 6 Sep 2012 14:45:55 +0200 (CEST) Subject: [FieldTrip] Having troubles with Emotiv + Fieldtrip + Matlab In-Reply-To: References: Message-ID: <49788.131.174.45.70.1346935555.squirrel@131.174.45.70> Hello Ricardo, I haven't tried to work with Emotiv, but I see an FtBuffer.h file in the latest version of FieldTrip in the realtime/src/buffer/cpp. I hope this helps. (It is also not clear for me if you downloaded only files related to emotive, or also the whole FieldTrip package (this latest is probably useful)). Best, Lilla > Hello there, > > I'm new to Fieldtrip: I've been assigned to work with signals acquired > by Emotiv in Matlab environment, specially in real-time - or at least > almost real-time - so I can work and study these signals with my own > Matlab's functions. However, here's the bad thing: we did not expect > it to be that complicated to extract signals directly to Matlab. > > While searching for any module, program, anything I could find, to > help our problem, I found Fieldtrip. Correct me if I am wrong, but it > seems that it is able to stream/buffer from emotiv's sdk to matlab. > > The problem is that we do not have that much experience with compiling > C programs, hence I am having a really hard time to understand what do > you mean with: > > "Compilation > We provide a simple Makefile for the MinGW compiler, but you will need > the Emotiv SDK. Please go to the realtime/datasource/emotiv directory > and type make or mingw32-make. Note that you might need to compile the > libbuffer library first." > > > Here's what I did so far: > > 1. I have installed Matlab r2011b 64-bit and Emotiv SDK Research Edition; > > 2. I installed MinGW and set the path of the /bin in environmental > variables; > > 3. I downloaded all these files from: > http://code.google.com/p/fieldtrip/source/browse/trunk/realtime/datasource/emotiv/?r=1742 > > 4. Then I went cmd and tried to do: mingw32-make -f makefile.gcc > SHARED=1 UNICODE=1 BUILD=release > which obviously failed: it said it was missing a file "Ftbuffer.h". I > assumed it was the libbuffer library, however I can't seem to find it > anywhere in the Internet (just some site that would ask me to install > Makestuff application, which I did and was unsuccessful. > I found a "buffer" folder in fieldtrip release but I dont think it's that. > Hence I tried to download the Ftbuffer.h itself from internet and put > it in the folder where emotiv2ft was. It worked, but then it started > to ask others files.... and more.. and more.. > > So, obviously I'm stuck right here. > Can you help me right here? What should I do? Have I done something wrong? > I've read this discussion list and found one thread quite related to > this - but his problem was not having research edition, which in fact, > I do have it. > > I'm sorry bothering you with probably authentic beginner questions, > but as I said, I only have high experience with Matlab. > > Best Regards, > Ricardo > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From r.oostenveld at donders.ru.nl Thu Sep 6 15:05:32 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 6 Sep 2012 15:05:32 +0200 Subject: [FieldTrip] Having troubles with Emotiv + Fieldtrip + Matlab In-Reply-To: References: Message-ID: <094D4EED-A39B-4788-BB7B-9C801AF65B78@donders.ru.nl> Dear Ricardo, We provide the full source code for you to investigate, modify and recompile, but we also provide pre-compiled binaries that you shoiuld be able to use to just get it to run. Rather than just grabbing a small section of the fieldtrip code, which you seem to have done, I suggest you get a complete fieldtrip version from http://fieldtrip.fcdonders.nl/download or through SVN (you want the complete trunk). In the fieldtrip/realtime/bin/win32 directory you will find the compiled emotiv2ft.exe program (it is present both in th ezip file from the ftp, as well as in the svn version). The emotiv2ft.exe application copies the data from the emotiv dll into the FT buffer, where you can access it from MATLAB using the methods described here http://fieldtrip.fcdonders.nl/getting_started/realtime for end-users and here http://fieldtrip.fcdonders.nl/development/realtime for developers. Hope this helps, Robert On 6 Sep 2012, at 12:25, Ricardo Jorge wrote: > Hello there, > > I'm new to Fieldtrip: I've been assigned to work with signals acquired > by Emotiv in Matlab environment, specially in real-time - or at least > almost real-time - so I can work and study these signals with my own > Matlab's functions. However, here's the bad thing: we did not expect > it to be that complicated to extract signals directly to Matlab. > > While searching for any module, program, anything I could find, to > help our problem, I found Fieldtrip. Correct me if I am wrong, but it > seems that it is able to stream/buffer from emotiv's sdk to matlab. > > The problem is that we do not have that much experience with compiling > C programs, hence I am having a really hard time to understand what do > you mean with: > > "Compilation > We provide a simple Makefile for the MinGW compiler, but you will need > the Emotiv SDK. Please go to the realtime/datasource/emotiv directory > and type make or mingw32-make. Note that you might need to compile the > libbuffer library first." > > > Here's what I did so far: > > 1. I have installed Matlab r2011b 64-bit and Emotiv SDK Research Edition; > > 2. I installed MinGW and set the path of the /bin in environmental variables; > > 3. I downloaded all these files from: > http://code.google.com/p/fieldtrip/source/browse/trunk/realtime/datasource/emotiv/?r=1742 > > 4. Then I went cmd and tried to do: mingw32-make -f makefile.gcc > SHARED=1 UNICODE=1 BUILD=release > which obviously failed: it said it was missing a file "Ftbuffer.h". I > assumed it was the libbuffer library, however I can't seem to find it > anywhere in the Internet (just some site that would ask me to install > Makestuff application, which I did and was unsuccessful. > I found a "buffer" folder in fieldtrip release but I dont think it's that. > Hence I tried to download the Ftbuffer.h itself from internet and put > it in the folder where emotiv2ft was. It worked, but then it started > to ask others files.... and more.. and more.. > > So, obviously I'm stuck right here. > Can you help me right here? What should I do? Have I done something wrong? > I've read this discussion list and found one thread quite related to > this - but his problem was not having research edition, which in fact, > I do have it. > > I'm sorry bothering you with probably authentic beginner questions, > but as I said, I only have high experience with Matlab. > > Best Regards, > Ricardo > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Jan.Hirschmann at med.uni-duesseldorf.de Thu Sep 6 15:06:02 2012 From: Jan.Hirschmann at med.uni-duesseldorf.de (Jan.Hirschmann at med.uni-duesseldorf.de) Date: Thu, 6 Sep 2012 15:06:02 +0200 Subject: [FieldTrip] phase difference between sources Message-ID: <72E993C35FB11743B79FF9286E5B6D8B04617307@Mail2-UKD.VMED.UKD> Dear fieldtrip experts, I was wondering how to get the mean phase difference between two sources A and B at a particular frequency f (mean across data segments). My idea was to use dics and to say cfg.refdip=A and cfg.keepcsd='yes'. Then I would get C, the cross spectral density between A and B, which is a 3x3 matrix with complex entries. Joachim Gross wrote that one could estimate csd in the dominant direction as the trace of C. So I guess I could get the phase difference by angle(trace(C)). Is this correct? If I wanted to use SVD to estimate the dominant direction instead of the trace, how would I get the phase difference then? And finally, if I wanted to have coherence not with the dipole orientation that maximizes power but with the orientation that maximizes phase difference, how would that work? Thanks for any remarks! Jan -- Jan Hirschmann MSc Neuroscience Institute of Clinical Neuroscience and Medical Psychology Heinrich Heine University Düsseldorf Universitätsstr. 1 40225 Düsseldorf Germany Tel: +49 (0)211 81 18415 Fax: +49 (0)211 81 19033 -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Sep 6 15:10:28 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 6 Sep 2012 15:10:28 +0200 Subject: [FieldTrip] left to right inversion after source interpolation In-Reply-To: <44E1ACF5-2C6D-4BA2-8FA7-B0886FB8AF20@uke.uni-hamburg.de> References: <075a92dd-147e-45e9-a4d1-726999c597b1@thalamus_p> <44E1ACF5-2C6D-4BA2-8FA7-B0886FB8AF20@uke.uni-hamburg.de> Message-ID: <7B18D5B7-9B69-4E09-AFD8-3B6D5B30D6A0@donders.ru.nl> Hi Fred, On http://fieldtrip.fcdonders.nl/faq/why_does_my_anatomical_mri_show_upside-down_when_plotting_it_with_ft_sourceplot there is an explanation to a related question. Also in your case FT_VOLUMERSLICE might be of use. See also http://fieldtrip.fcdonders.nl/faq/what_is_the_plotting_convention_for_anatomical_mris best Robert On 5 Sep 2012, at 16:30, Kathrin Müsch wrote: > Dear Fred, > > I encountered a similar thing a while ago and it was because spm8 seems to plot in radiological convention (i.e. left is plotted right and vice versa - http://mailman.science.ru.nl/pipermail/fieldtrip/2012-May/005229.html) so you're plots should actually be correct. > > If you use cfg.interactive = 'yes'; and click into the activated side of the brain, the first coordinate should be negative because you are in the left hemisphere. > > Hope that helps, > Kathrin > > > Am 05.09.2012 um 14:47 schrieb Frederic Roux: > >> Dear fieldtrip users, >> >> I have noticed that after interpolating a dummy source volume with ft_sourceinterpolate, >> voxels that were located in the left side of the volume, apear to be located in the right >> side of the volume. >> >> The code that I use is as following: >> >> dummy is a dummy structure of an lcmv beamformer map with the fields >> >> dummy = >> dim : [15 18 17] >> time: [1x272662 double] >> pos: [4590x3 double] >> inside: [1x2144 double] >> outside: [1x2446 double] >> method: 'average' >> avg: [1x1 struct] >> >> voxpos = dummy.pos(dummy.inside,1);% get the coordinates of voxels inside the volume >> dummy.avg.pow(dummy.inside(sign(voxpos)==1)) = 0; % set activity in the left hemisphere to 0 >> dummy.avg.pow(dummy.inside(sign(voxpos)==-1)) = 1; % set activity in the left hemisphere to 1 >> >> cfg = []; >> cfg.parameters = 'all'; >> >> int_dummy = ft_sourceinterpolate(cfg,dummy,template_MNI_mri); >> >> cfg = []; >> cfg.funparameter = 'avg.pow'; >> cfg.method = 'ortho'; >> >> %plot the non-interpolated volume >> figure; >> ft_sourceplot(cfg,dummy); >> >> %plot the interpolated volume >> figure; >> ft_sourceplot(cfg,int_dummy); >> >> As you can see from the figure in the attachement, the voxels that >> corresponded to the left hemisphere prior to the interpolation, >> no appear to be located in the rigth hemisphere. >> >> This is also something that I have observed in real data. >> >> Does anybody have an explanation why this is happening? >> Am I doing something wrong? >> >> Best, >> >> Fred >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): > > Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg > > Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From landpt at gmail.com Thu Sep 6 17:48:27 2012 From: landpt at gmail.com (Ricardo Jorge) Date: Thu, 6 Sep 2012 16:48:27 +0100 Subject: [FieldTrip] Having troubles with Emotiv + Fieldtrip + Matlab Message-ID: Hello there, Thanks! I'm a feeling a bit shamed because now they did seem like stupid questions but it really worked now - I had to read the walkthough to understand some definitions, and then I read your replies about the emotiv executable and really worked now! I was not understanding why I would need to compile again if there was an executable - I thought it was related to the fact that EPOC wouldn't allow the redistribution of their dlls or something like that, I don't know. Thanks again. Best, Ricardo Jorge From daria.laptinskaya at googlemail.com Thu Sep 6 18:52:44 2012 From: daria.laptinskaya at googlemail.com (Daria Laptinskaya) Date: Thu, 6 Sep 2012 18:52:44 +0200 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> Message-ID: Thanks you all for the answers! It seems to be a problem with reading the raw.-files. My collegue found a formula, maybe we can use it for microvolt-scaling. @Joe: It would be a great helf, if you could have a look at one of the files. Can I send you a dropbox-link? Best, Daria 2012/9/6 Joseph Dien > The Simple Binary (.raw) files don't get corrected for gain when imported > (I helped write them). I've experienced occasional unpredictable bugs with > NetStation export routines where the files are generated with amplitudes > many times too large, even with text format files. It's a bit > disconcerting to say the least. I could take a look at your files if you'd > like confirmation. > > Joe > > On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis > wrote: > > Hi Daria, > > Also, did you try looking at your raw data (so before the ERPs are made) > in FieldTrip and in Net Station? So open your .raw data in NetStation. You > can just look at a random participant's data, and check if the scale is the > same. I'm pretty sure no amplification takes place when reading in the data > into FieldTrip, this check can confirm that. Hope this helps, and let us > know what you find. > > Cheers, > Ingrid > > > On 9/3/2012 1:35 PM, Robert Oostenveld wrote: > > Hi Daria, > > There might indeed be an incompatibility in the gain value applied to > the data. > > If you are able to export the data using the EGI software in another > format (e.g. EDF), you could read them both into FieldTrip and compare the > timecourse aplitudes to check whether they are different. In case they are, > I suggest to involve EGI support. They are aware of the FieldTrip reading > functions and will know much more about the internals of their various file > formats. > > best regards > Robert > > > > > On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: > > Dear Fieldtrippers, > > I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip > toolbox. > The ERPs look perfect. > The 'only' problem is, that my signals look to strong. > It looks like if I get amplitutes (average) until 70 µV. > I think it must be an intern amplifier for the signals. > > Does anyone know this problem with EGI-data? > > Or does anyone know, where I can see the amplifier? > > > > Greetings, > Daria _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Ingrid Nieuwenhuis PhD > Postdoctoral Fellow > Sleep and Neuroimaging Laboratory > Department of Psychology > University of California, Berkeley > California 94720-1650 > Tolman Hall, room 5305 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mollison at gmail.com Thu Sep 6 19:01:42 2012 From: matt.mollison at gmail.com (Matt Mollison) Date: Thu, 6 Sep 2012 11:01:42 -0600 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> Message-ID: Joe, A few related questions: Does using the "calibrate data" option when exporting to raw (simple binary) correct for gain? Or is there a different solution/recommendation? Does exporting to MFF (Net Station 4.5.x only) or EGIS have this issue? I tend to use EGIS (faster to read than raw) and have no recollection of seeing unusually large voltages. Thanks, Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ On Wed, Sep 5, 2012 at 7:17 PM, Joseph Dien wrote: > The Simple Binary (.raw) files don't get corrected for gain when imported > (I helped write them). I've experienced occasional unpredictable bugs with > NetStation export routines where the files are generated with amplitudes > many times too large, even with text format files. It's a bit > disconcerting to say the least. I could take a look at your files if you'd > like confirmation. > > Joe > > On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis > wrote: > > Hi Daria, > > Also, did you try looking at your raw data (so before the ERPs are made) > in FieldTrip and in Net Station? So open your .raw data in NetStation. You > can just look at a random participant's data, and check if the scale is the > same. I'm pretty sure no amplification takes place when reading in the data > into FieldTrip, this check can confirm that. Hope this helps, and let us > know what you find. > > Cheers, > Ingrid > > > On 9/3/2012 1:35 PM, Robert Oostenveld wrote: > > Hi Daria, > > There might indeed be an incompatibility in the gain value applied to > the data. > > If you are able to export the data using the EGI software in another > format (e.g. EDF), you could read them both into FieldTrip and compare the > timecourse aplitudes to check whether they are different. In case they are, > I suggest to involve EGI support. They are aware of the FieldTrip reading > functions and will know much more about the internals of their various file > formats. > > best regards > Robert > > > > > On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: > > Dear Fieldtrippers, > > I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip > toolbox. > The ERPs look perfect. > The 'only' problem is, that my signals look to strong. > It looks like if I get amplitutes (average) until 70 µV. > I think it must be an intern amplifier for the signals. > > Does anyone know this problem with EGI-data? > > Or does anyone know, where I can see the amplifier? > > > > Greetings, > Daria _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Ingrid Nieuwenhuis PhD > Postdoctoral Fellow > Sleep and Neuroimaging Laboratory > Department of Psychology > University of California, Berkeley > California 94720-1650 > Tolman Hall, room 5305 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jdien07 at mac.com Fri Sep 7 02:58:43 2012 From: jdien07 at mac.com (Joseph Dien) Date: Thu, 06 Sep 2012 20:58:43 -0400 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> Message-ID: <293829E7-6D3C-4ED9-B592-5981F73098F8@mac.com> By all means! Joe On Sep 6, 2012, at 12:52 PM, Daria Laptinskaya wrote: > Thanks you all for the answers! > It seems to be a problem with reading the raw.-files. > My collegue found a formula, maybe we can use it for microvolt-scaling. > > @Joe: It would be a great helf, if you could have a look at one of the files. > Can I send you a dropbox-link? > > Best, > Daria > > > 2012/9/6 Joseph Dien > The Simple Binary (.raw) files don't get corrected for gain when imported (I helped write them). I've experienced occasional unpredictable bugs with NetStation export routines where the files are generated with amplitudes many times too large, even with text format files. It's a bit disconcerting to say the least. I could take a look at your files if you'd like confirmation. > > Joe > > On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis wrote: > >> Hi Daria, >> >> Also, did you try looking at your raw data (so before the ERPs are made) in FieldTrip and in Net Station? So open your .raw data in NetStation. You can just look at a random participant's data, and check if the scale is the same. I'm pretty sure no amplification takes place when reading in the data into FieldTrip, this check can confirm that. Hope this helps, and let us know what you find. >> >> Cheers, >> Ingrid >> >> >> On 9/3/2012 1:35 PM, Robert Oostenveld wrote: >>> Hi Daria, >>> >>> There might indeed be an incompatibility in the gain value applied to the data. >>> >>> If you are able to export the data using the EGI software in another format (e.g. EDF), you could read them both into FieldTrip and compare the timecourse aplitudes to check whether they are different. In case they are, I suggest to involve EGI support. They are aware of the FieldTrip reading functions and will know much more about the internals of their various file formats. >>> >>> best regards >>> Robert >>> >>> >>> >>> >>> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: >>> >>>> Dear Fieldtrippers, >>>> >>>> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip toolbox. >>>> The ERPs look perfect. >>>> The 'only' problem is, that my signals look to strong. >>>> It looks like if I get amplitutes (average) until 70 µV. >>>> I think it must be an intern amplifier for the signals. >>>> Does anyone know this problem with EGI-data? >>>> >>>> Or does anyone know, where I can see the amplifier? >>>> >>>> >>>> >>>> >>>> Greetings, >>>> >>>> Daria _______________________________________________ >>>> 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 >> >> -- >> Ingrid Nieuwenhuis PhD >> Postdoctoral Fellow >> Sleep and Neuroimaging Laboratory >> Department of Psychology >> University of California, Berkeley >> California 94720-1650 >> Tolman Hall, room 5305 >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07 at mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// -------------- next part -------------- An HTML attachment was scrubbed... URL: From jdien07 at mac.com Fri Sep 7 03:07:12 2012 From: jdien07 at mac.com (Joseph Dien) Date: Thu, 06 Sep 2012 21:07:12 -0400 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> Message-ID: <77D46473-6907-4AC1-96E1-F51756C119C0@mac.com> I don't recall ever seeing this problem with EGIS files, which is one of the reasons I prefer using this file format despite EGI's preference for newer Simple Binary format, but it's an unpredictable bug so I can't say it can't happen. I also can't say which versions of NetStation it happens with. It may have been fixed. I'm still trying to test out MFF so can't say anything about it. I had problems with the FieldTrip code for reading segmented MFF files (which is what I'm interested in). I also had trouble with writing them out from NetStation so I don't have a valid segmented test file and I'm still waiting for EGI to make one available so I can work them out. The simple binary file format (this is the original name for the EGI .raw file format and I prefer to use it over ".raw" as the BESA .raw file format is actually the .egis file format so it can get confusing) doesn't actually have separate calibration information for the channels (unlike EGIS), just one single gain value and no zeros values. So basically the simple binary format makes the assumption that calibration corrections have already been performed prior to generating the file. My understanding is that this is indeed what the "calibrate data" option is doing, but you'd have to confirm with EGI. Joe -------------------------------------------------------------------------------- On Sep 6, 2012, at 1:01 PM, Matt Mollison wrote: > Joe, > > A few related questions: > > Does using the "calibrate data" option when exporting to raw (simple binary) correct for gain? Or is there a different solution/recommendation? > Does exporting to MFF (Net Station 4.5.x only) or EGIS have this issue? I tend to use EGIS (faster to read than raw) and have no recollection of seeing unusually large voltages. > > Thanks, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > > On Wed, Sep 5, 2012 at 7:17 PM, Joseph Dien wrote: > The Simple Binary (.raw) files don't get corrected for gain when imported (I helped write them). I've experienced occasional unpredictable bugs with NetStation export routines where the files are generated with amplitudes many times too large, even with text format files. It's a bit disconcerting to say the least. I could take a look at your files if you'd like confirmation. > > Joe > > On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis wrote: > >> Hi Daria, >> >> Also, did you try looking at your raw data (so before the ERPs are made) in FieldTrip and in Net Station? So open your .raw data in NetStation. You can just look at a random participant's data, and check if the scale is the same. I'm pretty sure no amplification takes place when reading in the data into FieldTrip, this check can confirm that. Hope this helps, and let us know what you find. >> >> Cheers, >> Ingrid >> >> >> On 9/3/2012 1:35 PM, Robert Oostenveld wrote: >>> Hi Daria, >>> >>> There might indeed be an incompatibility in the gain value applied to the data. >>> >>> If you are able to export the data using the EGI software in another format (e.g. EDF), you could read them both into FieldTrip and compare the timecourse aplitudes to check whether they are different. In case they are, I suggest to involve EGI support. They are aware of the FieldTrip reading functions and will know much more about the internals of their various file formats. >>> >>> best regards >>> Robert >>> >>> >>> >>> >>> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: >>> >>>> Dear Fieldtrippers, >>>> >>>> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip toolbox. >>>> The ERPs look perfect. >>>> The 'only' problem is, that my signals look to strong. >>>> It looks like if I get amplitutes (average) until 70 µV. >>>> I think it must be an intern amplifier for the signals. >>>> Does anyone know this problem with EGI-data? >>>> >>>> Or does anyone know, where I can see the amplifier? >>>> >>>> >>>> >>>> >>>> Greetings, >>>> >>>> Daria _______________________________________________ >>>> 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 >> >> -- >> Ingrid Nieuwenhuis PhD >> Postdoctoral Fellow >> Sleep and Neuroimaging Laboratory >> Department of Psychology >> University of California, Berkeley >> California 94720-1650 >> Tolman Hall, room 5305 >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07 at mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// -------------- next part -------------- An HTML attachment was scrubbed... URL: From polomacnenad at gmail.com Fri Sep 7 12:36:05 2012 From: polomacnenad at gmail.com (Nenad Polomac) Date: Fri, 7 Sep 2012 12:36:05 +0200 Subject: [FieldTrip] problem with FT_MEGPLANAR Message-ID: Dear all, I would like to apply FT_MEGPLANAR on ERF data obtain from FT_TIMELOCKANALYSIS. According to tutorial that should be possible. This is the error I get: Error using ft_checkdata (line 376) This function requires ctf151, ctf275, bti148, bti248, itab153, yokogawa160 or yokogawa64 data as input, but you are giving ctf275 data. Error in ft_megplanar (line 109) data = ft_checkdata(data, 'datatype', {'raw' 'freq'}, 'feedback', 'yes', 'hassampleinfo', 'yes', 'ismeg', 'yes', 'senstype', {'ctf151', 'ctf275', 'bti148', 'bti248', 'itab153', 'yokogawa160', 'yokoga This is how looks like output form FT_TIMELOCKANALYSIS. On this data I would like to apply FT_MEGPLANAR. average32 = avg: [271x1440 double] var: [271x1440 double] time: [1x1440 double] dof: [271x1440 double] label: {271x1 cell} trial: [75x271x1440 double] dimord: 'rpt_chan_time' trialinfo: [75x1 double] cfg: [1x1 struct] My code: cfg = []; cfg.method = 'template'; cfg.template = 'CTF275_neighb.mat'; neighbours = ft_prepare_neighbours(cfg, grad); cfg=[]; cfg.neighbours=neighbours; cfg.planarmethod = 'orig'; cfg.trials = 'all'; planar32 = ft_megplanar(cfg, average32); *grad is structure obtained earlier with FT_PREPROCESSING Furthermore, I would also like to apply FT_MEGPLANAR on the other data obtained from ft_rejectcomponent (after ICA rejection) and this doesn't work as well. This error is the same as one I mentioned above. Thank you in advance! Nenad -------------- next part -------------- An HTML attachment was scrubbed... URL: From Markus.Butz at uni-duesseldorf.de Fri Sep 7 14:33:22 2012 From: Markus.Butz at uni-duesseldorf.de (Markus Butz) Date: Fri, 07 Sep 2012 13:33:22 +0100 Subject: [FieldTrip] Frontiers in Human Neuroscience - Research Topic: The Functional Role of Gamma Band Activity - Lessons from MEG Message-ID: <7620e04b44e3.5049f7a2@uni-duesseldorf.de> Dear FieldTrip list We are pleased to announce an upcoming Research Topic in Frontiers in Human Neuroscience on “The Functional Role of Gamma Band Activity – Lessons From MEG”. Further information can be found here: http://www.frontiersin.org/human_neuroscience/researchtopics/the_functional_role_of_gamma_b/962 Deadline for abstract submission: 01 Dec 2012 Deadline for full article submission: 01 Feb 2013 We are looking forward to your contributions! Please don’t hesitate to get in contact in case you have any further questions. Thank you very much for your consideration Krish & Markus -------------- next part -------------- An HTML attachment was scrubbed... URL: From tim.curran at Colorado.EDU Fri Sep 7 22:58:59 2012 From: tim.curran at Colorado.EDU (Tim Curran) Date: Fri, 7 Sep 2012 14:58:59 -0600 Subject: [FieldTrip] Colorado Computational Cognition Faculty Position In-Reply-To: References: Message-ID: <59F8E65D-69AE-4FCD-A985-1D0A28659020@colorado.edu> Computational Approaches to Cognition, Institute of Cognitive Science Tenure Track Position The Institute of Cognitive Science at the University of Colorado invites applications for a full-time tenure-track position in computational approaches to cognitive and/or affective processes at the assistant professor level with a starting date of Fall 2013. The Institute is a multidisciplinary unit with representation from the departments of Psychology & Neuroscience, Computer Science, Education, Philosophy, Linguistics, Architecture & Planning, and Speech, Language & Hearing Sciences. We seek applicants with a strong research program in theoretical and technical aspects of computational science. preferably with prior experience or interest in integrating cognitive science with state-of-the-art computational approaches. For example, individuals who utilize machine learning and statistical techniques to understand cognitive processes, such as language or learning, or to analyze high dimensional data from methods, such as functional magnetic resonance imaging, will be competitive for the position. Successful applicants could come from one of several fields, including cognitive science/cognitive neuroscience, computer science, statistics, biostatistics, physics, or other related disciplines. An ability for and commitment to interdisciplinary research is a priority, as is an approach that both exploits existing computational techniques to address questions relevant to cognitive science and advances machine-learning theory. Duties include research, research supervision, service, as well as graduate and undergraduate teaching. Applicants are directed to the CU online job application website: www.jobsatcu.com; Job Posting Number 818695. At this site you will be asked for a curriculum vitae, copies of representative publications, a teaching statement, a research summary, and letter from three referees. For fullest consideration, please apply by September 24th, 2012. Applications will continue to be accepted after this date until the position is filled. Email inquiries may be sent to Donna.Caccamise at colorado.edu. The University of Colorado is an Equal Opportunity Employer committed to building a diverse workforce. We encourage applications from women, racial and ethnic minorities, individuals with disabilities and veterans. Alternative formats of this ad can be provided upon request for individuals with disabilities by contacting the ADA Coordinator at hr-ada at colorado.edu. The University of Colorado Boulder conducts background checks on all final applicants being considered for employment. From jdien07 at mac.com Mon Sep 10 02:44:44 2012 From: jdien07 at mac.com (Joseph Dien) Date: Sun, 09 Sep 2012 20:44:44 -0400 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: <77D46473-6907-4AC1-96E1-F51756C119C0@mac.com> References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> <77D46473-6907-4AC1-96E1-F51756C119C0@mac.com> Message-ID: <3B494ED9-B6C3-46A3-840C-8EEEDAA85E5E@mac.com> Hey Daria, glad you were able to get it worked out! Thank Matt for his reminder (below) about the calibration option. Cheers! Joe > Hi Joe, > > > > I didn’t know that there is a function like this. > > The most of my colleagues use the RAW.-files they get from the file-exporter without problems. > > Not even NetStation-support could give me an answer. > > So I thought, it must be a problem between NetStation and fieldtrip. > > Because of your tip I opened an original datafile and tried to save a copy of the file. > > Doing so NetStation offers a possibility to ‘convert to microvolts’ and create a .ses –datafile. > > The .raw-files I get this way have microvolt as unit. > > I compared the signals I get this way with the signals I get by using the formula (5000 mircovolts / (2^16 bits) I send you. They are almost the same-that’s great!!! > > It seems to work now. > > Thank you very much!!! You were a great help!!! > > > Cheers, > > Daria > On Sep 6, 2012, at 9:07 PM, Joseph Dien wrote: > I don't recall ever seeing this problem with EGIS files, which is one of the reasons I prefer using this file format despite EGI's preference for newer Simple Binary format, but it's an unpredictable bug so I can't say it can't happen. I also can't say which versions of NetStation it happens with. It may have been fixed. I'm still trying to test out MFF so can't say anything about it. I had problems with the FieldTrip code for reading segmented MFF files (which is what I'm interested in). I also had trouble with writing them out from NetStation so I don't have a valid segmented test file and I'm still waiting for EGI to make one available so I can work them out. The simple binary file format (this is the original name for the EGI .raw file format and I prefer to use it over ".raw" as the BESA .raw file format is actually the .egis file format so it can get confusing) doesn't actually have separate calibration information for the channels (unlike EGIS), just one single gain value and no zeros values. So basically the simple binary format makes the assumption that calibration corrections have already been performed prior to generating the file. My understanding is that this is indeed what the "calibrate data" option is doing, but you'd have to confirm with EGI. > > Joe > > > -------------------------------------------------------------------------------- > > On Sep 6, 2012, at 1:01 PM, Matt Mollison wrote: > >> Joe, >> >> A few related questions: >> >> Does using the "calibrate data" option when exporting to raw (simple binary) correct for gain? Or is there a different solution/recommendation? >> Does exporting to MFF (Net Station 4.5.x only) or EGIS have this issue? I tend to use EGIS (faster to read than raw) and have no recollection of seeing unusually large voltages. >> >> Thanks, >> Matt >> >> -- >> Univ. of Colorado at Boulder >> Dept. of Psychology and Neuroscience >> matthew.mollison at colorado.edu >> http://psych.colorado.edu/~mollison/ >> >> On Wed, Sep 5, 2012 at 7:17 PM, Joseph Dien wrote: >> The Simple Binary (.raw) files don't get corrected for gain when imported (I helped write them). I've experienced occasional unpredictable bugs with NetStation export routines where the files are generated with amplitudes many times too large, even with text format files. It's a bit disconcerting to say the least. I could take a look at your files if you'd like confirmation. >> >> Joe >> >> On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis wrote: >> >>> Hi Daria, >>> >>> Also, did you try looking at your raw data (so before the ERPs are made) in FieldTrip and in Net Station? So open your .raw data in NetStation. You can just look at a random participant's data, and check if the scale is the same. I'm pretty sure no amplification takes place when reading in the data into FieldTrip, this check can confirm that. Hope this helps, and let us know what you find. >>> >>> Cheers, >>> Ingrid >>> >>> >>> On 9/3/2012 1:35 PM, Robert Oostenveld wrote: >>>> Hi Daria, >>>> >>>> There might indeed be an incompatibility in the gain value applied to the data. >>>> >>>> If you are able to export the data using the EGI software in another format (e.g. EDF), you could read them both into FieldTrip and compare the timecourse aplitudes to check whether they are different. In case they are, I suggest to involve EGI support. They are aware of the FieldTrip reading functions and will know much more about the internals of their various file formats. >>>> >>>> best regards >>>> Robert >>>> >>>> >>>> >>>> >>>> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: >>>> >>>>> Dear Fieldtrippers, >>>>> >>>>> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip toolbox. >>>>> The ERPs look perfect. >>>>> The 'only' problem is, that my signals look to strong. >>>>> It looks like if I get amplitutes (average) until 70 µV. >>>>> I think it must be an intern amplifier for the signals. >>>>> Does anyone know this problem with EGI-data? >>>>> >>>>> Or does anyone know, where I can see the amplifier? >>>>> >>>>> >>>>> >>>>> >>>>> Greetings, >>>>> >>>>> Daria _______________________________________________ >>>>> 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 >>> >>> -- >>> Ingrid Nieuwenhuis PhD >>> Postdoctoral Fellow >>> Sleep and Neuroimaging Laboratory >>> Department of Psychology >>> University of California, Berkeley >>> California 94720-1650 >>> Tolman Hall, room 5305 >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, >> Senior Research Scientist >> University of Maryland >> >> E-mail: jdien07 at mac.com >> Phone: 301-226-8848 >> Fax: 301-226-8811 >> http://joedien.com// >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07 at mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// -------------- next part -------------- An HTML attachment was scrubbed... URL: From sahand.babapoor at gmail.com Mon Sep 10 02:49:31 2012 From: sahand.babapoor at gmail.com (sahand babapoor) Date: Sun, 9 Sep 2012 20:49:31 -0400 Subject: [FieldTrip] Using WPLI od WPLI-debiased to do the coherence analysis Message-ID: Hi all, I am trying to do coherency analysis between ACC and FEF. I have tried both WPLI and WPLI-debiased methods to do the analysis. When I am using WPLI I find a very nice coherence pattern between ACC and FEF in the frequencies between ~11Hz to 20 Hz. However, when I am using WPLI-debiased method, the previous WPLI coherence pattern disappears and breaks into many sparse clusters across many time points and frequencies. Is there a way to know which method is the best for me. I should note that I am recording using tungsten microelectrodes advanced into the brain. I would appreciate if your help. Best, Sahand -------------- next part -------------- An HTML attachment was scrubbed... URL: From ivano_triggiani at yahoo.it Mon Sep 10 12:27:09 2012 From: ivano_triggiani at yahoo.it (Ivano Triggiani) Date: Mon, 10 Sep 2012 11:27:09 +0100 (BST) Subject: [FieldTrip] about overlap in PSD calculation In-Reply-To: References: Message-ID: <1347272829.31720.YahooMailNeo@web133103.mail.ir2.yahoo.com> Hi all. How can I obtain informations about the kind of overlapping performed by fiedltrip implemented method to obtain a Power Spectral Density ? I need to compare fieldtrip PSD with another spectral density, so I need to be sure of everything. I found docs about tapering, but I don't understand if using a kind of tapering the overlapping is given. Ivano   ------------------------------------------------------------------------ "No man can wear one face to himself and another to the multitude, without finally getting bewildered as to which one is true." Nathaniel Hawthorne ________________________________ Da: "fieldtrip-request at science.ru.nl" A: fieldtrip at science.ru.nl Inviato: Lunedì 10 Settembre 2012 12:00 Oggetto: fieldtrip Digest, Vol 22, Issue 17 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. Using WPLI od WPLI-debiased to do the coherence analysis       (sahand babapoor) ---------------------------------------------------------------------- Message: 1 Date: Sun, 9 Sep 2012 20:49:31 -0400 From: sahand babapoor To: fieldtrip at science.ru.nl Subject: [FieldTrip] Using WPLI od WPLI-debiased to do the coherence     analysis Message-ID:     Content-Type: text/plain; charset="iso-8859-1" Hi all, I am trying to do coherency analysis between ACC and FEF. I have tried both WPLI and WPLI-debiased methods to do the analysis. When I am using WPLI I find a very nice coherence pattern between ACC and FEF in the frequencies between ~11Hz to 20 Hz. However, when I am using WPLI-debiased method, the previous WPLI coherence pattern disappears and  breaks into many sparse clusters across many time points and frequencies. Is there a way to know which method is the best for me. I should note that I am recording using tungsten microelectrodes advanced into the brain. I would appreciate if your help. Best, Sahand -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip End of fieldtrip Digest, Vol 22, Issue 17 ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From bherrmann at cbs.mpg.de Mon Sep 10 13:16:09 2012 From: bherrmann at cbs.mpg.de (=?utf-8?Q?Bj=C3=B6rn_Herrmann?=) Date: Mon, 10 Sep 2012 13:16:09 +0200 (CEST) Subject: [FieldTrip] real-value spatial filter from FFT dipole localization? In-Reply-To: <380027886.2137.1347269068602.JavaMail.root@zimbra> Message-ID: <1396322041.3317.1347275769488.JavaMail.root@zimbra> Dear fieldtrip users, maybe someone can point me in the right direction. I try to obtain a spatial filter from localizing the sources of an auditory 3Hz peak in my FFT spectrum. I would like to apply the filter to my single trial real data, i.e. basically reducing my 204 gradiometer channels (neuromag system) to one or two channels in source space. I was using DICS beamformer and cfg.realfilter = 'yes' but the source localization results (NAI) looked not too well compared to the nice auditory gradiometer topographies. I then used ft_dipolefitting, however, I have trouble understanding the output. This is where I wondered whether someone could help me, in telling whether it is possible to obtain a real-value spatial filter from this: source = label: {204x1 cell} dip: [1x1 struct] Vdata: [204x408 double] Vmodel: [204x408 double] freq: 3 dimord: 'chan_freq' grad: [1x1 struct] cfg: [1x1 struct] source.dip = pos: [2x3 double] mom: [6x408 double] pot: [204x408 double] rv: [1x408 double] pow: 2.7948e+18 csd: [6x6 double] fourier: [6x204 double] I would appreciate helping comments, as I tested the different methods for some time now, but was unable to extract a reasonable real-value spatial filter for my auditory cortex activations. Best regards, Björn From wallisgj at gmail.com Mon Sep 10 14:22:20 2012 From: wallisgj at gmail.com (George Wallis) Date: Mon, 10 Sep 2012 13:22:20 +0100 Subject: [FieldTrip] Appending data.grad, after using D.ftraw(0) Message-ID: Dear fieldtrippers, if anyone can help me with this I'd be very grateful! I have a bunch of preprocessed and epoched data files in SPM format, and I'm converting them to fieldtrip format using the following: D = spm_eeg_load(fn); data = D.ftraw(0); ...which results in... data = fsample: 250 label: {350x1 cell} trial: {1x360 cell} time: {1x360 cell} Comparing this to data structures generated using fieldtrip alone, field like data.grad are missing. I can create something like a grad field by doing: D.sensors('MEG') ans = pnt: [510x3 double] ori: [510x3 double] tra: [306x510 double] unit: 'mm' label: {306x1 cell} If I then append this to the data: data.grad = D.sensors('MEG'); I get an error: --- Error using ft_chantype (line 56) the input that was provided to this function cannot be deciphered Error in ft_datatype_sens (line 128) sens.chantype = ft_chantype(sens); Error in ft_datatype_raw (line 99) data.grad = ft_datatype_sens(data.grad); Error in ft_checkdata (line 177) data = ft_datatype_raw(data, 'hassampleinfo', hassampleinfo); Error in ft_timelockanalysis (line 134) data = ft_checkdata(data, 'datatype', {'raw', 'comp'}, 'feedback', 'yes', 'hassampleinfo', 'yes'); Error in ft_SENS_ERF_grRep (line 82) avdat = ft_timelockanalysis(cfg,raw); --- ...when I try to do timelockanalysis on this data. If I leave the grad field off (i.e. not append it to the output of ftraw(0)) there's no problem, and the analysis runs fine. However, because I want to do spatial neighbour cluster analysis later, I think I need the .grad field, so I might as well get it incorporated at this stage. Going a bit further into the error messages above, the function ft_datatype_sens appears to convert the old format .ori, .pnt into the newer .coilori, .coilpos ... etc. But the next function in the chain, ft_chantype, looks for .pnt and .ori when doing: isgrad = isa(input, 'struct') && isfield(input, 'pnt') && isfield(input, 'ori'); I'm wondering if this could be the problem? Sorry for the long message! I'd be very grateful if anyone can help out. Best wishes, George -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Mon Sep 10 15:55:26 2012 From: smoratti at psi.ucm.es (smoratti at psi.ucm.es) Date: Mon, 10 Sep 2012 15:55:26 +0200 Subject: [FieldTrip] Appending data.grad, after using D.ftraw(0) In-Reply-To: References: Message-ID: <44D6E4E8-E44D-4D08-B012-C3B506F6E935@psi.ucm.es> Dear George, Your approach was right, and it would have worked with older versions of field trip. Now in field trip the grad field contents have changed a little bit. Now it contains balance: [1x1 struct] chanori: [306x3 double] chanpos: [306x3 double] chantype: {306x1 cell} chanunit: {306x1 cell} coilori: [510x3 double] coilpos: [510x3 double] label: {306x1 cell} tra: [306x510 double] unit: 'cm' so the field put would be chanpos, ori would be chanori (or coilpos/ coilori depending on your MEG system). So check this out and you can easily adapt the structure. I think SPM does not go with the últimate field trip version. I hope this helps, best, Stephan ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 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 10/09/2012, a las 14:22, George Wallis escribió: > Dear fieldtrippers, > > if anyone can help me with this I'd be very grateful! > > I have a bunch of preprocessed and epoched data files in SPM format, and I'm converting them to fieldtrip format using the following: > > D = spm_eeg_load(fn); > data = D.ftraw(0); > > ...which results in... > > data = > > fsample: 250 > label: {350x1 cell} > trial: {1x360 cell} > time: {1x360 cell} > > Comparing this to data structures generated using fieldtrip alone, field like data.grad are missing. > > I can create something like a grad field by doing: > > D.sensors('MEG') > > ans = > > pnt: [510x3 double] > ori: [510x3 double] > tra: [306x510 double] > unit: 'mm' > label: {306x1 cell} > > If I then append this to the data: > > data.grad = D.sensors('MEG'); > > I get an error: > > --- > > Error using ft_chantype (line 56) > the input that was provided to this function cannot be deciphered > > Error in ft_datatype_sens (line 128) > sens.chantype = ft_chantype(sens); > > Error in ft_datatype_raw (line 99) > data.grad = ft_datatype_sens(data.grad); > > Error in ft_checkdata (line 177) > data = ft_datatype_raw(data, 'hassampleinfo', hassampleinfo); > > Error in ft_timelockanalysis (line 134) > data = ft_checkdata(data, 'datatype', {'raw', 'comp'}, 'feedback', 'yes', 'hassampleinfo', > 'yes'); > > Error in ft_SENS_ERF_grRep (line 82) > avdat = ft_timelockanalysis(cfg,raw); > > --- > > ...when I try to do timelockanalysis on this data. If I leave the grad field off (i.e. not append it to the output of ftraw(0)) there's no problem, and the analysis runs fine. However, because I want to do spatial neighbour cluster analysis later, I think I need the .grad field, so I might as well get it incorporated at this stage. > > Going a bit further into the error messages above, the function ft_datatype_sens appears to convert the old format .ori, .pnt into the newer .coilori, .coilpos ... etc. But the next function in the chain, ft_chantype, looks for .pnt and .ori when doing: > > isgrad = isa(input, 'struct') && isfield(input, 'pnt') && isfield(input, 'ori'); > > I'm wondering if this could be the problem? > > Sorry for the long message! I'd be very grateful if anyone can help out. > > Best wishes, > George > _______________________________________________ > 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 wallisgj at gmail.com Mon Sep 10 18:21:36 2012 From: wallisgj at gmail.com (George Wallis) Date: Mon, 10 Sep 2012 17:21:36 +0100 Subject: [FieldTrip] Appending data.grad, after using D.ftraw(0) Message-ID: Hi Stephan, Thanks very much for your reply (and sorry for not replying to the thread; I get a digest, and couldn't figure out how to reply to an individual message). So, SPM will produce an outdated .grad format, which can be corrected. There is one thing I don't get, which is why ft_chantype looks for the older fields, viz: *isgrad = isa(input, 'struct') && isfield(input, 'pnt') && isfield(input, 'ori');* It seems like the function ft_chantype is called from, ft_datatype_sens, automatically corrects the old grad format before passing the structure (now called 'sens') to ft_chantype: % sensor description is a MEG sensor-array, containing oriented coils [chanpos, chanori, chanlab] = channelposition(sens, 'channel', 'all'); sens.coilori = sens.ori; sens = rmfield(sens, 'ori'); sens.coilpos = sens.pnt; sens = rmfield(sens, 'pnt'); sens.chanpos = chanpos; sens.chanori = chanori; Did the new format not propagate through? best wishes, George On Mon, Sep 10, 2012 at 2:55 PM, 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. about overlap in PSD calculation (Ivano Triggiani) > 2. real-value spatial filter from FFT dipole localization? > (Bj?rn Herrmann) > 3. Appending data.grad, after using D.ftraw(0) (George Wallis) > 4. Re: Appending data.grad, after using D.ftraw(0) > (smoratti at psi.ucm.es) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 10 Sep 2012 11:27:09 +0100 (BST) > From: Ivano Triggiani > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] about overlap in PSD calculation > Message-ID: > <1347272829.31720.YahooMailNeo at web133103.mail.ir2.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all. > > How can I obtain informations about the kind of overlapping performed by > fiedltrip implemented method to obtain a Power Spectral Density ? > > I need to compare fieldtrip PSD with another spectral density, so I need > to be sure of everything. I found docs about tapering, but I don't > understand if using a kind of tapering the overlapping is given. > Ivano > > ? > ------------------------------------------------------------------------ > > > > > "No man can wear one face to himself > and another to the multitude, > without finally getting bewildered > as to which one is true." > > > Nathaniel Hawthorne > > > ________________________________ > Da: "fieldtrip-request at science.ru.nl" > A: fieldtrip at science.ru.nl > Inviato: Luned? 10 Settembre 2012 12:00 > Oggetto: fieldtrip Digest, Vol 22, Issue 17 > > 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. Using WPLI od WPLI-debiased to do the coherence analysis > ? ? ? (sahand babapoor) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 9 Sep 2012 20:49:31 -0400 > From: sahand babapoor > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Using WPLI od WPLI-debiased to do the coherence > ??? analysis > Message-ID: > ??? > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > > I am trying to do coherency analysis between ACC and FEF. I have tried both > WPLI and WPLI-debiased methods to do the analysis. When I am using WPLI I > find a very nice coherence pattern between ACC and FEF in the frequencies > between ~11Hz to 20 Hz. However, when I am using WPLI-debiased method, the > previous WPLI coherence pattern disappears and? breaks into many sparse > clusters across many time points and frequencies. Is there a way to know > which method is the best for me. I should note that I am recording using > tungsten microelectrodes advanced into the brain. I would appreciate if > your help. > > Best, > Sahand > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120909/2a47bbc7/attachment-0001.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 22, Issue 17 > ***************************************** > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120910/448a5494/attachment-0001.html > > > > ------------------------------ > > Message: 2 > Date: Mon, 10 Sep 2012 13:16:09 +0200 (CEST) > From: Bj?rn Herrmann > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] real-value spatial filter from FFT dipole > localization? > Message-ID: <1396322041.3317.1347275769488.JavaMail.root at zimbra> > Content-Type: text/plain; charset=utf-8 > > Dear fieldtrip users, > > maybe someone can point me in the right direction. I try to obtain a > spatial filter from localizing the sources of an auditory 3Hz peak in my > FFT spectrum. I would like to apply the filter to my single trial real > data, i.e. basically reducing my 204 gradiometer channels (neuromag system) > to one or two channels in source space. > I was using DICS beamformer and cfg.realfilter = 'yes' but the source > localization results (NAI) looked not too well compared to the nice > auditory gradiometer topographies. > I then used ft_dipolefitting, however, I have trouble understanding the > output. This is where I wondered whether someone could help me, in telling > whether it is possible to obtain a real-value spatial filter from this: > > source = > label: {204x1 cell} > dip: [1x1 struct] > Vdata: [204x408 double] > Vmodel: [204x408 double] > freq: 3 > dimord: 'chan_freq' > grad: [1x1 struct] > cfg: [1x1 struct] > > source.dip = > pos: [2x3 double] > mom: [6x408 double] > pot: [204x408 double] > rv: [1x408 double] > pow: 2.7948e+18 > csd: [6x6 double] > fourier: [6x204 double] > > I would appreciate helping comments, as I tested the different methods for > some time now, but was unable to extract a reasonable real-value spatial > filter for my auditory cortex activations. > > Best regards, > > Bj?rn > > > > > > ------------------------------ > > Message: 3 > Date: Mon, 10 Sep 2012 13:22:20 +0100 > From: George Wallis > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Appending data.grad, after using D.ftraw(0) > Message-ID: > < > CADqk8UgZ-wUf-FAjLL9K0hScW6ZTWrOVJKaR0S+PVhvuKx31-w at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear fieldtrippers, > > if anyone can help me with this I'd be very grateful! > > I have a bunch of preprocessed and epoched data files in SPM format, and > I'm converting them to fieldtrip format using the following: > > D = spm_eeg_load(fn); > data = D.ftraw(0); > > ...which results in... > > data = > > fsample: 250 > label: {350x1 cell} > trial: {1x360 cell} > time: {1x360 cell} > > Comparing this to data structures generated using fieldtrip alone, field > like data.grad are missing. > > I can create something like a grad field by doing: > > D.sensors('MEG') > > ans = > > pnt: [510x3 double] > ori: [510x3 double] > tra: [306x510 double] > unit: 'mm' > label: {306x1 cell} > > If I then append this to the data: > > data.grad = D.sensors('MEG'); > > I get an error: > > --- > > Error using ft_chantype (line 56) > the input that was provided to this function cannot be deciphered > > Error in ft_datatype_sens (line 128) > sens.chantype = ft_chantype(sens); > > Error in ft_datatype_raw (line 99) > data.grad = ft_datatype_sens(data.grad); > > Error in ft_checkdata (line 177) > data = ft_datatype_raw(data, 'hassampleinfo', hassampleinfo); > > Error in ft_timelockanalysis (line 134) > data = ft_checkdata(data, 'datatype', {'raw', 'comp'}, 'feedback', 'yes', > 'hassampleinfo', > 'yes'); > > Error in ft_SENS_ERF_grRep (line 82) > avdat = ft_timelockanalysis(cfg,raw); > > --- > > ...when I try to do timelockanalysis on this data. If I leave the grad > field off (i.e. not append it to the output of ftraw(0)) there's no > problem, and the analysis runs fine. However, because I want to do spatial > neighbour cluster analysis later, I think I need the .grad field, so I > might as well get it incorporated at this stage. > > Going a bit further into the error messages above, the function > ft_datatype_sens appears to convert the old format .ori, .pnt into the > newer .coilori, .coilpos ... etc. But the next function in the chain, > ft_chantype, looks for .pnt and .ori when doing: > > isgrad = isa(input, 'struct') && isfield(input, 'pnt') && isfield(input, > 'ori'); > > I'm wondering if this could be the problem? > > Sorry for the long message! I'd be very grateful if anyone can help out. > > Best wishes, > George > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120910/8418e2de/attachment-0001.html > > > > ------------------------------ > > Message: 4 > Date: Mon, 10 Sep 2012 15:55:26 +0200 > From: "smoratti at psi.ucm.es" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Appending data.grad, after using D.ftraw(0) > Message-ID: <44D6E4E8-E44D-4D08-B012-C3B506F6E935 at psi.ucm.es> > Content-Type: text/plain; charset="iso-8859-1" > > Dear George, > > Your approach was right, and it would have worked with older versions of > field trip. Now in field trip the grad field contents have changed a little > bit. > > Now it contains > > balance: [1x1 struct] > chanori: [306x3 double] > chanpos: [306x3 double] > chantype: {306x1 cell} > chanunit: {306x1 cell} > coilori: [510x3 double] > coilpos: [510x3 double] > label: {306x1 cell} > tra: [306x510 double] > unit: 'cm' > > so the field put would be chanpos, ori would be chanori (or coilpos/ > coilori depending on your MEG system). > > So check this out and you can easily adapt the structure. I think SPM does > not go with the ?ltimate field trip version. > > I hope this helps, > > best, > > Stephan > > ________________________________________________________ > Stephan Moratti, PhD > > see also: http://web.me.com/smoratti/ > > Universidad Complutense de Madrid > Facultad de Psicolog?a > Departamento de Psicolog?a B?sica I > Campus de Somosaguas > 28223 Pozuelo de Alarc?n (Madrid) > Spain > > and > > Center for Biomedical Technology > Laboratory for Cognitive and Computational Neuroscience > Parque Cient?fico y Tecnol?gico de la Universidad Politecnica de Madrid > Campus Montegancedo > 28223 Pozuelo de Alarc?n (Madrid) > Spain > > > email: smoratti at psi.ucm.es > Tel.: +34 679219982 > > El 10/09/2012, a las 14:22, George Wallis escribi?: > > > Dear fieldtrippers, > > > > if anyone can help me with this I'd be very grateful! > > > > I have a bunch of preprocessed and epoched data files in SPM format, and > I'm converting them to fieldtrip format using the following: > > > > D = spm_eeg_load(fn); > > data = D.ftraw(0); > > > > ...which results in... > > > > data = > > > > fsample: 250 > > label: {350x1 cell} > > trial: {1x360 cell} > > time: {1x360 cell} > > > > Comparing this to data structures generated using fieldtrip alone, field > like data.grad are missing. > > > > I can create something like a grad field by doing: > > > > D.sensors('MEG') > > > > ans = > > > > pnt: [510x3 double] > > ori: [510x3 double] > > tra: [306x510 double] > > unit: 'mm' > > label: {306x1 cell} > > > > If I then append this to the data: > > > > data.grad = D.sensors('MEG'); > > > > I get an error: > > > > --- > > > > Error using ft_chantype (line 56) > > the input that was provided to this function cannot be deciphered > > > > Error in ft_datatype_sens (line 128) > > sens.chantype = ft_chantype(sens); > > > > Error in ft_datatype_raw (line 99) > > data.grad = ft_datatype_sens(data.grad); > > > > Error in ft_checkdata (line 177) > > data = ft_datatype_raw(data, 'hassampleinfo', hassampleinfo); > > > > Error in ft_timelockanalysis (line 134) > > data = ft_checkdata(data, 'datatype', {'raw', 'comp'}, 'feedback', > 'yes', 'hassampleinfo', > > 'yes'); > > > > Error in ft_SENS_ERF_grRep (line 82) > > avdat = ft_timelockanalysis(cfg,raw); > > > > --- > > > > ...when I try to do timelockanalysis on this data. If I leave the grad > field off (i.e. not append it to the output of ftraw(0)) there's no > problem, and the analysis runs fine. However, because I want to do spatial > neighbour cluster analysis later, I think I need the .grad field, so I > might as well get it incorporated at this stage. > > > > Going a bit further into the error messages above, the function > ft_datatype_sens appears to convert the old format .ori, .pnt into the > newer .coilori, .coilpos ... etc. But the next function in the chain, > ft_chantype, looks for .pnt and .ori when doing: > > > > isgrad = isa(input, 'struct') && isfield(input, 'pnt') && > isfield(input, 'ori'); > > > > I'm wondering if this could be the problem? > > > > Sorry for the long message! I'd be very grateful if anyone can help out. > > > > Best wishes, > > George > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120910/444962f9/attachment.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 22, Issue 18 > ***************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Mon Sep 10 18:36:02 2012 From: litvak.vladimir at gmail.com (litvak.vladimir at gmail.com) Date: Mon, 10 Sep 2012 16:36:02 +0000 Subject: [FieldTrip] Appending data.grad, after using D.ftraw(0) In-Reply-To: References: Message-ID: <1665240477-1347294953-cardhu_decombobulator_blackberry.rim.net-1232560809-@b18.c20.bise7.blackberry> Dear George, Yes, what you describe is still a bug in Fieldtrip because the conversion from the old to new grad format should be automatic. This might be related to a similar bug I reported on Bugzilla last Friday. The problem was specific to Neuromag data. The next SPM8 update will include an updated Fieldtrip version and will work with the new sensor formats. I hope the FT team will look at this soon. Vladimir Sent using BlackBerry® from Orange -----Original Message----- From: George Wallis Sender: fieldtrip-bounces at science.ru.nl Date: Mon, 10 Sep 2012 17:21:36 To: Reply-To: FieldTrip discussion list Subject: [FieldTrip] Appending data.grad, after using D.ftraw(0) _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From martin.maier at student.hu-berlin.de Tue Sep 11 14:06:38 2012 From: martin.maier at student.hu-berlin.de (Martin Maier) Date: Tue, 11 Sep 2012 14:06:38 +0200 Subject: [FieldTrip] example cross-frequency analysis In-Reply-To: References: Message-ID: Hi there, I'm trying to analyse my data for phase-amplitude cross-frequency coupling.The example script (http://fieldtrip.fcdonders.nl/example/crossfreq/phalow_amphigh) still uses ft_freqdescriptives to get the coherence-spectrum, but this has since been implemented in ft_connectivityanalysis. My question concerns the channelcombination when using ft_connectivityanalysis. When calculating the coherence between power and raw, I get the following error message: "??? Error using ==> univariate2bivariate at 25 no channel combinations are specified" I did specify channel combinations, but somehow ft_connectivityanalysis doesn't get them. Does the function need a different format when setting the channels to be combined? Or should I use a different function to calculate the coherence spectra (instead of ft_connectivityanalysis)? Thanks, Martin From member at linkedin.com Wed Sep 12 01:26:18 2012 From: member at linkedin.com (=?UTF-8?Q?Alicia_Gonz=C3=A1lez_Moreno_via_LinkedIn?=) Date: Tue, 11 Sep 2012 23:26:18 +0000 (UTC) Subject: [FieldTrip] Join my network on LinkedIn Message-ID: <1377830396.2855738.1347405978358.JavaMail.app@ela4-app2314.prod> LinkedIn ------------ Alicia González Moreno requested to add you as a connection on LinkedIn: ------------------------------------------ I'd like to add you to my professional network on LinkedIn. Accept invitation from Alicia González Moreno http://www.linkedin.com/e/-deyl8h-h6zmqar3-2j/2ql61bZWrtgNAx4NauUqWbaswiGNhc8KtyoV/blk/I214712724_50/0UcDpKqiRzolZKqiRybmRSrCBvrmRLoORIrmkZt5YCpnlOt3RApnhMpmdzgmhxrSNBszYMdlYQczsOcjsQcj99bTtdszl6sCl4bPsRc3oNcjsMdzwLrCBxbOYWrSlI/eml-comm_invm-b-in_ac-inv28/?hs=false&tok=2DIcL0uIu-Glo1 View profile of Alicia González Moreno http://www.linkedin.com/e/-deyl8h-h6zmqar3-2j/rso/203786050/UX0W/name/51465358_I214712724_50/?hs=false&tok=1RKIB_Kum-Glo1 ------------------------------------------ You are receiving Invitation emails. This email was intended for lin wang. Learn why this is included: http://www.linkedin.com/e/-deyl8h-h6zmqar3-2j/plh/http%3A%2F%2Fhelp%2Elinkedin%2Ecom%2Fapp%2Fanswers%2Fdetail%2Fa_id%2F4788/-GXI/?hs=false&tok=2C0EwII2W-Glo1 (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA. -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.hartmann at th-ht.de Wed Sep 12 14:57:37 2012 From: thomas.hartmann at th-ht.de (Thomas Hartmann) Date: Wed, 12 Sep 2012 14:57:37 +0200 Subject: [FieldTrip] units after beamforming Message-ID: <505086C1.9010004@th-ht.de> hi all, i do lcmv beamforming on meg data and use cfg.method='localspheres' and cfg.singlesphere='yes' as options to call ft_prepare_localspheres. i was wondering about the units of the resulting spatial filter. does anyone know, what those might be? thanks a lot! best, thomas -- Dr. Thomas Hartmann CIMeC - Center for Mind/Brain Sciences Università degli Studi di Trento via delle Regole, 101 38060 Mattarello (TN) ITALY Tel: +39 0461 28 2779 Fax: +39 0461 28 3066 Email: thomas.hartmann at th-ht.de Homepage: http://sites.google.com/site/obobcimec/ "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle) From elizabeth.bock at mcgill.ca Wed Sep 12 20:32:39 2012 From: elizabeth.bock at mcgill.ca (Elizabeth Anne Bock, Ms) Date: Wed, 12 Sep 2012 18:32:39 +0000 Subject: [FieldTrip] realtime buffer does not exit Message-ID: <86D86365C4E767468A79EB52DFBFB46F0510F73C@exmbx2010-8.campus.MCGILL.CA> I am using the realtime buffer and I have found I cannot exit the buffer within the Matlab command window. I am forced to exit Matlab or, more often, must kill the process manually from the windows task manager. I am using Windows XP to host the buffer and Linux to run acqftx. Here is what I am seeing: >> buffer('tcpserver', 'exit', ft_host, ft_port) In main: requesting cancelation of tcpserver thread >> buffer('tcpserver', 'init', ft_host, ft_port) ??? Error using ==> buffer thread is already running Any suggestions? Thanks, Elizabeth ------------------------------------------------------------------------------------------ Elizabeth Bock / MEG System Engineer McConnell Brain Imaging Centre / Montreal Neurological Institute McGill University / 3801 University St. / Montreal, QC H3A 2B4 MEG Lab: 514.398.6056 Mobile: 514.718.6342 From daria.laptinskaya at googlemail.com Thu Sep 13 09:21:00 2012 From: daria.laptinskaya at googlemail.com (Daria Laptinskaya) Date: Thu, 13 Sep 2012 09:21:00 +0200 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: <3B494ED9-B6C3-46A3-840C-8EEEDAA85E5E@mac.com> References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> <77D46473-6907-4AC1-96E1-F51756C119C0@mac.com> <3B494ED9-B6C3-46A3-840C-8EEEDAA85E5E@mac.com> Message-ID: Yes, it works fine now-thank you!!! @Matt: Do you know a calibration-function for existing raw-files? Best, Daria 2012/9/10 Joseph Dien > Hey Daria, > glad you were able to get it worked out! Thank Matt for his reminder > (below) about the calibration option. > > Cheers! > > Joe > > > Hi Joe, > > > I didn’t know that there is a function like this. > > The most of my colleagues use the RAW.-files they get from the > file-exporter without problems. > > Not even NetStation-support could give me an answer. > > So I thought, it must be a problem between NetStation and fieldtrip. > > Because of your tip I opened an original datafile and tried to save a copy > of the file. > > Doing so NetStation offers a possibility to ‘convert to microvolts’ and > create a .ses –datafile. > > The .raw-files I get this way have microvolt as unit. > > I compared the signals I get this way with the signals I get by using the > formula (5000 mircovolts / (2^16 bits) I send you. They are almost the > same-that’s great!!! > > It seems to work now. > > Thank you very much!!! You were a great help!!! > > > Cheers, > > Daria > > On Sep 6, 2012, at 9:07 PM, Joseph Dien wrote: > > I don't recall ever seeing this problem with EGIS files, which is one of > the reasons I prefer using this file format despite EGI's preference for > newer Simple Binary format, but it's an unpredictable bug so I can't say it > can't happen. I also can't say which versions of NetStation it happens > with. It may have been fixed. I'm still trying to test out MFF so can't > say anything about it. I had problems with the FieldTrip code for reading > segmented MFF files (which is what I'm interested in). I also had trouble > with writing them out from NetStation so I don't have a valid segmented > test file and I'm still waiting for EGI to make one available so I can work > them out. The simple binary file format (this is the original name for the > EGI .raw file format and I prefer to use it over ".raw" as the BESA .raw > file format is actually the .egis file format so it can get confusing) > doesn't actually have separate calibration information for the channels > (unlike EGIS), just one single gain value and no zeros values. So > basically the simple binary format makes the assumption that calibration > corrections have already been performed prior to generating the file. My > understanding is that this is indeed what the "calibrate data" option is > doing, but you'd have to confirm with EGI. > > Joe > > > > -------------------------------------------------------------------------------- > > On Sep 6, 2012, at 1:01 PM, Matt Mollison wrote: > > Joe, > > A few related questions: > > Does using the "calibrate data" option when exporting to raw (simple > binary) correct for gain? Or is there a different solution/recommendation? > Does exporting to MFF (Net Station 4.5.x only) or EGIS have this issue? I > tend to use EGIS (faster to read than raw) and have no recollection of > seeing unusually large voltages. > > Thanks, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > > On Wed, Sep 5, 2012 at 7:17 PM, Joseph Dien wrote: > >> The Simple Binary (.raw) files don't get corrected for gain when imported >> (I helped write them). I've experienced occasional unpredictable bugs with >> NetStation export routines where the files are generated with amplitudes >> many times too large, even with text format files. It's a bit >> disconcerting to say the least. I could take a look at your files if you'd >> like confirmation. >> >> Joe >> >> On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis >> wrote: >> >> Hi Daria, >> >> Also, did you try looking at your raw data (so before the ERPs are made) >> in FieldTrip and in Net Station? So open your .raw data in NetStation. You >> can just look at a random participant's data, and check if the scale is the >> same. I'm pretty sure no amplification takes place when reading in the data >> into FieldTrip, this check can confirm that. Hope this helps, and let us >> know what you find. >> >> Cheers, >> Ingrid >> >> >> On 9/3/2012 1:35 PM, Robert Oostenveld wrote: >> >> Hi Daria, >> >> There might indeed be an incompatibility in the gain value applied to >> the data. >> >> If you are able to export the data using the EGI software in another >> format (e.g. EDF), you could read them both into FieldTrip and compare the >> timecourse aplitudes to check whether they are different. In case they are, >> I suggest to involve EGI support. They are aware of the FieldTrip reading >> functions and will know much more about the internals of their various file >> formats. >> >> best regards >> Robert >> >> >> >> >> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: >> >> Dear Fieldtrippers, >> >> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip >> toolbox. >> The ERPs look perfect. >> The 'only' problem is, that my signals look to strong. >> It looks like if I get amplitutes (average) until 70 µV. >> I think it must be an intern amplifier for the signals. >> >> Does anyone know this problem with EGI-data? >> >> Or does anyone know, where I can see the amplifier? >> >> >> >> Greetings, >> Daria _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> _______________________________________________ >> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -- >> Ingrid Nieuwenhuis PhD >> Postdoctoral Fellow >> Sleep and Neuroimaging Laboratory >> Department of Psychology >> University of California, Berkeley >> California 94720-1650 >> Tolman Hall, room 5305 >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, >> Senior Research Scientist >> University of Maryland >> >> E-mail: jdien07 at mac.com >> Phone: 301-226-8848 >> Fax: 301-226-8811 >> http://joedien.com// >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > > > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joscha.schmiedt at esi-frankfurt.de Thu Sep 13 09:46:19 2012 From: joscha.schmiedt at esi-frankfurt.de (Schmiedt, Joscha) Date: Thu, 13 Sep 2012 07:46:19 +0000 Subject: [FieldTrip] Verbosity of fieldtrip functions Message-ID: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> Hi, I was wondering whether there is any option to suppress the printed output of a fieldtrip function or whether there are any plans for implementing a cfg.verbose option. Whenever I'm running some kind of loop I'd be glad to be able to use my own progress feedback without interruption from all the involved functions. Best, Joscha --------------------------- Joscha Schmiedt, MS 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 411 -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu Sep 13 10:03:19 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 13 Sep 2012 10:03:19 +0200 Subject: [FieldTrip] Verbosity of fieldtrip functions In-Reply-To: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> References: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> Message-ID: Hi Joscha, At the moment, we are thinking about implementing a generic logging mechanism in FieldTrip. Such a mechanism would allow you to specify the level of feedback you desire on the console, and also allow people to conveniently store log files for e.g. posting on this list for debugging. But given that (1) our thinking about this is still in its early stages, and (2) it requires a replace of all fprintf() statements in the entire codebase, it could be a while before this is fully implemented. But, to repeat, this is something we plan to do in the (near) future. Best, Eelke On 13 September 2012 09:46, Schmiedt, Joscha wrote: > Hi, > > I was wondering whether there is any option to suppress the printed output > of a fieldtrip function or whether there are any plans for implementing a > cfg.verbose option. Whenever I'm running some kind of loop I'd be glad to be > able to use my own progress feedback without interruption from all the > involved functions. > > Best, > Joscha > > > --------------------------- > Joscha Schmiedt, MS > 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 411 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From eelke.spaak at donders.ru.nl Thu Sep 13 10:03:19 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 13 Sep 2012 10:03:19 +0200 Subject: [FieldTrip] Verbosity of fieldtrip functions In-Reply-To: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> References: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> Message-ID: Hi Joscha, At the moment, we are thinking about implementing a generic logging mechanism in FieldTrip. Such a mechanism would allow you to specify the level of feedback you desire on the console, and also allow people to conveniently store log files for e.g. posting on this list for debugging. But given that (1) our thinking about this is still in its early stages, and (2) it requires a replace of all fprintf() statements in the entire codebase, it could be a while before this is fully implemented. But, to repeat, this is something we plan to do in the (near) future. Best, Eelke On 13 September 2012 09:46, Schmiedt, Joscha wrote: > Hi, > > I was wondering whether there is any option to suppress the printed output > of a fieldtrip function or whether there are any plans for implementing a > cfg.verbose option. Whenever I'm running some kind of loop I'd be glad to be > able to use my own progress feedback without interruption from all the > involved functions. > > Best, > Joscha > > > --------------------------- > Joscha Schmiedt, MS > 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 411 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From g.piantoni at nin.knaw.nl Thu Sep 13 10:28:31 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Thu, 13 Sep 2012 10:28:31 +0200 Subject: [FieldTrip] Verbosity of fieldtrip functions In-Reply-To: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> References: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> Message-ID: Hi Joscha, A quick and dirty solution is evalc: [~, data] = evalc('yourfunction(cfg)'); Cheers, Gio On Thu, Sep 13, 2012 at 9:46 AM, Schmiedt, Joscha wrote: > Hi, > > I was wondering whether there is any option to suppress the printed output > of a fieldtrip function or whether there are any plans for implementing a > cfg.verbose option. Whenever I'm running some kind of loop I'd be glad to be > able to use my own progress feedback without interruption from all the > involved functions. > > Best, > Joscha > > > --------------------------- > Joscha Schmiedt, MS > 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 411 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From smoratti at psi.ucm.es Thu Sep 13 10:36:05 2012 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Thu, 13 Sep 2012 10:36:05 +0200 Subject: [FieldTrip] Verbosity of fieldtrip functions In-Reply-To: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> References: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> Message-ID: <2EF4BF72-E8CE-4134-9DEB-7657B034C167@psi.ucm.es> Hi Joscha, Sometimes you can suppress some outputs with cfg.feedback = 'no'; Best, Stephan El 13/09/2012, a las 09:46, Schmiedt, Joscha escribió: > Hi, > > I was wondering whether there is any option to suppress the printed output of a fieldtrip function or whether there are any plans for implementing a cfg.verbose option. Whenever I'm running some kind of loop I'd be glad to be able to use my own progress feedback without interruption from all the involved functions. > > Best, > Joscha > > > --------------------------- > Joscha Schmiedt, MS > 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 411 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Thu Sep 13 10:36:05 2012 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Thu, 13 Sep 2012 10:36:05 +0200 Subject: [FieldTrip] Verbosity of fieldtrip functions In-Reply-To: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> References: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> Message-ID: <2EF4BF72-E8CE-4134-9DEB-7657B034C167@psi.ucm.es> Hi Joscha, Sometimes you can suppress some outputs with cfg.feedback = 'no'; Best, Stephan El 13/09/2012, a las 09:46, Schmiedt, Joscha escribió: > Hi, > > I was wondering whether there is any option to suppress the printed output of a fieldtrip function or whether there are any plans for implementing a cfg.verbose option. Whenever I'm running some kind of loop I'd be glad to be able to use my own progress feedback without interruption from all the involved functions. > > Best, > Joscha > > > --------------------------- > Joscha Schmiedt, MS > 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 411 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Thu Sep 13 10:55:55 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Thu, 13 Sep 2012 11:55:55 +0300 Subject: [FieldTrip] Making your own trialfun Message-ID: Hello, I tried to run the example in the following page: http://fieldtrip.fcdonders.nl/example/making_your_own_trialfun_for_conditional_trial_definition I did the required modifications so it can be run using biosemi system. But I don't know what to put instead of the variable "trigger" in the following statement: for j = 1:(length(trigger)-1) Could you help me Best, -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu Sep 13 11:02:32 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 13 Sep 2012 11:02:32 +0200 Subject: [FieldTrip] Making your own trialfun In-Reply-To: References: Message-ID: Hi Hamza, This is a bug in the example code; apologies. The "trigger" variable here actually refers to "value", so the vector of trigger values, assigned a few lines earlier. I will update the wiki. Best, Eelke On 13 September 2012 10:55, Hamza Fawzi Altakroury (Student) wrote: > Hello, > > I tried to run the example in the following page: > http://fieldtrip.fcdonders.nl/example/making_your_own_trialfun_for_conditional_trial_definition > > I did the required modifications so it can be run using biosemi system. > > But I don't know what to put instead of the variable "trigger" in the > following statement: > > for j = 1:(length(trigger)-1) > > > Could you help me > > Best, > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From eelke.spaak at donders.ru.nl Thu Sep 13 11:02:32 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 13 Sep 2012 11:02:32 +0200 Subject: [FieldTrip] Making your own trialfun In-Reply-To: References: Message-ID: Hi Hamza, This is a bug in the example code; apologies. The "trigger" variable here actually refers to "value", so the vector of trigger values, assigned a few lines earlier. I will update the wiki. Best, Eelke On 13 September 2012 10:55, Hamza Fawzi Altakroury (Student) wrote: > Hello, > > I tried to run the example in the following page: > http://fieldtrip.fcdonders.nl/example/making_your_own_trialfun_for_conditional_trial_definition > > I did the required modifications so it can be run using biosemi system. > > But I don't know what to put instead of the variable "trigger" in the > following statement: > > for j = 1:(length(trigger)-1) > > > Could you help me > > Best, > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From a.stolk at fcdonders.ru.nl Thu Sep 13 11:05:20 2012 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Thu, 13 Sep 2012 11:05:20 +0200 (CEST) Subject: [FieldTrip] realtime buffer does not exit In-Reply-To: <86D86365C4E767468A79EB52DFBFB46F0510F73C@exmbx2010-8.campus.MCGILL.CA> Message-ID: <3342976.328678.1347527120171.JavaMail.root@sculptor.zimbra.ru.nl> Hi Elizabeth, Could you try and start the buffer from outside matlab using 'demo_buffer.exe' (to be found in the 'realtime/bin/win32' directory)? This application may operate smoother than when starting the buffer from a single matlab thread. Best, Arjen ----- Oorspronkelijk bericht ----- > Van: "Elizabeth Anne Bock, Ms" > Aan: fieldtrip at science.ru.nl > Verzonden: Woensdag 12 september 2012 20:32:39 > Onderwerp: [FieldTrip] realtime buffer does not exit > I am using the realtime buffer and I have found I cannot exit the > buffer within the Matlab command window. I am forced to exit Matlab > or, more often, must kill the process manually from the windows task > manager. I am using Windows XP to host the buffer and Linux to run > acqftx. Here is what I am seeing: > > >> buffer('tcpserver', 'exit', ft_host, ft_port) > In main: requesting cancelation of tcpserver thread > > >> buffer('tcpserver', 'init', ft_host, ft_port) > ??? Error using ==> buffer > thread is already running > > Any suggestions? > Thanks, > Elizabeth > > > ------------------------------------------------------------------------------------------ > > Elizabeth Bock / MEG System Engineer > > McConnell Brain Imaging Centre / Montreal Neurological Institute > > McGill University / 3801 University St. / Montreal, QC H3A 2B4 > > > > MEG Lab: 514.398.6056 > > Mobile: 514.718.6342 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From hamzaf at sabanciuniv.edu Thu Sep 13 11:13:20 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Thu, 13 Sep 2012 12:13:20 +0300 Subject: [FieldTrip] Making your own trialfun In-Reply-To: References: Message-ID: Thank you Eelke, it works now. Best, Hamza On Thu, Sep 13, 2012 at 12:02 PM, Eelke Spaak wrote: > Hi Hamza, > > This is a bug in the example code; apologies. The "trigger" variable > here actually refers to "value", so the vector of trigger values, > assigned a few lines earlier. > > I will update the wiki. > > Best, > Eelke > > On 13 September 2012 10:55, Hamza Fawzi Altakroury (Student) > wrote: > > Hello, > > > > I tried to run the example in the following page: > > > http://fieldtrip.fcdonders.nl/example/making_your_own_trialfun_for_conditional_trial_definition > > > > I did the required modifications so it can be run using biosemi system. > > > > But I don't know what to put instead of the variable "trigger" in the > > following statement: > > > > for j = 1:(length(trigger)-1) > > > > > > Could you help me > > > > Best, > > > > -- > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabancı University > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Thu Sep 13 11:19:37 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Thu, 13 Sep 2012 12:19:37 +0300 Subject: [FieldTrip] ft_realtime_selectiveaverage Message-ID: Hello, I am tried to run the ft_realtime_selectiveaverage function but I got the following error: (note: the error appears after showing a plot with title: condition 255, ntrials = 1.) Could you tell me what is the problem. (exactly what does "connet read data before the begin of the file"). Best, ??? Error using ==> ft_read_data at 243 cannot read data before the begin of the file Error in ==> ft_realtime_selectiveaverage at 94 dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', chanindx, 'checkboundary', false); Error in ==> online1 at 48 ft_realtime_selectiveaverage(cfg) Statements: cfg = []; cfg.channel = {'A1'}; cfg.dataset = 'buffer://localhost:1972'; %cfg.trialfun = 'myfun'; cfg.trialdef.eventtype = 'stimulus'; % By placing '?' we can see the eventtype that we have. cfg.trialdef.eventvalue = 255; cfg.trialdef.pre = 0; cfg.trialdef.post = 1.0; cfg = ft_definetrial(cfg); ft_realtime_selectiveaverage(cfg) -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Sep 13 12:19:26 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 13 Sep 2012 05:19:26 -0500 Subject: [FieldTrip] Verbosity of fieldtrip functions In-Reply-To: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> References: <17F994D43E9ADA418DE0040CC6F4A96B0AEA51@UM-EXCDAG-A01.um.gwdg.de> Message-ID: <7638A242-2EF9-46AF-AB27-9448413A153E@donders.ru.nl> Hi Joscha There is indeed such a plan, see http://bugzilla.fcdonders.nl/show_bug.cgi?id=1686. If you want, you can provide your comments or ideas there. best Robert On 13 Sep 2012, at 2:46, Schmiedt, Joscha wrote: > Hi, > > I was wondering whether there is any option to suppress the printed output of a fieldtrip function or whether there are any plans for implementing a cfg.verbose option. Whenever I'm running some kind of loop I'd be glad to be able to use my own progress feedback without interruption from all the involved functions. > > Best, > Joscha > > > --------------------------- > Joscha Schmiedt, MS > 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 411 > > _______________________________________________ > 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 Duncan.Astle at mrc-cbu.cam.ac.uk Thu Sep 13 12:46:49 2012 From: Duncan.Astle at mrc-cbu.cam.ac.uk (Duncan Astle) Date: Thu, 13 Sep 2012 10:46:49 +0000 Subject: [FieldTrip] Problem with clustering across electrode neighbours Message-ID: Dear Fieldtrippers, I am rather new to this, but am attempting to do some cluster stats on my ERP sensor level data. It is working well, and I can cluster across time, but I can't get it to cluster across electrode locations. I think it is because of a mistake that I am making in my 'neighbours' file, although it looks fine when I inspect it. This is the error message that I get: ??? Cell contents reference from a non-cell array object. Error in ==> clusterstat>makechanneighbstructmat at 520 [seld] = match_str(cfg.channel, cfg.neighbours{chan}.label); Error in ==> clusterstat at 60 channeighbstructmat = makechanneighbstructmat(cfg); Error in ==> statistics_montecarlo at 322 [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); Error in ==> statistics_wrapper at 285 [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); Error in ==> ft_timelockstatistics at 119 [stat, cfg] = statistics_wrapper(cfg, varargin{:}); Can anyone spot what I am doing wrong? This is how I make my neighbour file: cfg = []; cfg.layout = 'EEG1010.lay'; % try 'distance' as well cfg.feedback = 'yes'; % show a neighbour plot cfg.method = 'template'; cfg.neighbourdist = 'number'; cfg.template = 'EEG1010_neighb.mat' cfg.channel = 'all' cfg.feedback = 'yes'; neighbours = ft_prepare_neighbours(cfg, Load5Hard); % define neighbouring channels This is how I then try the stats: cfg = []; cfg.channel = 'all'; cfg.latency = [0.1 1.3]; cfg.avgovertime = 'no'; cfg.avgoverchannel = 'no'; cfg.parameter = 'individual'; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT' cfg.alpha = 0.05; cfg.correctm = 'cluster'; cfg.correcttail = 'prob'; cfg.numrandomization = 1000; cfg.feedback = 'yes'; % show a neighbour plot cfg.neighbours = neighbours; %cfg.minnbchan = 2; cfg.clusterstatistic = 'maxsum'; cfg.clusterthreshold = 'nonparametric'; cfg.clusteralpha = 0.01; cfg.clustercritval = 0.06; % cfg.clustertail = 0; cfg.tail = 0; Nsub = 19; cfg.design(1,1:2*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub)]; cfg.design(2,1:2*Nsub) = [1:Nsub 1:Nsub]; cfg.ivar = 1; % the 1st row in cfg.design contains the independent variable cfg.uvar = 2; % the 2nd row in cfg.design contains the subject number [stat] = ft_timelockstatistics(cfg, Load3Hard, Load3Easy) Any suggestions very gratefully received. Thanks, Duncan ________________________________________________ Dr. Duncan Astle, Programme Leader Track, British Academy Research Fellow, MRC Cognition and Brain Sciences Unit, Chaucer Road, Cambridge. Duncan.Astle at mrc-cbu.cam.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu Sep 13 12:55:34 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 13 Sep 2012 12:55:34 +0200 Subject: [FieldTrip] Problem with clustering across electrode neighbours In-Reply-To: References: Message-ID: Dear Duncan, Jörn can correct me if I'm wrong, but I think it is sufficient to write cfg = []; cfg.method = 'template'; cfg.template = 'EEG1010_neighb.mat'; neighbours = ft_prepare_neighbours(cfg); if you want to use the neighbourhood structure template. So, specifying all those other options might have confused ft_prepare_neighbours. Best, Eelke On 13 September 2012 12:46, Duncan Astle wrote: > Dear Fieldtrippers, > > > > I am rather new to this, but am attempting to do some cluster stats on my > ERP sensor level data. It is working well, and I can cluster across time, > but I can’t get it to cluster across electrode locations. I think it is > because of a mistake that I am making in my ‘neighbours’ file, although it > looks fine when I inspect it. This is the error message that I get: > > > > ??? Cell contents reference from a non-cell array object. > > > > Error in ==> clusterstat>makechanneighbstructmat at 520 > > [seld] = match_str(cfg.channel, cfg.neighbours{chan}.label); > > > > Error in ==> clusterstat at 60 > > channeighbstructmat = makechanneighbstructmat(cfg); > > > > Error in ==> statistics_montecarlo at 322 > > [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); > > > > Error in ==> statistics_wrapper at 285 > > [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); > > > > Error in ==> ft_timelockstatistics at 119 > > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > > > Can anyone spot what I am doing wrong? > > > > This is how I make my neighbour file: > > > > cfg = []; > > cfg.layout = 'EEG1010.lay'; % try 'distance' as well > > cfg.feedback = 'yes'; % show a neighbour plot > > cfg.method = 'template'; > > cfg.neighbourdist = 'number'; > > cfg.template = 'EEG1010_neighb.mat' > > cfg.channel = 'all' > > cfg.feedback = 'yes'; > > neighbours = ft_prepare_neighbours(cfg, Load5Hard); % define > neighbouring channels > > > > This is how I then try the stats: > > > > cfg = []; > > cfg.channel = 'all'; > > cfg.latency = [0.1 1.3]; > > cfg.avgovertime = 'no'; > > cfg.avgoverchannel = 'no'; > > cfg.parameter = 'individual'; > > cfg.method = 'montecarlo'; > > cfg.statistic = 'depsamplesT' > > cfg.alpha = 0.05; > > cfg.correctm = 'cluster'; > > cfg.correcttail = 'prob'; > > cfg.numrandomization = 1000; > > cfg.feedback = 'yes'; % show a neighbour plot > > cfg.neighbours = neighbours; > > %cfg.minnbchan = 2; > > cfg.clusterstatistic = 'maxsum'; > > cfg.clusterthreshold = 'nonparametric'; > > cfg.clusteralpha = 0.01; > > cfg.clustercritval = 0.06; > > % cfg.clustertail = 0; > > cfg.tail = 0; > > Nsub = 19; > > cfg.design(1,1:2*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub)]; > > cfg.design(2,1:2*Nsub) = [1:Nsub 1:Nsub]; > > cfg.ivar = 1; % the 1st row in cfg.design contains the > independent variable > > cfg.uvar = 2; % the 2nd row in cfg.design contains the > subject number > > > > > > [stat] = ft_timelockstatistics(cfg, Load3Hard, Load3Easy) > > > > Any suggestions very gratefully received. > > > > Thanks, > > Duncan > > ________________________________________________ > > Dr. Duncan Astle, > > Programme Leader Track, > > British Academy Research Fellow, > > MRC Cognition and Brain Sciences Unit, > > Chaucer Road, > > Cambridge. > > Duncan.Astle at mrc-cbu.cam.ac.uk > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Thu Sep 13 13:11:15 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 13 Sep 2012 13:11:15 +0200 Subject: [FieldTrip] Problem with clustering across electrode neighbours In-Reply-To: References: Message-ID: <5051BF53.5030606@donders.ru.nl> Hey Duncan, it looks pretty much like you are using an old FieldTrip version with a new neighbourhood-structure. Could you check the with the most recent version again? Some months (about a year?) ago we changed the neighbour definition from cell arrays to structure arrays, so any attempt to access cfg.neighbours{i} will fail, cause it has to be cfg.neighbours(i) instead. But as I already said, this has been changed quite some time back in the past :) Essentially, your code is fine, but some note that cfg.neighbourdist should be a scalar, not the string 'number', but only if cfg.method='distance'. If you choose cfg.method = 'template' then cfg.neighbourdist is not used, cause a template is loaded. Best, Jörn On 9/13/2012 12:46 PM, Duncan Astle wrote: > > Dear Fieldtrippers, > > I am rather new to this, but am attempting to do some cluster stats on > my ERP sensor level data. It is working well, and I can cluster across > time, but I can't get it to cluster across electrode locations. I > think it is because of a mistake that I am making in my 'neighbours' > file, although it looks fine when I inspect it. This is the error > message that I get: > > ??? Cell contents reference from a non-cell array object. > > Error in ==> clusterstat>makechanneighbstructmat at 520 > > [seld] = match_str(cfg.channel, cfg.neighbours{chan}.label); > > Error in ==> clusterstat at 60 > > channeighbstructmat = makechanneighbstructmat(cfg); > > Error in ==> statistics_montecarlo at 322 > > [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); > > Error in ==> statistics_wrapper at 285 > > [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); > > Error in ==> ft_timelockstatistics at 119 > > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > Can anyone spot what I am doing wrong? > > This is how I make my neighbour file: > > cfg = []; > > cfg.layout = 'EEG1010.lay'; % try 'distance' as well > > cfg.feedback = 'yes'; % show a neighbour plot > > cfg.method = 'template'; > > cfg.neighbourdist = 'number'; > > cfg.template = 'EEG1010_neighb.mat' > > cfg.channel = 'all' > > cfg.feedback = 'yes'; > > neighbours = ft_prepare_neighbours(cfg, Load5Hard); % define > neighbouring channels > > This is how I then try the stats: > > cfg = []; > > cfg.channel = 'all'; > > cfg.latency = [0.1 1.3]; > > cfg.avgovertime = 'no'; > > cfg.avgoverchannel = 'no'; > > cfg.parameter = 'individual'; > > cfg.method = 'montecarlo'; > > cfg.statistic = 'depsamplesT' > > cfg.alpha = 0.05; > > cfg.correctm = 'cluster'; > > cfg.correcttail = 'prob'; > > cfg.numrandomization = 1000; > > cfg.feedback = 'yes'; % show a neighbour plot > > cfg.neighbours = neighbours; > > %cfg.minnbchan = 2; > > cfg.clusterstatistic = 'maxsum'; > > cfg.clusterthreshold = 'nonparametric'; > > cfg.clusteralpha = 0.01; > > cfg.clustercritval = 0.06; > > % cfg.clustertail = 0; > > cfg.tail = 0; > > Nsub = 19; > > cfg.design(1,1:2*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub)]; > > cfg.design(2,1:2*Nsub) = [1:Nsub 1:Nsub]; > > cfg.ivar = 1; % the 1st row in cfg.design contains > the independent variable > > cfg.uvar = 2; % the 2nd row in cfg.design contains > the subject number > > [stat] = ft_timelockstatistics(cfg, Load3Hard, Load3Easy) > > Any suggestions very gratefully received. > > Thanks, > > Duncan > > ________________________________________________ > > Dr. Duncan Astle, > > Programme Leader Track, > > British Academy Research Fellow, > > MRC Cognition and Brain Sciences Unit, > > Chaucer Road, > > Cambridge. > > Duncan.Astle at mrc-cbu.cam.ac.uk > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From elizabeth.bock at mcgill.ca Thu Sep 13 14:51:42 2012 From: elizabeth.bock at mcgill.ca (Elizabeth Anne Bock, Ms) Date: Thu, 13 Sep 2012 12:51:42 +0000 Subject: [FieldTrip] realtime buffer does not exit In-Reply-To: <3342976.328678.1347527120171.JavaMail.root@sculptor.zimbra.ru.nl> References: <86D86365C4E767468A79EB52DFBFB46F0510F73C@exmbx2010-8.campus.MCGILL.CA>, <3342976.328678.1347527120171.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <86D86365C4E767468A79EB52DFBFB46F05110836@exmbx2010-8.campus.MCGILL.CA> Thanks for the feedback. However, I would like to read the header and the data from the buffer into Matlab (I am doing realtime processing of the data). Is this possible to run the buffer in the windows environment and then read from it in Matlab? hdr = buffer('get_hdr', [], ft_host, ft_port) ??? Error using ==> buffer ERROR: failed to create socket (1) Thanks, Beth ------------------------------------------------------------------------------------------ Elizabeth Bock / MEG System Engineer McConnell Brain Imaging Centre / Montreal Neurological Institute McGill University / 3801 University St. / Montreal, QC H3A 2B4 MEG Lab: 514.398.6056 Mobile: 514.718.6342 ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Stolk, A. [a.stolk at fcdonders.ru.nl] Sent: Thursday, September 13, 2012 5:05 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] realtime buffer does not exit Hi Elizabeth, Could you try and start the buffer from outside matlab using 'demo_buffer.exe' (to be found in the 'realtime/bin/win32' directory)? This application may operate smoother than when starting the buffer from a single matlab thread. Best, Arjen ----- Oorspronkelijk bericht ----- > Van: "Elizabeth Anne Bock, Ms" > Aan: fieldtrip at science.ru.nl > Verzonden: Woensdag 12 september 2012 20:32:39 > Onderwerp: [FieldTrip] realtime buffer does not exit > I am using the realtime buffer and I have found I cannot exit the > buffer within the Matlab command window. I am forced to exit Matlab > or, more often, must kill the process manually from the windows task > manager. I am using Windows XP to host the buffer and Linux to run > acqftx. Here is what I am seeing: > > >> buffer('tcpserver', 'exit', ft_host, ft_port) > In main: requesting cancelation of tcpserver thread > > >> buffer('tcpserver', 'init', ft_host, ft_port) > ??? Error using ==> buffer > thread is already running > > Any suggestions? > Thanks, > Elizabeth > > > ------------------------------------------------------------------------------------------ > > Elizabeth Bock / MEG System Engineer > > McConnell Brain Imaging Centre / Montreal Neurological Institute > > McGill University / 3801 University St. / Montreal, QC H3A 2B4 > > > > MEG Lab: 514.398.6056 > > Mobile: 514.718.6342 > > _______________________________________________ > 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 wallisgj at gmail.com Thu Sep 13 15:26:55 2012 From: wallisgj at gmail.com (George Wallis) Date: Thu, 13 Sep 2012 14:26:55 +0100 Subject: [FieldTrip] Dimension mismatch in .grad struct for neuromag data Message-ID: Dear fieldtrippers, With neuromag306 data, after the old style of .grad gets converted to the new style, the field have dimensions as follows: data.grad: ans = unit: 'mm' label: {306x1 cell} coilori: [510x3 double] coilpos: [510x3 double] lab: {102x3 cell} chanpos: [102x3 double] chanori: [102x3 double] balance: [1x1 struct] Because there are three sensors in each location, there are 1/3 as many elements in chanpos as in coilpos. However, in ft_combineplanar, where the function remakes the .grad field to match the new list of channels (where the gradiometers have been combined), is uses a list of channel indices 'sel' which is concatenated vertically: sel = [sel_comb(:);sel_other(:)]; ...and indexes into newgrad.chanpos. As above, newgrad.chanpos is 102x3, but sel is 204x1: 102 combined gradiometers ('sel_comb') plus 102 magnetometers ('sel_other'). There is therefore a dimension mismatch, because the different channel types are 'overlaid' in 'chanpos' but not in 'sel'. Have I set up my .chanpos, .chanori incorrectly? Thanks for any tips, George -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mollison at gmail.com Thu Sep 13 16:50:58 2012 From: matt.mollison at gmail.com (Matt Mollison) Date: Thu, 13 Sep 2012 08:50:58 -0600 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> <77D46473-6907-4AC1-96E1-F51756C119C0@mac.com> <3B494ED9-B6C3-46A3-840C-8EEEDAA85E5E@mac.com> Message-ID: Daria, I do not know any calibration function for raw files that were exported without calibration, but maybe it is a simple formula? You might want to contact EGI. Let us know if you find anything out. Best, Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ On Thu, Sep 13, 2012 at 1:21 AM, Daria Laptinskaya < daria.laptinskaya at googlemail.com> wrote: > Yes, it works fine now-thank you!!! > > @Matt: Do you know a calibration-function for existing raw-files? > > > > Best, > > Daria > > > 2012/9/10 Joseph Dien > >> Hey Daria, >> glad you were able to get it worked out! Thank Matt for his reminder >> (below) about the calibration option. >> >> Cheers! >> >> Joe >> >> >> Hi Joe, >> >> >> I didn’t know that there is a function like this. >> >> The most of my colleagues use the RAW.-files they get from the >> file-exporter without problems. >> >> Not even NetStation-support could give me an answer. >> >> So I thought, it must be a problem between NetStation and fieldtrip. >> >> Because of your tip I opened an original datafile and tried to save a >> copy of the file. >> >> Doing so NetStation offers a possibility to ‘convert to microvolts’ and >> create a .ses –datafile. >> >> The .raw-files I get this way have microvolt as unit. >> >> I compared the signals I get this way with the signals I get by using the >> formula (5000 mircovolts / (2^16 bits) I send you. They are almost the >> same-that’s great!!! >> >> It seems to work now. >> >> Thank you very much!!! You were a great help!!! >> >> >> Cheers, >> >> Daria >> >> On Sep 6, 2012, at 9:07 PM, Joseph Dien wrote: >> >> I don't recall ever seeing this problem with EGIS files, which is one of >> the reasons I prefer using this file format despite EGI's preference for >> newer Simple Binary format, but it's an unpredictable bug so I can't say it >> can't happen. I also can't say which versions of NetStation it happens >> with. It may have been fixed. I'm still trying to test out MFF so can't >> say anything about it. I had problems with the FieldTrip code for reading >> segmented MFF files (which is what I'm interested in). I also had trouble >> with writing them out from NetStation so I don't have a valid segmented >> test file and I'm still waiting for EGI to make one available so I can work >> them out. The simple binary file format (this is the original name for the >> EGI .raw file format and I prefer to use it over ".raw" as the BESA .raw >> file format is actually the .egis file format so it can get confusing) >> doesn't actually have separate calibration information for the channels >> (unlike EGIS), just one single gain value and no zeros values. So >> basically the simple binary format makes the assumption that calibration >> corrections have already been performed prior to generating the file. My >> understanding is that this is indeed what the "calibrate data" option is >> doing, but you'd have to confirm with EGI. >> >> Joe >> >> >> >> -------------------------------------------------------------------------------- >> >> On Sep 6, 2012, at 1:01 PM, Matt Mollison >> wrote: >> >> Joe, >> >> A few related questions: >> >> Does using the "calibrate data" option when exporting to raw (simple >> binary) correct for gain? Or is there a different solution/recommendation? >> Does exporting to MFF (Net Station 4.5.x only) or EGIS have this issue? I >> tend to use EGIS (faster to read than raw) and have no recollection of >> seeing unusually large voltages. >> >> Thanks, >> Matt >> >> On Wed, Sep 5, 2012 at 7:17 PM, Joseph Dien wrote: >> >>> The Simple Binary (.raw) files don't get corrected for gain when >>> imported (I helped write them). I've experienced occasional unpredictable >>> bugs with NetStation export routines where the files are generated with >>> amplitudes many times too large, even with text format files. It's a bit >>> disconcerting to say the least. I could take a look at your files if you'd >>> like confirmation. >>> >>> Joe >>> >>> On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis < >>> inieuwenhuis at BERKELEY.EDU> wrote: >>> >>> Hi Daria, >>> >>> Also, did you try looking at your raw data (so before the ERPs are made) >>> in FieldTrip and in Net Station? So open your .raw data in NetStation. You >>> can just look at a random participant's data, and check if the scale is the >>> same. I'm pretty sure no amplification takes place when reading in the data >>> into FieldTrip, this check can confirm that. Hope this helps, and let us >>> know what you find. >>> >>> Cheers, >>> Ingrid >>> >>> >>> On 9/3/2012 1:35 PM, Robert Oostenveld wrote: >>> >>> Hi Daria, >>> >>> There might indeed be an incompatibility in the gain value applied to >>> the data. >>> >>> If you are able to export the data using the EGI software in another >>> format (e.g. EDF), you could read them both into FieldTrip and compare the >>> timecourse aplitudes to check whether they are different. In case they are, >>> I suggest to involve EGI support. They are aware of the FieldTrip reading >>> functions and will know much more about the internals of their various file >>> formats. >>> >>> best regards >>> Robert >>> >>> >>> >>> >>> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: >>> >>> Dear Fieldtrippers, >>> >>> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip >>> toolbox. >>> The ERPs look perfect. >>> The 'only' problem is, that my signals look to strong. >>> It looks like if I get amplitutes (average) until 70 µV. >>> I think it must be an intern amplifier for the signals. >>> >>> Does anyone know this problem with EGI-data? >>> >>> Or does anyone know, where I can see the amplifier? >>> >>> >>> >>> Greetings, >>> Daria _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> -- >>> Ingrid Nieuwenhuis PhD >>> Postdoctoral Fellow >>> Sleep and Neuroimaging Laboratory >>> Department of Psychology >>> University of California, Berkeley >>> California 94720-1650 >>> Tolman Hall, room 5305 >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> Joseph Dien, >>> Senior Research Scientist >>> University of Maryland >>> >>> E-mail: jdien07 at mac.com >>> Phone: 301-226-8848 >>> Fax: 301-226-8811 >>> http://joedien.com// >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, >> Senior Research Scientist >> University of Maryland >> >> E-mail: jdien07 at mac.com >> Phone: 301-226-8848 >> Fax: 301-226-8811 >> http://joedien.com// >> >> >> >> >> >> >> >> >> >> >> >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, >> Senior Research Scientist >> University of Maryland >> >> E-mail: jdien07 at mac.com >> Phone: 301-226-8848 >> Fax: 301-226-8811 >> http://joedien.com// >> >> >> >> >> >> >> >> >> >> >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From daria.laptinskaya at googlemail.com Thu Sep 13 17:14:37 2012 From: daria.laptinskaya at googlemail.com (Daria Laptinskaya) Date: Thu, 13 Sep 2012 17:14:37 +0200 Subject: [FieldTrip] Amplifier for EGI-data in fieldtrip??? In-Reply-To: References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> <77D46473-6907-4AC1-96E1-F51756C119C0@mac.com> <3B494ED9-B6C3-46A3-840C-8EEEDAA85E5E@mac.com> Message-ID: There is a formula in the NetStation-manual: (5000 mircovolts / (2^16 bits). You can convert bits to microvolts by multiplicating all signals with the factor 0,076293945 in fieldtrip. This solution isn't perfect, because it doesn't consider gains. We asked EGI for an other formula, but didn't yet get an answer. I compare the two methods and for little N the gains don't make a great difference. Best, Daria 2012/9/13 Matt Mollison > Daria, > > I do not know any calibration function for raw files that were exported > without calibration, but maybe it is a simple formula? You might want to > contact EGI. Let us know if you find anything out. > > Best, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > > On Thu, Sep 13, 2012 at 1:21 AM, Daria Laptinskaya < > daria.laptinskaya at googlemail.com> wrote: > >> Yes, it works fine now-thank you!!! >> >> @Matt: Do you know a calibration-function for existing raw-files? >> >> >> >> Best, >> >> Daria >> >> >> 2012/9/10 Joseph Dien >> >>> Hey Daria, >>> glad you were able to get it worked out! Thank Matt for his reminder >>> (below) about the calibration option. >>> >>> Cheers! >>> >>> Joe >>> >>> >>> Hi Joe, >>> >>> >>> I didn’t know that there is a function like this. >>> >>> The most of my colleagues use the RAW.-files they get from the >>> file-exporter without problems. >>> >>> Not even NetStation-support could give me an answer. >>> >>> So I thought, it must be a problem between NetStation and fieldtrip. >>> >>> Because of your tip I opened an original datafile and tried to save a >>> copy of the file. >>> >>> Doing so NetStation offers a possibility to ‘convert to microvolts’ and >>> create a .ses –datafile. >>> >>> The .raw-files I get this way have microvolt as unit. >>> >>> I compared the signals I get this way with the signals I get by using >>> the formula (5000 mircovolts / (2^16 bits) I send you. They are almost the >>> same-that’s great!!! >>> >>> It seems to work now. >>> >>> Thank you very much!!! You were a great help!!! >>> >>> >>> Cheers, >>> >>> Daria >>> >>> On Sep 6, 2012, at 9:07 PM, Joseph Dien wrote: >>> >>> I don't recall ever seeing this problem with EGIS files, which is one of >>> the reasons I prefer using this file format despite EGI's preference for >>> newer Simple Binary format, but it's an unpredictable bug so I can't say it >>> can't happen. I also can't say which versions of NetStation it happens >>> with. It may have been fixed. I'm still trying to test out MFF so can't >>> say anything about it. I had problems with the FieldTrip code for reading >>> segmented MFF files (which is what I'm interested in). I also had trouble >>> with writing them out from NetStation so I don't have a valid segmented >>> test file and I'm still waiting for EGI to make one available so I can work >>> them out. The simple binary file format (this is the original name for the >>> EGI .raw file format and I prefer to use it over ".raw" as the BESA .raw >>> file format is actually the .egis file format so it can get confusing) >>> doesn't actually have separate calibration information for the channels >>> (unlike EGIS), just one single gain value and no zeros values. So >>> basically the simple binary format makes the assumption that calibration >>> corrections have already been performed prior to generating the file. My >>> understanding is that this is indeed what the "calibrate data" option is >>> doing, but you'd have to confirm with EGI. >>> >>> Joe >>> >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> On Sep 6, 2012, at 1:01 PM, Matt Mollison >>> wrote: >>> >>> Joe, >>> >>> A few related questions: >>> >>> Does using the "calibrate data" option when exporting to raw (simple >>> binary) correct for gain? Or is there a different solution/recommendation? >>> Does exporting to MFF (Net Station 4.5.x only) or EGIS have this issue? >>> I tend to use EGIS (faster to read than raw) and have no recollection of >>> seeing unusually large voltages. >>> >>> Thanks, >>> Matt >>> >>> On Wed, Sep 5, 2012 at 7:17 PM, Joseph Dien wrote: >>> >>>> The Simple Binary (.raw) files don't get corrected for gain when >>>> imported (I helped write them). I've experienced occasional unpredictable >>>> bugs with NetStation export routines where the files are generated with >>>> amplitudes many times too large, even with text format files. It's a bit >>>> disconcerting to say the least. I could take a look at your files if you'd >>>> like confirmation. >>>> >>>> Joe >>>> >>>> On Sep 4, 2012, at 4:00 PM, Ingrid Nieuwenhuis < >>>> inieuwenhuis at BERKELEY.EDU> wrote: >>>> >>>> Hi Daria, >>>> >>>> Also, did you try looking at your raw data (so before the ERPs are >>>> made) in FieldTrip and in Net Station? So open your .raw data in >>>> NetStation. You can just look at a random participant's data, and check if >>>> the scale is the same. I'm pretty sure no amplification takes place when >>>> reading in the data into FieldTrip, this check can confirm that. Hope this >>>> helps, and let us know what you find. >>>> >>>> Cheers, >>>> Ingrid >>>> >>>> >>>> On 9/3/2012 1:35 PM, Robert Oostenveld wrote: >>>> >>>> Hi Daria, >>>> >>>> There might indeed be an incompatibility in the gain value applied >>>> to the data. >>>> >>>> If you are able to export the data using the EGI software in another >>>> format (e.g. EDF), you could read them both into FieldTrip and compare the >>>> timecourse aplitudes to check whether they are different. In case they are, >>>> I suggest to involve EGI support. They are aware of the FieldTrip reading >>>> functions and will know much more about the internals of their various file >>>> formats. >>>> >>>> best regards >>>> Robert >>>> >>>> >>>> >>>> >>>> On 3 Sep 2012, at 17:22, Daria Laptinskaya wrote: >>>> >>>> Dear Fieldtrippers, >>>> >>>> I analysed EGI-data (.raw-files, NetStation 4.3.) with the fieldtrip >>>> toolbox. >>>> The ERPs look perfect. >>>> The 'only' problem is, that my signals look to strong. >>>> It looks like if I get amplitutes (average) until 70 µV. >>>> I think it must be an intern amplifier for the signals. >>>> >>>> Does anyone know this problem with EGI-data? >>>> >>>> Or does anyone know, where I can see the amplifier? >>>> >>>> >>>> >>>> Greetings, >>>> Daria _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> >>>> -- >>>> Ingrid Nieuwenhuis PhD >>>> Postdoctoral Fellow >>>> Sleep and Neuroimaging Laboratory >>>> Department of Psychology >>>> University of California, Berkeley >>>> California 94720-1650 >>>> Tolman Hall, room 5305 >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> >>>> >>>> >>>> -------------------------------------------------------------------------------- >>>> >>>> Joseph Dien, >>>> Senior Research Scientist >>>> University of Maryland >>>> >>>> E-mail: jdien07 at mac.com >>>> Phone: 301-226-8848 >>>> Fax: 301-226-8811 >>>> http://joedien.com// >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> Joseph Dien, >>> Senior Research Scientist >>> University of Maryland >>> >>> E-mail: jdien07 at mac.com >>> Phone: 301-226-8848 >>> Fax: 301-226-8811 >>> http://joedien.com// >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> Joseph Dien, >>> Senior Research Scientist >>> University of Maryland >>> >>> E-mail: jdien07 at mac.com >>> Phone: 301-226-8848 >>> Fax: 301-226-8811 >>> http://joedien.com// >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bherrmann at cbs.mpg.de Fri Sep 14 10:23:14 2012 From: bherrmann at cbs.mpg.de (=?utf-8?Q?Bj=C3=B6rn_Herrmann?=) Date: Fri, 14 Sep 2012 10:23:14 +0200 (CEST) Subject: [FieldTrip] How to impove dics realfilter solution In-Reply-To: <612757646.1088.1347610775726.JavaMail.root@zimbra> Message-ID: <736231433.1128.1347610993969.JavaMail.root@zimbra> Dear fieldtrip user, I am using the DICS beamformer to localize a 3Hz FFT power topographical distribution (using a neuromag system). The topographies are very clear auditory in single subjects, thus it shouldn't be a problem finding the "right" solution. When I use the beamformer to obtain complex-value spatial filters, the solution looks very good (using NAI). No problem here. However, using cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real values, the localization completely breaks down, sometimes even finding a strong peak in the opposite hemisphere than visible in the sensor topography (the head is centered in the sensor array). Does someone have a suggestion how to improve the solution using realfilter = 'yes'. I use the following settings. They are rather standard I guess. cfg = []; cfg.method = 'dics'; cfg.frequency = 3; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.keepfilter = 'yes'; cfg.dics.realfilter = 'yes'; cfg.dics.fixedori = 'no'; If someone has a suggestion, I would appreciate it. Thanks in advance, best, Björn From r.oostenveld at donders.ru.nl Fri Sep 14 11:25:54 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 14 Sep 2012 04:25:54 -0500 Subject: [FieldTrip] fieldtrip wiki website unstable In-Reply-To: References: <63F6ADC4-BA8E-4299-973F-3DDAFE630C51@donders.ru.nl> <50465DC3.7080005@berkeley.edu> <3AAEF75C-181A-4768-948F-71A519FF0067@mac.com> <77D46473-6907-4AC1-96E1-F51756C119C0@mac.com> <3B494ED9-B6C3-46A3-840C-8EEEDAA85E5E@mac.com> Message-ID: <8FD34ABA-CEDF-4E8C-B024-9F175E1CD573@donders.ru.nl> Dear FieldTrip users, As you may have noticed, we have some issues with the FieldTrip wiki. The underlying cause is that the file server hosting the webserver, bugzilla, svn and the ftp server is acting weird, causing temporary failures of the online services. Our ICT group is working on it. So if you notice that either the FieldTrip wiki or one of the related servers is not doing what you expect, please try again later. best regards Robert From b.reuderink at donders.ru.nl Fri Sep 14 12:21:52 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Fri, 14 Sep 2012 12:21:52 +0200 Subject: [FieldTrip] realtime buffer does not exit In-Reply-To: <86D86365C4E767468A79EB52DFBFB46F05110836@exmbx2010-8.campus.MCGILL.CA> References: <86D86365C4E767468A79EB52DFBFB46F0510F73C@exmbx2010-8.campus.MCGILL.CA>, <3342976.328678.1347527120171.JavaMail.root@sculptor.zimbra.ru.nl> <86D86365C4E767468A79EB52DFBFB46F05110836@exmbx2010-8.campus.MCGILL.CA> Message-ID: <81D26A77-1088-4A8A-89FF-AA9B199F0320@donders.ru.nl> Dear Elizabeth, It is indeed possible (perhaps preferable) to run the FieldTrip buffer outside of the MATLAB environment. Basically, the 'demo_buffer.exe' functions as a stand-alone server that holds the neuro data. Then, you would need a client, that reads from your acquisition hardware and writes new samples and events to the server. FieldTrip has programs for many different acquisition systems, see [1]. Your MATLAB program can then act as another client and read form the buffer. The advantage of this setup is that you can restart your MATLAB session without disrupting the FieldTrip real-time buffer. You can even run the serving buffer and your MATLAB code on different computers in you lab. Without additional details I can only guess why you got the error message you described. Perhaps the ft_host and ft_port are not set correctly? For ft_host you could try 'localhost' or '127.0.0.1', and for ft_port the default is 1972. These settings tell FieldTrip to connect to a buffer (=server) on the same computer. If you can't get it to work, please don't hesitate to ask. BTW, some background information on real-time signal processing with FieldTrip can be found on [2] — perhaps that is useful. Best regards, Boris Reuderink [1] http://fieldtrip.fcdonders.nl/development/realtime/implementation [2] http://fieldtrip.fcdonders.nl/development/realtime/buffer_overview -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl On 13 sep. 2012, at 14:51, "Elizabeth Anne Bock, Ms" wrote: > Thanks for the feedback. However, I would like to read the header and the data from the buffer into Matlab (I am doing realtime processing of the data). Is this possible to run the buffer in the windows environment and then read from it in Matlab? > > hdr = buffer('get_hdr', [], ft_host, ft_port) > ??? Error using ==> buffer > ERROR: failed to create socket (1) > > Thanks, > Beth > > ------------------------------------------------------------------------------------------ > > Elizabeth Bock / MEG System Engineer > > McConnell Brain Imaging Centre / Montreal Neurological Institute > > McGill University / 3801 University St. / Montreal, QC H3A 2B4 > > > > MEG Lab: 514.398.6056 > > Mobile: 514.718.6342 > > ________________________________________ > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Stolk, A. [a.stolk at fcdonders.ru.nl] > Sent: Thursday, September 13, 2012 5:05 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] realtime buffer does not exit > > Hi Elizabeth, > > Could you try and start the buffer from outside matlab using 'demo_buffer.exe' (to be found in the 'realtime/bin/win32' directory)? This application may operate smoother than when starting the buffer from a single matlab thread. > > Best, > Arjen > > ----- Oorspronkelijk bericht ----- >> Van: "Elizabeth Anne Bock, Ms" >> Aan: fieldtrip at science.ru.nl >> Verzonden: Woensdag 12 september 2012 20:32:39 >> Onderwerp: [FieldTrip] realtime buffer does not exit >> I am using the realtime buffer and I have found I cannot exit the >> buffer within the Matlab command window. I am forced to exit Matlab >> or, more often, must kill the process manually from the windows task >> manager. I am using Windows XP to host the buffer and Linux to run >> acqftx. Here is what I am seeing: >> >>>> buffer('tcpserver', 'exit', ft_host, ft_port) >> In main: requesting cancelation of tcpserver thread >> >>>> buffer('tcpserver', 'init', ft_host, ft_port) >> ??? Error using ==> buffer >> thread is already running >> >> Any suggestions? >> Thanks, >> Elizabeth >> >> >> ------------------------------------------------------------------------------------------ >> >> Elizabeth Bock / MEG System Engineer >> >> McConnell Brain Imaging Centre / Montreal Neurological Institute >> >> McGill University / 3801 University St. / Montreal, QC H3A 2B4 >> >> >> >> MEG Lab: 514.398.6056 >> >> Mobile: 514.718.6342 >> >> _______________________________________________ >> 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 andrea.brovelli at univ-amu.fr Fri Sep 14 12:27:59 2012 From: andrea.brovelli at univ-amu.fr (andrea brovelli) Date: Fri, 14 Sep 2012 12:27:59 +0200 Subject: [FieldTrip] Data prewhitening Message-ID: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> Dear all, I was wondering whether we can whiten the data using the cfg options in the ft_preprocessing function. Does anyone know ? Or does anyone have some code for prewhitening raw data ? Thanks a lot Andrea From jan.schoffelen at donders.ru.nl Fri Sep 14 12:41:41 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 14 Sep 2012 12:41:41 +0200 Subject: [FieldTrip] Data prewhitening In-Reply-To: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> References: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> Message-ID: Caro Andrea, I think you could achieve this with ft_componentanalysis (but have never tried it myself): try: cfg = []; cfg.method = 'fastica'; cfg.fastica.only = 'white'; data2 = ft_componentanalysis(cfg, data); the fastica toolbox is in fieldtrip/external/ Check out the documentation in fastica.m Ciao, JM On Sep 14, 2012, at 12:27 PM, andrea brovelli wrote: > Dear all, > > I was wondering whether we can whiten the data using the cfg options in the ft_preprocessing function. Does anyone know ? > > Or does anyone have some code for prewhitening raw data ? > > Thanks a lot > > Andrea > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.vandermeij at donders.ru.nl Fri Sep 14 13:03:32 2012 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Fri, 14 Sep 2012 13:03:32 +0200 Subject: [FieldTrip] Data prewhitening In-Reply-To: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> References: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> Message-ID: Hi Andrea, Are you referring to pre-whitening by removing the first parameter of an auto-regressive model, thereby removing most (if not all) of the 1/f shape in the spectrum? If so, this can be done by taking the first temporal derivative of the raw-data, effectively setting the first AR parameter to 0. This is implemented by setting cfg.derivative = 'yes' in preprocessing. I don't know of any good references for this trick though, so if anybody else can help out, that'd be great. Best, Roemer On Fri, Sep 14, 2012 at 12:27 PM, andrea brovelli < andrea.brovelli at univ-amu.fr> wrote: > Dear all, > > I was wondering whether we can whiten the data using the cfg options in > the ft_preprocessing function. Does anyone know ? > > Or does anyone have some code for prewhitening raw data ? > > Thanks a lot > > Andrea > > > ______________________________**_________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip > -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri Sep 14 13:52:43 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 14 Sep 2012 13:52:43 +0200 Subject: [FieldTrip] Data prewhitening In-Reply-To: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> References: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> Message-ID: <55DE5D38-8A8E-4452-AE65-1326CE686A97@donders.ru.nl> Hi Andrea, As a follow up to my previous mail. There even seems to be a cfg.method = 'white' in ft_componentanalysis. As an addition to Roemers suggestion: if you want to spectrally whiten your data, his approach can be used. I interpreted your question as that you want to achieve spatial whitening. Best, JM On Sep 14, 2012, at 12:27 PM, andrea brovelli wrote: > Dear all, > > I was wondering whether we can whiten the data using the cfg options in the ft_preprocessing function. Does anyone know ? > > Or does anyone have some code for prewhitening raw data ? > > Thanks a lot > > Andrea > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrea.brovelli at univ-amu.fr Fri Sep 14 14:09:43 2012 From: andrea.brovelli at univ-amu.fr (andrea brovelli) Date: Fri, 14 Sep 2012 14:09:43 +0200 Subject: [FieldTrip] Data prewhitening In-Reply-To: References: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> Message-ID: <20120914140943.11107al822gjc39c@wmelperso1.univmed.fr> Thank you all for these suggestions, I'll try them out. bye Andrea ----- Message de r.vandermeij at donders.ru.nl --------- Date : Fri, 14 Sep 2012 13:03:32 +0200 De : Roemer van der Meij Répondre à : FieldTrip discussion list Objet : Re: [FieldTrip] Data prewhitening À : FieldTrip discussion list > Hi Andrea, > > Are you referring to pre-whitening by removing the first parameter of > an auto-regressive model, thereby removing most (if not all) of the 1/f > shape in the spectrum? If so, this can be done by taking the first > temporal derivative of the raw-data, effectively setting the first AR > parameter to 0. This is implemented by setting cfg.derivative = 'yes' in > preprocessing. > I don't know of any good references for this trick though, so if anybody > else can help out, that'd be great. > > Best, > Roemer > > > On Fri, Sep 14, 2012 at 12:27 PM, andrea brovelli < > andrea.brovelli at univ-amu.fr> wrote: > >> Dear all, >> >> I was wondering whether we can whiten the data using the cfg options in >> the ft_preprocessing function. Does anyone know ? >> >> Or does anyone have some code for prewhitening raw data ? >> >> Thanks a lot >> >> Andrea >> >> >> ______________________________**_________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip >> > > > > -- > Roemer van der Meij M.Sc. > PhD student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > Tel: +31(0)24 3655932 > E-mail: r.vandermeij at donders.ru.nl > ----- Fin du message de r.vandermeij at donders.ru.nl ----- -- NEW EMAIL: andrea.brovelli at univ-amu.fr From eelke.spaak at donders.ru.nl Fri Sep 14 14:27:54 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Fri, 14 Sep 2012 14:27:54 +0200 Subject: [FieldTrip] Data prewhitening In-Reply-To: <20120914140943.11107al822gjc39c@wmelperso1.univmed.fr> References: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> <20120914140943.11107al822gjc39c@wmelperso1.univmed.fr> Message-ID: Hi Andrea, To add to Roemer's suggestion: it's not exactly a reference perhaps, but Robert posted on the list a while ago some explanation behind using the temporal derivative to remove 1/f power (=whitening). See http://mailman.science.ru.nl/pipermail/fieldtrip/2011-October/004390.html Best, Eelke On 14 September 2012 14:09, andrea brovelli wrote: > Thank you all for these suggestions, I'll try them out. > > bye > > Andrea > > > ----- Message de r.vandermeij at donders.ru.nl --------- > Date : Fri, 14 Sep 2012 13:03:32 +0200 > De : Roemer van der Meij > Répondre à : FieldTrip discussion list > Objet : Re: [FieldTrip] Data prewhitening > À : FieldTrip discussion list > > >> Hi Andrea, >> >> Are you referring to pre-whitening by removing the first parameter of >> an auto-regressive model, thereby removing most (if not all) of the 1/f >> shape in the spectrum? If so, this can be done by taking the first >> temporal derivative of the raw-data, effectively setting the first AR >> parameter to 0. This is implemented by setting cfg.derivative = 'yes' in >> preprocessing. >> I don't know of any good references for this trick though, so if anybody >> else can help out, that'd be great. >> >> Best, >> Roemer >> >> >> On Fri, Sep 14, 2012 at 12:27 PM, andrea brovelli < >> andrea.brovelli at univ-amu.fr> wrote: >> >>> Dear all, >>> >>> I was wondering whether we can whiten the data using the cfg options in >>> the ft_preprocessing function. Does anyone know ? >>> >>> Or does anyone have some code for prewhitening raw data ? >>> >>> Thanks a lot >>> >>> Andrea >>> >>> >>> ______________________________**_________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> >>> http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> Roemer van der Meij M.Sc. >> PhD student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognition >> P.O. Box 9104 >> 6500 HE Nijmegen >> The Netherlands >> Tel: +31(0)24 3655932 >> E-mail: r.vandermeij at donders.ru.nl >> > > > ----- Fin du message de r.vandermeij at donders.ru.nl ----- > > > > -- > > NEW EMAIL: andrea.brovelli at univ-amu.fr > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Fri Sep 14 14:42:10 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 14 Sep 2012 14:42:10 +0200 Subject: [FieldTrip] improved edge behavior for cfg.boxcar in ft_preprocessing Message-ID: Dear all, I just pushed an improved version of boxcar smoothing to the svn-repository (will be available for download as of tonight). I just want to mention it, because it behaves slightly different from what you are used to (provided you actually ever use the option cfg.boxcar in ft_preprocessing). In a nutshell, the old implementation did an implicit zero-padding when performing the boxcar convolution. This could sometimes lead to ugly edges, if the local mean of the data (close to the edge) significantly deviated from 0. Therefore I implemented an explicit padding with the local mean value. You can read the code in ft_preproc_smooth. Since I think this change entails a significant improvement, and the old implementation was far from ideal, I decided to not support backward compatibility in this case. This means that you will not be able to reproduce the bad edge behavior of FT's boxcar functionality on your data anymore. Too bad. Happy computing and with best wishes, Jan-Mathijs Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.m.groppe at gmail.com Fri Sep 14 14:54:23 2012 From: david.m.groppe at gmail.com (David Groppe) Date: Fri, 14 Sep 2012 08:54:23 -0400 Subject: [FieldTrip] Data prewhitening In-Reply-To: References: <20120914122759.19107jzyjr2y0i9s@wmelperso1.univmed.fr> <20120914140943.11107al822gjc39c@wmelperso1.univmed.fr> Message-ID: Here's a reference for whitening: Applications of spectral methods in functional brain imaging. D. Kleinfeld and P. P. Mitra. In Imaging: A Laboratory Manual (Book 1) R. Yuste, editor and series editor, 2011, Cold Spring Harbor Laboratory Press, NY, Chapter 12, 143-158. http://physics.ucsd.edu/neurophysics/publications/12_08_IMG.pdf And thanks to Robert Oostenveld for that original email response to my question about removing 1/f power trends. -David On Fri, Sep 14, 2012 at 8:27 AM, Eelke Spaak wrote: > Hi Andrea, > > To add to Roemer's suggestion: it's not exactly a reference perhaps, > but Robert posted on the list a while ago some explanation behind > using the temporal derivative to remove 1/f power (=whitening). See > http://mailman.science.ru.nl/pipermail/fieldtrip/2011-October/004390.html > > Best, > Eelke > > On 14 September 2012 14:09, andrea brovelli wrote: >> Thank you all for these suggestions, I'll try them out. >> >> bye >> >> Andrea >> >> >> ----- Message de r.vandermeij at donders.ru.nl --------- >> Date : Fri, 14 Sep 2012 13:03:32 +0200 >> De : Roemer van der Meij >> Répondre à : FieldTrip discussion list >> Objet : Re: [FieldTrip] Data prewhitening >> À : FieldTrip discussion list >> >> >>> Hi Andrea, >>> >>> Are you referring to pre-whitening by removing the first parameter of >>> an auto-regressive model, thereby removing most (if not all) of the 1/f >>> shape in the spectrum? If so, this can be done by taking the first >>> temporal derivative of the raw-data, effectively setting the first AR >>> parameter to 0. This is implemented by setting cfg.derivative = 'yes' in >>> preprocessing. >>> I don't know of any good references for this trick though, so if anybody >>> else can help out, that'd be great. >>> >>> Best, >>> Roemer >>> >>> >>> On Fri, Sep 14, 2012 at 12:27 PM, andrea brovelli < >>> andrea.brovelli at univ-amu.fr> wrote: >>> >>>> Dear all, >>>> >>>> I was wondering whether we can whiten the data using the cfg options in >>>> the ft_preprocessing function. Does anyone know ? >>>> >>>> Or does anyone have some code for prewhitening raw data ? >>>> >>>> Thanks a lot >>>> >>>> Andrea >>>> >>>> >>>> ______________________________**_________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> >>>> http://mailman.science.ru.nl/**mailman/listinfo/fieldtrip >>>> >>> >>> >>> >>> -- >>> Roemer van der Meij M.Sc. >>> PhD student >>> Donders Institute for Brain, Cognition and Behaviour >>> Centre for Cognition >>> P.O. Box 9104 >>> 6500 HE Nijmegen >>> The Netherlands >>> Tel: +31(0)24 3655932 >>> E-mail: r.vandermeij at donders.ru.nl >>> >> >> >> ----- Fin du message de r.vandermeij at donders.ru.nl ----- >> >> >> >> -- >> >> NEW EMAIL: andrea.brovelli at univ-amu.fr >> >> >> _______________________________________________ >> 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 -- David Groppe, Ph.D. Postdoctoral Researcher North Shore LIJ Health System New Hyde Park, New York http://www.cogsci.ucsd.edu/~dgroppe/ From elizabeth.bock at mcgill.ca Fri Sep 14 16:23:51 2012 From: elizabeth.bock at mcgill.ca (Elizabeth Anne Bock, Ms) Date: Fri, 14 Sep 2012 14:23:51 +0000 Subject: [FieldTrip] realtime buffer does not exit In-Reply-To: <81D26A77-1088-4A8A-89FF-AA9B199F0320@donders.ru.nl> References: <86D86365C4E767468A79EB52DFBFB46F0510F73C@exmbx2010-8.campus.MCGILL.CA>, <3342976.328678.1347527120171.JavaMail.root@sculptor.zimbra.ru.nl> <86D86365C4E767468A79EB52DFBFB46F05110836@exmbx2010-8.campus.MCGILL.CA>, <81D26A77-1088-4A8A-89FF-AA9B199F0320@donders.ru.nl> Message-ID: <86D86365C4E767468A79EB52DFBFB46F05110DDE@exmbx2010-8.campus.MCGILL.CA> Thanks! This works great. Elizabeth ------------------------------------------------------------------------------------------ Elizabeth Bock / MEG System Engineer McConnell Brain Imaging Centre / Montreal Neurological Institute McGill University / 3801 University St. / Montreal, QC H3A 2B4 MEG Lab: 514.398.6056 Mobile: 514.718.6342 ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Boris Reuderink [b.reuderink at donders.ru.nl] Sent: Friday, September 14, 2012 6:21 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] realtime buffer does not exit Dear Elizabeth, It is indeed possible (perhaps preferable) to run the FieldTrip buffer outside of the MATLAB environment. Basically, the 'demo_buffer.exe' functions as a stand-alone server that holds the neuro data. Then, you would need a client, that reads from your acquisition hardware and writes new samples and events to the server. FieldTrip has programs for many different acquisition systems, see [1]. Your MATLAB program can then act as another client and read form the buffer. The advantage of this setup is that you can restart your MATLAB session without disrupting the FieldTrip real-time buffer. You can even run the serving buffer and your MATLAB code on different computers in you lab. Without additional details I can only guess why you got the error message you described. Perhaps the ft_host and ft_port are not set correctly? For ft_host you could try 'localhost' or '127.0.0.1', and for ft_port the default is 1972. These settings tell FieldTrip to connect to a buffer (=server) on the same computer. If you can't get it to work, please don't hesitate to ask. BTW, some background information on real-time signal processing with FieldTrip can be found on [2] — perhaps that is useful. Best regards, Boris Reuderink [1] http://fieldtrip.fcdonders.nl/development/realtime/implementation [2] http://fieldtrip.fcdonders.nl/development/realtime/buffer_overview -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl On 13 sep. 2012, at 14:51, "Elizabeth Anne Bock, Ms" wrote: > Thanks for the feedback. However, I would like to read the header and the data from the buffer into Matlab (I am doing realtime processing of the data). Is this possible to run the buffer in the windows environment and then read from it in Matlab? > > hdr = buffer('get_hdr', [], ft_host, ft_port) > ??? Error using ==> buffer > ERROR: failed to create socket (1) > > Thanks, > Beth > > ------------------------------------------------------------------------------------------ > > Elizabeth Bock / MEG System Engineer > > McConnell Brain Imaging Centre / Montreal Neurological Institute > > McGill University / 3801 University St. / Montreal, QC H3A 2B4 > > > > MEG Lab: 514.398.6056 > > Mobile: 514.718.6342 > > ________________________________________ > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Stolk, A. [a.stolk at fcdonders.ru.nl] > Sent: Thursday, September 13, 2012 5:05 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] realtime buffer does not exit > > Hi Elizabeth, > > Could you try and start the buffer from outside matlab using 'demo_buffer.exe' (to be found in the 'realtime/bin/win32' directory)? This application may operate smoother than when starting the buffer from a single matlab thread. > > Best, > Arjen > > ----- Oorspronkelijk bericht ----- >> Van: "Elizabeth Anne Bock, Ms" >> Aan: fieldtrip at science.ru.nl >> Verzonden: Woensdag 12 september 2012 20:32:39 >> Onderwerp: [FieldTrip] realtime buffer does not exit >> I am using the realtime buffer and I have found I cannot exit the >> buffer within the Matlab command window. I am forced to exit Matlab >> or, more often, must kill the process manually from the windows task >> manager. I am using Windows XP to host the buffer and Linux to run >> acqftx. Here is what I am seeing: >> >>>> buffer('tcpserver', 'exit', ft_host, ft_port) >> In main: requesting cancelation of tcpserver thread >> >>>> buffer('tcpserver', 'init', ft_host, ft_port) >> ??? Error using ==> buffer >> thread is already running >> >> Any suggestions? >> Thanks, >> Elizabeth >> >> >> ------------------------------------------------------------------------------------------ >> >> Elizabeth Bock / MEG System Engineer >> >> McConnell Brain Imaging Centre / Montreal Neurological Institute >> >> McGill University / 3801 University St. / Montreal, QC H3A 2B4 >> >> >> >> MEG Lab: 514.398.6056 >> >> Mobile: 514.718.6342 >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Duncan.Astle at mrc-cbu.cam.ac.uk Fri Sep 14 16:58:26 2012 From: Duncan.Astle at mrc-cbu.cam.ac.uk (Duncan Astle) Date: Fri, 14 Sep 2012 14:58:26 +0000 Subject: [FieldTrip] Problem with clustering across electrode neighbours In-Reply-To: <5051BF53.5030606@donders.ru.nl> References: <5051BF53.5030606@donders.ru.nl> Message-ID: Thanks for your help. You were spot on; now the version is updated it runs perfectly. Thanks, Duncan ________________________________________________ Dr. Duncan Astle, Programme Leader Track, British Academy Research Fellow, MRC Cognition and Brain Sciences Unit, Chaucer Road, Cambridge. Duncan.Astle at mrc-cbu.cam.ac.uk From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig" Sent: 13 September 2012 12:11 To: FieldTrip discussion list Subject: Re: [FieldTrip] Problem with clustering across electrode neighbours Hey Duncan, it looks pretty much like you are using an old FieldTrip version with a new neighbourhood-structure. Could you check the with the most recent version again? Some months (about a year?) ago we changed the neighbour definition from cell arrays to structure arrays, so any attempt to access cfg.neighbours{i} will fail, cause it has to be cfg.neighbours(i) instead. But as I already said, this has been changed quite some time back in the past :) Essentially, your code is fine, but some note that cfg.neighbourdist should be a scalar, not the string 'number', but only if cfg.method='distance'. If you choose cfg.method = 'template' then cfg.neighbourdist is not used, cause a template is loaded. Best, Jörn On 9/13/2012 12:46 PM, Duncan Astle wrote: Dear Fieldtrippers, I am rather new to this, but am attempting to do some cluster stats on my ERP sensor level data. It is working well, and I can cluster across time, but I can't get it to cluster across electrode locations. I think it is because of a mistake that I am making in my 'neighbours' file, although it looks fine when I inspect it. This is the error message that I get: ??? Cell contents reference from a non-cell array object. Error in ==> clusterstat>makechanneighbstructmat at 520 [seld] = match_str(cfg.channel, cfg.neighbours{chan}.label); Error in ==> clusterstat at 60 channeighbstructmat = makechanneighbstructmat(cfg); Error in ==> statistics_montecarlo at 322 [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); Error in ==> statistics_wrapper at 285 [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); Error in ==> ft_timelockstatistics at 119 [stat, cfg] = statistics_wrapper(cfg, varargin{:}); Can anyone spot what I am doing wrong? This is how I make my neighbour file: cfg = []; cfg.layout = 'EEG1010.lay'; % try 'distance' as well cfg.feedback = 'yes'; % show a neighbour plot cfg.method = 'template'; cfg.neighbourdist = 'number'; cfg.template = 'EEG1010_neighb.mat' cfg.channel = 'all' cfg.feedback = 'yes'; neighbours = ft_prepare_neighbours(cfg, Load5Hard); % define neighbouring channels This is how I then try the stats: cfg = []; cfg.channel = 'all'; cfg.latency = [0.1 1.3]; cfg.avgovertime = 'no'; cfg.avgoverchannel = 'no'; cfg.parameter = 'individual'; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT' cfg.alpha = 0.05; cfg.correctm = 'cluster'; cfg.correcttail = 'prob'; cfg.numrandomization = 1000; cfg.feedback = 'yes'; % show a neighbour plot cfg.neighbours = neighbours; %cfg.minnbchan = 2; cfg.clusterstatistic = 'maxsum'; cfg.clusterthreshold = 'nonparametric'; cfg.clusteralpha = 0.01; cfg.clustercritval = 0.06; % cfg.clustertail = 0; cfg.tail = 0; Nsub = 19; cfg.design(1,1:2*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub)]; cfg.design(2,1:2*Nsub) = [1:Nsub 1:Nsub]; cfg.ivar = 1; % the 1st row in cfg.design contains the independent variable cfg.uvar = 2; % the 2nd row in cfg.design contains the subject number [stat] = ft_timelockstatistics(cfg, Load3Hard, Load3Easy) Any suggestions very gratefully received. Thanks, Duncan ________________________________________________ Dr. Duncan Astle, Programme Leader Track, British Academy Research Fellow, MRC Cognition and Brain Sciences Unit, Chaucer Road, Cambridge. Duncan.Astle at mrc-cbu.cam.ac.uk _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sat Sep 15 07:49:07 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sat, 15 Sep 2012 08:49:07 +0300 Subject: [FieldTrip] example: ft_realtime_selectiveaverage Message-ID: Hello, Did any of you dealt before with ft_realtime_selectiveaverage function. If so, could I have a simple code so I can see how it is run? Best, -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From dmitri89 at ut.ee Tue Sep 18 10:00:35 2012 From: dmitri89 at ut.ee (Dmitri Filimonov) Date: Tue, 18 Sep 2012 11:00:35 +0300 Subject: [FieldTrip] channel repair script Message-ID: <259e43dd8af0ecf135e3965765705a76.squirrel@mailhost.ut.ee> Dear Sir/Madam, My name is Dmitri Filimonov, I am a master student in University of Tartu (Estonia), using fieldtrip for EEG data analysis. I would like to ask some assistance with fieldtrip script. The task is to repair some EEG channels, so need to use ft_channelrepair. And I tried to do that after artifact rejection, so I could first see, which channels are noisy or disabled. I tried multiple combinations, yet there are still problems with the script. It looks like: >> channels_to_repair={'Fp1', 'Fp2'}; layout_file=('C:\ fieldtrip-20120703\template\layout\EEG1010.lay'); cfg=[]; cfg.layout = 'EEG1010.lay'; data.elec = ft_prepare_layout(cfg); neighbours = ft_prepare_neighbours(cfg, good_data) cfg = ft_checkconfig(cfg, 'required', {'method'}); cfg.method = 'distance'; (or ‘nearest’) cfg.badchannel=channels_to_repair; cfg.neighbours = ft_prepare_neighbours (cfg, good_data); G_data = ft_channelrepair(cfg, dood_data); (Good_data –is a processed and filtered data, yet containing channels, which have to be repaired.) After processing the program gives me several errors: reading layout from file EEG1010.lay the call to "ft_prepare_layout" took 0 seconds and an estimated NaN MB ??? Error using ==> ft_checkconfig at 151 The field cfg.method is required Error in ==> ft_prepare_neighbours at 77 cfg = ft_checkconfig(cfg, 'required', {'method'}); Other combinations emerge similar errors, or Error in ==> ft_neighbourselection at 30 neighbours = ft_prepare_neighbours(varargin{:}); Can you give me some help, what kind of ‘method’ exactly program wants me to mention (type)? Yours sincerely, Dmitri From Joachim.Gross at glasgow.ac.uk Tue Sep 18 11:00:34 2012 From: Joachim.Gross at glasgow.ac.uk (Joachim Gross) Date: Tue, 18 Sep 2012 10:00:34 +0100 Subject: [FieldTrip] Five PostDoc Positions in Glasgow Message-ID: Research Associate (5 posts available) University of Glasgow - Institute of Neuroscience and Psychology You will contribute to Wellcome Trust funded research entitled "Natural and modulated neural communication: State-dependent decoding and driving of human Brain Oscillations" (Joint Investigators: Gregor Thut, Joachim Gross). This is one of 5 simultaneously filled 5-year Research Associate positions covering different aspects of the above project. The job requires working in an interdisciplinary team of researchers on longstanding questions of how brain oscillations orchestrate brain functions, or relate to brain dysfunction. Depending on the position within the team, this will involve the development and/or application of new analysis methods to eavesdrop on brain communication and decode some of the information coded in brain oscillations (MEG/EEG), or using this knowledge for controlled intervention into brain oscillations by transcranial stimulation to modulate brain function (combined TMS/tACS-EEG). For more information on the position and environment please write to Joachim.Gross at glasgow.ac.uk, or Gregor.Thut at glasgow.ac.uk This post has funding available until 31 December 2017 Ref: 002653 Please apply here: http://www.gla.ac.uk/about/jobs/ Salary: Grade 7, £31,948 - £35,938 per annum Closing date: 15 October 2012 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Tue Sep 18 12:34:01 2012 From: jm.horschig at donders.ru.nl (=?UTF-8?B?IkrDtnJuIE0uIEhvcnNjaGlnIg==?=) Date: Tue, 18 Sep 2012 12:34:01 +0200 Subject: [FieldTrip] channel repair script In-Reply-To: <259e43dd8af0ecf135e3965765705a76.squirrel@mailhost.ut.ee> References: <259e43dd8af0ecf135e3965765705a76.squirrel@mailhost.ut.ee> Message-ID: <50584E19.3090300@donders.ru.nl> Dear Dmitri, I think you are confusing things here. Note that you are calling two FieldTrip functions subsequently. The error message you are receiving results from ft_prepare_neighbours. ft_prepare_neighbours needs a different cfg than ft_channelrepair. The call you are making, does however not make much sense, because you already called that function a few lines before. So just drop that cfg.neighbours = ft_prepare_neighbours(...) line and replace it by cfg.neighbours = neighbours. Thereby, you are removing the function call that results in an error (and you already did that call), and I guess everything will work fine. Best, Jörn On 9/18/2012 10:00 AM, Dmitri Filimonov wrote: > Dear Sir/Madam, > > My name is Dmitri Filimonov, I am a master student in University of Tartu > (Estonia), using fieldtrip for EEG data analysis. I would like to ask some > assistance with fieldtrip script. > The task is to repair some EEG channels, so need to use ft_channelrepair. > And I tried to do that after artifact rejection, so I could first see, > which channels are noisy or disabled. I tried multiple combinations, yet > there are still problems with the script. > It looks like: > >>> channels_to_repair={'Fp1', 'Fp2'}; > layout_file=('C:\ fieldtrip-20120703\template\layout\EEG1010.lay'); > > cfg=[]; > cfg.layout = 'EEG1010.lay'; > data.elec = ft_prepare_layout(cfg); > neighbours = ft_prepare_neighbours(cfg, good_data) > cfg = ft_checkconfig(cfg, 'required', {'method'}); > cfg.method = 'distance'; (or ‘nearest’) > cfg.badchannel=channels_to_repair; > cfg.neighbours = ft_prepare_neighbours (cfg, good_data); > G_data = ft_channelrepair(cfg, dood_data); > (Good_data –is a processed and filtered data, yet containing channels, > which have to be repaired.) > After processing the program gives me several errors: > > reading layout from file EEG1010.lay > the call to "ft_prepare_layout" took 0 seconds and an estimated NaN MB > ??? Error using ==> ft_checkconfig at 151 > The field cfg.method is required > Error in ==> ft_prepare_neighbours at 77 > cfg = ft_checkconfig(cfg, 'required', {'method'}); > > Other combinations emerge similar errors, or > > Error in ==> ft_neighbourselection at 30 > neighbours = ft_prepare_neighbours(varargin{:}); > > Can you give me some help, what kind of ‘method’ exactly program wants me > to mention (type)? > > Yours sincerely, > Dmitri > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From r.vandermeij at donders.ru.nl Wed Sep 19 11:20:12 2012 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Wed, 19 Sep 2012 11:20:12 +0200 Subject: [FieldTrip] Question of implementing Fieldtrip In-Reply-To: <201209190328.q8J3SNa4008385@melipona.ucdavis.edu> References: <201209190328.q8J3SNa4008385@melipona.ucdavis.edu> Message-ID: Hi Jinghao, I forwarded your question to the Fieldtrip mailing list. I don't entirely understand what you mean only saving clusters with psychological meaning. Given the parameters that you chose, you get a certain number of clusters, all of which are significant as a whole. In analogy, this means that the whole 'mountain range' is significant or not, not the 'individual peaks'. You could of course focus on a few of those clusters in your report, as long as you mention the other clusters. You could also try to set your parameters a little more stringent (i.e. a lower cfg.clusteralpha), this would 'reduce the number of peaks in your mountain range', as some peaks would then fall below the threshold. Hopefully, your clusters with 'psychological meaning' would still show up, albeit a little smaller/shorter. Hope this helps, Roemer > Well in fact I'm doing an intracranial EEG project currently where the data > should be analyzed statistically. The permutation analysis seems a good > choice and first I ran it with sample-specific independent t-test to get a > rough idea of the data in different conditions. > > I'm wondering how to apply cluster-based permutation in single sensor > analysis where I would like to save only the time clusters with > psychological meaning. I could not find the guidance of how to do this in > Fieldtrip. Could you please share with me the approach? That'll be really > helpful. > > Best Regards, > Jinghao Lu > > > Dept. of Physics > Zhejiang University > 866 Yuhangtang Road > Hangzhou > 310058 ZHEJIANG > CHINA > > Temporary Affiliate > Dynamic Memory Lab > UC Davis > > > Jinghao Lu > > > Dept. of Physics > Zhejiang University > 866 Yuhangtang Road > Hangzhou > 310058 ZHEJIANG > CHINA > > Temporary Affiliate > Dynamic Memory Lab > UC Davis > -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From politzerahless at gmail.com Wed Sep 19 13:46:19 2012 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Wed, 19 Sep 2012 06:46:19 -0500 Subject: [FieldTrip] Question of implementing Fieldtrip Message-ID: Hi Jinghao, You can use cfg.latency to limit the time period in which the test will look for clusters (for example, if you expect a difference to show up in a particular small time window and you are only interested in that difference, and don't want to test earlier or later differences); the tutorial has some more information. The choice of time window should be made based on predictions you had before the experiment, not based on inspection of the data. But like Roemer points out, it's not possible to save "only clusters with psychological meaning", as the statistical test doesn't know whether or not clusters have psychological meaning. Best, Steve > Message: 2 > Date: Wed, 19 Sep 2012 11:20:12 +0200 > From: Roemer van der Meij > To: Email discussion list for the FieldTrip project > > Cc: Jinghao Lu > Subject: Re: [FieldTrip] Question of implementing Fieldtrip > Message-ID: > < > CA+WpQ37dfrEoQV4gLuVTHWbMrBKexo8HFRprSJ9d5t8w45ZvYg at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Jinghao, > > I forwarded your question to the Fieldtrip mailing list. I don't entirely > understand what you mean only saving clusters with psychological meaning. > Given the parameters that you chose, you get a certain number of clusters, > all of which are significant as a whole. In analogy, this means that the > whole 'mountain range' is significant or not, not the 'individual peaks'. > You could of course focus on a few of those clusters in your report, as > long as you mention the other clusters. You could also try to set your > parameters a little more stringent (i.e. a lower cfg.clusteralpha), this > would 'reduce the number of peaks in your mountain range', as some peaks > would then fall below the threshold. Hopefully, your clusters with > 'psychological meaning' would still show up, albeit a little > smaller/shorter. > > Hope this helps, > Roemer > > > > > > Well in fact I'm doing an intracranial EEG project currently where the > data > > should be analyzed statistically. The permutation analysis seems a good > > choice and first I ran it with sample-specific independent t-test to get > a > > rough idea of the data in different conditions. > > > > I'm wondering how to apply cluster-based permutation in single sensor > > analysis where I would like to save only the time clusters with > > psychological meaning. I could not find the guidance of how to do this in > > Fieldtrip. Could you please share with me the approach? That'll be really > > helpful. > > > > Best Regards, > > Jinghao Lu > > > > > > Dept. of Physics > > Zhejiang University > > 866 Yuhangtang Road > > Hangzhou > > 310058 ZHEJIANG > > CHINA > > > > Temporary Affiliate > > Dynamic Memory Lab > > UC Davis > > > > > > Jinghao Lu > > > > > > Dept. of Physics > > Zhejiang University > > 866 Yuhangtang Road > > Hangzhou > > 310058 ZHEJIANG > > CHINA > > > > Temporary Affiliate > > Dynamic Memory Lab > > UC Davis > > > > > > -- > Roemer van der Meij M.Sc. > PhD student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > Tel: +31(0)24 3655932 > E-mail: r.vandermeij at donders.ru.nl > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120919/bc3080b9/attachment-0001.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 22, Issue 35 > ***************************************** > -- Stephen Politzer-Ahles University of Kansas Linguistics Department http://www.linguistics.ku.edu/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From haiteng.jiang at gmail.com Wed Sep 19 15:39:15 2012 From: haiteng.jiang at gmail.com (Haiteng Jiang) Date: Wed, 19 Sep 2012 15:39:15 +0200 Subject: [FieldTrip] Problems plotting TFR with different frequency sacle Message-ID: Dear Fieldtripers , I try to plot the TFR with Fieldtrip , but I find the frequency shift in the plotting when I use different frequency scale. Please see the attached two examples (4-30Hz versus 4-100Hz). The TFR within 4-30Hz is centered in alpha band while it is switched to beta band with the 4-100Hz. scale . Regarding to the TFR, I calculate it by using an adaptive sliding time window of four cycles length (Δt = 4/f) and a Hanning taper for lower frequencies (4–30 Hz), and a sliding time window of fixed length (200ms) and three orthogonal Slepian tapers resulting in ±10 Hz smoothing (29) for higher frequencies (30–100 Hz). Any suggestion ? All the best, Haiteng -- Haiteng Jiang PhD candidate Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Visiting address Room 2.32 Donders Centre for Cognitive Neuroimaging Kapittelweg 29 6525 EN Nijmegen the Netherlands Tel.: +31 (0)243668291 Web: https://sites.google.com/site/haitengjiang/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TFR_4-30.jpg Type: image/jpeg Size: 84855 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TFR_4-100.jpg Type: image/jpeg Size: 76534 bytes Desc: not available URL: From r.vandermeij at donders.ru.nl Wed Sep 19 16:04:19 2012 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Wed, 19 Sep 2012 16:04:19 +0200 Subject: [FieldTrip] Question of implementing Fieldtrip In-Reply-To: <201209191150.q8JBoQsp022660@phaenicia.ucdavis.edu> References: <201209191150.q8JBoQsp022660@phaenicia.ucdavis.edu> Message-ID: Hi Jinghao, If you are talking about only looking at a single channel and using those for analyses, you can use cfg.channel for this purpose. It might be a good idea as well to run through the respective tutorial, which can be found at: http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock. My previous suggestion will also aid in reducing small clusters popping up. Best, Roemer On Wed, Sep 19, 2012 at 1:50 PM, Jinghao Lu wrote: > > > As for my question, what I mean is that I want to apply the cluster-based > permutation on the data from a single intracranial electrode just like what > Maris did in his paper 'Nonparametric statistical testing of EEG- and MEG- > data'. In this way, the scattered clusters will reduce to only several. > Some discrete sample with significant difference may disappear as well. > > In Fieldtrip, if I choose cfg.correctm = 'cluster', then a neighborhood is > required. However, I only have one electrode and want to apply it on > time(or further frequency). How can I set cfg? > > -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Wed Sep 19 16:07:09 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 19 Sep 2012 16:07:09 +0200 Subject: [FieldTrip] Problems plotting TFR with different frequency sacle In-Reply-To: References: Message-ID: <5059D18D.4070705@donders.ru.nl> Hi Haiteng, I'm gonna drop by since you are in the office next door ;) Best, Jörn On 9/19/2012 3:39 PM, Haiteng Jiang wrote: > Dear Fieldtripers , > I try to plot the TFR with Fieldtrip , but I find the frequency > shift in the plotting when I use different frequency scale. Please > see the attached two examples (4-30Hz versus 4-100Hz). The TFR within > 4-30Hz is centered in alpha band while it is switched to beta band > with the 4-100Hz. scale . Regarding to the TFR, I calculate it by > using an adaptive sliding time window of four cycles length (?t = 4/f) > and a Hanning taper for lower frequencies (4--30 Hz), and a sliding > time window of fixed length (200ms) and three orthogonal Slepian > tapers resulting in ±10 Hz smoothing (29) for higher frequencies > (30--100 Hz). > Any suggestion ? > All the best, > Haiteng > -- > Haiteng Jiang > PhD candidate > Neuronal Oscillations Group > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > > Visiting address > Room 2.32 > Donders Centre for Cognitive Neuroimaging > Kapittelweg 29 > 6525 EN Nijmegen > the Netherlands > > Tel.: +31 (0)243668291 > Web: https://sites.google.com/site/haitengjiang/ > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From Markus.Butz at uni-duesseldorf.de Wed Sep 19 16:25:33 2012 From: Markus.Butz at uni-duesseldorf.de (Markus Butz) Date: Wed, 19 Sep 2012 15:25:33 +0100 Subject: [FieldTrip] ft_checkcoordsys outdated? Message-ID: <7630d250a5f1.5059e3ed@uni-duesseldorf.de> Dear list the headmodel tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the function ft_checkcoordsys. This function is also explained here http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. However, as far as I can see it is not existent in the fieldtrip version I am using right now, ie 20111101. How come? Is it outdated or do I miss something here? Best wishes Markus -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at donders.ru.nl Wed Sep 19 18:17:43 2012 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Wed, 19 Sep 2012 18:17:43 +0200 Subject: [FieldTrip] ft_checkcoordsys outdated? In-Reply-To: <7630d250a5f1.5059e3ed@uni-duesseldorf.de> References: <7630d250a5f1.5059e3ed@uni-duesseldorf.de> Message-ID: Hi Markus, Indeed it is outdated. It has been renamed to ft_determine_coordsys and moved to utilities: http://code.google.com/p/fieldtrip/source/detail?spec=svn3219&r=3219 Thanks for spotting that on the tutorial, as it should be updated. Cheers, Johanna 2012/9/19 Markus Butz > Dear list > > the headmodel tutorial ( > http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the > function ft_checkcoordsys. > This function is also explained here > http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. > However, as far as I can see it is not existent in the fieldtrip version I > am using right now, ie 20111101. > How come? Is it outdated or do I miss something here? > > Best wishes > Markus > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Sep 19 19:06:12 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 19 Sep 2012 19:06:12 +0200 Subject: [FieldTrip] ft_checkcoordsys outdated? In-Reply-To: References: <7630d250a5f1.5059e3ed@uni-duesseldorf.de> Message-ID: ...and the good thing about a wiki is: anybody can update it! ;-) Best, Jan-Mathijs On Sep 19, 2012, at 6:17 PM, Johanna Zumer wrote: > Hi Markus, > > Indeed it is outdated. It has been renamed to ft_determine_coordsys and moved to utilities: http://code.google.com/p/fieldtrip/source/detail?spec=svn3219&r=3219 > Thanks for spotting that on the tutorial, as it should be updated. > > Cheers, > Johanna > > 2012/9/19 Markus Butz > Dear list > > the headmodel tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the function ft_checkcoordsys. > This function is also explained here http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. > However, as far as I can see it is not existent in the fieldtrip version I am using right now, ie 20111101. > How come? Is it outdated or do I miss something here? > > Best wishes > Markus > > > > > > _______________________________________________ > 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 Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jhlu at ucdavis.edu Thu Sep 20 00:29:25 2012 From: jhlu at ucdavis.edu (Jinghao Lu) Date: Wed, 19 Sep 2012 15:29:25 -0700 (PDT) Subject: [FieldTrip] problem of implementing fieldtrip Message-ID: <201209192229.q8JMTPtA023532@syrphus.ucdavis.edu> Hi Roemer, the more exact problem may be like this: 1. I used eeglab to do all the erps and time-frequency and then used 'eeglab2fieldtrip(preprocessing, which seems the only way)' 2. then ran ft_timelockanalysis to generate erps, with cfg.channel = {'naLeft1'}(only one channel) 3. ran permutation with cfg.correctm = 'cluster' and subsequent cfg settings. However, an error message came out saying: "Error using ==> statistics_wrapper at 249 You need to specify a neighbourstructure" Which part did I set wrong? Best, Jinghao > 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: Question of implementing Fieldtrip (Roemer van der Meij) > 2. Re: Problems plotting TFR with different frequency sacle > (J?rn M. Horschig) > 3. ft_checkcoordsys outdated? (Markus Butz) > 4. Re: ft_checkcoordsys outdated? (Johanna Zumer) > 5. Re: ft_checkcoordsys outdated? (jan-mathijs schoffelen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 19 Sep 2012 16:04:19 +0200 > From: Roemer van der Meij > To: Email discussion list for the FieldTrip project > > Subject: Re: [FieldTrip] Question of implementing Fieldtrip > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Jinghao, > > If you are talking about only looking at a single channel and using those > for analyses, you can use cfg.channel for this purpose. It might be a > good > idea as well to run through the respective tutorial, which can be found > at: http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock. > My previous suggestion will also aid in reducing small clusters popping > up. > > Best, > Roemer > > > > On Wed, Sep 19, 2012 at 1:50 PM, Jinghao Lu wrote: > > > > > > > As for my question, what I mean is that I want to apply the > cluster-based > > permutation on the data from a single intracranial electrode just like > what > > Maris did in his paper 'Nonparametric statistical testing of EEG- and > MEG- > > data'. In this way, the scattered clusters will reduce to only several. > > Some discrete sample with significant difference may disappear as well. > > > > In Fieldtrip, if I choose cfg.correctm = 'cluster', then a neighborhood > is > > required. However, I only have one electrode and want to apply it on > > time(or further frequency). How can I set cfg? > > > > > -- > Roemer van der Meij M.Sc. > PhD student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > Tel: +31(0)24 3655932 > E-mail: r.vandermeij at donders.ru.nl > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Message: 2 > Date: Wed, 19 Sep 2012 16:07:09 +0200 > From: "J?rn M. Horschig" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Problems plotting TFR with different > frequency sacle > Message-ID: <5059D18D.4070705 at donders.ru.nl> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hi Haiteng, > > I'm gonna drop by since you are in the office next door ;) > > Best, > J?rn > > On 9/19/2012 3:39 PM, Haiteng Jiang wrote: > > Dear Fieldtripers , > > I try to plot the TFR with Fieldtrip , but I find the frequency > > shift in the plotting when I use different frequency scale. Please > > see the attached two examples (4-30Hz versus 4-100Hz). The TFR within > > 4-30Hz is centered in alpha band while it is switched to beta band > > with the 4-100Hz. scale . Regarding to the TFR, I calculate it by > > using an adaptive sliding time window of four cycles length (?t = 4/f) > > and a Hanning taper for lower frequencies (4--30 Hz), and a sliding > > time window of fixed length (200ms) and three orthogonal Slepian > > tapers resulting in ?10 Hz smoothing (29) for higher frequencies > > (30--100 Hz). > > Any suggestion ? > > All the best, > > Haiteng > > -- > > Haiteng Jiang > > PhD candidate > > Neuronal Oscillations Group > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > > > Visiting address > > Room 2.32 > > Donders Centre for Cognitive Neuroimaging > > Kapittelweg 29 > > 6525 EN Nijmegen > > the Netherlands > > > > Tel.: +31 (0)243668291 > > Web: https://sites.google.com/site/haitengjiang/ > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > J?rn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Message: 3 > Date: Wed, 19 Sep 2012 15:25:33 +0100 > From: Markus Butz > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] ft_checkcoordsys outdated? > Message-ID: <7630d250a5f1.5059e3ed at uni-duesseldorf.de> > Content-Type: text/plain; charset="us-ascii" > > Dear list > > the headmodel tutorial > (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the > function ft_checkcoordsys. > This function is also explained here > http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. > However, as far as I can see it is not existent in the fieldtrip version I > am using right now, ie 20111101. > How come? Is it outdated or do I miss something here? > > Best wishes > Markus > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Message: 4 > Date: Wed, 19 Sep 2012 18:17:43 +0200 > From: Johanna Zumer > To: Markus.Butz at uni-duesseldorf.de, FieldTrip discussion list > > Subject: Re: [FieldTrip] ft_checkcoordsys outdated? > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Markus, > > Indeed it is outdated. It has been renamed to ft_determine_coordsys and > moved to utilities: > http://code.google.com/p/fieldtrip/source/detail?spec=svn3219&r=3219 > Thanks for spotting that on the tutorial, as it should be updated. > > Cheers, > Johanna > > 2012/9/19 Markus Butz > > > Dear list > > > > the headmodel tutorial ( > > http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the > > function ft_checkcoordsys. > > This function is also explained here > > http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. > > However, as far as I can see it is not existent in the fieldtrip version > I > > am using right now, ie 20111101. > > How come? Is it outdated or do I miss something here? > > > > Best wishes > > Markus > > > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Message: 5 > Date: Wed, 19 Sep 2012 19:06:12 +0200 > From: jan-mathijs schoffelen > To: FieldTrip discussion list > Subject: Re: [FieldTrip] ft_checkcoordsys outdated? > Message-ID: > Content-Type: text/plain; charset="us-ascii" > > ...and the good thing about a wiki is: anybody can update it! ;-) > > Best, > Jan-Mathijs > > > On Sep 19, 2012, at 6:17 PM, Johanna Zumer wrote: > > > Hi Markus, > > > > Indeed it is outdated. It has been renamed to ft_determine_coordsys and > moved to utilities: > http://code.google.com/p/fieldtrip/source/detail?spec=svn3219&r=3219 > > Thanks for spotting that on the tutorial, as it should be updated. > > > > Cheers, > > Johanna > > > > 2012/9/19 Markus Butz > > Dear list > > > > the headmodel tutorial > (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the > function ft_checkcoordsys. > > This function is also explained here > http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. > > However, as far as I can see it is not existent in the fieldtrip version > I am using right now, ie 20111101. > > How come? Is it outdated or do I miss something here? > > > > Best wishes > > Markus > > > > > > > > > > > > _______________________________________________ > > 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 > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 22, Issue 37 > ***************************************** > Jinghao Lu Dept. of Physics Zhejiang University 866 Yuhangtang Road Hangzhou 310058 ZHEJIANG CHINA Temporary Affiliate Dynamic Memory Lab UC Davis From dmitri89 at ut.ee Thu Sep 20 09:54:59 2012 From: dmitri89 at ut.ee (Dmitri Filimonov) Date: Thu, 20 Sep 2012 10:54:59 +0300 Subject: [FieldTrip] channel repair script In-Reply-To: <50584E19.3090300@donders.ru.nl> References: <259e43dd8af0ecf135e3965765705a76.squirrel@mailhost.ut.ee> <50584E19.3090300@donders.ru.nl> Message-ID: Dear Jörn, Thank you for answering, but unfortunately it doesn't work anyway. I tried that also. It always gives "The field cfg.method is required" I've put several possible cfg.methods = *(like cfg.method = 'mtmfft' (in case if program wants me to set spectra calculating parameters); or 'nearest' (in case of neighbour selection method). Non of this works, yet I am trying to deal with it now. Best wishes, Dmitri > Dear Dmitri, > > I think you are confusing things here. > Note that you are calling two FieldTrip functions subsequently. The > error message you are receiving results from ft_prepare_neighbours. > ft_prepare_neighbours needs a different cfg than ft_channelrepair. The > call you are making, does however not make much sense, because you > already called that function a few lines before. So just drop that > cfg.neighbours = ft_prepare_neighbours(...) line and replace it by > cfg.neighbours = neighbours. Thereby, you are removing the function call > that results in an error (and you already did that call), and I guess > everything will work fine. > > Best, > Jörn > > On 9/18/2012 10:00 AM, Dmitri Filimonov wrote: >> Dear Sir/Madam, >> >> My name is Dmitri Filimonov, I am a master student in University of >> Tartu >> (Estonia), using fieldtrip for EEG data analysis. I would like to ask >> some >> assistance with fieldtrip script. >> The task is to repair some EEG channels, so need to use >> ft_channelrepair. >> And I tried to do that after artifact rejection, so I could first see, >> which channels are noisy or disabled. I tried multiple combinations, yet >> there are still problems with the script. >> It looks like: >> >>>> channels_to_repair={'Fp1', 'Fp2'}; >> layout_file=('C:\ fieldtrip-20120703\template\layout\EEG1010.lay'); >> >> cfg=[]; >> cfg.layout = 'EEG1010.lay'; >> data.elec = ft_prepare_layout(cfg); >> neighbours = ft_prepare_neighbours(cfg, good_data) >> cfg = ft_checkconfig(cfg, 'required', {'method'}); >> cfg.method = 'distance'; (or ‘nearest’) >> cfg.badchannel=channels_to_repair; >> cfg.neighbours = ft_prepare_neighbours (cfg, good_data); >> G_data = ft_channelrepair(cfg, dood_data); >> (Good_data –is a processed and filtered data, yet containing channels, >> which have to be repaired.) >> After processing the program gives me several errors: >> >> reading layout from file EEG1010.lay >> the call to "ft_prepare_layout" took 0 seconds and an estimated NaN MB >> ??? Error using ==> ft_checkconfig at 151 >> The field cfg.method is required >> Error in ==> ft_prepare_neighbours at 77 >> cfg = ft_checkconfig(cfg, 'required', {'method'}); >> >> Other combinations emerge similar errors, or >> >> Error in ==> ft_neighbourselection at 30 >> neighbours = ft_prepare_neighbours(varargin{:}); >> >> Can you give me some help, what kind of ‘method’ exactly program wants >> me >> to mention (type)? >> >> Yours sincerely, >> Dmitri >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Thu Sep 20 09:59:27 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 20 Sep 2012 09:59:27 +0200 Subject: [FieldTrip] problem of implementing fieldtrip In-Reply-To: <201209192229.q8JMTPtA023532@syrphus.ucdavis.edu> References: <201209192229.q8JMTPtA023532@syrphus.ucdavis.edu> Message-ID: <505ACCDF.6020100@donders.ru.nl> Dear Jinghao, you need to specify cfg.avgoverchan='yes' prior to calling ft_timelockstatistics to tell fieldtrip that no clustering in space is needed. It should work fine then. Best, Jörn On 9/20/2012 12:29 AM, Jinghao Lu wrote: > Hi Roemer, > > the more exact problem may be like this: > > 1. I used eeglab to do all the erps and time-frequency and then used > 'eeglab2fieldtrip(preprocessing, which seems the only way)' > > 2. then ran ft_timelockanalysis to generate erps, with cfg.channel = > {'naLeft1'}(only one channel) > > 3. ran permutation with cfg.correctm = 'cluster' and subsequent cfg > settings. However, an error message came out saying: > > > "Error using ==> statistics_wrapper at 249 > You need to specify a neighbourstructure" > > Which part did I set wrong? > > Best, > Jinghao > > > > > >> 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: Question of implementing Fieldtrip (Roemer van der Meij) >> 2. Re: Problems plotting TFR with different frequency sacle >> (J?rn M. Horschig) >> 3. ft_checkcoordsys outdated? (Markus Butz) >> 4. Re: ft_checkcoordsys outdated? (Johanna Zumer) >> 5. Re: ft_checkcoordsys outdated? (jan-mathijs schoffelen) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Wed, 19 Sep 2012 16:04:19 +0200 >> From: Roemer van der Meij >> To: Email discussion list for the FieldTrip project >> >> Subject: Re: [FieldTrip] Question of implementing Fieldtrip >> Message-ID: >> XXYb5Wb0vcyG_j=8g at mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi Jinghao, >> >> If you are talking about only looking at a single channel and using those >> for analyses, you can use cfg.channel for this purpose. It might be a >> good >> idea as well to run through the respective tutorial, which can be found >> at: http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock. >> My previous suggestion will also aid in reducing small clusters popping >> up. >> >> Best, >> Roemer >> >> >> >> On Wed, Sep 19, 2012 at 1:50 PM, Jinghao Lu wrote: >> >>> >>> As for my question, what I mean is that I want to apply the >> cluster-based >>> permutation on the data from a single intracranial electrode just like >> what >>> Maris did in his paper 'Nonparametric statistical testing of EEG- and >> MEG- >>> data'. In this way, the scattered clusters will reduce to only several. >>> Some discrete sample with significant difference may disappear as well. >>> >>> In Fieldtrip, if I choose cfg.correctm = 'cluster', then a neighborhood >> is >>> required. However, I only have one electrode and want to apply it on >>> time(or further frequency). How can I set cfg? >>> >>> >> -- >> Roemer van der Meij M.Sc. >> PhD student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognition >> P.O. Box 9104 >> 6500 HE Nijmegen >> The Netherlands >> Tel: +31(0)24 3655932 >> E-mail: r.vandermeij at donders.ru.nl >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> > 56cf/attachment-0001.html> >> ------------------------------ >> >> Message: 2 >> Date: Wed, 19 Sep 2012 16:07:09 +0200 >> From: "J?rn M. Horschig" >> To: FieldTrip discussion list >> Subject: Re: [FieldTrip] Problems plotting TFR with different >> frequency sacle >> Message-ID: <5059D18D.4070705 at donders.ru.nl> >> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" >> >> Hi Haiteng, >> >> I'm gonna drop by since you are in the office next door ;) >> >> Best, >> J?rn >> >> On 9/19/2012 3:39 PM, Haiteng Jiang wrote: >>> Dear Fieldtripers , >>> I try to plot the TFR with Fieldtrip , but I find the frequency >>> shift in the plotting when I use different frequency scale. Please >>> see the attached two examples (4-30Hz versus 4-100Hz). The TFR within >>> 4-30Hz is centered in alpha band while it is switched to beta band >>> with the 4-100Hz. scale . Regarding to the TFR, I calculate it by >>> using an adaptive sliding time window of four cycles length (?t = 4/f) >>> and a Hanning taper for lower frequencies (4--30 Hz), and a sliding >>> time window of fixed length (200ms) and three orthogonal Slepian >>> tapers resulting in ?10 Hz smoothing (29) for higher frequencies >>> (30--100 Hz). >>> Any suggestion ? >>> All the best, >>> Haiteng >>> -- >>> Haiteng Jiang >>> PhD candidate >>> Neuronal Oscillations Group >>> Donders Institute for Brain, Cognition and Behaviour >>> Centre for Cognitive Neuroimaging >>> Radboud University Nijmegen >>> >>> Visiting address >>> Room 2.32 >>> Donders Centre for Cognitive Neuroimaging >>> Kapittelweg 29 >>> 6525 EN Nijmegen >>> the Netherlands >>> >>> Tel.: +31 (0)243668291 >>> Web: https://sites.google.com/site/haitengjiang/ >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> -- >> J?rn M. Horschig >> PhD Student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> Neuronal Oscillations Group >> FieldTrip Development Team >> >> P.O. Box 9101 >> NL-6500 HB Nijmegen >> The Netherlands >> >> Contact: >> E-Mail: jm.horschig at donders.ru.nl >> Tel: +31-(0)24-36-68493 >> Web: http://www.ru.nl/donders >> >> Visiting address: >> Trigon, room 2.30 >> Kapittelweg 29 >> NL-6525 EN Nijmegen >> The Netherlands >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> > dfd7/attachment-0001.html> >> ------------------------------ >> >> Message: 3 >> Date: Wed, 19 Sep 2012 15:25:33 +0100 >> From: Markus Butz >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] ft_checkcoordsys outdated? >> Message-ID: <7630d250a5f1.5059e3ed at uni-duesseldorf.de> >> Content-Type: text/plain; charset="us-ascii" >> >> Dear list >> >> the headmodel tutorial >> (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the >> function ft_checkcoordsys. >> This function is also explained here >> http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. >> However, as far as I can see it is not existent in the fieldtrip version > I >> am using right now, ie 20111101. >> How come? Is it outdated or do I miss something here? >> >> Best wishes >> Markus >> >> >> >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> > 9565/attachment-0001.html> >> ------------------------------ >> >> Message: 4 >> Date: Wed, 19 Sep 2012 18:17:43 +0200 >> From: Johanna Zumer >> To: Markus.Butz at uni-duesseldorf.de, FieldTrip discussion list >> >> Subject: Re: [FieldTrip] ft_checkcoordsys outdated? >> Message-ID: >> 8FHxUvcAhG0Or35B=Ow at mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi Markus, >> >> Indeed it is outdated. It has been renamed to ft_determine_coordsys and >> moved to utilities: >> http://code.google.com/p/fieldtrip/source/detail?spec=svn3219&r=3219 >> Thanks for spotting that on the tutorial, as it should be updated. >> >> Cheers, >> Johanna >> >> 2012/9/19 Markus Butz >> >>> Dear list >>> >>> the headmodel tutorial ( >>> http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the >>> function ft_checkcoordsys. >>> This function is also explained here >>> http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. >>> However, as far as I can see it is not existent in the fieldtrip > version >> I >>> am using right now, ie 20111101. >>> How come? Is it outdated or do I miss something here? >>> >>> Best wishes >>> Markus >>> >>> >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> > 1c05/attachment-0001.html> >> ------------------------------ >> >> Message: 5 >> Date: Wed, 19 Sep 2012 19:06:12 +0200 >> From: jan-mathijs schoffelen >> To: FieldTrip discussion list >> Subject: Re: [FieldTrip] ft_checkcoordsys outdated? >> Message-ID: >> Content-Type: text/plain; charset="us-ascii" >> >> ...and the good thing about a wiki is: anybody can update it! ;-) >> >> Best, >> Jan-Mathijs >> >> >> On Sep 19, 2012, at 6:17 PM, Johanna Zumer wrote: >> >>> Hi Markus, >>> >>> Indeed it is outdated. It has been renamed to ft_determine_coordsys > and >> moved to utilities: >> http://code.google.com/p/fieldtrip/source/detail?spec=svn3219&r=3219 >>> Thanks for spotting that on the tutorial, as it should be updated. >>> >>> Cheers, >>> Johanna >>> >>> 2012/9/19 Markus Butz >>> Dear list >>> >>> the headmodel tutorial >> (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the >> function ft_checkcoordsys. >>> This function is also explained here >> http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys. >>> However, as far as I can see it is not existent in the fieldtrip > version >> I am using right now, ie 20111101. >>> How come? Is it outdated or do I miss something here? >>> >>> Best wishes >>> Markus >>> >>> >>> >>> >>> >>> _______________________________________________ >>> 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 >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> > 674f/attachment.html> >> ------------------------------ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> End of fieldtrip Digest, Vol 22, Issue 37 >> ***************************************** >> > Jinghao Lu > > > Dept. of Physics > Zhejiang University > 866 Yuhangtang Road > Hangzhou > 310058 ZHEJIANG > CHINA > > Temporary Affiliate > Dynamic Memory Lab > UC Davis > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From jm.horschig at donders.ru.nl Thu Sep 20 10:09:53 2012 From: jm.horschig at donders.ru.nl (=?UTF-8?B?IkrDtnJuIE0uIEhvcnNjaGlnIg==?=) Date: Thu, 20 Sep 2012 10:09:53 +0200 Subject: [FieldTrip] channel repair script In-Reply-To: References: <259e43dd8af0ecf135e3965765705a76.squirrel@mailhost.ut.ee> <50584E19.3090300@donders.ru.nl> Message-ID: <505ACF51.4040706@donders.ru.nl> Hi Dmitri, looking at your script it seems that the error occurs even right at the start. You said you are doing this (the very first lines that you pasted) cfg=[]; cfg.layout = 'EEG1010.lay'; data.elec = ft_prepare_layout(cfg); neighbours = ft_prepare_neighbours(cfg, good_data) which means that you call ft_prepare_neighbours with a configuration structure which only has cfg.layout and nothing else. However, you did not specify a method how neighbours should be defined. If you look up the help from ft_prepare_neighbours, you will see what methods are available. Note that these are distinct from cfg.method for other functions. Every function has it's own cfg-settings, which are mostly independent from those of other functions. For example 'nearest' is not an method for ft_prepare_neighbours but for ft_channelrepair. Likewise, 'mtmfft' is a method for ft_freqanalysis, but not for any other method. I would strongly advise you to start with FieldTrip by going through our tutorials: http://fieldtrip.fcdonders.nl/tutorial This is the easiest way to get acquainted and used to the way FieldTrip works with cfg-and data-structures. And then check our frequently asked questions: http://fieldtrip.fcdonders.nl/faq In your case, especially http://fieldtrip.fcdonders.nl/faq/how_can_i_define_neighbouring_sensors http://fieldtrip.fcdonders.nl/faq/how_does_ft_prepare_neighbours_work Should you need any more assistance, feel free to ask. Best, Jörn On 9/20/2012 9:54 AM, Dmitri Filimonov wrote: > Dear Jörn, > > Thank you for answering, but unfortunately it doesn't work anyway. I tried > that also. It always gives > > "The field cfg.method is required" > > I've put several possible cfg.methods = *(like cfg.method = 'mtmfft' (in > case if program wants me to set spectra calculating parameters); or > 'nearest' (in case of neighbour selection method). Non of this works, yet > I am trying to deal with it now. > > Best wishes, > Dmitri > > > > >> Dear Dmitri, >> >> I think you are confusing things here. >> Note that you are calling two FieldTrip functions subsequently. The >> error message you are receiving results from ft_prepare_neighbours. >> ft_prepare_neighbours needs a different cfg than ft_channelrepair. The >> call you are making, does however not make much sense, because you >> already called that function a few lines before. So just drop that >> cfg.neighbours = ft_prepare_neighbours(...) line and replace it by >> cfg.neighbours = neighbours. Thereby, you are removing the function call >> that results in an error (and you already did that call), and I guess >> everything will work fine. >> >> Best, >> Jörn >> >> On 9/18/2012 10:00 AM, Dmitri Filimonov wrote: >>> Dear Sir/Madam, >>> >>> My name is Dmitri Filimonov, I am a master student in University of >>> Tartu >>> (Estonia), using fieldtrip for EEG data analysis. I would like to ask >>> some >>> assistance with fieldtrip script. >>> The task is to repair some EEG channels, so need to use >>> ft_channelrepair. >>> And I tried to do that after artifact rejection, so I could first see, >>> which channels are noisy or disabled. I tried multiple combinations, yet >>> there are still problems with the script. >>> It looks like: >>> >>>>> channels_to_repair={'Fp1', 'Fp2'}; >>> layout_file=('C:\ fieldtrip-20120703\template\layout\EEG1010.lay'); >>> >>> cfg=[]; >>> cfg.layout = 'EEG1010.lay'; >>> data.elec = ft_prepare_layout(cfg); >>> neighbours = ft_prepare_neighbours(cfg, good_data) >>> cfg = ft_checkconfig(cfg, 'required', {'method'}); >>> cfg.method = 'distance'; (or ‘nearest’) >>> cfg.badchannel=channels_to_repair; >>> cfg.neighbours = ft_prepare_neighbours (cfg, good_data); >>> G_data = ft_channelrepair(cfg, dood_data); >>> (Good_data –is a processed and filtered data, yet containing channels, >>> which have to be repaired.) >>> After processing the program gives me several errors: >>> >>> reading layout from file EEG1010.lay >>> the call to "ft_prepare_layout" took 0 seconds and an estimated NaN MB >>> ??? Error using ==> ft_checkconfig at 151 >>> The field cfg.method is required >>> Error in ==> ft_prepare_neighbours at 77 >>> cfg = ft_checkconfig(cfg, 'required', {'method'}); >>> >>> Other combinations emerge similar errors, or >>> >>> Error in ==> ft_neighbourselection at 30 >>> neighbours = ft_prepare_neighbours(varargin{:}); >>> >>> Can you give me some help, what kind of ‘method’ exactly program wants >>> me >>> to mention (type)? >>> >>> Yours sincerely, >>> Dmitri >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> -- >> Jörn M. Horschig >> PhD Student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> Neuronal Oscillations Group >> FieldTrip Development Team >> >> P.O. Box 9101 >> NL-6500 HB Nijmegen >> The Netherlands >> >> Contact: >> E-Mail: jm.horschig at donders.ru.nl >> Tel: +31-(0)24-36-68493 >> Web: http://www.ru.nl/donders >> >> Visiting address: >> Trigon, room 2.30 >> Kapittelweg 29 >> NL-6525 EN Nijmegen >> The Netherlands >> >> _______________________________________________ >> 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 -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From b.reuderink at donders.ru.nl Thu Sep 20 11:16:27 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Thu, 20 Sep 2012 11:16:27 +0200 Subject: [FieldTrip] ft_realtime_selectiveaverage In-Reply-To: References: Message-ID: Dear Hamza, I guess that the function is trying to samples form the FieldTrip buffer form the period before it was started, i.e. samples with negative indices. This might be related to the triggers you have and your trial fun. Your best bet is to start the MATLAB debugger, and just step through the code until the error occurs. Inspection of variables might give a clue on what is happening. In the mean-time, I'll try to update the examples with some extra information on how to call these functions. Best regards, Boris -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl On 13 sep. 2012, at 11:19, Hamza Fawzi Altakroury (Student) wrote: > Hello, > > I am tried to run the ft_realtime_selectiveaverage function but I got the following error: > (note: the error appears after showing a plot with title: condition 255, ntrials = 1.) > > Could you tell me what is the problem. (exactly what does "connet read data before the begin of the file"). > > Best, > > ??? Error using ==> ft_read_data at 243 > cannot read data before the begin of the file > > Error in ==> ft_realtime_selectiveaverage at 94 > dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', chanindx, 'checkboundary', false); > > Error in ==> online1 at 48 > ft_realtime_selectiveaverage(cfg) > > Statements: > > cfg = []; > cfg.channel = {'A1'}; > cfg.dataset = 'buffer://localhost:1972'; > %cfg.trialfun = 'myfun'; > cfg.trialdef.eventtype = 'stimulus'; % By placing '?' we can see the eventtype that we have. > cfg.trialdef.eventvalue = 255; > cfg.trialdef.pre = 0; > cfg.trialdef.post = 1.0; > cfg = ft_definetrial(cfg); > ft_realtime_selectiveaverage(cfg) > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From hamzaf at sabanciuniv.edu Thu Sep 20 11:29:48 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Thu, 20 Sep 2012 12:29:48 +0300 Subject: [FieldTrip] ft_realtime_selectiveaverage In-Reply-To: References: Message-ID: Thank you Boris Best, Hamza On Thu, Sep 20, 2012 at 12:16 PM, Boris Reuderink wrote: > Dear Hamza, > > I guess that the function is trying to samples form the FieldTrip buffer > form the period before it was started, i.e. samples with negative indices. > This might be related to the triggers you have and your trial fun. > > Your best bet is to start the MATLAB debugger, and just step through the > code until the error occurs. Inspection of variables might give a clue on > what is happening. > > In the mean-time, I'll try to update the examples with some extra > information on how to call these functions. > > Best regards, > > Boris > > -- > twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl > > On 13 sep. 2012, at 11:19, Hamza Fawzi Altakroury (Student) < > hamzaf at sabanciuniv.edu> wrote: > > > Hello, > > > > I am tried to run the ft_realtime_selectiveaverage function but I got > the following error: > > (note: the error appears after showing a plot with title: condition 255, > ntrials = 1.) > > > > Could you tell me what is the problem. (exactly what does "connet read > data before the begin of the file"). > > > > Best, > > > > ??? Error using ==> ft_read_data at 243 > > cannot read data before the begin of the file > > > > Error in ==> ft_realtime_selectiveaverage at 94 > > dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', > begsample, 'endsample', endsample, 'chanindx', chanindx, 'checkboundary', > false); > > > > Error in ==> online1 at 48 > > ft_realtime_selectiveaverage(cfg) > > > > Statements: > > > > cfg = []; > > cfg.channel = {'A1'}; > > cfg.dataset = 'buffer://localhost:1972'; > > %cfg.trialfun = 'myfun'; > > cfg.trialdef.eventtype = 'stimulus'; % By placing '?' we > can see the eventtype that we have. > > cfg.trialdef.eventvalue = 255; > > cfg.trialdef.pre = 0; > > cfg.trialdef.post = 1.0; > > cfg = ft_definetrial(cfg); > > ft_realtime_selectiveaverage(cfg) > > > > -- > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabancı University > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Thu Sep 20 14:46:17 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 20 Sep 2012 14:46:17 +0200 Subject: [FieldTrip] Problems plotting TFR with different frequency sacle In-Reply-To: <5059D18D.4070705@donders.ru.nl> References: <5059D18D.4070705@donders.ru.nl> Message-ID: <505B1019.2050904@donders.ru.nl> For those having similar problems, note that FieldTrip (actually Matlab's image function) cannot handle unequal axis, e.g. a data.freq may not be [1 2 3 4 5 10 15 20]. Therefore, ladies and gentlemen, let me introduce bug number 1729: http://bugzilla.fcdonders.nl/show_bug.cgi?id=1729 On 9/19/2012 4:07 PM, "Jörn M. Horschig" wrote: > Hi Haiteng, > > I'm gonna drop by since you are in the office next door ;) > > Best, > Jörn > > On 9/19/2012 3:39 PM, Haiteng Jiang wrote: >> Dear Fieldtripers , >> I try to plot the TFR with Fieldtrip , but I find the frequency >> shift in the plotting when I use different frequency scale. Please >> see the attached two examples (4-30Hz versus 4-100Hz). The TFR >> within 4-30Hz is centered in alpha band while it is switched to beta >> band with the 4-100Hz. scale . Regarding to the TFR, I calculate it >> by using an adaptive sliding time window of four cycles length (?t = >> 4/f) and a Hanning taper for lower frequencies (4--30 Hz), and a >> sliding time window of fixed length (200ms) and three orthogonal >> Slepian tapers resulting in ±10 Hz smoothing (29) for higher >> frequencies (30--100 Hz). >> Any suggestion ? >> All the best, >> Haiteng >> -- >> Haiteng Jiang >> PhD candidate >> Neuronal Oscillations Group >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> >> Visiting address >> Room 2.32 >> Donders Centre for Cognitive Neuroimaging >> Kapittelweg 29 >> 6525 EN Nijmegen >> the Netherlands >> >> Tel.: +31 (0)243668291 >> Web: https://sites.google.com/site/haitengjiang/ >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail:jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web:http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From pgoodin at swin.edu.au Sun Sep 23 15:14:28 2012 From: pgoodin at swin.edu.au (Peter Goodin) Date: Sun, 23 Sep 2012 13:14:28 +0000 Subject: [FieldTrip] Neuromag sensor level stats Message-ID: Hi Fieldtrippers, I'm at a stage where I'd like to do statistical analysis on my ERF neuromag data, but don't really know where to begin. I'd like to do a cluster analysis, but the tutorial material is for a CTF system. I'm using a neuromag 306 channel which complicates matters somewhat due to the different sensor types. I've searched the mailing list but can't find any solid answers / example scripts. The most pressing questions I have are: 1. Despite running the data through maxfilter and entering in the bad channels, occasionally one gets through (not the same one). I've used Fieldtrip's repairchannel function on the data, making sure to replace the channel only with like sensor neighbouring sensors. While I know this is a common method for fixing bad channels in EEG, does the same hold for MEG due to non-existent smearing of the signal? Is it best to keep the fixed channel(s) or just remove them from the stats analysis across all participants? 2. Given the three sensor types on the neuromag system, do I need to run three different cluster analyses (one for mags, one for xgrads, one for ygrads), each time specifying like sensor neighbours? Alternatively, If I'm not interested in the mags data, can I just run one using the data from the combined gradiometers? 3. When examining for group x condition effects, would I use a three row design matrix with row 1 containing group, row 2 containing participants and row 3 conditions? Thanks for any help, Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Sun Sep 23 16:49:02 2012 From: smoratti at psi.ucm.es (smoratti at psi.ucm.es) Date: Sun, 23 Sep 2012 16:49:02 +0200 Subject: [FieldTrip] Neuromag sensor level stats In-Reply-To: References: Message-ID: <2007ABA6-22AA-480F-9DC8-64BFA482CA07@psi.ucm.es> Dear Peter, I would do the stats on Magnetometers and Gradiometers separately. Use cfg.layout = 'neuromag_306mag' for magnetometers. Before using the gradiometers I would use ft_combineplanar and then use the combined planar topographies for the stats (cfg.layout = 'neuromag_306cmb'). Hope that helps, Best, Stephan ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 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 23/09/2012, a las 15:14, Peter Goodin escribió: > Hi Fieldtrippers, > > I'm at a stage where I'd like to do statistical analysis on my ERF neuromag data, but don't really know where to begin. I'd like to do a cluster analysis, but the tutorial material is for a CTF system. I'm using a neuromag 306 channel which complicates matters somewhat due to the different sensor types. I've searched the mailing list but can't find any solid answers / example scripts. > > The most pressing questions I have are: > > 1. Despite running the data through maxfilter and entering in the bad channels, occasionally one gets through (not the same one). I've used Fieldtrip's repairchannel function on the data, making sure to replace the channel only with like sensor neighbouring sensors. While I know this is a common method for fixing bad channels in EEG, does the same hold for MEG due to non-existent smearing of the signal? Is it best to keep the fixed channel(s) or just remove them from the stats analysis across all participants? > > 2. Given the three sensor types on the neuromag system, do I need to run three different cluster analyses (one for mags, one for xgrads, one for ygrads), each time specifying like sensor neighbours? Alternatively, If I'm not interested in the mags data, can I just run one using the data from the combined gradiometers? > > 3. When examining for group x condition effects, would I use a three row design matrix with row 1 containing group, row 2 containing participants and row 3 conditions? > > Thanks for any help, > > Peter > _______________________________________________ > 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 jm.horschig at donders.ru.nl Mon Sep 24 14:15:05 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 24 Sep 2012 14:15:05 +0200 Subject: [FieldTrip] Neuromag sensor level stats In-Reply-To: References: Message-ID: <50604EC9.7050705@donders.ru.nl> Dear Peter, regarding your first question, most people here at the Donders actually repair bad channels. When computing the grandaverage over subjects or doing some statistics across subjects, only those channels which are in common for all datasets are used. Thus, if having different channels damaged/rejected per subjects, you can end up with a fairly low amount of channels. But, in the end it depends pretty much on what channels you reject wrt your hypothesis, e.g. having few occipital channels while being interested in motor regions won't constitute a big problem, so no need to interpolate. I leave the question whether it's a correct thing to do up to you (imho: I wouldn't worry too much about it). Regarding your third question: In FieldTrip you can only compare two conditions directly (at least when doing cluster-based permutation testing). Also, any interaction needs to be setup manually. Best, Jörn On 9/23/2012 3:14 PM, Peter Goodin wrote: > Hi Fieldtrippers, > > I'm at a stage where I'd like to do statistical analysis on my ERF > neuromag data, but don't really know where to begin. I'd like to do a > cluster analysis, but the tutorial material is for a CTF system. I'm > using a neuromag 306 channel which complicates matters somewhat due to > the different sensor types. I've searched the mailing list but can't > find any solid answers / example scripts. > > The most pressing questions I have are: > > 1. Despite running the data through maxfilter and entering in the bad > channels, occasionally one gets through (not the same one). I've used > Fieldtrip's repairchannel function on the data, making sure to replace > the channel only with like sensor neighbouring sensors. While I know > this is a common method for fixing bad channels in EEG, does the same > hold for MEG due to non-existent smearing of the signal? Is it best to > keep the fixed channel(s) or just remove them from the stats analysis > across all participants? > > 2. Given the three sensor types on the neuromag system, do I need to > run three different cluster analyses (one for mags, one for xgrads, > one for ygrads), each time specifying like sensor neighbours? > Alternatively, If I'm not interested in the mags data, can I just run > one using the data from the combined gradiometers? > > 3. When examining for group x condition effects, would I use a three > row design matrix with row 1 containing group, row 2 containing > participants and row 3 conditions? > > Thanks for any help, > > Peter > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From f.roux at bcbl.eu Mon Sep 24 16:29:52 2012 From: f.roux at bcbl.eu (Frederic Roux) Date: Mon, 24 Sep 2012 16:29:52 +0200 (CEST) Subject: [FieldTrip] model order for autoregressive model In-Reply-To: <20f3c578-3f8d-4f9b-8ad6-337627c79057@thalamus_p> Message-ID: Dear all, i am planning to do granger causality on source space time series, and wanted to know if anyone could tell me how to find/chose the right model order when using the ft_mvaranalysis? Any help/advice would be highly appreciated! Best, Fred From sherrykhan78 at gmail.com Mon Sep 24 19:22:01 2012 From: sherrykhan78 at gmail.com (Sheraz Khan) Date: Mon, 24 Sep 2012 13:22:01 -0400 Subject: [FieldTrip] model order for autoregressive model In-Reply-To: References: <20f3c578-3f8d-4f9b-8ad6-337627c79057@thalamus_p> Message-ID: Dear Fred, It is best to use AIC or BIC to determine model. http://en.wikipedia.org/wiki/Akaike_information_criterion Sheraz On Mon, Sep 24, 2012 at 10:29 AM, Frederic Roux wrote: > Dear all, > > i am planning to do granger causality on source space > time series, and wanted to know if anyone could tell me > how to find/chose the right model order when using the > ft_mvaranalysis? > > Any help/advice would be highly appreciated! > > Best, > > Fred > > _______________________________________________ > 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 f.roux at bcbl.eu Mon Sep 24 23:17:52 2012 From: f.roux at bcbl.eu (Frederic Roux) Date: Mon, 24 Sep 2012 23:17:52 +0200 (CEST) Subject: [FieldTrip] model order for autoregressive model In-Reply-To: Message-ID: Dear Sheraz, thank you for your reply and the link. How do you obtain the AIC / BIC from the output of ft_mvaranalyis? Best, Fred ----- Original Message ----- From: "Sheraz Khan" To: "FieldTrip discussion list" Sent: Monday, September 24, 2012 7:22:01 PM Subject: Re: [FieldTrip] model order for autoregressive model Dear Fred, It is best to use AIC or BIC to determine model. http://en.wikipedia.org/wiki/Akaike_information_criterion Sheraz On Mon, Sep 24, 2012 at 10:29 AM, Frederic Roux < f.roux at bcbl.eu > wrote: BeDear all, i am planning to do granger causality on source space time series, and wanted to know if anyone could tell me how to find/chose the right model order when using the ft_mvaranalysis? Any help/advice would be highly appreciated! Best, Fred _______________________________________________ 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 pgoodin at swin.edu.au Tue Sep 25 02:37:14 2012 From: pgoodin at swin.edu.au (Peter Goodin) Date: Tue, 25 Sep 2012 00:37:14 +0000 Subject: [FieldTrip] Neuromag sensor level stats In-Reply-To: <50604EC9.7050705@donders.ru.nl> References: <50604EC9.7050705@donders.ru.nl> Message-ID: Thanks very much for the responses Stephan and Jörn! One last question if possible Jörn. In your opinion, will doing several (at the most 5) cluster based t-tests affect the validity of permutation method testing to control for multiple comparisons? Would being more conservative regarding my alpha (for example a combination of permutation AND Bonferroni) possibly alleviate this? Thanks again for the responses, Peter. From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig" Sent: Monday, 24 September 2012 10:15 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] Neuromag sensor level stats Dear Peter, regarding your first question, most people here at the Donders actually repair bad channels. When computing the grandaverage over subjects or doing some statistics across subjects, only those channels which are in common for all datasets are used. Thus, if having different channels damaged/rejected per subjects, you can end up with a fairly low amount of channels. But, in the end it depends pretty much on what channels you reject wrt your hypothesis, e.g. having few occipital channels while being interested in motor regions won't constitute a big problem, so no need to interpolate. I leave the question whether it's a correct thing to do up to you (imho: I wouldn't worry too much about it). Regarding your third question: In FieldTrip you can only compare two conditions directly (at least when doing cluster-based permutation testing). Also, any interaction needs to be setup manually. Best, Jörn On 9/23/2012 3:14 PM, Peter Goodin wrote: Hi Fieldtrippers, I'm at a stage where I'd like to do statistical analysis on my ERF neuromag data, but don't really know where to begin. I'd like to do a cluster analysis, but the tutorial material is for a CTF system. I'm using a neuromag 306 channel which complicates matters somewhat due to the different sensor types. I've searched the mailing list but can't find any solid answers / example scripts. The most pressing questions I have are: 1. Despite running the data through maxfilter and entering in the bad channels, occasionally one gets through (not the same one). I've used Fieldtrip's repairchannel function on the data, making sure to replace the channel only with like sensor neighbouring sensors. While I know this is a common method for fixing bad channels in EEG, does the same hold for MEG due to non-existent smearing of the signal? Is it best to keep the fixed channel(s) or just remove them from the stats analysis across all participants? 2. Given the three sensor types on the neuromag system, do I need to run three different cluster analyses (one for mags, one for xgrads, one for ygrads), each time specifying like sensor neighbours? Alternatively, If I'm not interested in the mags data, can I just run one using the data from the combined gradiometers? 3. When examining for group x condition effects, would I use a three row design matrix with row 1 containing group, row 2 containing participants and row 3 conditions? Thanks for any help, Peter _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From sherrykhan78 at gmail.com Tue Sep 25 02:56:51 2012 From: sherrykhan78 at gmail.com (Sheraz Khan) Date: Mon, 24 Sep 2012 20:56:51 -0400 Subject: [FieldTrip] model order for autoregressive model In-Reply-To: References: Message-ID: Please look at bsmart tutorial ( http://brain-smart.org/ ) for more detail, It has step by step procedure. fieldtrip also support bsmart based mutivariate model. Sheraz On Mon, Sep 24, 2012 at 5:17 PM, Frederic Roux wrote: > Dear Sheraz, > > thank you for your reply and the link. > > How do you obtain the AIC / BIC from > the output of ft_mvaranalyis? > > Best, > Fred > ----- Original Message ----- > From: "Sheraz Khan" > To: "FieldTrip discussion list" > Sent: Monday, September 24, 2012 7:22:01 PM > Subject: Re: [FieldTrip] model order for autoregressive model > > > Dear Fred, > > > It is best to use AIC or BIC to determine model. > > > http://en.wikipedia.org/wiki/Akaike_information_criterion > > > Sheraz > > > On Mon, Sep 24, 2012 at 10:29 AM, Frederic Roux < f.roux at bcbl.eu > wrote: > > > BeDear all, > > i am planning to do granger causality on source space > time series, and wanted to know if anyone could tell me > how to find/chose the right model order when using the > ft_mvaranalysis? > > Any help/advice would be highly appreciated! > > Best, > > Fred > > _______________________________________________ > 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 eelke.spaak at donders.ru.nl Tue Sep 25 09:21:12 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 25 Sep 2012 09:21:12 +0200 Subject: [FieldTrip] Neuromag sensor level stats In-Reply-To: References: <50604EC9.7050705@donders.ru.nl> Message-ID: Hi Peter, The cluster-based permutation test by itself is fully corrected for multiple comparisons. You mention "cluster based t-tests", but the exact test statistic (in your case, t) is irrelevant for this method. >From your comment I think you already understand this, but I thought it good to point out nonetheless :) Strictly speaking, when doing several cluster-based permutation tests, the cluster-level p-values you get out are uncorrected with respect to the several different tests, so actually I think it would be formally appropriate to correct them (with the number of cluster tests, *not* number of clusters of course), using Bonferroni or Holm-Bonferroni correction or so. I don't think this is commonly done, though. Best, Eelke On 25 September 2012 02:37, Peter Goodin wrote: > Thanks very much for the responses Stephan and Jörn! > > > > One last question if possible Jörn. In your opinion, will doing several (at > the most 5) cluster based t-tests affect the validity of permutation method > testing to control for multiple comparisons? Would being more conservative > regarding my alpha (for example a combination of permutation AND Bonferroni) > possibly alleviate this? > > > Thanks again for the responses, > > > > Peter. > > > > From: fieldtrip-bounces at science.ru.nl > [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig" > Sent: Monday, 24 September 2012 10:15 PM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Neuromag sensor level stats > > > > Dear Peter, > > regarding your first question, most people here at the Donders actually > repair bad channels. When computing the grandaverage over subjects or doing > some statistics across subjects, only those channels which are in common for > all datasets are used. Thus, if having different channels damaged/rejected > per subjects, you can end up with a fairly low amount of channels. But, in > the end it depends pretty much on what channels you reject wrt your > hypothesis, e.g. having few occipital channels while being interested in > motor regions won't constitute a big problem, so no need to interpolate. I > leave the question whether it's a correct thing to do up to you (imho: I > wouldn't worry too much about it). > > Regarding your third question: In FieldTrip you can only compare two > conditions directly (at least when doing cluster-based permutation testing). > Also, any interaction needs to be setup manually. > > Best, > Jörn > > On 9/23/2012 3:14 PM, Peter Goodin wrote: > > Hi Fieldtrippers, > > > > I'm at a stage where I'd like to do statistical analysis on my ERF neuromag > data, but don't really know where to begin. I'd like to do a cluster > analysis, but the tutorial material is for a CTF system. I'm using a > neuromag 306 channel which complicates matters somewhat due to the different > sensor types. I've searched the mailing list but can't find any solid > answers / example scripts. > > > > The most pressing questions I have are: > > > > 1. Despite running the data through maxfilter and entering in the bad > channels, occasionally one gets through (not the same one). I've used > Fieldtrip's repairchannel function on the data, making sure to replace the > channel only with like sensor neighbouring sensors. While I know this is a > common method for fixing bad channels in EEG, does the same hold for MEG due > to non-existent smearing of the signal? Is it best to keep the fixed > channel(s) or just remove them from the stats analysis across all > participants? > > > > 2. Given the three sensor types on the neuromag system, do I need to run > three different cluster analyses (one for mags, one for xgrads, one for > ygrads), each time specifying like sensor neighbours? Alternatively, If I'm > not interested in the mags data, can I just run one using the data from the > combined gradiometers? > > > > 3. When examining for group x condition effects, would I use a three row > design matrix with row 1 containing group, row 2 containing participants and > row 3 conditions? > > > > Thanks for any help, > > > > Peter > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > > Jörn M. Horschig > > PhD Student > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > Neuronal Oscillations Group > > FieldTrip Development Team > > > > P.O. Box 9101 > > NL-6500 HB Nijmegen > > The Netherlands > > > > Contact: > > E-Mail: jm.horschig at donders.ru.nl > > Tel: +31-(0)24-36-68493 > > Web: http://www.ru.nl/donders > > > > Visiting address: > > Trigon, room 2.30 > > Kapittelweg 29 > > NL-6525 EN Nijmegen > > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From g.piantoni at nin.knaw.nl Tue Sep 25 12:21:54 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Tue, 25 Sep 2012 12:21:54 +0200 Subject: [FieldTrip] How to impove dics realfilter solution In-Reply-To: <736231433.1128.1347610993969.JavaMail.root@zimbra> References: <612757646.1088.1347610775726.JavaMail.root@zimbra> <736231433.1128.1347610993969.JavaMail.root@zimbra> Message-ID: Hi Björn, It's not surprising that the results are pretty bad after using real filters. The fourier transform and DICS are intrinsically complex-valued, so using only the real part means throwing away half of the information (and getting meaningless results). The realfilter option was implemented in order to allow to pass the time-domain signal through the complex-value spatial filter and obtain a "virtual electrode". A virtual electrode with complex values is "weird to say the least", see: http://mailman.science.ru.nl/pipermail/fieldtrip/2006-May/000510.html Robert considered it an error in the algorithm and fixed it by providing the realfilter option. However, to me it seems more correct to think that complex spatial filters requires complex input (i.e. frequency-domain signal), so don't use DICS spatial filters on time-domain real-valued MEG recordings to generate time-domain virtual electrodes. If you want time-domain virtual electrodes, use LCMV spatial filters centered at the location of interest. Other smart people might disagree though. I suggest not to use realfilter option at all, but I'd be happy to hear other meaningful applications of this option. Hope this helps, Gio On Fri, Sep 14, 2012 at 10:23 AM, Björn Herrmann wrote: > Dear fieldtrip user, > > I am using the DICS beamformer to localize a 3Hz FFT power topographical distribution (using a neuromag system). The topographies are very clear auditory in single subjects, thus it shouldn't be a problem finding the "right" solution. When I use the beamformer to obtain complex-value spatial filters, the solution looks very good (using NAI). No problem here. However, using cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real values, the localization completely breaks down, sometimes even finding a strong peak in the opposite hemisphere than visible in the sensor topography (the head is centered in the sensor array). > > Does someone have a suggestion how to improve the solution using realfilter = 'yes'. I use the following settings. They are rather standard I guess. > > cfg = []; > cfg.method = 'dics'; > cfg.frequency = 3; > cfg.dics.projectnoise = 'yes'; > cfg.dics.lambda = '5%'; > cfg.dics.keepfilter = 'yes'; > cfg.dics.realfilter = 'yes'; > cfg.dics.fixedori = 'no'; > > > If someone has a suggestion, I would appreciate it. > Thanks in advance, > best, > > Björn > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From landpt at gmail.com Wed Sep 26 20:53:05 2012 From: landpt at gmail.com (Ricardo Jorge) Date: Wed, 26 Sep 2012 19:53:05 +0100 Subject: [FieldTrip] Emotiv and Fieldtrip - filter in the streamer/buffer? Message-ID: Hello there once again, I've contacted you some days ago because I was having troubles reading the data from the Emotiv in the Fieldtrip toolbox, which you replied and solved my trouble. Thanks once again. However, being worked on the data, I've noticed something odd that I cannot understand what exactly is happening: - I did not activate or put any filter (even removed the preprocessing baseline command) and the signals that I get in the fieldtrip have around 4000-5000 of mean and the variance is almost 0.05, something like that. - At the same time, I was running Emotiv Testbench and for some weird reason, the signals that I get in there have exactly the same mean, but its variance is more than 1 (something like between 1 and 1.5). - At the same time, I did run OpenVibe, which was similar to the Testbench. Seeing their plots, there are clearly some variations: Testbench/Openvibe gave much more "peaks" and spread, whereas Fieldtrip (streamer) looks less noisy, as if it was almost-perfect. But I did not apply any filter... Can I have any information about what could be happening here? Does the streamer/buffer apply some filter that I don't know? I've seen that it is not possible to acquire raw data from Emotiv, except using Emotiv SDK, Openvibe or Emokit. Is it related? Thanks in advance. Ricardo Jorge From Jan.Hirschmann at med.uni-duesseldorf.de Thu Sep 27 09:40:46 2012 From: Jan.Hirschmann at med.uni-duesseldorf.de (Jan.Hirschmann at med.uni-duesseldorf.de) Date: Thu, 27 Sep 2012 09:40:46 +0200 Subject: [FieldTrip] How to impove dics realfilter solution In-Reply-To: References: <612757646.1088.1347610775726.JavaMail.root@zimbra><736231433.1128.1347610993969.JavaMail.root@zimbra> Message-ID: <72E993C35FB11743B79FF9286E5B6D8B04772649@Mail2-UKD.VMED.UKD> Hi Gio, What about the application of projecting frequency domain data through a common filter? This is described in the beamformer tutorial on the fieldtrip website and has worked fine for me. After commenting out the realfilter line the group statistical results looked worse in my case (although I also changed lambda on this second try). >From the tutorial: "Then we compute the inverse filter based on both conditions. Note the use of cfg.keepfilter so that the output saves this computed filter. cfg = []; cfg.method = 'dics'; cfg.frequency = 18; cfg.grid = grid; cfg.vol = vol; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '5%'; cfg.dics.keepfilter = 'yes'; cfg.dics.realfilter = 'yes'; sourceAll = ft_sourceanalysis(cfg, freqAll); By placing this pre-computed filter inside cfg.grid.filter, it can now be applied to each condition separately. cfg.grid.filter = sourceAll.avg.filter; sourcePre_con = ft_sourceanalysis(cfg, freqPre ); sourcePost_con = ft_sourceanalysis(cfg, freqPost);" Best, Jan -----Ursprüngliche Nachricht----- Von: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] Im Auftrag von Gio Piantoni Gesendet: Dienstag, 25. September 2012 12:22 An: FieldTrip discussion list Betreff: Re: [FieldTrip] How to impove dics realfilter solution Hi Björn, It's not surprising that the results are pretty bad after using real filters. The fourier transform and DICS are intrinsically complex-valued, so using only the real part means throwing away half of the information (and getting meaningless results). The realfilter option was implemented in order to allow to pass the time-domain signal through the complex-value spatial filter and obtain a "virtual electrode". A virtual electrode with complex values is "weird to say the least", see: http://mailman.science.ru.nl/pipermail/fieldtrip/2006-May/000510.html Robert considered it an error in the algorithm and fixed it by providing the realfilter option. However, to me it seems more correct to think that complex spatial filters requires complex input (i.e. frequency-domain signal), so don't use DICS spatial filters on time-domain real-valued MEG recordings to generate time-domain virtual electrodes. If you want time-domain virtual electrodes, use LCMV spatial filters centered at the location of interest. Other smart people might disagree though. I suggest not to use realfilter option at all, but I'd be happy to hear other meaningful applications of this option. Hope this helps, Gio On Fri, Sep 14, 2012 at 10:23 AM, Björn Herrmann wrote: > Dear fieldtrip user, > > I am using the DICS beamformer to localize a 3Hz FFT power topographical distribution (using a neuromag system). The topographies are very clear auditory in single subjects, thus it shouldn't be a problem finding the "right" solution. When I use the beamformer to obtain complex-value spatial filters, the solution looks very good (using NAI). No problem here. However, using cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real values, the localization completely breaks down, sometimes even finding a strong peak in the opposite hemisphere than visible in the sensor topography (the head is centered in the sensor array). > > Does someone have a suggestion how to improve the solution using realfilter = 'yes'. I use the following settings. They are rather standard I guess. > > cfg = []; > cfg.method = 'dics'; > cfg.frequency = 3; > cfg.dics.projectnoise = 'yes'; > cfg.dics.lambda = '5%'; > cfg.dics.keepfilter = 'yes'; > cfg.dics.realfilter = 'yes'; > cfg.dics.fixedori = 'no'; > > > If someone has a suggestion, I would appreciate it. > Thanks in advance, > best, > > Björn > > > > _______________________________________________ > 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 b.reuderink at donders.ru.nl Thu Sep 27 11:24:34 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Thu, 27 Sep 2012 11:24:34 +0200 Subject: [FieldTrip] Emotiv and Fieldtrip - filter in the streamer/buffer? In-Reply-To: References: Message-ID: Dear Ricardo, If I understand your remark correctly, there is a scaling difference between other software (OpenVibe & Emotiv Testbench) and FieldTrip's real-time signal from the Emotiv. Would could see if we can find this difference in scaling. But, are there other signal characteristics that are different? You mention 'less noisy' — could that be caused just by scaling, or do you have a clear indication that the signal is filtered? Screenshots would be helpful. There are some places were filtering could take place. The viewer (bufferViewer.exe) has an option to enable a high-pass filter, and the FieldTrip's shared ODM code for streaming can down-sample the signal which also involves filtering, but it should be disabled by default. Can you provide some additional info? Best, Boris PS: emotiv2ft.exe is based on the Emotiv SDK (EDK). -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl On 26 sep. 2012, at 20:53, Ricardo Jorge wrote: > Hello there once again, > > I've contacted you some days ago because I was having troubles reading > the data from the Emotiv in the Fieldtrip toolbox, which you replied > and solved my trouble. Thanks once again. > > However, being worked on the data, I've noticed something odd that I > cannot understand what exactly is happening: > - I did not activate or put any filter (even removed the preprocessing > baseline command) and the signals that I get in the fieldtrip have > around 4000-5000 of mean and the variance is almost 0.05, something > like that. > - At the same time, I was running Emotiv Testbench and for some weird > reason, the signals that I get in there have exactly the same mean, > but its variance is more than 1 (something like between 1 and 1.5). > - At the same time, I did run OpenVibe, which was similar to the Testbench. > > Seeing their plots, there are clearly some variations: > Testbench/Openvibe gave much more "peaks" and spread, whereas > Fieldtrip (streamer) looks less noisy, as if it was almost-perfect. > But I did not apply any filter... > > Can I have any information about what could be happening here? Does > the streamer/buffer apply some filter that I don't know? I've seen > that it is not possible to acquire raw data from Emotiv, except using > Emotiv SDK, Openvibe or Emokit. Is it related? > > Thanks in advance. > > Ricardo Jorge > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Thu Sep 27 13:39:07 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 27 Sep 2012 13:39:07 +0200 Subject: [FieldTrip] How to impove dics realfilter solution In-Reply-To: References: <612757646.1088.1347610775726.JavaMail.root@zimbra> <736231433.1128.1347610993969.JavaMail.root@zimbra> Message-ID: Dear Björn, caro Gio, I don't agree with you, Gio, that one should use complex-valued filters. The reason for this is that they don't make sense from a biophysical point of view. The mixing from sources to channels (as represented in the leadfields) is strictly real-valued, because it is (near-)instantaneous. I think that the unmixing from channels to sources also should be real-valued, for the same argument. When you allow filter coefficients to be complex-valued, this is equivalent to allowing the sensor-level signals to be shifted in time with respect to one another. I consider this a bit odd. In Joachim's seminal paper (on which FieldTrip's initial DICS implementation is based), this was not really explicit in the methods description. However, based on personal communications with said Joachim, I at least distilled that the filters should be real-valued. The complex-valued filters were kept in (as default) for backward compatibilitiy reasons. Although mathematically possible (perhaps even more strictly answering to the minimum variance and unit gain constraints), and sometimes seemingly giving nicer subjective results, I'd advice against using them. Cheers, JM On Sep 25, 2012, at 12:21 PM, Gio Piantoni wrote: > Hi Björn, > > It's not surprising that the results are pretty bad after using real > filters. The fourier transform and DICS are intrinsically > complex-valued, so using only the real part means throwing away half > of the information (and getting meaningless results). > > The realfilter option was implemented in order to allow to pass the > time-domain signal through the complex-value spatial filter and obtain > a "virtual electrode". A virtual electrode with complex values is > "weird to say the least", see: > http://mailman.science.ru.nl/pipermail/fieldtrip/2006-May/000510.html > Robert considered it an error in the algorithm and fixed it by > providing the realfilter option. However, to me it seems more correct > to think that complex spatial filters requires complex input (i.e. > frequency-domain signal), so don't use DICS spatial filters on > time-domain real-valued MEG recordings to generate time-domain virtual > electrodes. If you want time-domain virtual electrodes, use LCMV > spatial filters centered at the location of interest. Other smart > people might disagree though. > > I suggest not to use realfilter option at all, but I'd be happy to > hear other meaningful applications of this option. > > Hope this helps, > > Gio > > On Fri, Sep 14, 2012 at 10:23 AM, Björn Herrmann wrote: >> Dear fieldtrip user, >> >> I am using the DICS beamformer to localize a 3Hz FFT power topographical distribution (using a neuromag system). The topographies are very clear auditory in single subjects, thus it shouldn't be a problem finding the "right" solution. When I use the beamformer to obtain complex-value spatial filters, the solution looks very good (using NAI). No problem here. However, using cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real values, the localization completely breaks down, sometimes even finding a strong peak in the opposite hemisphere than visible in the sensor topography (the head is centered in the sensor array). >> >> Does someone have a suggestion how to improve the solution using realfilter = 'yes'. I use the following settings. They are rather standard I guess. >> >> cfg = []; >> cfg.method = 'dics'; >> cfg.frequency = 3; >> cfg.dics.projectnoise = 'yes'; >> cfg.dics.lambda = '5%'; >> cfg.dics.keepfilter = 'yes'; >> cfg.dics.realfilter = 'yes'; >> cfg.dics.fixedori = 'no'; >> >> >> If someone has a suggestion, I would appreciate it. >> Thanks in advance, >> best, >> >> Björn >> >> >> >> _______________________________________________ >> 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 Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Duncan.Astle at mrc-cbu.cam.ac.uk Thu Sep 27 15:17:08 2012 From: Duncan.Astle at mrc-cbu.cam.ac.uk (Duncan Astle) Date: Thu, 27 Sep 2012 13:17:08 +0000 Subject: [FieldTrip] Transfering SPM TF data into Fieldtrip Message-ID: Dear FieldTrippers, I have some nice time frequency data in SPM8. It is averaged for each subject. I would really like to bring it into fieldtrip to do some stats, but I am struggling. When I use the spm2fieldtrip function it treats my 73 frequencies as 73 different trials. Does anyone have any suggestions about how to get in to fieldtrip? Best, Duncan ________________________________________________ Dr. Duncan Astle, Programme Leader Track, British Academy Research Fellow, MRC Cognition and Brain Sciences Unit, Chaucer Road, Cambridge. Duncan.Astle at mrc-cbu.cam.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Thu Sep 27 15:18:54 2012 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Thu, 27 Sep 2012 14:18:54 +0100 Subject: [FieldTrip] Transfering SPM TF data into Fieldtrip In-Reply-To: References: Message-ID: Dear Duncan, In SPM do: D = spm_eeg_load; ftdata = D.fttimelock; Best, Vladimir On Thu, Sep 27, 2012 at 2:17 PM, Duncan Astle wrote: > Dear FieldTrippers, > > > > I have some nice time frequency data in SPM8. It is averaged for each > subject. I would really like to bring it into fieldtrip to do some stats, > but I am struggling. When I use the spm2fieldtrip function it treats my 73 > frequencies as 73 different trials. > > > > Does anyone have any suggestions about how to get in to fieldtrip? > > > > Best, > > Duncan > > ________________________________________________ > > Dr. Duncan Astle, > > Programme Leader Track, > > British Academy Research Fellow, > > MRC Cognition and Brain Sciences Unit, > > Chaucer Road, > > Cambridge. > > Duncan.Astle at mrc-cbu.cam.ac.uk > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Duncan.Astle at mrc-cbu.cam.ac.uk Thu Sep 27 17:08:55 2012 From: Duncan.Astle at mrc-cbu.cam.ac.uk (Duncan Astle) Date: Thu, 27 Sep 2012 15:08:55 +0000 Subject: [FieldTrip] Update - transfering TF data from SPM Message-ID: Dear all, I keep thinking that I have done it, in that I think that I have recreated all the information that should be needed in a field trip TF object. I did this by bringing in the extra information from D.fttimelock, and creating the cfg field as if I had run it through FT_FREQANALYSIS. The structure has these fields: l5d19 = fsample: 250.0000 label: {68x1 cell} trial: {[68x73 single]} time: {[1x376 double]} trialinfo: 1 cfg: [1x1 struct] powspctrm: [68x73x376 single] freq: [1x73 double] dimord: 'chan_freq_time' However, when I try and use my file in 'FT_FREQGRANDAVERAGE' , it does not recognise this as a TF object, and produces this error message: ??? Error using ==> ft_checkdata at 324 This function requires freq data as input. Error in ==> ft_freqgrandaverage at 66 varargin{i} = ft_checkdata(varargin{i}, 'datatype', 'freq', 'feedback', 'no'); What is it that I am missing?? Best, Duncan ________________________________________________ Dr. Duncan Astle, Programme Leader Track, British Academy Research Fellow, MRC Cognition and Brain Sciences Unit, Chaucer Road, Cambridge. Duncan.Astle at mrc-cbu.cam.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Thu Sep 27 17:32:02 2012 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Thu, 27 Sep 2012 16:32:02 +0100 Subject: [FieldTrip] Update - transfering TF data from SPM In-Reply-To: References: Message-ID: Dear Duncan, You should look in the code how FT differentiates between different structures and what goes wrong. For instance it might be that it is confused by the fsample field that shouldn't be there. It's been a while since I did something like that and FT code has evolved with more stringent checks now. Best, Vladimir On Thu, Sep 27, 2012 at 4:08 PM, Duncan Astle wrote: > Dear all, > > > > I keep thinking that I have done it, in that I think that I have recreated > all the information that should be needed in a field trip TF object. I did > this by bringing in the extra information from D.fttimelock, and creating > the cfg field as if I had run it through FT_FREQANALYSIS. The structure has > these fields: > > > > l5d19 = > > > > fsample: 250.0000 > > label: {68x1 cell} > > trial: {[68x73 single]} > > time: {[1x376 double]} > > trialinfo: 1 > > cfg: [1x1 struct] > > powspctrm: [68x73x376 single] > > freq: [1x73 double] > > dimord: 'chan_freq_time' > > > > However, when I try and use my file in ‘FT_FREQGRANDAVERAGE’ , it does not > recognise this as a TF object, and produces this error message: > > > > ??? Error using ==> ft_checkdata at 324 > > This function requires freq data as input. > > > > Error in ==> ft_freqgrandaverage at 66 > > varargin{i} = ft_checkdata(varargin{i}, 'datatype', 'freq', 'feedback', > 'no'); > > > > What is it that I am missing?? > > > > Best, > > Duncan > > > > ________________________________________________ > > Dr. Duncan Astle, > > Programme Leader Track, > > British Academy Research Fellow, > > MRC Cognition and Brain Sciences Unit, > > Chaucer Road, > > Cambridge. > > Duncan.Astle at mrc-cbu.cam.ac.uk > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Duncan.Astle at mrc-cbu.cam.ac.uk Thu Sep 27 17:55:12 2012 From: Duncan.Astle at mrc-cbu.cam.ac.uk (Duncan Astle) Date: Thu, 27 Sep 2012 15:55:12 +0000 Subject: [FieldTrip] Update - transfering TF data from SPM In-Reply-To: References: Message-ID: Dear Vladimir, Thanks for your help; I worked out what it wanted. Anyone who is interested should contact me and I will take them through it. Best, Duncan ________________________________________________ Dr. Duncan Astle, Programme Leader Track, British Academy Research Fellow, MRC Cognition and Brain Sciences Unit, Chaucer Road, Cambridge. Duncan.Astle at mrc-cbu.cam.ac.uk -----Original Message----- From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Vladimir Litvak Sent: 27 September 2012 16:32 To: FieldTrip discussion list Subject: Re: [FieldTrip] Update - transfering TF data from SPM Dear Duncan, You should look in the code how FT differentiates between different structures and what goes wrong. For instance it might be that it is confused by the fsample field that shouldn't be there. It's been a while since I did something like that and FT code has evolved with more stringent checks now. Best, Vladimir On Thu, Sep 27, 2012 at 4:08 PM, Duncan Astle wrote: > Dear all, > > > > I keep thinking that I have done it, in that I think that I have > recreated all the information that should be needed in a field trip TF > object. I did this by bringing in the extra information from > D.fttimelock, and creating the cfg field as if I had run it through > FT_FREQANALYSIS. The structure has these fields: > > > > l5d19 = > > > > fsample: 250.0000 > > label: {68x1 cell} > > trial: {[68x73 single]} > > time: {[1x376 double]} > > trialinfo: 1 > > cfg: [1x1 struct] > > powspctrm: [68x73x376 single] > > freq: [1x73 double] > > dimord: 'chan_freq_time' > > > > However, when I try and use my file in 'FT_FREQGRANDAVERAGE' , it does > not recognise this as a TF object, and produces this error message: > > > > ??? Error using ==> ft_checkdata at 324 > > This function requires freq data as input. > > > > Error in ==> ft_freqgrandaverage at 66 > > varargin{i} = ft_checkdata(varargin{i}, 'datatype', 'freq', > 'feedback', 'no'); > > > > What is it that I am missing?? > > > > Best, > > Duncan > > > > ________________________________________________ > > Dr. Duncan Astle, > > Programme Leader Track, > > British Academy Research Fellow, > > MRC Cognition and Brain Sciences Unit, > > Chaucer Road, > > Cambridge. > > Duncan.Astle at mrc-cbu.cam.ac.uk > > > > > _______________________________________________ > 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 michael.wibral at web.de Thu Sep 27 20:03:43 2012 From: michael.wibral at web.de (Michael Wibral) Date: Thu, 27 Sep 2012 20:03:43 +0200 Subject: [FieldTrip] Fwd: Re: How to impove dics realfilter solution In-Reply-To: <50649472.3050502@em.uni-frankfurt.de> References: <50649472.3050502@em.uni-frankfurt.de> Message-ID: <506494FF.7070308@web.de> -------- Original Message -------- Subject: Re: [FieldTrip] How to impove dics realfilter solution Date: Thu, 27 Sep 2012 20:01:22 +0200 From: wibral Reply-To: wibral at em.uni-frankfurt.de To: FieldTrip discussion list Dear Filedtrip users, I fully agree with jan Mathijs, in principle when using DICS to reconstruct source power, the nature of the physical processes (forward model) should guarantee that filters are automatically real-valued, because this reflects the quasi-static approximation of maxwell's equations which holds pretty well in MEG. In practice filter coeffcients only deviate from being real because of sensor noise, which is not a desirable effect. Best, Michael On 09/27/2012 01:39 PM, jan-mathijs schoffelen wrote: > Dear Björn, caro Gio, > > I don't agree with you, Gio, that one should use complex-valued > filters. The reason for this is that they don't make sense from a > biophysical point of view. The mixing from sources to channels (as > represented in the leadfields) is strictly real-valued, because it is > (near-)instantaneous. I think that the unmixing from channels to > sources also should be real-valued, for the same argument. When you > allow filter coefficients to be complex-valued, this is equivalent to > allowing the sensor-level signals to be shifted in time with respect > to one another. I consider this a bit odd. In Joachim's seminal paper > (on which FieldTrip's initial DICS implementation is based), this was > not really explicit in the methods description. However, based on > personal communications with said Joachim, I at least distilled that > the filters should be real-valued. The complex-valued filters were > kept in (as default) for backward compatibilitiy reasons. Although > mathematically possible (perhaps even more strictly answering to the > minimum variance and unit gain constraints), and sometimes seemingly > giving nicer subjective results, I'd advice against using them. > > Cheers, > > JM > > > > On Sep 25, 2012, at 12:21 PM, Gio Piantoni wrote: > >> Hi Björn, >> >> It's not surprising that the results are pretty bad after using real >> filters. The fourier transform and DICS are intrinsically >> complex-valued, so using only the real part means throwing away half >> of the information (and getting meaningless results). >> >> The realfilter option was implemented in order to allow to pass the >> time-domain signal through the complex-value spatial filter and obtain >> a "virtual electrode". A virtual electrode with complex values is >> "weird to say the least", see: >> http://mailman.science.ru.nl/pipermail/fieldtrip/2006-May/000510.html >> Robert considered it an error in the algorithm and fixed it by >> providing the realfilter option. However, to me it seems more correct >> to think that complex spatial filters requires complex input (i.e. >> frequency-domain signal), so don't use DICS spatial filters on >> time-domain real-valued MEG recordings to generate time-domain virtual >> electrodes. If you want time-domain virtual electrodes, use LCMV >> spatial filters centered at the location of interest. Other smart >> people might disagree though. >> >> I suggest not to use realfilter option at all, but I'd be happy to >> hear other meaningful applications of this option. >> >> Hope this helps, >> >> Gio >> >> On Fri, Sep 14, 2012 at 10:23 AM, Björn Herrmann >> wrote: >>> Dear fieldtrip user, >>> >>> I am using the DICS beamformer to localize a 3Hz FFT power >>> topographical distribution (using a neuromag system). The >>> topographies are very clear auditory in single subjects, thus it >>> shouldn't be a problem finding the "right" solution. When I use the >>> beamformer to obtain complex-value spatial filters, the solution >>> looks very good (using NAI). No problem here. However, using >>> cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real >>> values, the localization completely breaks down, sometimes even >>> finding a strong peak in the opposite hemisphere than visible in the >>> sensor topography (the head is centered in the sensor array). >>> >>> Does someone have a suggestion how to improve the solution using >>> realfilter = 'yes'. I use the following settings. They are rather >>> standard I guess. >>> >>> cfg = []; >>> cfg.method = 'dics'; >>> cfg.frequency = 3; >>> cfg.dics.projectnoise = 'yes'; >>> cfg.dics.lambda = '5%'; >>> cfg.dics.keepfilter = 'yes'; >>> cfg.dics.realfilter = 'yes'; >>> cfg.dics.fixedori = 'no'; >>> >>> >>> If someone has a suggestion, I would appreciate it. >>> Thanks in advance, >>> best, >>> >>> Björn >>> >>> >>> >>> _______________________________________________ >>> 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 > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > > _______________________________________________ > 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 g.piantoni at nin.knaw.nl Thu Sep 27 21:05:02 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Thu, 27 Sep 2012 21:05:02 +0200 Subject: [FieldTrip] How to impove dics realfilter solution In-Reply-To: References: <612757646.1088.1347610775726.JavaMail.root@zimbra> <736231433.1128.1347610993969.JavaMail.root@zimbra> Message-ID: Well, the people disagreeing with me are indeed very smart! Jan-Mathijs, your argument is very subtle and I agree with you that the imaginary part of the filter contains the non-instantaneous unmixing. However, for frequency-domain data it makes sense to use the non-instantaneous information, for the very reason that frequency-domain data are not instantaneous. If you take the fourier transform of a signal at 10 Hz, you're not computing it at one specific instant but over a period of time. I'd imagine that the imaginary part contains information about the frequency-domain data over that period of time. I see Michael's point as well, but would it be possible for the quasi-static approximation of Maxwell's equations to contain the imaginary part only when applied to frequency-domain data instead of time-domain data? In the end, the complex-value spatial filters are specific to one frequency band over a period of time and maybe the imaginary part accounts for the time-shift (phase-shift) implicit in the frequency-domain representation. Thanks for the interesting discussion! Happy to hear if you have further thoughts on this. Cheers, Gio On Thu, Sep 27, 2012 at 1:39 PM, jan-mathijs schoffelen wrote: > Dear Björn, caro Gio, > > I don't agree with you, Gio, that one should use complex-valued filters. The > reason for this is that they don't make sense from a biophysical point of > view. The mixing from sources to channels (as represented in the leadfields) > is strictly real-valued, because it is (near-)instantaneous. I think that > the unmixing from channels to sources also should be real-valued, for the > same argument. When you allow filter coefficients to be complex-valued, this > is equivalent to allowing the sensor-level signals to be shifted in time > with respect to one another. I consider this a bit odd. In Joachim's seminal > paper (on which FieldTrip's initial DICS implementation is based), this was > not really explicit in the methods description. However, based on personal > communications with said Joachim, I at least distilled that the filters > should be real-valued. The complex-valued filters were kept in (as default) > for backward compatibilitiy reasons. Although mathematically possible > (perhaps even more strictly answering to the minimum variance and unit gain > constraints), and sometimes seemingly giving nicer subjective results, I'd > advice against using them. > > Cheers, > > JM > > > > On Sep 25, 2012, at 12:21 PM, Gio Piantoni wrote: > > Hi Björn, > > It's not surprising that the results are pretty bad after using real > filters. The fourier transform and DICS are intrinsically > complex-valued, so using only the real part means throwing away half > of the information (and getting meaningless results). > > The realfilter option was implemented in order to allow to pass the > time-domain signal through the complex-value spatial filter and obtain > a "virtual electrode". A virtual electrode with complex values is > "weird to say the least", see: > http://mailman.science.ru.nl/pipermail/fieldtrip/2006-May/000510.html > Robert considered it an error in the algorithm and fixed it by > providing the realfilter option. However, to me it seems more correct > to think that complex spatial filters requires complex input (i.e. > frequency-domain signal), so don't use DICS spatial filters on > time-domain real-valued MEG recordings to generate time-domain virtual > electrodes. If you want time-domain virtual electrodes, use LCMV > spatial filters centered at the location of interest. Other smart > people might disagree though. > > I suggest not to use realfilter option at all, but I'd be happy to > hear other meaningful applications of this option. > > Hope this helps, > > Gio > > On Fri, Sep 14, 2012 at 10:23 AM, Björn Herrmann > wrote: > > Dear fieldtrip user, > > > I am using the DICS beamformer to localize a 3Hz FFT power topographical > distribution (using a neuromag system). The topographies are very clear > auditory in single subjects, thus it shouldn't be a problem finding the > "right" solution. When I use the beamformer to obtain complex-value spatial > filters, the solution looks very good (using NAI). No problem here. However, > using cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real > values, the localization completely breaks down, sometimes even finding a > strong peak in the opposite hemisphere than visible in the sensor topography > (the head is centered in the sensor array). > > > Does someone have a suggestion how to improve the solution using realfilter > = 'yes'. I use the following settings. They are rather standard I guess. > > > cfg = []; > > cfg.method = 'dics'; > > cfg.frequency = 3; > > cfg.dics.projectnoise = 'yes'; > > cfg.dics.lambda = '5%'; > > cfg.dics.keepfilter = 'yes'; > > cfg.dics.realfilter = 'yes'; > > cfg.dics.fixedori = 'no'; > > > > If someone has a suggestion, I would appreciate it. > > Thanks in advance, > > best, > > > Björn > > > > > _______________________________________________ > > 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 > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From bherrmann at cbs.mpg.de Thu Sep 27 21:19:06 2012 From: bherrmann at cbs.mpg.de (=?utf-8?Q?Bj=C3=B6rn_Herrmann?=) Date: Thu, 27 Sep 2012 21:19:06 +0200 (CEST) Subject: [FieldTrip] How to impove dics realfilter solution (Michael Wibral) In-Reply-To: Message-ID: <1079339450.6815.1348773546422.JavaMail.root@zimbra> Thank you Gio, Jan and Michael, This is very helpful input. I understand that it makes sense from a biological point of view and also from thinking about leadfields that the filter should be real-valued. What I find surprising though is that just from an application point of view, the localization results really look in my case much better (auditory cortex; for a very clear auditory topography of the FFT to a 3Hz modulated sound) for the complex than the real filter. I used the standard parameters for the localization, maybe something could be impoved there, but this is what really surprises me, also following this interesting discussion here. Just by looking into the struct in fieldtrip and what kind of data goes into the DICS beamformer, then there is mainly the CSD, which is complex, and the power, which is positive real-valued. Thus, thinking of a classical leadfield being generated by a source and which is then compared to the observed topography (i.e. biological meaningful and real-valed), does not completely fit here, at least in my current thinking. Therefore, I was not fully surprised seeing the realfilter producing the more puzzling localization result in my case. Can the DICS beamformer really be thought of in the "classical" way, i.e. that the source produces a real-value leadfield (positive and negative values)? I somehow understood it as localizing a power topography, which is only positive, thus in a way different from a classical leadfield. All the best, BJörn ------ Björn Herrmann Auditory Cognition Group Max Planck Institute for Human Cognitive and Brain Sciences Stephanstrasse 1a, 04103 Leipzig, Germany phone: ++49 (0)341 9940 2606 email: bherrmann at cbs.mpg.de ----- Ursprüngliche Mail ----- Von: fieldtrip-request at science.ru.nl An: fieldtrip at science.ru.nl Gesendet: Donnerstag, 27. September 2012 20:04:01 Betreff: fieldtrip Digest, Vol 22, Issue 47 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: Update - transfering TF data from SPM (Vladimir Litvak) 2. Re: Update - transfering TF data from SPM (Duncan Astle) 3. Fwd: Re: How to impove dics realfilter solution (Michael Wibral) ---------------------------------------------------------------------- Message: 1 Date: Thu, 27 Sep 2012 16:32:02 +0100 From: Vladimir Litvak To: FieldTrip discussion list Subject: Re: [FieldTrip] Update - transfering TF data from SPM Message-ID: Content-Type: text/plain; charset=windows-1252 Dear Duncan, You should look in the code how FT differentiates between different structures and what goes wrong. For instance it might be that it is confused by the fsample field that shouldn't be there. It's been a while since I did something like that and FT code has evolved with more stringent checks now. Best, Vladimir On Thu, Sep 27, 2012 at 4:08 PM, Duncan Astle wrote: > Dear all, > > > > I keep thinking that I have done it, in that I think that I have recreated > all the information that should be needed in a field trip TF object. I did > this by bringing in the extra information from D.fttimelock, and creating > the cfg field as if I had run it through FT_FREQANALYSIS. The structure has > these fields: > > > > l5d19 = > > > > fsample: 250.0000 > > label: {68x1 cell} > > trial: {[68x73 single]} > > time: {[1x376 double]} > > trialinfo: 1 > > cfg: [1x1 struct] > > powspctrm: [68x73x376 single] > > freq: [1x73 double] > > dimord: 'chan_freq_time' > > > > However, when I try and use my file in ?FT_FREQGRANDAVERAGE? , it does not > recognise this as a TF object, and produces this error message: > > > > ??? Error using ==> ft_checkdata at 324 > > This function requires freq data as input. > > > > Error in ==> ft_freqgrandaverage at 66 > > varargin{i} = ft_checkdata(varargin{i}, 'datatype', 'freq', 'feedback', > 'no'); > > > > What is it that I am missing?? > > > > Best, > > Duncan > > > > ________________________________________________ > > Dr. Duncan Astle, > > Programme Leader Track, > > British Academy Research Fellow, > > MRC Cognition and Brain Sciences Unit, > > Chaucer Road, > > Cambridge. > > Duncan.Astle at mrc-cbu.cam.ac.uk > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ------------------------------ Message: 2 Date: Thu, 27 Sep 2012 15:55:12 +0000 From: Duncan Astle To: FieldTrip discussion list Subject: Re: [FieldTrip] Update - transfering TF data from SPM Message-ID: Content-Type: text/plain; charset="us-ascii" Dear Vladimir, Thanks for your help; I worked out what it wanted. Anyone who is interested should contact me and I will take them through it. Best, Duncan ________________________________________________ Dr. Duncan Astle, Programme Leader Track, British Academy Research Fellow, MRC Cognition and Brain Sciences Unit, Chaucer Road, Cambridge. Duncan.Astle at mrc-cbu.cam.ac.uk -----Original Message----- From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Vladimir Litvak Sent: 27 September 2012 16:32 To: FieldTrip discussion list Subject: Re: [FieldTrip] Update - transfering TF data from SPM Dear Duncan, You should look in the code how FT differentiates between different structures and what goes wrong. For instance it might be that it is confused by the fsample field that shouldn't be there. It's been a while since I did something like that and FT code has evolved with more stringent checks now. Best, Vladimir On Thu, Sep 27, 2012 at 4:08 PM, Duncan Astle wrote: > Dear all, > > > > I keep thinking that I have done it, in that I think that I have > recreated all the information that should be needed in a field trip TF > object. I did this by bringing in the extra information from > D.fttimelock, and creating the cfg field as if I had run it through > FT_FREQANALYSIS. The structure has these fields: > > > > l5d19 = > > > > fsample: 250.0000 > > label: {68x1 cell} > > trial: {[68x73 single]} > > time: {[1x376 double]} > > trialinfo: 1 > > cfg: [1x1 struct] > > powspctrm: [68x73x376 single] > > freq: [1x73 double] > > dimord: 'chan_freq_time' > > > > However, when I try and use my file in 'FT_FREQGRANDAVERAGE' , it does > not recognise this as a TF object, and produces this error message: > > > > ??? Error using ==> ft_checkdata at 324 > > This function requires freq data as input. > > > > Error in ==> ft_freqgrandaverage at 66 > > varargin{i} = ft_checkdata(varargin{i}, 'datatype', 'freq', > 'feedback', 'no'); > > > > What is it that I am missing?? > > > > Best, > > Duncan > > > > ________________________________________________ > > Dr. Duncan Astle, > > Programme Leader Track, > > British Academy Research Fellow, > > MRC Cognition and Brain Sciences Unit, > > Chaucer Road, > > Cambridge. > > Duncan.Astle at mrc-cbu.cam.ac.uk > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ------------------------------ Message: 3 Date: Thu, 27 Sep 2012 20:03:43 +0200 From: Michael Wibral To: FieldTrip discussion list Subject: [FieldTrip] Fwd: Re: How to impove dics realfilter solution Message-ID: <506494FF.7070308 at web.de> Content-Type: text/plain; charset="iso-8859-1" -------- Original Message -------- Subject: Re: [FieldTrip] How to impove dics realfilter solution Date: Thu, 27 Sep 2012 20:01:22 +0200 From: wibral Reply-To: wibral at em.uni-frankfurt.de To: FieldTrip discussion list Dear Filedtrip users, I fully agree with jan Mathijs, in principle when using DICS to reconstruct source power, the nature of the physical processes (forward model) should guarantee that filters are automatically real-valued, because this reflects the quasi-static approximation of maxwell's equations which holds pretty well in MEG. In practice filter coeffcients only deviate from being real because of sensor noise, which is not a desirable effect. Best, Michael On 09/27/2012 01:39 PM, jan-mathijs schoffelen wrote: > Dear Bj?rn, caro Gio, > > I don't agree with you, Gio, that one should use complex-valued > filters. The reason for this is that they don't make sense from a > biophysical point of view. The mixing from sources to channels (as > represented in the leadfields) is strictly real-valued, because it is > (near-)instantaneous. I think that the unmixing from channels to > sources also should be real-valued, for the same argument. When you > allow filter coefficients to be complex-valued, this is equivalent to > allowing the sensor-level signals to be shifted in time with respect > to one another. I consider this a bit odd. In Joachim's seminal paper > (on which FieldTrip's initial DICS implementation is based), this was > not really explicit in the methods description. However, based on > personal communications with said Joachim, I at least distilled that > the filters should be real-valued. The complex-valued filters were > kept in (as default) for backward compatibilitiy reasons. Although > mathematically possible (perhaps even more strictly answering to the > minimum variance and unit gain constraints), and sometimes seemingly > giving nicer subjective results, I'd advice against using them. > > Cheers, > > JM > > > > On Sep 25, 2012, at 12:21 PM, Gio Piantoni wrote: > >> Hi Bj?rn, >> >> It's not surprising that the results are pretty bad after using real >> filters. The fourier transform and DICS are intrinsically >> complex-valued, so using only the real part means throwing away half >> of the information (and getting meaningless results). >> >> The realfilter option was implemented in order to allow to pass the >> time-domain signal through the complex-value spatial filter and obtain >> a "virtual electrode". A virtual electrode with complex values is >> "weird to say the least", see: >> http://mailman.science.ru.nl/pipermail/fieldtrip/2006-May/000510.html >> Robert considered it an error in the algorithm and fixed it by >> providing the realfilter option. However, to me it seems more correct >> to think that complex spatial filters requires complex input (i.e. >> frequency-domain signal), so don't use DICS spatial filters on >> time-domain real-valued MEG recordings to generate time-domain virtual >> electrodes. If you want time-domain virtual electrodes, use LCMV >> spatial filters centered at the location of interest. Other smart >> people might disagree though. >> >> I suggest not to use realfilter option at all, but I'd be happy to >> hear other meaningful applications of this option. >> >> Hope this helps, >> >> Gio >> >> On Fri, Sep 14, 2012 at 10:23 AM, Bj?rn Herrmann >> wrote: >>> Dear fieldtrip user, >>> >>> I am using the DICS beamformer to localize a 3Hz FFT power >>> topographical distribution (using a neuromag system). The >>> topographies are very clear auditory in single subjects, thus it >>> shouldn't be a problem finding the "right" solution. When I use the >>> beamformer to obtain complex-value spatial filters, the solution >>> looks very good (using NAI). No problem here. However, using >>> cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real >>> values, the localization completely breaks down, sometimes even >>> finding a strong peak in the opposite hemisphere than visible in the >>> sensor topography (the head is centered in the sensor array). >>> >>> Does someone have a suggestion how to improve the solution using >>> realfilter = 'yes'. I use the following settings. They are rather >>> standard I guess. >>> >>> cfg = []; >>> cfg.method = 'dics'; >>> cfg.frequency = 3; >>> cfg.dics.projectnoise = 'yes'; >>> cfg.dics.lambda = '5%'; >>> cfg.dics.keepfilter = 'yes'; >>> cfg.dics.realfilter = 'yes'; >>> cfg.dics.fixedori = 'no'; >>> >>> >>> If someone has a suggestion, I would appreciate it. >>> Thanks in advance, >>> best, >>> >>> Bj?rn >>> >>> >>> >>> _______________________________________________ >>> 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 > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip End of fieldtrip Digest, Vol 22, Issue 47 ***************************************** From g.piantoni at nin.knaw.nl Fri Sep 28 10:50:35 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Fri, 28 Sep 2012 10:50:35 +0200 Subject: [FieldTrip] Fwd: Re: How to impove dics realfilter solution In-Reply-To: <506494FF.7070308@web.de> References: <50649472.3050502@em.uni-frankfurt.de> <506494FF.7070308@web.de> Message-ID: Hi Michael, Thanks for your suggestion! In fact, the contribution of the imaginary part increases with higher levels of noise (and it's zero when the noise is zero). I tested with a simulation (see code below). The imaginary part derives from the uncorrelated sensor noise and seem to contain no meaningful information, sorry if I had given wrong information before, my intuition tricked me. Thanks for the interesting discussion! Cheers, Gio %-----------------% %-forward model fieldtripdir = '/path/to/fieldtrip/'; elec = ft_read_sens([fieldtripdir 'template/electrode/standard_1020.elc']); load([fieldtripdir 'template/headmodel/standard_bem.mat']); cfg = []; cfg.elec = elec; cfg.vol = vol; cfg.grid.xgrid = -80:10:80; cfg.grid.ygrid = -110:10:80; cfg.grid.zgrid = -70:10:90; cfg.inwardshift = 1; lead = ft_prepare_leadfield(cfg); %-----------------% %-------------------------------------% %-loop over relative noise relnoise = 0:.05:1; realfilter = zeros(size(relnoise)); imagfilter = zeros(size(relnoise)); for i = 1:numel(relnoise) %-----------------% %-create data cfg = []; cfg.dip.pos = [10 30 30]; cfg.dip.mom = [1 0 0]'; cfg.dip.frequency = 10; cfg.vol = vol; cfg.relnoise = relnoise(i); cfg.elec = elec; data = ft_dipolesimulation(cfg); %-----------------% %-----------------% %-fourier freq cfg = []; cfg.method = 'mtmfft'; cfg.output = 'fourier'; cfg.taper = 'hanning'; cfg.foilim = [10 10]; freq = ft_freqanalysis(cfg, data); %-----------------% %-----------------% %-beamformer cfg = []; cfg.method = 'dics'; cfg.frequency = 10; cfg.grid = lead; cfg.vol = vol; cfg.elec = elec; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = '1%'; cfg.dics.keepfilter = 'yes'; source = ft_sourceanalysis(cfg, freq); %-take one dipole as example realfilter(i) = sum(abs(real(source.avg.filter{source.inside(100)}(:)))); imagfilter(i) = sum(abs(imag(source.avg.filter{source.inside(100)}(:)))); %-----------------% end plot(relnoise, realfilter) hold on plot(relnoise, imagfilter, 'r') %-------------------------------------% On Thu, Sep 27, 2012 at 8:03 PM, Michael Wibral wrote: > > > > > -------- Original Message -------- > Subject: Re: [FieldTrip] How to impove dics realfilter solution > Date: Thu, 27 Sep 2012 20:01:22 +0200 > From: wibral > Reply-To: wibral at em.uni-frankfurt.de > To: FieldTrip discussion list > > > > Dear Filedtrip users, > > I fully agree with jan Mathijs, > > in principle when using DICS to reconstruct source power, the nature of > the physical processes (forward model) should guarantee that filters are > automatically real-valued, because this reflects the quasi-static > approximation of maxwell's equations which holds pretty well in MEG. In > practice filter coeffcients only deviate from being real because of sensor > noise, which is not a desirable effect. > > Best, > Michael > > > On 09/27/2012 01:39 PM, jan-mathijs schoffelen wrote: > > Dear Björn, caro Gio, > > I don't agree with you, Gio, that one should use complex-valued filters. > The reason for this is that they don't make sense from a biophysical point > of view. The mixing from sources to channels (as represented in the > leadfields) is strictly real-valued, because it is (near-)instantaneous. I > think that the unmixing from channels to sources also should be real-valued, > for the same argument. When you allow filter coefficients to be > complex-valued, this is equivalent to allowing the sensor-level signals to > be shifted in time with respect to one another. I consider this a bit odd. > In Joachim's seminal paper (on which FieldTrip's initial DICS implementation > is based), this was not really explicit in the methods description. However, > based on personal communications with said Joachim, I at least distilled > that the filters should be real-valued. The complex-valued filters were kept > in (as default) for backward compatibilitiy reasons. Although mathematically > possible (perhaps even more strictly answering to the minimum variance and > unit gain constraints), and sometimes seemingly giving nicer subjective > results, I'd advice against using them. > > Cheers, > > JM > > > > On Sep 25, 2012, at 12:21 PM, Gio Piantoni wrote: > > Hi Björn, > > It's not surprising that the results are pretty bad after using real > filters. The fourier transform and DICS are intrinsically > complex-valued, so using only the real part means throwing away half > of the information (and getting meaningless results). > > The realfilter option was implemented in order to allow to pass the > time-domain signal through the complex-value spatial filter and obtain > a "virtual electrode". A virtual electrode with complex values is > "weird to say the least", see: > http://mailman.science.ru.nl/pipermail/fieldtrip/2006-May/000510.html > Robert considered it an error in the algorithm and fixed it by > providing the realfilter option. However, to me it seems more correct > to think that complex spatial filters requires complex input (i.e. > frequency-domain signal), so don't use DICS spatial filters on > time-domain real-valued MEG recordings to generate time-domain virtual > electrodes. If you want time-domain virtual electrodes, use LCMV > spatial filters centered at the location of interest. Other smart > people might disagree though. > > I suggest not to use realfilter option at all, but I'd be happy to > hear other meaningful applications of this option. > > Hope this helps, > > Gio > > On Fri, Sep 14, 2012 at 10:23 AM, Björn Herrmann > wrote: > > Dear fieldtrip user, > > > I am using the DICS beamformer to localize a 3Hz FFT power topographical > distribution (using a neuromag system). The topographies are very clear > auditory in single subjects, thus it shouldn't be a problem finding the > "right" solution. When I use the beamformer to obtain complex-value spatial > filters, the solution looks very good (using NAI). No problem here. However, > using cfg.dics.realfilter = 'yes', i.e. the spatial filter will have real > values, the localization completely breaks down, sometimes even finding a > strong peak in the opposite hemisphere than visible in the sensor topography > (the head is centered in the sensor array). > > > Does someone have a suggestion how to improve the solution using > realfilter = 'yes'. I use the following settings. They are rather standard I > guess. > > > cfg = []; > > cfg.method = 'dics'; > > cfg.frequency = 3; > > cfg.dics.projectnoise = 'yes'; > > cfg.dics.lambda = '5%'; > > cfg.dics.keepfilter = 'yes'; > > cfg.dics.realfilter = 'yes'; > > cfg.dics.fixedori = 'no'; > > > > If someone has a suggestion, I would appreciate it. > > Thanks in advance, > > best, > > > Björn > > > > > _______________________________________________ > > 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 > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > > _______________________________________________ > 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 landpt at gmail.com Fri Sep 28 11:39:58 2012 From: landpt at gmail.com (Ricardo Jorge) Date: Fri, 28 Sep 2012 10:39:58 +0100 Subject: [FieldTrip] Emotiv and Fieldtrip - filter in the streamer/buffer? In-Reply-To: References: Message-ID: Dear Boris, Sorry for the late response, I tried to reply as earliest as possible. Thank for the answer, by the way. I don't think it's a scaling issue: it shouldn't affect the variance that much and Power spectral seem to be different from both ways. Absolutely that I can give you additional information; I am starting with explaining almost everything I've done: 1st: I picked up the function ft_realtime_signalviewer in "fieldtrip-20120904\realtime\example" and adapted it slightly so I could view it in realtime but at the same time, I could see the previous 20 seconds. Besides that, I disabled the ft_preproc_baselinecorrect(data.trial{1}) step in that function and added some steps that allowed me to save the whole record into a file at the same time (is there any function in fieldtrip that does that at the same time as realtime?). I'm not sure if I can send files through this discussion list: tell me if you want to try it. Just for visualization issues, I multiplied the signal in the plot by a factor, so it could be similar to Testbench visually, but it doesn't matter because I'm not changing any data, just the plot. 2nd: I opened Testbench and OpenVibe. In order to compare the results, I saved them into EDF an opened it in matlab. Testbench has an option to set an high-pass filter, but it does not alter the recording, only the visualization in real time. 3rd: I did put the emotiv in the table so it could be at the rest. 4th: I started all 3 of them. They're not be all exactly at the same time because I can't press it all at once (but almost) and so I'll record during a reasonable time so I can get enough samples. Results: 1. There is a weird thing in the testbench/openvibe data, all values in AF3 channel (for instance) are integer numbers, whereas Fieldtrip are not: Fieldtrip: 1.0e+03 * 4.030540530271679 4.030428591191215 4.030553469018260 4.030684982830449 4.030580735490210 4.030495361159973 Testbench: 4029 4030 4031 4031 4032 4032 They're almost the same and it isn't a problem since they didnt start exactly at the same time. However, analyzing their mean/variance, we have: Fieldtrip: Mean: 4.030526515189773e+03 Variance: 0.011920664040352 Offline (Testbench): Mean: 4.030526118470382e+03 Variance:1.641380154961390 Their mean are great but the same cannot be said to their variance: in fact it seems that it spreads way too much while offline. Let's see their min and max through a sample: Fieldtrip: [4.027692307692308e+03 ; 4.032307692307693e+03] Testbench: [4025 ; 4037] I've put a plot in my dropbox folder if you want to check it: https://dl.dropbox.com/u/846911/comparision.jpg I've checked if the signalviewer has any filter, but I can't find any, so I cannot understand exactly what could be happening. Their FFT is similar but not exactly the same as well. What do you think it could be happening? Thanks in advance, Best Regards Ricardo Jorge From b.reuderink at donders.ru.nl Fri Sep 28 13:14:37 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Fri, 28 Sep 2012 13:14:37 +0200 Subject: [FieldTrip] Emotiv and Fieldtrip - filter in the streamer/buffer? In-Reply-To: References: Message-ID: <11DBE635-CEA4-4580-B5B3-19C31E6259F1@donders.ru.nl> Dear Ricardo, No problem, and thank you for your elaborate response :). When I look at your screenshot, the right subplot seems to show a rounding issue; all the values are indeed integers, while on the left a more continuous signal is displayed. So, I would say that the difference between the signals is at least a rounding issue, and I assume that the FieldTrip signal is the more precise one. This might explain the difference in variance. For me this raises the question where this rounding comes from. You say that both OpenVibe and Emotiv's Testbench have these integer valued samples? Could this rounding to integers happen at some other stage (e.g. after importing in MATLAB?). Best, Boris -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl On 28 sep. 2012, at 11:39, Ricardo Jorge wrote: > Dear Boris, > > Sorry for the late response, I tried to reply as earliest as possible. > Thank for the answer, by the way. > > I don't think it's a scaling issue: it shouldn't affect the variance > that much and Power spectral seem to be different from both ways. > Absolutely that I can give you additional information; I am starting > with explaining almost everything I've done: > > 1st: I picked up the function ft_realtime_signalviewer in > "fieldtrip-20120904\realtime\example" and adapted it slightly so I > could view it in realtime but at the same time, I could see the > previous 20 seconds. Besides that, I disabled the > ft_preproc_baselinecorrect(data.trial{1}) step in that function and > added some steps that allowed me to save the whole record into a file > at the same time (is there any function in fieldtrip that does that at > the same time as realtime?). I'm not sure if I can send files through > this discussion list: tell me if you want to try it. Just for > visualization issues, I multiplied the signal in the plot by a factor, > so it could be similar to Testbench visually, but it doesn't matter > because I'm not changing any data, just the plot. > > 2nd: I opened Testbench and OpenVibe. In order to compare the results, > I saved them into EDF an opened it in matlab. Testbench has an option > to set an high-pass filter, but it does not alter the recording, only > the visualization in real time. > > 3rd: I did put the emotiv in the table so it could be at the rest. > > 4th: I started all 3 of them. They're not be all exactly at the same > time because I can't press it all at once (but almost) and so I'll > record during a reasonable time so I can get enough samples. > > Results: > > 1. There is a weird thing in the testbench/openvibe data, all values > in AF3 channel (for instance) are integer numbers, whereas Fieldtrip > are not: > > Fieldtrip: > 1.0e+03 * > > 4.030540530271679 4.030428591191215 4.030553469018260 > 4.030684982830449 4.030580735490210 4.030495361159973 > > Testbench: > 4029 4030 4031 4031 4032 4032 > > They're almost the same and it isn't a problem since they didnt start > exactly at the same time. > However, analyzing their mean/variance, we have: > > Fieldtrip: > > Mean: 4.030526515189773e+03 > Variance: 0.011920664040352 > > Offline (Testbench): > > Mean: 4.030526118470382e+03 > Variance:1.641380154961390 > > Their mean are great but the same cannot be said to their variance: in > fact it seems that it spreads way too much while offline. Let's see > their min and max through a sample: > Fieldtrip: [4.027692307692308e+03 ; 4.032307692307693e+03] > Testbench: [4025 ; 4037] > > I've put a plot in my dropbox folder if you want to check it: > https://dl.dropbox.com/u/846911/comparision.jpg > > > I've checked if the signalviewer has any filter, but I can't find any, > so I cannot understand exactly what could be happening. > > Their FFT is similar but not exactly the same as well. > > What do you think it could be happening? > > Thanks in advance, > > Best Regards > > Ricardo Jorge > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From landpt at gmail.com Fri Sep 28 14:16:10 2012 From: landpt at gmail.com (Ricardo Jorge) Date: Fri, 28 Sep 2012 13:16:10 +0100 Subject: [FieldTrip] Emotiv and Fieldtrip - filter in the streamer/buffer? In-Reply-To: References: Message-ID: Hi again, I'm not sure, to be honest! I would say fieldtrip is the most precise one, but why would it happen - I mean, how could it be better than the testbench? That's what's confusing me: it makes no sense that a signal such as EEG has only integer values indeed. But there are weirder things: In the EDF/CSV files from testbench, the first channel (AF3) has only integer values, the second channel doesn't have only integer values, but have mean 260 around, the third channel goes back to the integer values and 4000 mean again, fourth chan back to ~200 mean, non-integer and it goes on... which makes me thinking that they probably apply something, either the baseline and rounding, or something more. In the EDF files from Openvibe, all numbers are integers as independently of the channel, but variance's different as well. In fact, estimating it right now, it says that it has variance around 3. In the MAT file recorded by Fieldtrip, all numbers are non integer but with an extremely low variance comparing to the others. So, for some reason all methods are different but to be honest I feel that fieldtrip's results are correct and so I'm going to give it a try and use them in my investigation to see if they can confirm what I expect. Thanks once again! Best regards, Ricardo Jorge On Fri, Sep 28, 2012 at 10:39 AM, Ricardo Jorge wrote: > Dear Boris, > > Sorry for the late response, I tried to reply as earliest as possible. > Thank for the answer, by the way. > > I don't think it's a scaling issue: it shouldn't affect the variance > that much and Power spectral seem to be different from both ways. > Absolutely that I can give you additional information; I am starting > with explaining almost everything I've done: > > 1st: I picked up the function ft_realtime_signalviewer in > "fieldtrip-20120904\realtime\example" and adapted it slightly so I > could view it in realtime but at the same time, I could see the > previous 20 seconds. Besides that, I disabled the > ft_preproc_baselinecorrect(data.trial{1}) step in that function and > added some steps that allowed me to save the whole record into a file > at the same time (is there any function in fieldtrip that does that at > the same time as realtime?). I'm not sure if I can send files through > this discussion list: tell me if you want to try it. Just for > visualization issues, I multiplied the signal in the plot by a factor, > so it could be similar to Testbench visually, but it doesn't matter > because I'm not changing any data, just the plot. > > 2nd: I opened Testbench and OpenVibe. In order to compare the results, > I saved them into EDF an opened it in matlab. Testbench has an option > to set an high-pass filter, but it does not alter the recording, only > the visualization in real time. > > 3rd: I did put the emotiv in the table so it could be at the rest. > > 4th: I started all 3 of them. They're not be all exactly at the same > time because I can't press it all at once (but almost) and so I'll > record during a reasonable time so I can get enough samples. > > Results: > > 1. There is a weird thing in the testbench/openvibe data, all values > in AF3 channel (for instance) are integer numbers, whereas Fieldtrip > are not: > > Fieldtrip: > 1.0e+03 * > > 4.030540530271679 4.030428591191215 4.030553469018260 > 4.030684982830449 4.030580735490210 4.030495361159973 > > Testbench: > 4029 4030 4031 4031 4032 4032 > > They're almost the same and it isn't a problem since they didnt start > exactly at the same time. > However, analyzing their mean/variance, we have: > > Fieldtrip: > > Mean: 4.030526515189773e+03 > Variance: 0.011920664040352 > > Offline (Testbench): > > Mean: 4.030526118470382e+03 > Variance:1.641380154961390 > > Their mean are great but the same cannot be said to their variance: in > fact it seems that it spreads way too much while offline. Let's see > their min and max through a sample: > Fieldtrip: [4.027692307692308e+03 ; 4.032307692307693e+03] > Testbench: [4025 ; 4037] > > I've put a plot in my dropbox folder if you want to check it: > https://dl.dropbox.com/u/846911/comparision.jpg > > > I've checked if the signalviewer has any filter, but I can't find any, > so I cannot understand exactly what could be happening. > > Their FFT is similar but not exactly the same as well. > > What do you think it could be happening? > > Thanks in advance, > > Best Regards > > Ricardo Jorge From mark.noordenbos at gmail.com Sun Sep 30 11:30:35 2012 From: mark.noordenbos at gmail.com (Mark Noordenbos) Date: Sun, 30 Sep 2012 11:30:35 +0200 Subject: [FieldTrip] cluster analysis Message-ID: Dear Fieldtrippers, I was wondering how you report the results of the cluster analysis in your papers. I have seen different types of how the results are reported. For example, some report only the p-value of the cluster whereas others report clusters as T(degrees of freedom) = [clusterstat value], p-value. Is T (multivariate t) the correct test statisic for the cluster analysis (like F for anova)? Where can I find (or calculate) the degrees of freedom of the clusterstat value? Thanks Best, Mark -------------- next part -------------- An HTML attachment was scrubbed... URL: From politzerahless at gmail.com Sun Sep 30 15:46:09 2012 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Sun, 30 Sep 2012 08:46:09 -0500 Subject: [FieldTrip] cluster analysis Message-ID: Hi Mark, The Fieldtrip wiki has examples of published papers that report cluster analyses. In what I've seen, usually just the *p* is reported (if even that), along with the latency and topography of the cluster. See e.g. Pijnacker et al. (2011, *Journal of Cognitive Neuroscience*) and Meltzer & Braun (2011, *Frontiers in Human Neuroscience*). There may be others in http://fieldtrip.fcdonders.nl/publications As for your second question, my understanding is that the test statistic doesn't matter (one of the points of the cluster test is that it works no matter which test statistic you use (Maris & Oostenveld, 2007)). Also, to the best of my knowledge, there are no degrees of freedom for the cluster test, since it's non-parametric (it's not based on the distribution of a test statistic, it's based on Monte Carlo estimation). Best, Steve Message: 1 > Date: Sun, 30 Sep 2012 11:30:35 +0200 > From: Mark Noordenbos > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] cluster analysis > Message-ID: > 7qVRZp7goj3AhoE7xaq8tqTPsg at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Fieldtrippers, > > I was wondering how you report the results of the cluster analysis in your > papers. I have seen different types of how the results are reported. > For example, some report only the p-value of the cluster whereas others > report clusters as T(degrees of freedom) = [clusterstat value], p-value. > > Is T (multivariate t) the correct test statisic for the cluster analysis > (like F for anova)? > Where can I find (or calculate) the degrees of freedom of the clusterstat > value? > > Thanks > > Best, > Mark > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120930/fe6908ab/attachment-0001.html > > > > ------------------------------ > -------------- next part -------------- An HTML attachment was scrubbed... URL: