From odidodi at hotmail.com Wed Jun 1 09:10:30 2011 From: odidodi at hotmail.com (odelia nakar) Date: Wed, 1 Jun 2011 07:10:30 +0000 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>, <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl>, , , <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com>, , <4DDB5A14.3090102@uni-oldenburg.de>, <34CEBDBD-7738-403D-A563-4A6FDBD83C04@mac.com>, , Message-ID: Hi all, Thank you all for the discussion. I'm sorry I response only now, I went on a vacation... I actually didn't want to run the ICA on trials with blinks, rather on all trials, but to remove the component only for trials with a blink. Your critics concern my idea as well, since if I have any kind of correlation between condition and blink I might yield a difference that does not exist between conditions... Considering your suggestion, Mahesh, unfortunately I don't have EOG recording for this experiment. Thanks again for the discussion, Odelia. Date: Fri, 27 May 2011 00:32:01 -0400 From: mahesh.casiraghi at gmail.com To: yuvharpaz at gmail.com; fieldtrip at donders.ru.nl Subject: Re: [FieldTrip] ICA+frqanalysis questions Dear Yuval and discussion group, it seems to me that what you are proposing is getting close to what proposed by the hybrid approach of regica described here: Manousos A. Klados, Christos Papadelis, Christoph Braun, Panagiotis D. Bamidis, REG-ICA: A hybrid methodology combining Blind Source Separation and regression techniques for the rejection of ocular artifacts, Biomedical Signal Processing and Control, In Press, Corrected Proof, Available online 16 March 2011, ISSN 1746-8094, DOI: 10.1016/j.bspc.2011.02.001. They suggest to selectively run regression based AR only on those components which correlate with EOG signals. This makes sense to me and I have been trying to experiment that on some old data, although with no clear conclusions yet. It may be worth a try for Odelia: Anybody out there with some insights for this - or maybe a similar - approach? Cheers, Mahesh Mahesh M. CasiraghiPhD candidate - Cognitive Sciences Roberto Dell'Acqua Lab, University of PadovaPierre Jolicoeur Lab, Univesité de Montréal mahesh.casiraghi at umontreal.ca I have the conviction that when Physiology will be far enough advanced, the poet, the philosopher, and the physiologist will all understand each other. Claude Bernard On Thu, May 26, 2011 at 11:40 PM, Yuval Harpaz wrote: Dear discussion groupDid anybody consider smoothing or filtering the component trace before rejecting it? it seems that the added noise to no-blink trials is in a frequency higher than that typical to blinks. what if we evaluate the component weight, creating a trace for the eyeblink component for every trial, then bandpass filter the blink trace , say 0.1-25Hz, and only then remove the component from the data? yuval On 27 May 2011 06:16, Joseph Dien wrote: Stefan, just to be clear, I don't think any of us were saying not to use ICA to correct blinks. David was just saying that there are potential concerns when one only applies the ICA to the blink trials rather than to all the trials. I myself use EEGlab's infomax implementation in the automatic eyeblink correction tool of my EP Toolkit (http://sourceforge.net/projects/erppcatoolkit/). Now that said, I should add a little more nuance to my response. One of the things I observed (or rather, that Tim Curran pointed out to me) is that when you apply ICA to remove eyeblink artifacts in this manner, it can actually substantially increase the noise level in the data, so for the trials without eyeblinks it can have a considerable cost. So in order to balance the cost/benefit ratio, what I did was to include a trial by trial criterion that the putative eyeblink factors would only be removed if doing so reduced the overall variance of the trial. This approach does still have some potential for causing the concerns that David raises but not as much as only applying the ICA to blink trials since it does end up getting applied to non-blink trials too. This does mean that one should be cautious about any apparent effects in the artifact corrected data that are centered around the eyes (that have a blink topography) but that goes without saying in any case. So anyway, I agree, it's not perfect but seems to be the best available option. Cheers! Joe On May 24, 2011, at 3:11 AM, Stefan Debener wrote: Hi Odelia, I have a slightly different opinion here. It is certainly true that any filter has the tendency to distort data (with distortion I mean that data consists of a mixture of some wanted, true signal and some unwanted signal, and that the removal of the unwanted part of the signal is neither complete nor specific). In our lab we regularly use ICA for artefact removal (and more), and the benefit/gain is clearly are much larger than the distortion. In fact there are a number of examples out showing that currently only ICA (or related tools) can recover the study of (a substantial fraction of the wanted) EEG signal (but again, it is NOT a perfect tool at all), in particular in cases where other means of SNR enhancement don't work well (averaging, spectral analysis). I am happy to provide references if you are interested... For the evaluation of outcome it would be reasonable to not evaluate the ERP alone, as this could be misleading. Better evaluate the sensitivity and specificity of an eye blink attentuation approach on the single trial (and single subject) level, this will give you good insight. And it is worth keeping in mind that the preprocessing of the data (among other issues, like the quality of the recording and so on) largely determines the quality of the output (for some introduction you may look up chapter 3.1 in Ullsperger & Debener, 2010, Simultaneous EEG and FMRI, Oxford University Press). Just by a different preprocessing ICA output could vary between crap and excellent unmixing. Thus a poor ICA eye blink attenuation would make me a bit suspicious... Best, Stefan Am 5/24/11 4:00 AM, schrieb Alexander J. Shackman: And for a related perspective, see McMenamin, B. W., Shackman, A. J., Greischar, L. L. & Davidson, R. J. (2011). Electromyogenic artifacts and electroencephalographic inferences revisited, Neuroimage, 54, 4-9. http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf On Mon, May 23, 2011 at 8:07 PM, Joseph Dien wrote: I agree with David's reasoning. You may find the following article to be of help as well in understanding the issues involved: Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of simulated ERPs: Promax versus Infomax rotations. Human Brain Mapping, 28(8), 742-763. Cheers! Joe On May 23, 2011, at 11:57 AM, David Groppe wrote: Hi Odelia, When you use ICA (or any other spatial filter) to correct for EEG artifacts, you're going to distort your data some by removing true EEG activity in addition to the artifact (for an explanation, see: http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). So to minimize distortion, it would be better not to apply ICA artifact correction to artifact-free data. However, if the frequency of the artifact differs across experimental conditions, it could confound your analysis. For example, I suspect people blink more often to targets in an oddball experiment than standards. Thus if you apply ICA only to blinky trials, you could find a difference between the EEG response to standards and targets that simply reflects the fact ICA removed more EEG activity in the target trials (i.e., it wouldn't reflect a true difference in neural processing). hope this helps, -David On Mon, May 23, 2011 at 1:44 AM, odelia nakar wrote: Hi all, I'm troubled by the fact that when I use ICA for blinks\eyes movements removal, I remove the relevant components also from trials that do not contain blinks\eyes movements. In order to avoid this bias we thought to combine the data before ICA ("data" structure) with the data after ICA ("dataica" structure), only in specific trials, as follows: datall=dataica; datall.trial=data.trial; datall.time=data.time; blinks=[2 4 5 8 bla bla 156]; for ind=1:length(blinks) datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; end To my first question: I just wanted to check that there is no problem with that, or any reason not to use it. Another issue- I use motor learning task, and I'm trying to understand what happens through the process, in terms of power-frequency changes through the process. How would you recommend that I'd use the ft_freqanalysis function? What method to use (or what do I need to consider when choosing the method field)? Thanks a lot, Odelia. _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- David Groppe, Ph.D. Postdoctoral Researcher Kutaslab Dept. of Cognitive Science University of California, San Diego http://www.cogsci.ucsd.edu/~dgroppe/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------------------------------------------------------------------------- Joseph Dien E-mail: jdien07 at mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://homepage.mac.com/jdien07/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Alexander J. Shackman, Ph.D. Wisconsin Psychiatric Institute & Clinics and Department of Psychology University of Wisconsin-Madison 1202 West Johnson Street Madison, Wisconsin 53706 Telephone: +1 (608) 358-5025 Fax: +1 (608) 265-2875 Email: shackman at wisc.edu http://psyphz.psych.wisc.edu/~shackman _______________________________________________ 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 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Y.Harpaz a link to the BIU MEG lab: http://faculty.biu.ac.il/~goldsa/index.html "Many were increasingly of the opinion that they'd all made a big mistake in coming down from the trees in the first place. And some said that even the trees had been a bad move, and that no one should ever have left the oceans". Douglas Adams _______________________________________________ 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 suforraxi at gmail.com Wed Jun 1 11:23:54 2011 From: suforraxi at gmail.com (Matteo Demuru) Date: Wed, 1 Jun 2011 11:23:54 +0200 Subject: [FieldTrip] WPLI question Message-ID: Hi, I have question about the WPLI: I would like to know why it can have either positive or negative value? It seems to me that it could be due from the relation (lagging or leading) between two signals, but I am not sure. Taking the absolute value of the WPLI is it a way to preserve the 'synchronization infomation' discardig which signal is leading or lagging? Thanks Matteo -------------- next part -------------- An HTML attachment was scrubbed... URL: From martinvinck at gmail.com Wed Jun 1 12:07:17 2011 From: martinvinck at gmail.com (Martin Vinck) Date: Wed, 1 Jun 2011 12:07:17 +0200 Subject: [FieldTrip] WPLI question In-Reply-To: References: Message-ID: <345B36F9-D0E3-43F4-8B7B-25333BB5681E@gmail.com> Hi Mateo, As it is computed in ft_connectivity_wpli it preserves the information about the sign, i.e. whether the average imaginary component of the cross-spectrum is positive or negative. That is, it estimates the average imaginary component of the cross-spectrum divided by the average magnitude of this imaginary component. By taking the absolute value over the output one gets a measure of the strength of the interaction,- WPLI as it is defined in the paper, by taking the sign one gets a measure of the direction of the interaction. The debiased WPLI estimator gets negative however as a consequence of the debiasing method - different issue. Best, Martin. From Elena.Orekhova at neuro.gu.se Wed Jun 1 12:23:29 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Wed, 1 Jun 2011 10:23:29 +0000 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECA991@exchccr1.neuro.gu.se> Dear fieldtrippers, This message is mainly for Neuromag users. When I do 'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. If I combine the two types of sensors without weighting, the result is meaningless. Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements. Does anybody know how to deal with this problem? Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.wibral at web.de Wed Jun 1 16:04:46 2011 From: michael.wibral at web.de (Michael Wibral) Date: Wed, 1 Jun 2011 16:04:46 +0200 (CEST) Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis Message-ID: <1960081272.1639684.1306937086986.JavaMail.fmail@mwmweb084> An HTML attachment was scrubbed... URL: From zechuan_he at hotmail.com Wed Jun 1 15:35:07 2011 From: zechuan_he at hotmail.com (Zeddy He) Date: Wed, 1 Jun 2011 11:35:07 -0200 Subject: [FieldTrip] Emotiv headset realtime capture In-Reply-To: References: Message-ID: Hi Valentin, I am not entirely sure exactly what part of the process you're not sure about. I'm new to fieldtrip as well and I have never heard of emotiv until today. I have, however, been playing around with FieldTrip's realtime acquisition part for the last couple of weeks(acq2ft, AcqBuffer), and maybe able to offer some pointers in getting it set up on your system. It seems that to use emotive2ft, you would have to compile it first, call upon it in matlab before starting your emotive software, and then start the emotiv software. I am not exactly sure what can read the bufferdata, though ft_realtime_signalviewer as well as viewer.exe may be good functions/programs to start off with. If you're using acq2ft or Acqbuffer already for realtime acquistion from another CTF device, you could try running one of those first either by standalone or their MATLAB equivilent functions, and then run emotiv2ft in matlab without any passed in parameters(unless you didn't decide to put the buffer on localhost:1972). You also might be able to just let the function create it's own buffer by giving it a new port, and then draw from that port seperately later on. Some troubles I've ran into while using FieldTrip's realtime functions include: shmget() errors on linux systems firewall blocking port number type in-compatibility and perhaps a couple others I can't recall at the moment. If you think I might be capable of assisting you, let me know and I'll see if I can give you additional details. Regards Zeddy > From: valentin.umbach at hu-berlin.de > Date: Tue, 31 May 2011 18:51:17 +0200 > To: fieldtrip at donders.ru.nl > Subject: [FieldTrip] Emotiv headset realtime capture > > Hi, I'm new to FieldTrip and I'm interested in using it to capture > realtime data from the Emotiv headset using this interface: > http://fieldtrip.fcdonders.nl/development/realtime/emotiv > I'm not clear about how to make calls to this interface from within > Matlab. Also, I would like to know if it's possible to access not just > the raw EEG, but also the API output of the detection libraries > (Affectiv Suite...). > Any help is greatly appreciated! > > Best, Valentin > > -- > Dipl.-Psych. Valentin J. Umbach > Institut für Psychologie > Humboldt-Universität zu Berlin > Rudower Chaussee 18 > 12489 Berlin > Tel. +49 30 2093 9438 > E-Mail: valentin.umbach at hu-berlin.de > > _______________________________________________ > 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 michael.wibral at web.de Thu Jun 2 13:18:04 2011 From: michael.wibral at web.de (michael.wibral at web.de) Date: Thu, 2 Jun 2011 13:18:04 +0200 (CEST) Subject: [FieldTrip] Poblem with options for ft_volumesegment Message-ID: <511684614.2148844.1307013484440.JavaMail.fmail@mwmweb077> An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Jun 2 13:26:45 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 2 Jun 2011 13:26:45 +0200 Subject: [FieldTrip] Poblem with options for ft_volumesegment In-Reply-To: <511684614.2148844.1307013484440.JavaMail.fmail@mwmweb077> References: <511684614.2148844.1307013484440.JavaMail.fmail@mwmweb077> Message-ID: Dear Michael, Thanks for reporting this; we'll look into it. Best, JM On Jun 2, 2011, at 1:18 PM, michael.wibral at web.de wrote: > Dear FT'ers, > > Davide Rivolta posted a problem with ft_volumesegment a while ago. > We have meanwhile solved this problem. > > There is (FT from may 31st) a problem with the handling of the > > cfg.smooth > > option. > > It's default is 'no', according to the function HELP. > However in line 434 of ft_volumesegment, this option is put into a > numerical array - this makes sense for a smoothing value. Also if no > specification is given at all, then a NaN is inserted into the > array. However if "no" is set explicitely then ft_getopt tries to > insert the string 'no' into the array which leads to an error. Below > is a script that is running and the error is once again detailed in > the commets. > In my opinion this could be fixed by simply updating te function HELP. > > Michael > > %%Brain segmentation – MRI > > > mri = ft_read_mri('NPD18_V2.mri'); > > cfg = []; > > cfg.spmversion = 'spm8'; > > cfg.output = 'tpm'; > > cfg.template = 'T1.nii'; > > cfg.units = 'mm'; > > cfg.write = 'no'; > > cfg.coordsys = 'ctf'; > > cfg.downsample = 2; > > cfg.smooth = NaN; % works. option 'no' as recommended (!) in > the function HELP throws an > > % error because ft_getopt > on line 434 of ft_volumesegment > > % tries to put a string of > length two into an array that is for numbers > > % leaving out this option > also worked, but some > > % people might try to use > this option > > segmentedmri = ft_volumesegment(cfg, mri); > > save ('segmentedmri'); > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Thu Jun 2 18:22:03 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Thu, 2 Jun 2011 16:22:03 +0000 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <1960081272.1639684.1306937086986.JavaMail.fmail@mwmweb084> References: <1960081272.1639684.1306937086986.JavaMail.fmail@mwmweb084> Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECAB58@exchccr1.neuro.gu.se> Dear Michael, I have tried to multiply the leadfield by -1 as you suggested: for i = 1 : size (grid.leadfield, 2) grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); end This had no effect on the 'lcmv' output. I attached the pictures for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ In this experiment I measured evoked field in response to the unilateral (left) click. The source is expected to be in the right superior temporal cortex. This is the case for ‘GRA only' and ’MAG only’ datasets. The combined sensors give meaningless result. Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Wednesday, June 01, 2011 4:04 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Elena, could you give the following a try: invert (*-1) the leadfileds for one of the two sensor types. Let me know what happens. I would also be interested in taking a look at the results - maybe you could sent images off-list: Michael.Wibral web.de. Michael ________________________________ Von: "Elena Orekhova" Gesendet: Jun 1, 2011 12:23:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "Arial"; }@font-face { font-family: "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: Times; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear fieldtrippers, This message is mainly for Neuromag users. When I do 'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. If I combine the two types of sensors without weighting, the result is meaningless. Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements. Does anybody know how to deal with this problem? Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: lcmv_St1_gra_1p2-1p5.jpg Type: image/jpeg Size: 22987 bytes Desc: lcmv_St1_gra_1p2-1p5.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: lcmv_St1_mag_1p2-1p5.jpg Type: image/jpeg Size: 22978 bytes Desc: lcmv_St1_mag_1p2-1p5.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: lcmv_St1_mag+gra_1p2-1p5.jpg Type: image/jpeg Size: 22576 bytes Desc: lcmv_St1_mag+gra_1p2-1p5.jpg URL: From michael.wibral at web.de Thu Jun 2 19:20:07 2011 From: michael.wibral at web.de (Michael Wibral) Date: Thu, 2 Jun 2011 19:20:07 +0200 (CEST) Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis Message-ID: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Thu Jun 2 20:03:16 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Thu, 2 Jun 2011 18:03:16 +0000 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F03ECAB58@exchccr1.neuro.gu.se> References: <1960081272.1639684.1306937086986.JavaMail.fmail@mwmweb084>, <32CC77C0C8A7AD4B9410934642608E1F03ECAB58@exchccr1.neuro.gu.se> Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECAB81@exchccr1.neuro.gu.se> Dear Michael, I did normalize the data (sourcepst.avg.nai=sourcepst.avg.pow./sourcepre.avg.pow) as it was suggested in the tutorial. I used the same scales in all plots for comparison purposes. If automatic scaling is used the result for MAG+GRA does not look any better (see attachment). >What you could do as a workaround is to average the separate results with a weighting per voxel and that >is corresponding to the squared norms of the leadfields for the respective modalities for a given voxel , this >would guarantee equal amounts of backprojected noise from both modalities (if I'm not mistaken). Thank you for your suggestion. I may use it as a last resort. Hopefully, there is still a way to get more optimal solution using both GRA and MAG in the same analysis... Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Elena Orekhova [Elena.Orekhova at neuro.gu.se] Sent: Thursday, June 02, 2011 6:22 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Michael, I have tried to multiply the leadfield by -1 as you suggested: for i = 1 : size (grid.leadfield, 2) grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); end This had no effect on the 'lcmv' output. I attached the pictures for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ In this experiment I measured evoked field in response to the unilateral (left) click. The source is expected to be in the right superior temporal cortex. This is the case for ‘GRA only' and ’MAG only’ datasets. The combined sensors give meaningless result. Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Wednesday, June 01, 2011 4:04 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Elena, could you give the following a try: invert (*-1) the leadfileds for one of the two sensor types. Let me know what happens. I would also be interested in taking a look at the results - maybe you could sent images off-list: Michael.Wibral web.de. Michael ________________________________ Von: "Elena Orekhova" Gesendet: Jun 1, 2011 12:23:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "Arial"; }@font-face { font-family: "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: Times; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear fieldtrippers, This message is mainly for Neuromag users. When I do 'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. If I combine the two types of sensors without weighting, the result is meaningless. Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements. Does anybody know how to deal with this problem? Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: lcmv_St1_mag+gra_autoscale.jpg Type: image/jpeg Size: 22257 bytes Desc: lcmv_St1_mag+gra_autoscale.jpg URL: From smoratti at psi.ucm.es Fri Jun 3 11:00:18 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Fri, 03 Jun 2011 11:00:18 +0200 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> References: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> Message-ID: <722801BA-5C22-4A69-8F87-18C1C54A7F00@psi.ucm.es> Hi Michael y Elena, I am following your discussion with great interest as I have just started to work with Neuromag data. As FT uses the MNE toolbox to read the data I assume that the SSP vectors are applied to the data during reading the data. However, the SSP vectors are stored in "data.hdr.orig.projs". However, when I go on with averaging in the ERF from timelockanalysis I cannot find this info. So my question is, does FT apply the SSP vectors later on also to the leadfield when calculating it? I assume that not, as the SSP vectors are not passed on further. How can I apply the SSP vectors to the leadfield to get correct results? Best and thanks, STephan El 02/06/2011, a las 19:20, Michael Wibral escribió: > Hi Elena, > > I assume that you were well aware of the difficulties in beamforming evoked activty and baseline normalisation and these things, your results really look that way. I mus say I am quite puzzled by the results - could it be a color scaling problem in the plot? I think this mmay be a problem because most of your plot is a peak power, only a tiny corner seems to be in a low-amplitude range. > > What you could do as a workaround is to average the separate results with a weighting per voxel and that is corresponding to the squared norms of the leadfields for the respective modalities for a given voxel , this would guarantee equal amounts of backprojected noise from both modalities (if I'm not mistaken). > > Michael > PS: I am away for a couple of days, but after that, I'll be happy to resume this discussion. > > > Von: "Elena Orekhova" > Gesendet: Jun 2, 2011 6:22:03 PM > An: "Email discussion list for the FieldTrip project" > Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis > > @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } > Dear Michael, > > > I have tried to multiply the leadfield by -1 as you suggested: > > > for i = 1 : size (grid.leadfield, 2) > > grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); > > end > > > This had no effect on the 'lcmv' output. I attached the pictures for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ > > > In this experiment I measured evoked field in response to the unilateral (left) click. > > The source is expected to be in the right superior temporal cortex. This is the case for ‘GRA only' and ’MAG only’ datasets. The combined sensors give meaningless result. > > > Elena > > > From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] > Sent: Wednesday, June 01, 2011 4:04 PM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis > > > Dear Elena, > > could you give the following a try: invert (*-1) the leadfileds for one of the two sensor types. Let me know what happens. > I would also be interested in taking a look at the results - maybe you could sent images off-list: Michael.Wibral web.de. > > Michael > > > > Von: "Elena Orekhova" > Gesendet: Jun 1, 2011 12:23:29 PM > An: "fieldtrip at donders.ru.nl" > Betreff: [FieldTrip] combining magnetometers and planad gradiometers for analysis > > @font-face { font-family: "Arial"; }@font-face { font-family: "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: Times; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } > Dear fieldtrippers, > > This message is mainly for Neuromag users. > > > When I do 'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. > > If I combine the two types of sensors without weighting, the result is meaningless. > > Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements. Does anybody know how to deal with this problem? > > > > Elena > > > > _______________________________________________ > 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 jan.schoffelen at donders.ru.nl Fri Jun 3 13:11:02 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 3 Jun 2011 13:11:02 +0200 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <722801BA-5C22-4A69-8F87-18C1C54A7F00@psi.ucm.es> References: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> <722801BA-5C22-4A69-8F87-18C1C54A7F00@psi.ucm.es> Message-ID: <77A55ECC-5A84-4839-9093-75FA499D3D31@donders.ru.nl> Hi Stephan et al, Any balancing coefficients (e.g. the digital weights for the bti- system, or ctf's 3d order gradient coefficients) are only applied to the leadfield if they end up in the data.grad.tra matrix. These .tra matrices will be compiled when reading the data header, by functions like XXX2grad (in fileio/private: ctf2grad, bti2grad, fif2grad). You can check whether it is constructed using hdr.orig.projs. If not, it may be worthwile to implement I guess. Best, JM On Jun 3, 2011, at 11:00 AM, Stephan Moratti wrote: > Hi Michael y Elena, > > I am following your discussion with great interest as I have just > started to work with Neuromag data. As FT uses the MNE toolbox to > read the data I assume that the SSP vectors are applied to the data > during reading the data. However, the SSP vectors are stored in > "data.hdr.orig.projs". However, when I go on with averaging in the > ERF from timelockanalysis I cannot find this info. So my question > is, does FT apply the SSP vectors later on also to the leadfield > when calculating it? I assume that not, as the SSP vectors are not > passed on further. How can I apply the SSP vectors to the leadfield > to get correct results? > > Best and thanks, > > STephan > > El 02/06/2011, a las 19:20, Michael Wibral escribió: > >> Hi Elena, >> >> I assume that you were well aware of the difficulties in >> beamforming evoked activty and baseline normalisation and these >> things, your results really look that way. I mus say I am quite >> puzzled by the results - could it be a color scaling problem in the >> plot? I think this mmay be a problem because most of your plot is a >> peak power, only a tiny corner seems to be in a low-amplitude range. >> >> What you could do as a workaround is to average the separate >> results with a weighting per voxel and that is corresponding to >> the squared norms of the leadfields for the respective modalities >> for a given voxel , this would guarantee equal amounts of >> backprojected noise from both modalities (if I'm not mistaken). >> >> Michael >> PS: I am away for a couple of days, but after that, I'll be happy >> to resume this discussion. >> >> >> Von: "Elena Orekhova" >> Gesendet: Jun 2, 2011 6:22:03 PM >> An: "Email discussion list for the FieldTrip project" > > >> Betreff: Re: [FieldTrip] combining magnetometers and planad >> gradiometers for analysis >> >> @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face >> { font-family: "Cambria Math"; }@font-face { font-family: >> "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal, >> li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: >> 12pt; font-family: Cambria; }.MsoChpDefault { font-family: >> Cambria; }div.WordSection1 { page: WordSection1; } >> Dear Michael, >> >> >> I have tried to multiply the leadfield by -1 as you suggested: >> >> >> for i = 1 : size (grid.leadfield, 2) >> >> grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); >> >> end >> >> >> This had no effect on the 'lcmv' output. I attached the pictures >> for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ >> >> >> In this experiment I measured evoked field in response to the >> unilateral (left) click. >> >> The source is expected to be in the right superior temporal >> cortex. This is the case for ‘GRA only' and ’MAG only’ datasets. >> The combined sensors give meaningless result. >> >> >> Elena >> >> >> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl >> ] on behalf of Michael Wibral [michael.wibral at web.de] >> Sent: Wednesday, June 01, 2011 4:04 PM >> To: Email discussion list for the FieldTrip project >> Subject: Re: [FieldTrip] combining magnetometers and planad >> gradiometers for analysis >> >> >> Dear Elena, >> >> could you give the following a try: invert (*-1) the leadfileds for >> one of the two sensor types. Let me know what happens. >> I would also be interested in taking a look at the results - maybe >> you could sent images off-list: Michael.Wibral web.de. >> >> Michael >> >> >> >> Von: "Elena Orekhova" >> Gesendet: Jun 1, 2011 12:23:29 PM >> An: "fieldtrip at donders.ru.nl" >> Betreff: [FieldTrip] combining magnetometers and planad >> gradiometers for analysis >> >> @font-face { font-family: "Arial"; }@font-face { font-family: >> "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D >> "; }@font-face { font-family: "Cambria Math"; }@font-face { font- >> family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal >> { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: >> Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; >> font-family: Times; }.MsoChpDefault { font-family: >> Cambria; }div.WordSection1 { page: WordSection1; } >> Dear fieldtrippers, >> >> This message is mainly for Neuromag users. >> >> >> When I do 'lcmv' beamforming analysis separately on planar >> gradiometers or magnetometers, I get quite meaningful results. >> >> If I combine the two types of sensors without weighting, the result >> is meaningless. >> >> Apparently, the algorithm does not take care of different scales >> and units of the GRA and MAG measurements. Does anybody know how >> to deal with this problem? >> >> >> >> Elena >> >> >> >> _______________________________________________ >> 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 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Fri Jun 3 14:25:46 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Fri, 3 Jun 2011 12:25:46 +0000 Subject: [FieldTrip] cfg.method = 'sam' Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECAC4F@exchccr1.neuro.gu.se> Dear colleagues, Sorry, I posted much on the list recent time. I want to figure out howto run SAM analysis on my data. When I run 'lcmv' beamformer on my averaged dataset it works fine: cfg = []; cfg.grad = hdr.grad; cfg.method = 'lcmv'; cfg.grid = grid; cfg.vol = vol_cm; cfg.reducerank=2; cfg.keepfilter = 'yes' cfg.channel = MAG; %MAG = {'MEG0721', 'MEG0731',... } source = ft_sourceanalysis(cfg, tlckavg); When I do the same with cfg.method = 'lcmv' option, I get the error: ***************************** ??? Undefined function or method 'beamformer_sam' for input arguments of type 'struct'. Error in ==> sourceanalysis at 1158 dip(i) = beamformer_sam(grid, sens, vol, squeeze(avg(i,:,:)), squeeze(Cy(i,:,:)), optarg{:}); Error in ==> ft_sourceanalysis at 11 [varargout{1:nargout}] = funhandle(varargin{:}); Does anybody know how to make the ‘SAM’ option to work? Does anybody used cfg.method = 'lcmv' option in the Fieldtrip??? Regards, Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Fri Jun 3 14:57:47 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Fri, 3 Jun 2011 12:57:47 +0000 Subject: [FieldTrip] cfg.method = 'sam' Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECAC6B@exchccr1.neuro.gu.se> Dear colleagues, Sorry, I posted much on the list recent time. I want to figure out how to run SAM analysis on my data. When I run 'lcmv' beamformer on my averaged dataset it works fine: cfg = []; cfg.grad = hdr.grad; cfg.method = 'lcmv'; cfg.grid = grid; cfg.vol = vol_cm; cfg.reducerank=2; cfg.keepfilter = 'yes' cfg.channel = MAG; %MAG = {'MEG0721', 'MEG0731',... } source = ft_sourceanalysis(cfg, tlckavg); When I do the same with cfg.method = 'sam' option, I get the error: ***************************** ??? Undefined function or method 'beamformer_sam' for input arguments of type 'struct'. Error in ==> sourceanalysis at 1158 dip(i) = beamformer_sam(grid, sens, vol, squeeze(avg(i,:,:)), squeeze(Cy(i,:,:)), optarg{:}); Error in ==> ft_sourceanalysis at 11 [varargout{1:nargout}] = funhandle(varargin{:}); Does anybody know how to make the ‘SAM’ option to work? Does anybody used cfg.method = 'sam' option in the Fieldtrip??? Regards, Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Fri Jun 3 15:08:53 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Fri, 03 Jun 2011 15:08:53 +0200 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <77A55ECC-5A84-4839-9093-75FA499D3D31@donders.ru.nl> References: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> <722801BA-5C22-4A69-8F87-18C1C54A7F00@psi.ucm.es> <77A55ECC-5A84-4839-9093-75FA499D3D31@donders.ru.nl> Message-ID: <32BF5576-A020-41A6-AF11-0879E03067FD@psi.ucm.es> Hi Jan-Mathijs, I had just a look at fif2grad.m and it seems to me that the information of hdr.orig.projs is not used to construct the .tra field. It only codes for magnetometers 1 and for the two gradiometers 1 and -1 (to get the difference). Going through the code I found out that FT uses mne2grad.m rather than fif2grad.m. But mne2grad.m does not use the info in hdr.orig.projs. Thus, it seems the information does not go into grad.tra. (So I guess the topographies and leadfields will not be correct when SSP vectors are used). Best, Stephan El 03/06/2011, a las 13:11, jan-mathijs schoffelen escribió: > Hi Stephan et al, > > Any balancing coefficients (e.g. the digital weights for the bti-system, or ctf's 3d order gradient coefficients) are only applied to the leadfield if they end up in the data.grad.tra matrix. These .tra matrices will be compiled when reading the data header, by functions like XXX2grad (in fileio/private: ctf2grad, bti2grad, fif2grad). > You can check whether it is constructed using hdr.orig.projs. > If not, it may be worthwile to implement I guess. > > Best, > > JM > > > > On Jun 3, 2011, at 11:00 AM, Stephan Moratti wrote: > >> Hi Michael y Elena, >> >> I am following your discussion with great interest as I have just started to work with Neuromag data. As FT uses the MNE toolbox to read the data I assume that the SSP vectors are applied to the data during reading the data. However, the SSP vectors are stored in "data.hdr.orig.projs". However, when I go on with averaging in the ERF from timelockanalysis I cannot find this info. So my question is, does FT apply the SSP vectors later on also to the leadfield when calculating it? I assume that not, as the SSP vectors are not passed on further. How can I apply the SSP vectors to the leadfield to get correct results? >> >> Best and thanks, >> >> STephan >> >> El 02/06/2011, a las 19:20, Michael Wibral escribió: >> >>> Hi Elena, >>> >>> I assume that you were well aware of the difficulties in beamforming evoked activty and baseline normalisation and these things, your results really look that way. I mus say I am quite puzzled by the results - could it be a color scaling problem in the plot? I think this mmay be a problem because most of your plot is a peak power, only a tiny corner seems to be in a low-amplitude range. >>> >>> What you could do as a workaround is to average the separate results with a weighting per voxel and that is corresponding to the squared norms of the leadfields for the respective modalities for a given voxel , this would guarantee equal amounts of backprojected noise from both modalities (if I'm not mistaken). >>> >>> Michael >>> PS: I am away for a couple of days, but after that, I'll be happy to resume this discussion. >>> >>> >>> Von: "Elena Orekhova" >>> Gesendet: Jun 2, 2011 6:22:03 PM >>> An: "Email discussion list for the FieldTrip project" >>> Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis >>> >>> @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } >>> Dear Michael, >>> >>> >>> I have tried to multiply the leadfield by -1 as you suggested: >>> >>> >>> for i = 1 : size (grid.leadfield, 2) >>> >>> grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); >>> >>> end >>> >>> >>> This had no effect on the 'lcmv' output. I attached the pictures for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ >>> >>> >>> In this experiment I measured evoked field in response to the unilateral (left) click. >>> >>> The source is expected to be in the right superior temporal cortex. This is the case for ‘GRA only' and ’MAG only’ datasets. The combined sensors give meaningless result. >>> >>> >>> Elena >>> >>> >>> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] >>> Sent: Wednesday, June 01, 2011 4:04 PM >>> To: Email discussion list for the FieldTrip project >>> Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis >>> >>> >>> Dear Elena, >>> >>> could you give the following a try: invert (*-1) the leadfileds for one of the two sensor types. Let me know what happens. >>> I would also be interested in taking a look at the results - maybe you could sent images off-list: Michael.Wibral web.de. >>> >>> Michael >>> >>> >>> >>> Von: "Elena Orekhova" >>> Gesendet: Jun 1, 2011 12:23:29 PM >>> An: "fieldtrip at donders.ru.nl" >>> Betreff: [FieldTrip] combining magnetometers and planad gradiometers for analysis >>> >>> @font-face { font-family: "Arial"; }@font-face { font-family: "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: Times; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } >>> Dear fieldtrippers, >>> >>> This message is mainly for Neuromag users. >>> >>> >>> When I do 'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. >>> >>> If I combine the two types of sensors without weighting, the result is meaningless. >>> >>> Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements. Does anybody know how to deal with this problem? >>> >>> >>> >>> Elena >>> >>> >>> >>> _______________________________________________ >>> 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 >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > _______________________________________________ > 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 jan.schoffelen at donders.ru.nl Fri Jun 3 15:22:10 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 3 Jun 2011 15:22:10 +0200 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <32BF5576-A020-41A6-AF11-0879E03067FD@psi.ucm.es> References: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> <722801BA-5C22-4A69-8F87-18C1C54A7F00@psi.ucm.es> <77A55ECC-5A84-4839-9093-75FA499D3D31@donders.ru.nl> <32BF5576-A020-41A6-AF11-0879E03067FD@psi.ucm.es> Message-ID: <9A770E4F-6106-4136-BADB-5BBCBE84862D@donders.ru.nl> Dear Stephan, Ah, you're right. I forgot about the mne2grad... Sorry. Regarding the SSP vectors I forgot to mention that of course the sensor data needs to have the SSP vectors incorporated as well, if such info is to be applied to the leadfields too? Either the data on disk is already balanced, or the coefficients need to be applied after reading in the unbalanced data. I don't know enough about the elekta- software/mne-software to know what is happening to the data when the ssp vectors are computed, but once we know enough details it should be straightforward to build it into fieldtrip. Best, JM On Jun 3, 2011, at 3:08 PM, Stephan Moratti wrote: > Hi Jan-Mathijs, > > I had just a look at fif2grad.m and it seems to me that the > information of hdr.orig.projs is not used to construct the .tra > field. It only codes for magnetometers 1 and for the two > gradiometers 1 and -1 (to get the difference). Going through the > code I found out that FT uses mne2grad.m rather than fif2grad.m. But > mne2grad.m does not use the info in hdr.orig.projs. Thus, it seems > the information does not go into grad.tra. (So I guess the > topographies and leadfields will not be correct when SSP vectors are > used). > > Best, > > Stephan > > El 03/06/2011, a las 13:11, jan-mathijs schoffelen escribió: > >> Hi Stephan et al, >> >> Any balancing coefficients (e.g. the digital weights for the bti- >> system, or ctf's 3d order gradient coefficients) are only applied >> to the leadfield if they end up in the data.grad.tra matrix. >> These .tra matrices will be compiled when reading the data header, >> by functions like XXX2grad (in fileio/private: ctf2grad, bti2grad, >> fif2grad). >> You can check whether it is constructed using hdr.orig.projs. >> If not, it may be worthwile to implement I guess. >> >> Best, >> >> JM >> >> >> >> On Jun 3, 2011, at 11:00 AM, Stephan Moratti wrote: >> >>> Hi Michael y Elena, >>> >>> I am following your discussion with great interest as I have just >>> started to work with Neuromag data. As FT uses the MNE toolbox to >>> read the data I assume that the SSP vectors are applied to the >>> data during reading the data. However, the SSP vectors are stored >>> in "data.hdr.orig.projs". However, when I go on with averaging in >>> the ERF from timelockanalysis I cannot find this info. So my >>> question is, does FT apply the SSP vectors later on also to the >>> leadfield when calculating it? I assume that not, as the SSP >>> vectors are not passed on further. How can I apply the SSP vectors >>> to the leadfield to get correct results? >>> >>> Best and thanks, >>> >>> STephan >>> >>> El 02/06/2011, a las 19:20, Michael Wibral escribió: >>> >>>> Hi Elena, >>>> >>>> I assume that you were well aware of the difficulties in >>>> beamforming evoked activty and baseline normalisation and these >>>> things, your results really look that way. I mus say I am quite >>>> puzzled by the results - could it be a color scaling problem in >>>> the plot? I think this mmay be a problem because most of your >>>> plot is a peak power, only a tiny corner seems to be in a low- >>>> amplitude range. >>>> >>>> What you could do as a workaround is to average the separate >>>> results with a weighting per voxel and that is corresponding to >>>> the squared norms of the leadfields for the respective modalities >>>> for a given voxel , this would guarantee equal amounts of >>>> backprojected noise from both modalities (if I'm not mistaken). >>>> >>>> Michael >>>> PS: I am away for a couple of days, but after that, I'll be happy >>>> to resume this discussion. >>>> >>>> >>>> Von: "Elena Orekhova" >>>> Gesendet: Jun 2, 2011 6:22:03 PM >>>> An: "Email discussion list for the FieldTrip project" >>> > >>>> Betreff: Re: [FieldTrip] combining magnetometers and planad >>>> gradiometers for analysis >>>> >>>> @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face >>>> { font-family: "Cambria Math"; }@font-face { font-family: >>>> "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal, >>>> li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font- >>>> size: 12pt; font-family: Cambria; }.MsoChpDefault { font-family: >>>> Cambria; }div.WordSection1 { page: WordSection1; } >>>> Dear Michael, >>>> >>>> >>>> I have tried to multiply the leadfield by -1 as you suggested: >>>> >>>> >>>> for i = 1 : size (grid.leadfield, 2) >>>> >>>> grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i} >>>> (3:3:306, :); >>>> >>>> end >>>> >>>> >>>> This had no effect on the 'lcmv' output. I attached the pictures >>>> for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ >>>> >>>> >>>> In this experiment I measured evoked field in response to the >>>> unilateral (left) click. >>>> >>>> The source is expected to be in the right superior temporal >>>> cortex. This is the case for ‘GRA only' and ’MAG only’ >>>> datasets. The combined sensors give meaningless result. >>>> >>>> >>>> Elena >>>> >>>> >>>> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl >>>> ] on behalf of Michael Wibral [michael.wibral at web.de] >>>> Sent: Wednesday, June 01, 2011 4:04 PM >>>> To: Email discussion list for the FieldTrip project >>>> Subject: Re: [FieldTrip] combining magnetometers and planad >>>> gradiometers for analysis >>>> >>>> >>>> Dear Elena, >>>> >>>> could you give the following a try: invert (*-1) the leadfileds >>>> for one of the two sensor types. Let me know what happens. >>>> I would also be interested in taking a look at the results - >>>> maybe you could sent images off-list: Michael.Wibral web.de. >>>> >>>> Michael >>>> >>>> >>>> >>>> Von: "Elena Orekhova" >>>> Gesendet: Jun 1, 2011 12:23:29 PM >>>> An: "fieldtrip at donders.ru.nl" >>>> Betreff: [FieldTrip] combining magnetometers and planad >>>> gradiometers for analysis >>>> >>>> @font-face { font-family: "Arial"; }@font-face { font-family: >>>> "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D >>>> "; }@font-face { font-family: "Cambria Math"; }@font-face { font- >>>> family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal >>>> { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: >>>> Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: >>>> 10pt; font-family: Times; }.MsoChpDefault { font-family: >>>> Cambria; }div.WordSection1 { page: WordSection1; } >>>> Dear fieldtrippers, >>>> >>>> This message is mainly for Neuromag users. >>>> >>>> >>>> When I do 'lcmv' beamforming analysis separately on planar >>>> gradiometers or magnetometers, I get quite meaningful results. >>>> >>>> If I combine the two types of sensors without weighting, the >>>> result is meaningless. >>>> >>>> Apparently, the algorithm does not take care of different scales >>>> and units of the GRA and MAG measurements. Does anybody know how >>>> to deal with this problem? >>>> >>>> >>>> >>>> Elena >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> Dr. J.M. (Jan-Mathijs) Schoffelen >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> J.Schoffelen at donders.ru.nl >> Telephone: 0031-24-3614793 >> >> _______________________________________________ >> 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 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri Jun 3 15:23:34 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 3 Jun 2011 15:23:34 +0200 Subject: [FieldTrip] cfg.method = 'sam' In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F03ECAC6B@exchccr1.neuro.gu.se> References: <32CC77C0C8A7AD4B9410934642608E1F03ECAC6B@exchccr1.neuro.gu.se> Message-ID: Hi Elena, At some point we had an implementation for sam in FieldTrip. Apparently, this has been taken out of the release version. I don't know whether this was on purpose, or whether there was a good reason to do so. The reason you get an error is that the function is missing. We will look into the missing function issue. For the time being, you could try lcmv, which is very similar to sam. Best, Jan-Mathijs On Jun 3, 2011, at 2:57 PM, Elena Orekhova wrote: > Dear colleagues, > Sorry, I posted much on the list recent time. I want to figure out > how to run SAM analysis on my data. > > When I run 'lcmv' beamformer on my averaged dataset it works fine: > cfg = []; > cfg.grad = hdr.grad; > cfg.method = 'lcmv'; > cfg.grid = grid; > cfg.vol = vol_cm; > cfg.reducerank=2; > cfg.keepfilter = 'yes' > cfg.channel = MAG; %MAG = {'MEG0721', 'MEG0731',... } > source = ft_sourceanalysis(cfg, tlckavg); > > > When I do the same with cfg.method = 'sam' option, > I get the error: > ***************************** > ??? Undefined function or method 'beamformer_sam' for input > arguments of type 'struct'. > > Error in ==> sourceanalysis at 1158 > dip(i) = beamformer_sam(grid, sens, vol, squeeze(avg(i,:,:)), > squeeze(Cy(i,:,:)), > optarg{:}); > > Error in ==> ft_sourceanalysis at 11 > [varargout{1:nargout}] = funhandle(varargin{:}); > > Does anybody know how to make the ‘SAM’ option to work? > Does anybody used cfg.method = 'sam' option in the Fieldtrip??? > > Regards, > Elena > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at inria.fr Fri Jun 3 15:30:25 2011 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Fri, 3 Jun 2011 09:30:25 -0400 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <9A770E4F-6106-4136-BADB-5BBCBE84862D@donders.ru.nl> References: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> <722801BA-5C22-4A69-8F87-18C1C54A7F00@psi.ucm.es> <77A55ECC-5A84-4839-9093-75FA499D3D31@donders.ru.nl> <32BF5576-A020-41A6-AF11-0879E03067FD@psi.ucm.es> <9A770E4F-6106-4136-BADB-5BBCBE84862D@donders.ru.nl> Message-ID: Hi everyone, > I don't know enough about the elekta-software/mne-software to know what is > happening to the data when the ssp vectors are computed, but once we know > enough details it should be straightforward to build it into fieldtrip. SSP vectors are stored in fif files and applied to data only if requested. In a typical MNE workflow, the SSP vectors are no directly applied to the raw file (avoid data duplication on disk) but rather to the noise covariance matrix and consequently in the whitening matrix. When computing an inverse solution, the whitening matrix is used on the data and the lead field, hence taking into account the SSP vectors. Hope this helps. -- Alexandre Gramfort, PhD gramfort at nmr.mgh.harvard.edu Dept. of Radiology MGH Martinos Center / Harvard Medical School http://www-sop.inria.fr/members/Alexandre.Gramfort/ From smoratti at psi.ucm.es Fri Jun 3 16:06:28 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Fri, 03 Jun 2011 16:06:28 +0200 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: References: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> <722801BA-5C22-4A69-8F87-18C1C54A7F00@psi.ucm.es> <77A55ECC-5A84-4839-9093-75FA499D3D31@donders.ru.nl> <32BF5576-A020-41A6-AF11-0879E03067FD@psi.ucm.es> <9A770E4F-6106-4136-BADB-5BBCBE84862D@donders.ru.nl> Message-ID: Hi everyone, Thanks Alexandre for the info. I went a little bit through the FT code and it seems that it reads the raw data without applying the SSP vectors on the data (raw.proj is empty!!). I saw in mne_ex_read_raw.m that you have to activate the projectors and then get the proj matrix with mne_make_projector_info .m It is a chan by chan matrix. So adding the proj matrix to the raw structure I understand that by using fiff_read_raw_segment .m I get the data filtered by the SSP vectors. So now my stupid? question: If I just multiply the grad.tra matrix by the proj matrix, this would fix everything (plotting topos and leadfield calculation???) best, Stephan El 03/06/2011, a las 15:30, Alexandre Gramfort escribió: > Hi everyone, > >> I don't know enough about the elekta-software/mne-software to know what is >> happening to the data when the ssp vectors are computed, but once we know >> enough details it should be straightforward to build it into fieldtrip. > > SSP vectors are stored in fif files and applied to data only if requested. > > In a typical MNE workflow, the SSP vectors are no directly applied to the raw > file (avoid data duplication on disk) but rather to the noise covariance matrix > and consequently in the whitening matrix. When computing an inverse solution, > the whitening matrix is used on the data and the lead field, hence taking > into account the SSP vectors. > > Hope this helps. > > -- > Alexandre Gramfort, PhD > gramfort at nmr.mgh.harvard.edu > Dept. of Radiology MGH Martinos Center / Harvard Medical School > http://www-sop.inria.fr/members/Alexandre.Gramfort/ > _______________________________________________ > 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 sylvana.schister at utah.edu Fri Jun 3 19:09:21 2011 From: sylvana.schister at utah.edu (Sylvana) Date: Fri, 03 Jun 2011 11:09:21 -0600 Subject: [FieldTrip] Question about layout for Neuromag data Message-ID: <1307120961.4481.1.camel@weston-desktop> Greetings - I have preprocessed and computed TF analysis on a set of neuromag data that I will like to visualize using ft_multiplotTFR. I found out that the function crashes when I try to plot the data. After trying to understand the source of the problem and comparing my analysis to the ones explained in the different tutorials, I found out that the layout produced for these data contains fields 'lay.width' and 'lay.height' that are zero vectors. These vectors are used in ft_multiplotTFR to define the axes of the different plots. Has anyone encountered this problem before? Any clue how to overcome it? I am a just getting familiar with FT and although I have read and followed the tutorials, I wouldn't exclude the possibility that I am doing something wrong. I will appreciate any help you can offer. Have a great day! Sylvana From michael.wibral at web.de Fri Jun 3 23:05:05 2011 From: michael.wibral at web.de (michael.wibral at web.de) Date: Fri, 3 Jun 2011 23:05:05 +0200 (CEST) Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis Message-ID: <533029427.749303.1307135105021.JavaMail.www-data@mwebmailfe05.dlan.cinetic.de> dear neuromag / fieldtrip community, just a small question so I can keep up with the dsicussion: I thought that (t)SSS would nor project in a classical sense, i.e. for activities from inside the head leadfields would not have to be corrected? at least this I have read on the neuromeg list. So in most respcts the data should be treated just like rawdata - with standard coil positions after the motion correction ? maybe someone can shed more light on this? michael -----Ursprüngliche Nachricht----- Von: "Alexandre Gramfort" Gesendet: 03.06.11 15:30:25 An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis >Hi everyone, > > > I don't know enough about the elekta-software/mne-software to know what is > > happening to the data when the ssp vectors are computed, but once we know > > enough details it should be straightforward to build it into fieldtrip. > > SSP vectors are stored in fif files and applied to data only if requested. > > In a typical MNE workflow, the SSP vectors are no directly applied to the raw > file (avoid data duplication on disk) but rather to the noise covariance matrix > and consequently in the whitening matrix. When computing an inverse solution, > the whitening matrix is used on the data and the lead field, hence taking > into account the SSP vectors. > > Hope this helps. > > -- > Alexandre Gramfort, PhD > gramfort at nmr.mgh.harvard.edu > Dept. of Radiology MGH Martinos Center / Harvard Medical School > http://www-sop.inria.fr/members/Alexandre.Gramfort/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: From tony.w.wilson at gmail.com Sat Jun 4 00:09:08 2011 From: tony.w.wilson at gmail.com (Tony W. Wilson) Date: Fri, 3 Jun 2011 17:09:08 -0500 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <533029427.749303.1307135105021.JavaMail.www-data@mwebmailfe05.dlan.cinetic.de> References: <533029427.749303.1307135105021.JavaMail.www-data@mwebmailfe05.dlan.cinetic.de> Message-ID: Dear Michael, everyone, I believe you are correct. Most Neuromag sites have SSP vectors computed for data acquisitions; some groups occasionally recompute these per subject. These acquisition SSP vectors are stored in the fif file, but not applied w/o user intervention. In addition, I believe the tag relating to these vectors is removed from the fif file if you apply (t)SSS (through Maxfilter). However, I am not totally certain because I have never tried to apply these SSP vectors after applying SSS. Regardless, during analysis I treat the motion corrected t(SSS) output files just like raw data files. ... It is also worth noting here that one can compute new sets of SSP vectors in the MNE software (not directly related to the data acquisition vectors) and save these with the fif file for later use. I am not sure if these SSP vectors can be used outside of the MNE software. Tony On Fri, Jun 3, 2011 at 4:05 PM, wrote: > dear neuromag / fieldtrip community, > > just a small question so I can keep up with the dsicussion: > I thought that (t)SSS would nor project in a classical sense, i.e. for > activities from inside the head leadfields would not have to be corrected? > at least this I have read on the neuromeg list. So in most respcts the data > should be treated just like rawdata - with standard coil positions after the > motion correction ? > > maybe someone can shed more light on this? > > michael > > -----Ursprüngliche Nachricht----- > Von: "Alexandre Gramfort" > Gesendet: 03.06.11 15:30:25 > An: "Email discussion list for the FieldTrip project" < > fieldtrip at donders.ru.nl> > Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers > for analysis > > >Hi everyone, > > > > > I don't know enough about the elekta-software/mne-software to know what > is > > > happening to the data when the ssp vectors are computed, but once we > know > > > enough details it should be straightforward to build it into fieldtrip. > > > > SSP vectors are stored in fif files and applied to data only if > requested. > > > > In a typical MNE workflow, the SSP vectors are no directly applied to the > raw > > file (avoid data duplication on disk) but rather to the noise covariance > matrix > > and consequently in the whitening matrix. When computing an inverse > solution, > > the whitening matrix is used on the data and the lead field, hence taking > > into account the SSP vectors. > > > > Hope this helps. > > > > -- > > Alexandre Gramfort, PhD > > gramfort at nmr.mgh.harvard.edu > > Dept. of Radiology MGH Martinos Center / Harvard Medical School > > http://www-sop.inria.fr/members/Alexandre.Gramfort/ > > _______________________________________________ > > 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 smoratti at psi.ucm.es Sat Jun 4 11:54:55 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Sat, 04 Jun 2011 11:54:55 +0200 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: References: <533029427.749303.1307135105021.JavaMail.www-data@mwebmailfe05.dlan.cinetic.de> Message-ID: <60211D3C-5BDA-49AE-8F17-B83594F7DB09@psi.ucm.es> Dear everyone, It would be cool to have the possibility to choose if one wants to apply the SSP vectors or not. Some sites use them, others use SSS or tSSS, depends how noisy your environment is. I think it is good that the data is read in raw format and that the SSP vectors are not applied as default, but it would be great to have the possibility to do so. What do you think? Stephan El 04/06/2011, a las 0:09, Tony W. Wilson escribió: > Dear Michael, everyone, > I believe you are correct. Most Neuromag sites have SSP vectors > computed for data acquisitions; some groups occasionally recompute > these per subject. These acquisition SSP vectors are stored in the > fif file, but not applied w/o user intervention. In addition, I > believe the tag relating to these vectors is removed from the fif > file if you apply (t)SSS (through Maxfilter). However, I am not > totally certain because I have never tried to apply these SSP > vectors after applying SSS. Regardless, during analysis I treat the > motion corrected t(SSS) output files just like raw data files. ... > It is also worth noting here that one can compute new sets of SSP > vectors in the MNE software (not directly related to the data > acquisition vectors) and save these with the fif file for later > use. I am not sure if these SSP vectors can be used outside of the > MNE software. > > Tony > > On Fri, Jun 3, 2011 at 4:05 PM, wrote: > dear neuromag / fieldtrip community, > > just a small question so I can keep up with the dsicussion: > I thought that (t)SSS would nor project in a classical sense, i.e. > for activities from inside the head leadfields would not have to be > corrected? at least this I have read on the neuromeg list. So in > most respcts the data should be treated just like rawdata - with > standard coil positions after the motion correction ? > > maybe someone can shed more light on this? > > michael > > -----Ursprüngliche Nachricht----- > Von: "Alexandre Gramfort" > Gesendet: 03.06.11 15:30:25 > An: "Email discussion list for the FieldTrip project" > > Betreff: Re: [FieldTrip] combining magnetometers and planad > gradiometers for analysis > > >Hi everyone, > > > > > I don't know enough about the elekta-software/mne-software to > know what is > > > happening to the data when the ssp vectors are computed, but > once we know > > > enough details it should be straightforward to build it into > fieldtrip. > > > > SSP vectors are stored in fif files and applied to data only if > requested. > > > > In a typical MNE workflow, the SSP vectors are no directly applied > to the raw > > file (avoid data duplication on disk) but rather to the noise > covariance matrix > > and consequently in the whitening matrix. When computing an > inverse solution, > > the whitening matrix is used on the data and the lead field, hence > taking > > into account the SSP vectors. > > > > Hope this helps. > > > > -- > > Alexandre Gramfort, PhD > > gramfort at nmr.mgh.harvard.edu > > Dept. of Radiology MGH Martinos Center / Harvard Medical School > > http://www-sop.inria.fr/members/Alexandre.Gramfort/ > > _______________________________________________ > > 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 ________________________________________________________ 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 Mon Jun 6 12:37:53 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Mon, 06 Jun 2011 12:37:53 +0200 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: References: <533029427.749303.1307135105021.JavaMail.www-data@mwebmailfe05.dlan.cinetic.de> Message-ID: <6B0B1BCA-8D99-4123-93CA-830E7E4D07B8@psi.ucm.es> Dear all, Looking at the MNE toolbox code, I think the following could be done to get the SSP projection if wanted: %% do SSP projection on data %%%% added by stephan moratti to do SSP for k = 1:length(data.hdr.orig.projs) data.hdr.orig.projs(k).active = true; end fprintf(1,'%d projection items activated\n',length(data.hdr.orig.projs)); [proj,nproj] = mne_make_projector_info(data.hdr.orig); data.hdr.orig.raw.proj = proj; % now apply to data for i = 1:length(data.trial) data.trial{i} = proj*data.trial{i}; end However, I am not sure how to put them into the grad.tra field. Best, Stephan El 04/06/2011, a las 00:09, Tony W. Wilson escribió: > Dear Michael, everyone, > I believe you are correct. Most Neuromag sites have SSP vectors computed for data acquisitions; some groups occasionally recompute these per subject. These acquisition SSP vectors are stored in the fif file, but not applied w/o user intervention. In addition, I believe the tag relating to these vectors is removed from the fif file if you apply (t)SSS (through Maxfilter). However, I am not totally certain because I have never tried to apply these SSP vectors after applying SSS. Regardless, during analysis I treat the motion corrected t(SSS) output files just like raw data files. ... It is also worth noting here that one can compute new sets of SSP vectors in the MNE software (not directly related to the data acquisition vectors) and save these with the fif file for later use. I am not sure if these SSP vectors can be used outside of the MNE software. > > Tony > > On Fri, Jun 3, 2011 at 4:05 PM, wrote: > dear neuromag / fieldtrip community, > > just a small question so I can keep up with the dsicussion: > I thought that (t)SSS would nor project in a classical sense, i.e. for activities from inside the head leadfields would not have to be corrected? at least this I have read on the neuromeg list. So in most respcts the data should be treated just like rawdata - with standard coil positions after the motion correction ? > > maybe someone can shed more light on this? > > michael > > -----Ursprüngliche Nachricht----- > Von: "Alexandre Gramfort" > Gesendet: 03.06.11 15:30:25 > An: "Email discussion list for the FieldTrip project" > Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis > > >Hi everyone, > > > > > I don't know enough about the elekta-software/mne-software to know what is > > > happening to the data when the ssp vectors are computed, but once we know > > > enough details it should be straightforward to build it into fieldtrip. > > > > SSP vectors are stored in fif files and applied to data only if requested. > > > > In a typical MNE workflow, the SSP vectors are no directly applied to the raw > > file (avoid data duplication on disk) but rather to the noise covariance matrix > > and consequently in the whitening matrix. When computing an inverse solution, > > the whitening matrix is used on the data and the lead field, hence taking > > into account the SSP vectors. > > > > Hope this helps. > > > > -- > > Alexandre Gramfort, PhD > > gramfort at nmr.mgh.harvard.edu > > Dept. of Radiology MGH Martinos Center / Harvard Medical School > > http://www-sop.inria.fr/members/Alexandre.Gramfort/ > > _______________________________________________ > > 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 ________________________________________________________ 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 valentin.umbach at hu-berlin.de Mon Jun 6 14:18:51 2011 From: valentin.umbach at hu-berlin.de (Valentin J. Umbach) Date: Mon, 6 Jun 2011 14:18:51 +0200 Subject: [FieldTrip] Emotiv headset realtime capture Message-ID: Hi Zeddy, thanks alot for your reply. FieldTrip comes with a precompiled version of emotiv2ft.exe. However, I can't get this to connect with my hardware. I've been trying to change some code in emotiv2ft.cc, but I couldn't compile it using mingw (as suggested here: http://fieldtrip.fcdonders.nl/development/realtime/emotiv). If you haven't worked with the Emotiv headset, this might be too specific. I wonder who wrote the interface to FieldTrip - someone must have connected the two before... Best, Valentin - Zitierten Text ausblenden - > > Message: 4 > Date: Wed, 1 Jun 2011 11:35:07 -0200 > From: Zeddy He > To: > Subject: Re: [FieldTrip] Emotiv headset realtime capture > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > > Hi Valentin, > > I am not entirely sure exactly what part of the process you're not sure about. I'm new to fieldtrip as well and I have never heard of emotiv until today. I have, however, been playing around with FieldTrip's realtime acquisition part for the last couple of weeks(acq2ft, AcqBuffer), and maybe able to offer some pointers in getting it set up on your system. > It seems that to use emotive2ft, you would have to compile it first, call upon it in matlab before starting your emotive software, and then start the emotiv software. I am not exactly sure what can read the bufferdata, though ft_realtime_signalviewer as well as viewer.exe may be good functions/programs to start off with. > If you're using acq2ft or Acqbuffer already for realtime acquistion from another CTF device, you could try running one of those first either by standalone or their MATLAB equivilent functions, and then run emotiv2ft in matlab without any passed in parameters(unless you didn't decide to put the buffer on localhost:1972). You also might be able to just let the function create it's own buffer by giving it a new port, and then draw from that port seperately later on. > Some troubles I've ran into while using FieldTrip's realtime functions include: > shmget() errors on linux systems > firewall blocking port > number type in-compatibility > and perhaps a couple others I can't recall at the moment. > > If you think I might be capable of assisting you, let me know and I'll see if I can give you additional details. > > Regards > > Zeddy > > >> From: valentin.umbach at hu-berlin.de >> Date: Tue, 31 May 2011 18:51:17 +0200 >> To: fieldtrip at donders.ru.nl >> Subject: [FieldTrip] Emotiv headset realtime capture >> >> Hi, I'm new to FieldTrip and I'm interested in using it to capture >> realtime data from the Emotiv headset using this interface: >> http://fieldtrip.fcdonders.nl/development/realtime/emotiv >> I'm not clear about how to make calls to this interface from within >> Matlab. Also, I would like to know if it's possible to access not just >> the raw EEG, but also the API output of the detection libraries >> (Affectiv Suite...). >> Any help is greatly appreciated! >> >> Best, Valentin >> >> -- >> Dipl.-Psych. Valentin J. Umbach >> Institut f?r Psychologie >> Humboldt-Universit?t zu Berlin >> Rudower Chaussee 18 >> 12489 Berlin >> Tel. +49 30 2093 9438 >> E-Mail: valentin.umbach at hu-berlin.de >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From n.a.kloosterman at uva.nl Mon Jun 6 15:28:41 2011 From: n.a.kloosterman at uva.nl (Kloosterman, Niels) Date: Mon, 6 Jun 2011 13:28:41 +0000 Subject: [FieldTrip] Problem passing arguments to peerslave command line executable Message-ID: Dear Fieldtrippers, Although I have succesfully used the command-line ./peerslave.glnxa64 to launch slaves for parallel analysis of my batch jobs, I am somehow not able to pass arguments to the command, for example ./peerslave.glnxa64 --number 8, to launch 8 slaves at once. Could anybody tell me what’s going on? When I execute without arguments this line pops up: peerslave[9705]: peerinit: niels at gb-r35n18.irc.sara.nl, id = 4020038417 All seems fine: the master is indeed able to send jobs to the slave. No other information is printed to the shell when it gets a job or whatever (is this normal?). Now when I try to run the --help I get this: niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./peerslave.glnxa64 --help peerslave[9753]: peerinit: niels at gb-r35n18.irc.sara.nl, id = 2887682376 parser: cannot open file --help peerslave[9753]: cannot read the configuration file And when I try to do --number 8: niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./peerslave.glnxa64 --number 8 peerslave[9759]: peerinit: niels at gb-r35n18.irc.sara.nl, id = 3997336815 ./peerslave.glnxa64: unrecognized option '--number' peerslave[9759]: invalid command line options I have recompiled the peerslave.glnxa64 by editing the Makefile and using make, but the problem stays. I am using MATLAB 2011a on a 64 bit linux node with 8 cores on a grid computer, which I access using ssh –X. Any ideas would be appreciated! Best, Niels Kloosterman -- Niels A. Kloosterman MSc.| PhD student | University of Amsterdam | Cognitive Neuroscience Group | Dept. of Psychology | Roetersstraat 15, A614 | 1018 WB Amsterdam | Tel: +31 20 525 6847 -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Mon Jun 6 20:32:07 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 6 Jun 2011 20:32:07 +0200 Subject: [FieldTrip] Emotiv headset realtime capture In-Reply-To: References: Message-ID: Dear Valentin The interface was implemented by Stefan Klanke here at the Donders for the BrainGain project, but he is not working with us any more. He has been testing it and it worked for him. I don't have an emotiv headset myself, but think that Ali Bahramisharif (CC), one of our colleagues, is in possession of the headset that Stefan used for testing. I checked the fieldtrip/realtime/acquisition/emotiv/emotiv2ft.cc source code, and from what I see it it requires additional software from emotiv that is not included with the fieldtrip release. See http://emotiv.com/developer/SDK/UserManual.pdf and specifically chapter 5. If that emotiv software developers kit is missing from your computer, you'll be getting errors that the compiler cannot find the edk.h, EmoStateDLL.h and/or edkErrorCode.h header files. It might also be that you need import libraries on your compile path. Please have a look in fieldtrip/realtime/acquisition/emotiv/Makefile for some further instructions. Hope this helps. If not, Ali (CC) might be able to provide some additional information. best, Robert On 6 Jun 2011, at 14:18, Valentin J. Umbach wrote: > Hi Zeddy, > > thanks alot for your reply. > FieldTrip comes with a precompiled version of emotiv2ft.exe. However, > I can't get this to connect with my hardware. I've been trying to > change some code in emotiv2ft.cc, but I couldn't compile it using > mingw (as suggested here: > http://fieldtrip.fcdonders.nl/development/realtime/emotiv). > If you haven't worked with the Emotiv headset, this might be too > specific. I wonder who wrote the interface to FieldTrip - someone must > have connected the two before... > > Best, Valentin > - Zitierten Text ausblenden - > >> >> Message: 4 >> Date: Wed, 1 Jun 2011 11:35:07 -0200 >> From: Zeddy He >> To: >> Subject: Re: [FieldTrip] Emotiv headset realtime capture >> Message-ID: >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Hi Valentin, >> >> I am not entirely sure exactly what part of the process you're not sure about. I'm new to fieldtrip as well and I have never heard of emotiv until today. I have, however, been playing around with FieldTrip's realtime acquisition part for the last couple of weeks(acq2ft, AcqBuffer), and maybe able to offer some pointers in getting it set up on your system. >> It seems that to use emotive2ft, you would have to compile it first, call upon it in matlab before starting your emotive software, and then start the emotiv software. I am not exactly sure what can read the bufferdata, though ft_realtime_signalviewer as well as viewer.exe may be good functions/programs to start off with. >> If you're using acq2ft or Acqbuffer already for realtime acquistion from another CTF device, you could try running one of those first either by standalone or their MATLAB equivilent functions, and then run emotiv2ft in matlab without any passed in parameters(unless you didn't decide to put the buffer on localhost:1972). You also might be able to just let the function create it's own buffer by giving it a new port, and then draw from that port seperately later on. >> Some troubles I've ran into while using FieldTrip's realtime functions include: >> shmget() errors on linux systems >> firewall blocking port >> number type in-compatibility >> and perhaps a couple others I can't recall at the moment. >> >> If you think I might be capable of assisting you, let me know and I'll see if I can give you additional details. >> >> Regards >> >> Zeddy >> >> >>> From: valentin.umbach at hu-berlin.de >>> Date: Tue, 31 May 2011 18:51:17 +0200 >>> To: fieldtrip at donders.ru.nl >>> Subject: [FieldTrip] Emotiv headset realtime capture >>> >>> Hi, I'm new to FieldTrip and I'm interested in using it to capture >>> realtime data from the Emotiv headset using this interface: >>> http://fieldtrip.fcdonders.nl/development/realtime/emotiv >>> I'm not clear about how to make calls to this interface from within >>> Matlab. Also, I would like to know if it's possible to access not just >>> the raw EEG, but also the API output of the detection libraries >>> (Affectiv Suite...). >>> Any help is greatly appreciated! >>> >>> Best, Valentin >>> >>> -- >>> Dipl.-Psych. Valentin J. Umbach >>> Institut f?r Psychologie >>> Humboldt-Universit?t zu Berlin >>> Rudower Chaussee 18 >>> 12489 Berlin >>> Tel. +49 30 2093 9438 >>> E-Mail: valentin.umbach at hu-berlin.de >>> >>> _______________________________________________ >>> 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 r.oostenveld at donders.ru.nl Mon Jun 6 20:39:18 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 6 Jun 2011 20:39:18 +0200 Subject: [FieldTrip] cfg.method = 'sam' In-Reply-To: References: <32CC77C0C8A7AD4B9410934642608E1F03ECAC6B@exchccr1.neuro.gu.se> Message-ID: Dear Elena The SAM implementation was contributed some time ago by Gareth Barnes, but apaprently went missing in the release version. I found the missing files in an older versionand just added them to the latest release version(*). Note that I did not test them for some time and also did not test them right now. It might be that you'll get follow up problems. If so, better report them on bugzilla.fcdonders.nl and not on the email list. best regards, Robert PS (*) please download the FT version of this evening, which will include the beamformer_sam function which you need for cfg.method='sam' in ft_sourceanalysis. On 3 Jun 2011, at 15:23, jan-mathijs schoffelen wrote: > Hi Elena, > > At some point we had an implementation for sam in FieldTrip. Apparently, this has been taken out of the release version. I don't know whether this was on purpose, or whether there was a good reason to do so. > The reason you get an error is that the function is missing. We will look into the missing function issue. > For the time being, you could try lcmv, which is very similar to sam. > > Best, > > Jan-Mathijs > > > On Jun 3, 2011, at 2:57 PM, Elena Orekhova wrote: > >> Dear colleagues, >> Sorry, I posted much on the list recent time. I want to figure out how to run SAM analysis on my data. >> >> When I run 'lcmv' beamformer on my averaged dataset it works fine: >> cfg = []; >> cfg.grad = hdr.grad; >> cfg.method = 'lcmv'; >> cfg.grid = grid; >> cfg.vol = vol_cm; >> cfg.reducerank=2; >> cfg.keepfilter = 'yes' >> cfg.channel = MAG; %MAG = {'MEG0721', 'MEG0731',... } >> source = ft_sourceanalysis(cfg, tlckavg); >> >> >> When I do the same with cfg.method = 'sam' option, >> I get the error: >> ***************************** >> ??? Undefined function or method 'beamformer_sam' for input arguments of type 'struct'. >> >> Error in ==> sourceanalysis at 1158 >> dip(i) = beamformer_sam(grid, sens, vol, squeeze(avg(i,:,:)), squeeze(Cy(i,:,:)), >> optarg{:}); >> >> Error in ==> ft_sourceanalysis at 11 >> [varargout{1:nargout}] = funhandle(varargin{:}); >> >> Does anybody know how to make the ‘SAM’ option to work? >> Does anybody used cfg.method = 'sam' option in the Fieldtrip??? >> >> Regards, >> Elena >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > _______________________________________________ > 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 r.oostenveld at donders.ru.nl Mon Jun 6 21:18:53 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 6 Jun 2011 21:18:53 +0200 Subject: [FieldTrip] questions about realtime buffer In-Reply-To: References: Message-ID: Dear Amelie > I’m implementing a realtime buffer in C++ pretty much like in “demo_combined” : my application creates a buffer server and an acquisition client. > I encountered a first problem when trying to close the buffer server cleanly, but with some small changes in tcpsocket.c and tcpserver.c, I think I solved the problem. > If these modifications can be useful for other users and do not create other problems, I will share them. If you have changes that don't break the ANSI-C compilation then I am certainly happy to include them in our version. Please go to http://bugzilla.fcdonders.nl and submit a bug/request in which you attach the updated files. > I encounter now a new problem : what if there are several acquisition clients ? > I tried to create several couples “buffer-server + acquisition client” in different threads in my application, but it does not work at all, because of global variables (I suppose). > It seems that one buffer server can not manage several acquisition clients, but I’m not sure of this point. > Did anyone encounter this problem (or solve it) ? > Or do anyone have an idea ? You are right about the global variables. The buffer is implemented using multithreading and to ensure that incoming data (Write) does not interfere with outgoing (read) data a mutex (http://en.wikipedia.org/wiki/Mutual_exclusion) is set. That mutex is shared throughout the code so that all pieces of code are aware of when they are allowed to change the buffer content. Having multiple buffers would require multiple mutexes and multiple (separately identifyable) memory segments for the actual data. That would require a lot of changes to the code. You can run multiple buffers on the same computer, but you would have to start them separately and they would have to have different TCP ports. The application you are writing could write different aspects to the different TCP ports. You can use fieldtrip/realtime/general/buffer.exe, which in fact is a compiled version of fieldtrip/realtime/buffer/test/demo_buffer. Note that you would use it as buffer.exe localhost 2340 buffer.exe localhost 2341 buffer.exe localhost 2342 buffer.exe localhost 2343 to start 4 buffers on ports 2340-2343. The "localhost" argument is not used, but still appears to be required according to the demo_buffer.c source code. Of course it is cumbersome to have to start the 4 seperate processes on top of your own application. On unix-like computers you should be able to write a single application that at the beginning forks into a parent and child, where the parent continues as your application and where the child (which is then a separate process) can start the buffer. You can fork multiple times, to have multiple buffers (one per child). best Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: From batrod at gmail.com Tue Jun 7 00:51:20 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Mon, 6 Jun 2011 17:51:20 -0500 Subject: [FieldTrip] Weird trialfun_general error Message-ID: Dear fieldtrippers, i just noticed and found the origin of a weird error obtained with the trialfun_general function, i thought it could be useful to send it here. I use the ft_definetrial function on a file obtained using the merge function in EEGlab. Apparently, this function is adding some triggers with the value 'boundary' in the new file, indicating the old frontier between the dataset that have been merged. The funny part is that the trialfun_general() function in fieltrip is using the intersect() matlab function to match event values. Moreover, im using 27 different event values to indicate point of interest (112,114,116,122,etc...) All of my event values dont create any problems except the value 114 because intersect('boundary',114) = 114 whereas it gives an empty result with any other of my values... Therefore, for that particular event value, there was a dimension mismatch between trl and val in trialfun_general. I just removed events with 'boundary' values and it worked. Best regards, Rodolphe Nenert, Ph.D. -------------- next part -------------- An HTML attachment was scrubbed... URL: From johemart at gmail.com Tue Jun 7 01:36:51 2011 From: johemart at gmail.com (=?ISO-8859-1?Q?Johann_Heinz_Mart=EDnez_Huartos?=) Date: Tue, 7 Jun 2011 01:36:51 +0200 Subject: [FieldTrip] Reference to non-existent field 'statistic' !????? Message-ID: Hello dear fieldtrip guys. Im new using this toolbox and i dont understand why is happened this error that i think it must be easy to solve but I have tryed and nothing happend. The thing is that im following (step by step) the tutorial for multivariableanalysis from fieldtrip wiki using the data that web link offer us. But when I run the command: stat = ft_timelockstatistics(cfg,tleft,tright); there are appear those errors: ??? Reference to non-existent field 'statistic'. Error in ==> prepare_design at 67 if any(strcmp(cfg.statistic,{'indepsamplesT','indepsamplesregrT','indepsamplesZcoh','indepsamplesF'})) Error in ==> statistics_wrapper at 249 [cfg] = prepare_design(cfg); Error in ==> ft_timelockstatistics at 123 [stat, cfg] = statistics_wrapper(cfg, varargin{:}); Error in ==> JohannTestFieldtrip at 45 stat = ft_timelockstatistics(cfg,tleft,tright); and i Dunno what can i do... Im using Matlab (R2011a) and the (fieldtrip-20110603). I have been looking for the documentation and i coundt find out how to fix it. Is it probably the matlab version very new? Which would be the last matlab version available using for? Thanks -- Atentamente: Johann Martínez. -------------- next part -------------- An HTML attachment was scrubbed... URL: From n.a.kloosterman at uva.nl Tue Jun 7 10:33:39 2011 From: n.a.kloosterman at uva.nl (Kloosterman, Niels) Date: Tue, 7 Jun 2011 08:33:39 +0000 Subject: [FieldTrip] Problem passing arguments to peerslave command line executable Message-ID: Dear Fieldtrippers, Although I have succesfully used the command-line ./peerslave.glnxa64 to launch slaves for parallel analysis of my batch jobs, I am somehow not able to pass arguments to the command, for example ./peerslave.glnxa64 --number 8, to launch 8 slaves at once. Could anybody tell me what’s going on? When I execute without arguments this line pops up: niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./peerslave.glnxa64 peerslave[9705]: peerinit: niels at gb-r35n18.irc.sara.nl, id = 4020038417 All seems fine: the master is indeed able to send jobs to the slave. No other information is printed to the shell when it gets a job or whatever (is this normal?). Now when I try to run the --help I get this: niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./peerslave.glnxa64 --help peerslave[9753]: peerinit: niels at gb-r35n18.irc.sara.nl, id = 2887682376 parser: cannot open file --help peerslave[9753]: cannot read the configuration file And when I try to do --number 8: niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./peerslave.glnxa64 --number 8 peerslave[9759]: peerinit: niels at gb-r35n18.irc.sara.nl, id = 3997336815 ./peerslave.glnxa64: unrecognized option '--number' peerslave[9759]: invalid command line options I have recompiled the peerslave.glnxa64 by editing the Makefile and using make, but the problem persists. I am using MATLAB 2011a on a 64 bit linux node with 8 cores, which I access interactively using ssh –X. Any ideas would be appreciated! Best, Niels Kloosterman -- Niels A. Kloosterman MSc.| PhD student | University of Amsterdam | Cognitive Neuroscience Group | Dept. of Psychology | Roetersstraat 15, A614 | 1018 WB Amsterdam | Tel: +31 20 525 6847 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Tue Jun 7 12:53:24 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Tue, 7 Jun 2011 10:53:24 +0000 Subject: [FieldTrip] courses Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECAF47@exchccr1.neuro.gu.se> Dear FieldTrip gurus, Are you planning any FieldTrip courses for the users in the nearest future? Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From valentin.umbach at hu-berlin.de Tue Jun 7 13:47:18 2011 From: valentin.umbach at hu-berlin.de (Valentin J. Umbach) Date: Tue, 7 Jun 2011 13:47:18 +0200 Subject: [FieldTrip] fieldtrip Digest, Vol 7, Issue 13 In-Reply-To: References: Message-ID: Dear Robert, thank you for your helpful information. The Problem seems to be that I only have the "Developer" version of the headset (and the accompanying SDK), whereas the one used in the interface is the "Researcher" version (or above). The DLL (and header files) supplied in my SDK lacks some of the functions used in emotiv2ft. So I either have to upgrade my SDK or rewrite the interface to only use my functionality (at this point I'm not interested in the "raw" EEG, but rather the output of Emotiv's own "EmoEngine" - this should work with my version). Best, Valentin > Message: 1 > Date: Mon, 6 Jun 2011 20:32:07 +0200 > From: Robert Oostenveld > To: Email discussion list for the FieldTrip project >         > Cc: Ali Bahramisharif > Subject: Re: [FieldTrip] Emotiv headset realtime capture > Message-ID: > Content-Type: text/plain; charset=us-ascii > > Dear Valentin > > The interface was implemented by Stefan Klanke here at the Donders for the BrainGain project, but he is not  working with us any more. He has been testing it and it worked for him. I don't have an emotiv headset myself, but think that Ali Bahramisharif (CC), one of our colleagues, is in possession of the headset that Stefan used for testing. > > I checked the fieldtrip/realtime/acquisition/emotiv/emotiv2ft.cc source code, and from what I see it it requires additional software from emotiv that is not included with the fieldtrip release. See http://emotiv.com/developer/SDK/UserManual.pdf and specifically chapter 5. If that emotiv software developers kit is missing from your computer, you'll be getting errors that the compiler cannot find the edk.h, EmoStateDLL.h and/or edkErrorCode.h header files. It might also be that you need import libraries on your compile path. Please have a look in fieldtrip/realtime/acquisition/emotiv/Makefile for some further instructions. > > Hope this helps. If not, Ali (CC) might be able to provide some additional information. > > best, > Robert From bornalikundu at gmail.com Tue Jun 7 22:01:46 2011 From: bornalikundu at gmail.com (Bornali Kundu) Date: Tue, 7 Jun 2011 15:01:46 -0500 Subject: [FieldTrip] Test interactions for multi-level factors Message-ID: Greetings, We are interested in testing the main effects and interactions between 2 factors that have more than 2 levels (a 2x4 within subjects design) using the cluster-based permutation test for either time domain or time-frequency domain data. Has anyone done this using Fieldtrip scripts? There is only one such contrast for a 2x2 design thus the interaction effects can be tested using a t test on design cell differences. However, for a factor with more levels, is there a way to perhaps specify contrasts to test the full effect of the interaction? Would setting cfg.contrastcoefs to something work? Otherwise, is there a way to specify this in cfg.design? Thanks so much for your time, Bornali Kundu -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at donders.ru.nl Wed Jun 8 14:54:48 2011 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Wed, 8 Jun 2011 14:54:48 +0200 Subject: [FieldTrip] Reference to non-existent field 'statistic' !????? In-Reply-To: References: Message-ID: Dear Johann, The function prepare_design should not be called by statistics_wrapper in this specific case, since the cfg.design is specified in this tutorial example. cfg.design = [ones(size(tleft.trial,1),1); 2*ones(size(tright.trial,1),1)]; Be sure to specifically add the multivariate directory and subdirectories to your path for this example, otherwise it will crash complaining of not finding other functions (for example ft_mv_standardizer.m) Best, Johanna On 7 June 2011 01:36, Johann Heinz Martínez Huartos wrote: > Hello dear fieldtrip guys. > > Im new using this toolbox and i dont understand why is happened this error > that i think it must be easy to solve but I have tryed and nothing happend. > The thing is that im following (step by step) the tutorial for > multivariableanalysis from fieldtrip wiki using the data that web link offer > us. But when I run the command: > > stat = ft_timelockstatistics(cfg,tleft,tright); > > there are appear those errors: > > ??? Reference to non-existent field 'statistic'. > > Error in ==> prepare_design at 67 > if > any(strcmp(cfg.statistic,{'indepsamplesT','indepsamplesregrT','indepsamplesZcoh','indepsamplesF'})) > > Error in ==> statistics_wrapper at 249 > [cfg] = prepare_design(cfg); > > Error in ==> ft_timelockstatistics at 123 > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > Error in ==> JohannTestFieldtrip at 45 > stat = ft_timelockstatistics(cfg,tleft,tright); > > and i Dunno what can i do... > > Im using Matlab (R2011a) and the (fieldtrip-20110603). I have been looking > for the documentation and i coundt find out how to fix it. > > Is it probably the matlab version very new? > Which would be the last matlab version available using for? > > Thanks > > > -- > Atentamente: > Johann Martínez. > > _______________________________________________ > 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 johemart at gmail.com Wed Jun 8 22:14:18 2011 From: johemart at gmail.com (=?ISO-8859-1?Q?Johann_Heinz_Mart=EDnez_Huartos?=) Date: Wed, 8 Jun 2011 22:14:18 +0200 Subject: [FieldTrip] Reference to non-existent field 'statistic' !????? In-Reply-To: References: Message-ID: Hello dear. Thnks a lot for your comments. I was very useful, eventually i was added all the fieldtrip directory including its subdirectories in order to avoid future problems and at the end it was succesfully instaled in my Matlab R2011b version. Best. Johann. On 8 June 2011 14:54, Johanna Zumer wrote: > Dear Johann, > > The function prepare_design should not be called by statistics_wrapper in > this specific case, since the cfg.design is specified in this tutorial > example. > > cfg.design = [ones(size(tleft.trial,1),1); 2*ones(size(tright.trial,1),1)]; > > > Be sure to specifically add the multivariate directory and subdirectories > to your path for this example, otherwise it will crash complaining of not > finding other functions (for example ft_mv_standardizer.m) > > Best, > Johanna > > > On 7 June 2011 01:36, Johann Heinz Martínez Huartos wrote: > >> Hello dear fieldtrip guys. >> >> Im new using this toolbox and i dont understand why is happened this error >> that i think it must be easy to solve but I have tryed and nothing happend. >> The thing is that im following (step by step) the tutorial for >> multivariableanalysis from fieldtrip wiki using the data that web link offer >> us. But when I run the command: >> >> stat = ft_timelockstatistics(cfg,tleft,tright); >> >> there are appear those errors: >> >> ??? Reference to non-existent field 'statistic'. >> >> Error in ==> prepare_design at 67 >> if >> any(strcmp(cfg.statistic,{'indepsamplesT','indepsamplesregrT','indepsamplesZcoh','indepsamplesF'})) >> >> Error in ==> statistics_wrapper at 249 >> [cfg] = prepare_design(cfg); >> >> Error in ==> ft_timelockstatistics at 123 >> [stat, cfg] = statistics_wrapper(cfg, varargin{:}); >> >> Error in ==> JohannTestFieldtrip at 45 >> stat = ft_timelockstatistics(cfg,tleft,tright); >> >> and i Dunno what can i do... >> >> Im using Matlab (R2011a) and the (fieldtrip-20110603). I have been looking >> for the documentation and i coundt find out how to fix it. >> >> Is it probably the matlab version very new? >> Which would be the last matlab version available using for? >> >> Thanks >> >> >> -- >> Atentamente: >> Johann Martínez. >> >> _______________________________________________ >> 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 > -- Atentamente: Johann Martínez. M.Sc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From amelie.serpollet at cea.fr Thu Jun 9 10:52:42 2011 From: amelie.serpollet at cea.fr (=?iso-8859-1?Q?SERPOLLET_Am=E9lie_228173?=) Date: Thu, 9 Jun 2011 10:52:42 +0200 Subject: [FieldTrip] questions about realtime buffer In-Reply-To: References: Message-ID: Dear Robert, Thank you for your answer. I was trying to run several buffers in the same process, but running them in different processes as you describe it seems to be very easier. The modifications I did to close the buffer cleanly make possible to run a new buffer after closing one, in the same process. Maybe it is not necessary if buffers are created in different processes, but they are few modifications and I find it is still convenient, so I submit it. Best regards Amélie ________________________________ De : Robert Oostenveld [mailto:r.oostenveld at donders.ru.nl] Envoyé : lundi 6 juin 2011 21:19 À : Email discussion list for the FieldTrip project Cc : SERPOLLET Amélie 228173 Objet : Re: [FieldTrip] questions about realtime buffer Dear Amelie I'm implementing a realtime buffer in C++ pretty much like in "demo_combined" : my application creates a buffer server and an acquisition client. I encountered a first problem when trying to close the buffer server cleanly, but with some small changes in tcpsocket.c and tcpserver.c, I think I solved the problem. If these modifications can be useful for other users and do not create other problems, I will share them. If you have changes that don't break the ANSI-C compilation then I am certainly happy to include them in our version. Please go to http://bugzilla.fcdonders.nl and submit a bug/request in which you attach the updated files. I encounter now a new problem : what if there are several acquisition clients ? I tried to create several couples "buffer-server + acquisition client" in different threads in my application, but it does not work at all, because of global variables (I suppose). It seems that one buffer server can not manage several acquisition clients, but I'm not sure of this point. Did anyone encounter this problem (or solve it) ? Or do anyone have an idea ? You are right about the global variables. The buffer is implemented using multithreading and to ensure that incoming data (Write) does not interfere with outgoing (read) data a mutex (http://en.wikipedia.org/wiki/Mutual_exclusion) is set. That mutex is shared throughout the code so that all pieces of code are aware of when they are allowed to change the buffer content. Having multiple buffers would require multiple mutexes and multiple (separately identifyable) memory segments for the actual data. That would require a lot of changes to the code. You can run multiple buffers on the same computer, but you would have to start them separately and they would have to have different TCP ports. The application you are writing could write different aspects to the different TCP ports. You can use fieldtrip/realtime/general/buffer.exe, which in fact is a compiled version of fieldtrip/realtime/buffer/test/demo_buffer. Note that you would use it as buffer.exe localhost 2340 buffer.exe localhost 2341 buffer.exe localhost 2342 buffer.exe localhost 2343 to start 4 buffers on ports 2340-2343. The "localhost" argument is not used, but still appears to be required according to the demo_buffer.c source code. Of course it is cumbersome to have to start the 4 seperate processes on top of your own application. On unix-like computers you should be able to write a single application that at the beginning forks into a parent and child, where the parent continues as your application and where the child (which is then a separate process) can start the buffer. You can fork multiple times, to have multiple buffers (one per child). best Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Jun 9 15:19:14 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 9 Jun 2011 15:19:14 +0200 Subject: [FieldTrip] courses In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F03ECAF47@exchccr1.neuro.gu.se> References: <32CC77C0C8A7AD4B9410934642608E1F03ECAF47@exchccr1.neuro.gu.se> Message-ID: <5B0A148A-D4F0-454F-B60B-E47ECCA47E75@donders.ru.nl> Dear Elena For 2011 there are no courses planned any more in Nijmege, which are open to external participants (there will be a course for local studens in the Donders Graduate School in the autumn). The next course in Nijmegen will be the MEG Toolkit course, which most likely will be somewhere in the spring of 2012. For 2011 we are currently considering a course in Paris at the end of this year. I believe that Stefan and Saskia are considering to do another course in New York later this year, although I don't know any details for the New York plans. At the upcoming HBM meeting in Quebec there will be an educational course in which FieldTrip and the other open source academic toolboxes will play a (relatively small) role. Although I don't think it is efficient to travel to Quebec just for this part, it might be interesting for you to attend if you are attending the HBM conference anyway. See http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3437 and for the program one of the last pages of http://www.humanbrainmapping.org/files/2011MeetingFiles/Descriptions/HBM%202011%20Educational%20Program.pdf Please note that we are open to invitations for presenting the FieldTrip course at external sites. This year we have already been in Tuebingen, St Louis, and New York, and if there is an interesting venue, an enthousiastic local organizer and funding can be arranged to cover the expenses, most likely some experienced users/developers from Nijmegen can be found or appointed to present a 2,5 day course at the external site. best regards, Robert On 7 Jun 2011, at 12:53, Elena Orekhova wrote: > Dear FieldTrip gurus, > > Are you planning any FieldTrip courses for the users in the nearest > future? > > Elena > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From r.oostenveld at donders.ru.nl Thu Jun 9 17:02:38 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 9 Jun 2011 17:02:38 +0200 Subject: [FieldTrip] Problem passing arguments to peerslave command line executable In-Reply-To: References: Message-ID: <33AD75FB-959A-4F3B-AD5B-1ABBD9F2C1DE@donders.ru.nl> Hi Niels On 7 Jun 2011, at 10:33, Kloosterman, Niels wrote: > Although I have succesfully used the command-line ./ > peerslave.glnxa64 to launch slaves for parallel analysis of my batch > jobs, I am somehow not able to pass arguments to the command, for > example ./peerslave.glnxa64 --number 8, to launch 8 slaves at once. > Could anybody tell me what’s going on? I'll give it a try. > When I execute without arguments this line pops up: > > niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./ > peerslave.glnxa64 > peerslave[9705]: peerinit: niels at gb-r35n18.irc.sara.nl, id = > 4020038417 > > All seems fine: the master is indeed able to send jobs to the slave. > No other information is printed to the shell when it gets a job or > whatever (is this normal?). Yes, that is normal. Since we are running the peerslaves at the Donders on our ~50 node cluster on the background, the default (compiled) behaviour is to use the syslog facility. If I were to start them from a cronjob, I would either get very lengthy mails (which cron sends if the process finishes), or not get any information (when I redirect the output to /dev/null). To keep track of all processes on all nodes, we use a syslog server. The peerslave messages are all sent to a single syslog server where I can track them all in /var/log/ peerslave.log Note however that if you recompile, you can change this. Have a look at this section in peer.h #if SYSLOG == 0 #define PANIC(format, ...) {exit(-1);} #define DEBUG(level, format, ...) { } #elif SYSLOG == 1 #define PANIC(format, ...) {syslog(LOG_ERR, format, ## __VA_ARGS__); exit(-1);} #define DEBUG(level, format, ...) {syslog(level, format, ## __VA_ARGS__);} #elif SYSLOG == 2 #define PANIC(format, ...) {fprintf(stderr, format"\n", ## __VA_ARGS__); exit(-1);} #define DEBUG(level, format, ...) {fprintf(stderr, format"\n", ## __VA_ARGS__);} #elif SYSLOG == 3 #define PANIC(format, ...) {mexPrintf(format"\n", ## __VA_ARGS__); exit(-1);} #define DEBUG(level, format, ...) {if (level<=syslog_level) mexPrintf(format"\n", ## __VA_ARGS__);} #endif At compile time you can specify whether the output goes to syslog (1), stderr (2) or whether mexPrintf shoudl be used (for the mex file, 3). Probably you'll want to add -DSYSLOG=2 to the compile flags. Furthermore note that the syslog level is used to control how much info is given. That is controlled with the --verbose=number option on the peerslave command line. > Now when I try to run the --help I get this: > > niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./ > peerslave.glnxa64 --help > peerslave[9753]: peerinit: niels at gb-r35n18.irc.sara.nl, id = > 2887682376 > parser: cannot open file --help > peerslave[9753]: cannot read the configuration file Hmm, this is not good. It appears that it misinterprets the cmd line option. > And when I try to do --number 8: > > niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./ > peerslave.glnxa64 --number 8 > peerslave[9759]: peerinit: niels at gb-r35n18.irc.sara.nl, id = > 3997336815 > ./peerslave.glnxa64: unrecognized option '--number' > peerslave[9759]: invalid command line options Again here the cmd line option is misinterpreted. This one I can reproduce roboos at mentat258> ../bin/peerslave.glnxa64 --number 8 peerslave[14690]: peerinit: roboos at mentat258.dccn.nl, id = 2375758516 ../bin/peerslave.glnxa64: unrecognized option `--number' peerslave[14690]: invalid command line options I'll file a bug for it. For the meantime, I suggest you look into the configuration files. That is also how we are using them at the Donders, you can find an example below. best Robert ------------------------ cut here ------------------------ # has 12GB of RAM, one CPU and 4 cores # Intel(R) Xeon(R) CPU W3530 @ 2.80GHz [peer] matlab=/opt/cluster/matlab2010b -nodisplay -singleCompThread timavail=86399 smartcpu=1 smartmem=1 udsserver=1 [peer] matlab=/opt/cluster/matlab2010b -nodisplay -singleCompThread timavail=3599 smartcpu=1 smartmem=1 udsserver=1 [peer] matlab=/opt/cluster/matlab2010b -nodisplay -singleCompThread timavail=3599 smartcpu=1 smartmem=1 udsserver=1 [peer] matlab=/opt/cluster/matlab2010b -nodisplay -singleCompThread timavail=599 smartcpu=1 smartmem=1 udsserver=1 ------------------------ cut here ------------------------ From michael.wibral at web.de Thu Jun 9 17:05:49 2011 From: michael.wibral at web.de (Michael Wibral) Date: Thu, 9 Jun 2011 17:05:49 +0200 (CEST) Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis Message-ID: <327769233.351093.1307631949517.JavaMail.fmail@mwmweb082> An HTML attachment was scrubbed... URL: From michael.wibral at web.de Thu Jun 9 17:06:47 2011 From: michael.wibral at web.de (Michael Wibral) Date: Thu, 9 Jun 2011 17:06:47 +0200 (CEST) Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis Message-ID: <619181926.351452.1307632007849.JavaMail.fmail@mwmweb082> An HTML attachment was scrubbed... URL: From johan.bergmann at yahoo.com Thu Jun 9 20:35:54 2011 From: johan.bergmann at yahoo.com (Johan Bergmann) Date: Thu, 9 Jun 2011 11:35:54 -0700 (PDT) Subject: [FieldTrip] Converting time stamps into NCS. Message-ID: <213089.20008.qm@web45503.mail.sp1.yahoo.com> Hello, I have a .mat file containing a single column of voltage values which i wish to convert to the ncs file format. I cannot seem to achieve this, please can someone show me a usage example. Cheers, Johan. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Thu Jun 9 22:48:34 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Thu, 9 Jun 2011 20:48:34 +0000 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <619181926.351452.1307632007849.JavaMail.fmail@mwmweb082> References: <619181926.351452.1307632007849.JavaMail.fmail@mwmweb082> Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECB515@exchccr1.neuro.gu.se> Dear Michael, I still have not resolved this problem and do not know whether is specific for my data(or program bag) or the other Neuromag users also had it. Do you use Neuromag? Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Thursday, June 09, 2011 5:06 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Hi Elena, disregard my last email, I overlooked the att. Michael ________________________________ Von: "Elena Orekhova" Gesendet: Jun 2, 2011 8:03:16 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Verdana"; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear Michael, I did normalize the data (sourcepst.avg.nai=sourcepst.avg.pow./sourcepre.avg.pow) as it was suggested in the tutorial. I used the same scales in all plots for comparison purposes. If automatic scaling is used the result for MAG+GRA does not look any better (see attachment). >What you could do as a workaround is to average the separate results with a weighting per voxel and that >is corresponding to the squared norms of the leadfields for the respective modalities for a given voxel , this >would guarantee equal amounts of backprojected noise from both modalities (if I'm not mistaken). Thank you for your suggestion. I may use it as a last resort. Hopefully, there is still a way to get more optimal solution using both GRA and MAG in the same analysis... Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Elena Orekhova [Elena.Orekhova at neuro.gu.se] Sent: Thursday, June 02, 2011 6:22 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis BODY {direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;} Dear Michael, I have tried to multiply the leadfield by -1 as you suggested: for i = 1 : size (grid.leadfield, 2) grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); end This had no effect on the 'lcmv' output. I attached the pictures for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ In this experiment I measured evoked field in response to the unilateral (left) click. The source is expected to be in the right superior temporal cortex. This is the case for ‘GRA only' and ’MAG only’ datasets. The combined sensors give meaningless result. Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Wednesday, June 01, 2011 4:04 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Elena, could you give the following a try: invert (*-1) the leadfileds for one of the two sensor types. Let me know what happens. I would also be interested in taking a look at the results - maybe you could sent images off-list: Michael.Wibral web.de. Michael ________________________________ Von: "Elena Orekhova" Gesendet: Jun 1, 2011 12:23:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "Arial"; }@font-face { font-family: "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: Times; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear fieldtrippers, This message is mainly for Neuromag users. When I do 'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. If I combine the two types of sensors without weighting, the result is meaningless. Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements. Does anybody know how to deal with this problem? Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri Jun 10 09:45:30 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 10 Jun 2011 09:45:30 +0200 Subject: [FieldTrip] Converting time stamps into NCS. In-Reply-To: <213089.20008.qm@web45503.mail.sp1.yahoo.com> References: <213089.20008.qm@web45503.mail.sp1.yahoo.com> Message-ID: <550011EB-7B66-40F1-87BB-77974ED41D1B@donders.ru.nl> Dear Johan You can use ft_write_data(FILENAME, DAT, 'header', HDR, 'dataformat', 'neuralynx_ncs') where you have to provide the filename, the data (as 1*Nsamples matrix) and the header (i.e. everything in upper case in the example). For the header you have to provide a matlab structure such as the one that is returned by ft_read_header returns when you read an original neuralynx ncs file. I suggest that you look into the ft_write_data function at line 529 for further details. best Robert On 9 Jun 2011, at 20:35, Johan Bergmann wrote: > Hello, > > I have a .mat file containing a single column of voltage values > which i wish to convert to the ncs file format. I cannot seem to > achieve this, please can someone show me a usage example. > > Cheers, > > Johan. > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From johan.bergmann at yahoo.com Fri Jun 10 12:39:37 2011 From: johan.bergmann at yahoo.com (Johan Bergmann) Date: Fri, 10 Jun 2011 03:39:37 -0700 (PDT) Subject: [FieldTrip] Converting time stamps into NCS. In-Reply-To: <550011EB-7B66-40F1-87BB-77974ED41D1B@donders.ru.nl> References: <213089.20008.qm@web45503.mail.sp1.yahoo.com> <550011EB-7B66-40F1-87BB-77974ED41D1B@donders.ru.nl> Message-ID: <629642.35556.qm@web45515.mail.sp1.yahoo.com> Dear Robert, Thanks for your response. I have taken a look at the code in ft_write_data. My original file was not from a .ncs file format it was from a .mcd file format, scaled in micro volts and a continuous recording. So, i have a "900x1 double" voltage values as a variable called "data" in Matlab. I call: ft_write_data(new_file.ncs, data, '?', ? , 'matlab', '?') ft_write_data(FILENAME, DAT, 'header', HDR, 'dataformat', 'neuralynx_ncs') sorry for the simplistic question. Thanks, Johan. ________________________________ From: Robert Oostenveld To: Email discussion list for the FieldTrip project Sent: Fri, June 10, 2011 8:45:30 AM Subject: Re: [FieldTrip] Converting time stamps into NCS. Dear Johan You can use ft_write_data(FILENAME, DAT, 'header', HDR, 'dataformat', 'neuralynx_ncs') where you have to provide the filename, the data (as 1*Nsamples matrix) and the header (i.e. everything in upper case in the example). For the header you have to provide a matlab structure such as the one that is returned by ft_read_header returns when you read an original neuralynx ncs file. I suggest that you look into the ft_write_data function at line 529 for further details. best Robert On 9 Jun 2011, at 20:35, Johan Bergmann wrote: > Hello, > > I have a .mat file containing a single column of voltage values which i wish to >convert to the ncs file format. I cannot seem to achieve this, please can >someone show me a usage example. > > Cheers, > > Johan. > _______________________________________________ > 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 tobias.staudigl at uni-konstanz.de Fri Jun 10 12:42:51 2011 From: tobias.staudigl at uni-konstanz.de (Tobias Staudigl) Date: Fri, 10 Jun 2011 12:42:51 +0200 Subject: [FieldTrip] granger causality Message-ID: <4DF1F52B.3000406@uni-konstanz.de> Dear all, I am trying to make sense out of a granger-causality analysis i did using ft-functions. I have two condition in which i already identified a sig. difference in plv. now i would like to know the directionality of the coupling in one of the conditions. To this end, I use granger causality as implemented in fieldtrip (see below for details). At the moment, i have 3 questions. (As i am not very familiar with using fieldtrip, i may have missed something obvious). Q 1: If I understood correctly, the grangerspectrum (granger.grangerspctrm) gives me values for the granger-causality in a matrix [nChannel, nChannel, Freqs]. Does [1,2,:] give me the granger-causality of Channel1 predicting Channel2, or the other way round? Q2: The plotting function gives me an error: ft_connectivityplot(cfg, granger) ??? Error using ==> seloverdim at 36 cannot select over multiple dimensions at the same time Error in ==> ft_selectdata at 528 if selectchan, data = seloverdim(data, 'chan', selchan, fb); end Error in ==> ft_connectivityplot at 79 data = ft_selectdata(data, 'channel', cfg.channel); Q3: How do i statistically validate the measures i get fromthe granger-analysis? Is there some recommended statistical test? Is it correct to do bootstrapping / permutation testing? What I could do on my data is shuffle the trials across conditions, compute granger causality on the shuffeld data, and compair this distribution with the value i get from the data. Maybe, somebody is experienced in using granger and could help me out! Any advice appreciated! Thanks a lot! tobi I used the following ft_functions according to the online tutorial: %% MVAR cfg = []; cfg.order = 2; cfg.toolbox = 'bsmart'; mdata = ft_mvaranalysis(cfg, data); %% transfer function cfg = []; cfg.method = 'mvar'; mfreq = ft_freqanalysis(cfg, mdata); %% granger cfg = []; cfg.method = 'granger'; granger = ft_connectivityanalysis(cfg, mfreq); %% cfg = []; cfg.zparam = 'grangerspctrm'; %cfg.channel = 'all'; ft_connectivityplot(cfg, granger); -- Tobias Staudigl Fachbereich Psychologie - ZPR Postfach ZPR 78457 Konstanz ZPR, Haus 12 Tel.: +49 (0)7531 / 88 - 5703 From jan.schoffelen at donders.ru.nl Fri Jun 10 13:00:12 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 10 Jun 2011 13:00:12 +0200 Subject: [FieldTrip] granger causality In-Reply-To: <4DF1F52B.3000406@uni-konstanz.de> References: <4DF1F52B.3000406@uni-konstanz.de> Message-ID: <01F5D123-C4D5-42B2-9D93-CC3B4E86BD66@donders.ru.nl> Hi Tobias, > > Q 1: > If I understood correctly, the grangerspectrum > (granger.grangerspctrm) gives me values for the granger-causality in > a matrix [nChannel, nChannel, Freqs]. > Does [1,2,:] give me the granger-causality of Channel1 predicting > Channel2, or the other way round? > The FieldTrip convention is indeed (1,2,:) relates to 1->2 > Q2: > The plotting function gives me an error: > > ft_connectivityplot(cfg, granger) > > ??? Error using ==> seloverdim at 36 > cannot select over multiple dimensions at the same time > > Error in ==> ft_selectdata at 528 > if selectchan, data = seloverdim(data, 'chan', selchan, fb); end > > Error in ==> ft_connectivityplot at 79 > data = ft_selectdata(data, 'channel', cfg.channel); Please update your fieldtrip version. There is a fix (dated 22-04) that should take care of this > Q3: > How do i statistically validate the measures i get fromthe granger- > analysis? > Is there some recommended statistical test? > Is it correct to do bootstrapping / permutation testing? > What I could do on my data is shuffle the trials across conditions, > compute granger causality on the shuffeld data, and compair this > distribution with the value i get from the data. This is a very relevant issue. From what you describe it seems as if you want to compare across conditions. The shuffling across conditions is what we do as well, although it remains open to debate how meaningful it is to compare granger causality indices across conditions. And, also, if you are able to reject your null-hypothesis, whether your decision to reject it is actually due to the actual granger causality being different, or by some other confounding quantity. Best wishes, Jan-Mathijs > Maybe, somebody is experienced in using granger and could help me out! > Any advice appreciated! > > Thanks a lot! > tobi > > > I used the following ft_functions according to the online tutorial: > > %% MVAR > cfg = []; > cfg.order = 2; > cfg.toolbox = 'bsmart'; > mdata = ft_mvaranalysis(cfg, data); > > %% transfer function > cfg = []; > cfg.method = 'mvar'; > mfreq = ft_freqanalysis(cfg, mdata); > > %% granger > cfg = []; > cfg.method = 'granger'; > granger = ft_connectivityanalysis(cfg, mfreq); > > %% > cfg = []; > cfg.zparam = 'grangerspctrm'; > %cfg.channel = 'all'; > ft_connectivityplot(cfg, granger); > > -- > Tobias Staudigl > Fachbereich Psychologie - ZPR > Postfach ZPR > 78457 Konstanz > ZPR, Haus 12 > Tel.: +49 (0)7531 / 88 - 5703 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From jan.schoffelen at donders.ru.nl Fri Jun 10 13:01:58 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 10 Jun 2011 13:01:58 +0200 Subject: [FieldTrip] Weird trialfun_general error In-Reply-To: References: Message-ID: <59055861-365E-4FD7-A85C-C57C2FF430C4@donders.ru.nl> Hi Rodolphe, This is a funny bug. It goes wrong in trialfun_general when the intersect() tries to compare a string (event(i).vale being 'boundary') with a list of numbers (your event values). This leads in your case to unwanted behavior, and I can imagine that this will cause problems elsewhere too. We'll look into it and fix it. Thanks for the notification. Best, Jan-Mathijs On Jun 7, 2011, at 12:51 AM, Rodolphe Nenert wrote: > Dear fieldtrippers, > > i just noticed and found the origin of a weird error obtained with > the trialfun_general function, i thought it could be useful to send > it here. > I use the ft_definetrial function on a file obtained using the merge > function in EEGlab. Apparently, this function is adding some > triggers with the value 'boundary' in the new file, indicating the > old frontier between the dataset that have been merged. > The funny part is that the trialfun_general() function in fieltrip > is using the intersect() matlab function to match event values. > Moreover, im using 27 different event values to indicate point of > interest (112,114,116,122,etc...) > All of my event values dont create any problems except the value > 114 because intersect('boundary',114) = 114 whereas it gives an > empty result with any other of my values... > Therefore, for that particular event value, there was a dimension > mismatch between trl and val in trialfun_general. > > I just removed events with 'boundary' values and it worked. > > Best regards, > > Rodolphe Nenert, Ph.D. > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From g.dimitriadis at donders.ru.nl Fri Jun 10 16:52:54 2011 From: g.dimitriadis at donders.ru.nl (George Dimitriadis) Date: Fri, 10 Jun 2011 16:52:54 +0200 Subject: [FieldTrip] (no subject) In-Reply-To: <550011EB-7B66-40F1-87BB-77974ED41D1B@donders.ru.nl> References: <213089.20008.qm@web45503.mail.sp1.yahoo.com> <550011EB-7B66-40F1-87BB-77974ED41D1B@donders.ru.nl> Message-ID: <00ed01cc277e$170492c0$450db840$@dimitriadis@donders.ru.nl> Hello guys, In ft_plot_topo.m at line 69 you say if isempty(tag), tag=''; Could you please turn the comma into a ; because it breaks my code. Thanks From TAVABIK at email.chop.edu Fri Jun 10 18:59:03 2011 From: TAVABIK at email.chop.edu (Tavabi, Kambiz) Date: Fri, 10 Jun 2011 12:59:03 -0400 Subject: [FieldTrip] working with neuromag data In-Reply-To: <887659131.308634.1301386835573.JavaMail.root@sculptor.zimbra.ru.nl> References: <717208384.308488.1301386421578.JavaMail.root@sculptor.zimbra.ru.nl>, <887659131.308634.1301386835573.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: As per advise from Arjen, I was able to use following steps 1) ft_preprocessing on your stimulus averaged epoch data. This should give you a data structure with 6 trials (which are actually the averages per condition). 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat this so you end up with 6 timelocked structures representing the 6 different conditions. to create individual condition averaged ft data structures which I can visualize using ft_topoplotER(cfg,data) data: avg: [338x651 double] var: [338x651 double] fsample: 1000 time: [1x651 double] dof: [338x651 double] label: {338x1 cell} dimord: 'chan_time' grad: [1x1 struct] cfg: [1x1 struct] however when i use; cfg = []; cfg.showlabels = 'yes'; cfg.fontsize = 6; cfg.ylim = [-10e-13 10e-13] ft_multiplotER(cfg, data); Fieldtrip chruns through creating the selection avg along dimension 1 selection dof along dimension 1 selection var along dimension 1 creating layout from data.grad creating layout for neuromag306 system but the resutling figure is an empty figure containing only layout with ch lables without any data what so ever. Any ideas why this might be? -Kambiz. ------------------------------------------------------------- Kambiz Tavabi PhD Biomedical Imaging Laboratory The Children's Hospital of Philadelphia 34th Street and Civic Center Boulevard Philadelphia, Pa. 19104 Tel: 267.426.0302 email: tavabik at email.chop.edu ------------------------------------------------------------- ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. [a.stolk at fcdonders.ru.nl] Sent: Tuesday, March 29, 2011 4:20 AM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] working with neuromag data Dear Kambiz, I think I see your point. Your data presumably is already preprocessed and timelocked (averaged over trials) with neuromag software. I then take it that you have 6 different conditions which you would like to plot separately and possibly test at the group level. Since the data is already averaged, I'd recommend to do the following to get your data back on track. 1) ft_preprocessing on your stimulus averaged epoch data. This should give you a data structure with 6 trials (which are actually the averages per condition). 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat this so you end up with 6 timelocked structures representing the 6 different conditions. 3) plot or grandaverage (see tutorials how to proceed as your data now should be 'ft-friendly'). Goodluck, Arjen ----- "Kambiz Tavabi" schreef: > Van: "Kambiz Tavabi" > Aan: "Email discussion list for the FieldTrip project" > Verzonden: Dinsdag 29 maart 2011 01:10:14 > Onderwerp: Re: [FieldTrip] working with neuromag data > > Dear Arjen - Thanks for your response. Just to clarify the low level > functions ft_read_header & ft_read_data are mentioned in the ft > getting started tutorial. I believe they're recommended to make sure > the data is ft friendly. In my case the data is ft friendly. My data > is also pre-processed and already 'time-locked'--meaning that I have > stimulus averaged epoch data in fif format for all my subjects. My > question is how to proceed from there? I've been through the pages you > refer to but have not been able to piece together my data in such a > way to proceed with grand-averaging and carrying out stats. > -Kambiz. > ------------------------------------------------------------- > Kambiz Tavabi PhD > Biomedical Imaging Laboratory > The Children's Hospital of Philadelphia > 34th Street and Civic Center Boulevard > Philadelphia, Pa. 19104 > Tel: 267.426.0302 > email: tavabik at email.chop.edu > ------------------------------------------------------------- > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > [a.stolk at fcdonders.ru.nl] > Sent: Monday, March 28, 2011 4:05 PM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] working with neuromag data > > Dear Kambiz, > > While you are able to use the 'low level' ft_read_header and > ft_read_data functions, you should be able to preprocess and analyze > your neuromag data using the 'high level' functions such as > ft_preprocessing (which calls the low level functions mentioned > above). > > How to proceed depends on what you want to do with your data. If you > have triggers stored in your dataset that are synchronuous with the > recorded brain activity, it'd be recommended to start with the > following tutorial on how to select your trials: > > http://fieldtrip.fcdonders.nl/tutorial/preprocessing > > Since your experience with FT is still limited as you say, I believe > the following text may provide a good overview of what the data, once > read in to FT (i.e. matlab) environment, may look like: > > http://fieldtrip.fcdonders.nl/walkthrough > > Typically, your next steps involve single-subject timelocked analysis, > then grand-average and perform statistics at the group level. For an > overview of the steps and protocols, see: > > http://fieldtrip.fcdonders.nl/tutorial/analysis_protocols > > Hope this has helped for a start, > > Arjen > > > ----- "Kambiz Tavabi" schreef: > > > Van: "Kambiz Tavabi" > > Aan: "Email discussion list for the FieldTrip project" > > > Verzonden: Maandag 28 maart 2011 20:59:36 > > Onderwerp: [FieldTrip] working with neuromag data > > > > Greetings - I have preprocessed/averaged neuromag data for a group > of > > subjects that I'd like to visualize, compute grandaverage and carry > > out sensor level statistics on. The only help I managed to find on > the > > Fieldtrip site/list Re: neurmag data concerns getting started e.g., > > with ft_read_header and ft_read_data. In my case these programs > work > > fine meaning that I can proceed with further analysis. > > On a side, in my limited experience with FT, a major problem I run > > into frequently is that there is no clear suggestion(s) on how to > > proceed with data that is not raw. I understand it is impossible to > > cover all analysis scenarios, but it is often the case that working > > with CTF, or in particular Elekta system, the data is likely to be > in > > a post-preprocessed phase. Everytime I've tried to work with ft, It > > seems to me that if I don't start with square one in fieldtrip, it > is > > difficult to figure out how to use downstream programs to work on > the > > data. > > That said, in my case I have the output from ft_read_header: > > > > label: {338x1 cell} > > nChans: 338 > > Fs: 1000 > > grad: [1x1 struct] > > unit: {1x338 cell} > > nSamples: 651 > > nSamplesPre: 100 > > nTrials: 6 > > orig: [1x1 struct] > > > > and output from ft_read_data > > > > [338x651x6] that being channels by samples by number of stimulus > > averaged epochs. To proceed, ideally I'd like to compute a > > grandaverage for each condition, visualize them in a multiplot, and > > carry out sensor level stats. To be able to do this I understand I > > need the output from ft_timelockanalysis, how do I arrange my data > as > > such? I am assuming it is already in that state. Thanks for your > > time. > > > > -Kambiz. > > ------------------------------------------------------------- > > Kambiz Tavabi PhD > > Biomedical Imaging Laboratory > > The Children's Hospital of Philadelphia > > 34th Street and Civic Center Boulevard > > Philadelphia, Pa. 19104 > > Tel: 267.426.0302 > > email: tavabik at email.chop.edu > > ------------------------------------------------------------- > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- A non-text attachment was scrubbed... Name: multiplot.jpg Type: image/jpeg Size: 47066 bytes Desc: multiplot.jpg URL: From TAVABIK at email.chop.edu Fri Jun 10 20:21:30 2011 From: TAVABIK at email.chop.edu (Tavabi, Kambiz) Date: Fri, 10 Jun 2011 14:21:30 -0400 Subject: [FieldTrip] working with neuromag data In-Reply-To: References: <717208384.308488.1301386421578.JavaMail.root@sculptor.zimbra.ru.nl>, <887659131.308634.1301386835573.JavaMail.root@sculptor.zimbra.ru.nl>, Message-ID: As per advise from Arjen, I was able to use following steps 1) ft_preprocessing on your stimulus averaged epoch data. This should give you a data structure with 6 trials (which are actually the averages per condition). 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat this so you end up with 6 timelocked structures representing the 6 different conditions. to create individual condition averaged ft data structures which I can visualize using ft_topoplotER(cfg,data) data: avg: [338x651 double] var: [338x651 double] fsample: 1000 time: [1x651 double] dof: [338x651 double] label: {338x1 cell} dimord: 'chan_time' grad: [1x1 struct] cfg: [1x1 struct] however when i use; cfg = []; cfg.showlabels = 'yes'; cfg.fontsize = 6; cfg.ylim = [-10e-13 10e-13] ft_multiplotER(cfg, data); Fieldtrip chruns through creating the selection avg along dimension 1 selection dof along dimension 1 selection var along dimension 1 creating layout from data.grad creating layout for neuromag306 system but the resutling figure is an empty figure containing only layout with ch lables without any data what so ever. Any ideas why this might be? Following up my question on plotting: Why would the granaverge structure lose the channel layout information instead of carrying it over from the Timelock structure? ft_topoplotER(cfg,grandavgc1) ??? Error using ==> ft_prepare_layout at 532 no layout detected, please specify cfg.layout Error in ==> ft_topoplotER at 408 lay = ft_prepare_layout(cfg, data); -Kambiz. ------------------------------------------------------------- Kambiz Tavabi PhD Biomedical Imaging Laboratory The Children's Hospital of Philadelphia 34th Street and Civic Center Boulevard Philadelphia, Pa. 19104 Tel: 267.426.0302 email: tavabik at email.chop.edu ------------------------------------------------------------- ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. [a.stolk at fcdonders.ru.nl] Sent: Tuesday, March 29, 2011 4:20 AM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] working with neuromag data Dear Kambiz, I think I see your point. Your data presumably is already preprocessed and timelocked (averaged over trials) with neuromag software. I then take it that you have 6 different conditions which you would like to plot separately and possibly test at the group level. Since the data is already averaged, I'd recommend to do the following to get your data back on track. 1) ft_preprocessing on your stimulus averaged epoch data. This should give you a data structure with 6 trials (which are actually the averages per condition). 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat this so you end up with 6 timelocked structures representing the 6 different conditions. 3) plot or grandaverage (see tutorials how to proceed as your data now should be 'ft-friendly'). Goodluck, Arjen ----- "Kambiz Tavabi" schreef: > Van: "Kambiz Tavabi" > Aan: "Email discussion list for the FieldTrip project" > Verzonden: Dinsdag 29 maart 2011 01:10:14 > Onderwerp: Re: [FieldTrip] working with neuromag data > > Dear Arjen - Thanks for your response. Just to clarify the low level > functions ft_read_header & ft_read_data are mentioned in the ft > getting started tutorial. I believe they're recommended to make sure > the data is ft friendly. In my case the data is ft friendly. My data > is also pre-processed and already 'time-locked'--meaning that I have > stimulus averaged epoch data in fif format for all my subjects. My > question is how to proceed from there? I've been through the pages you > refer to but have not been able to piece together my data in such a > way to proceed with grand-averaging and carrying out stats. > -Kambiz. > ------------------------------------------------------------- > Kambiz Tavabi PhD > Biomedical Imaging Laboratory > The Children's Hospital of Philadelphia > 34th Street and Civic Center Boulevard > Philadelphia, Pa. 19104 > Tel: 267.426.0302 > email: tavabik at email.chop.edu > ------------------------------------------------------------- > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > [a.stolk at fcdonders.ru.nl] > Sent: Monday, March 28, 2011 4:05 PM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] working with neuromag data > > Dear Kambiz, > > While you are able to use the 'low level' ft_read_header and > ft_read_data functions, you should be able to preprocess and analyze > your neuromag data using the 'high level' functions such as > ft_preprocessing (which calls the low level functions mentioned > above). > > How to proceed depends on what you want to do with your data. If you > have triggers stored in your dataset that are synchronuous with the > recorded brain activity, it'd be recommended to start with the > following tutorial on how to select your trials: > > http://fieldtrip.fcdonders.nl/tutorial/preprocessing > > Since your experience with FT is still limited as you say, I believe > the following text may provide a good overview of what the data, once > read in to FT (i.e. matlab) environment, may look like: > > http://fieldtrip.fcdonders.nl/walkthrough > > Typically, your next steps involve single-subject timelocked analysis, > then grand-average and perform statistics at the group level. For an > overview of the steps and protocols, see: > > http://fieldtrip.fcdonders.nl/tutorial/analysis_protocols > > Hope this has helped for a start, > > Arjen > > > ----- "Kambiz Tavabi" schreef: > > > Van: "Kambiz Tavabi" > > Aan: "Email discussion list for the FieldTrip project" > > > Verzonden: Maandag 28 maart 2011 20:59:36 > > Onderwerp: [FieldTrip] working with neuromag data > > > > Greetings - I have preprocessed/averaged neuromag data for a group > of > > subjects that I'd like to visualize, compute grandaverage and carry > > out sensor level statistics on. The only help I managed to find on > the > > Fieldtrip site/list Re: neurmag data concerns getting started e.g., > > with ft_read_header and ft_read_data. In my case these programs > work > > fine meaning that I can proceed with further analysis. > > On a side, in my limited experience with FT, a major problem I run > > into frequently is that there is no clear suggestion(s) on how to > > proceed with data that is not raw. I understand it is impossible to > > cover all analysis scenarios, but it is often the case that working > > with CTF, or in particular Elekta system, the data is likely to be > in > > a post-preprocessed phase. Everytime I've tried to work with ft, It > > seems to me that if I don't start with square one in fieldtrip, it > is > > difficult to figure out how to use downstream programs to work on > the > > data. > > That said, in my case I have the output from ft_read_header: > > > > label: {338x1 cell} > > nChans: 338 > > Fs: 1000 > > grad: [1x1 struct] > > unit: {1x338 cell} > > nSamples: 651 > > nSamplesPre: 100 > > nTrials: 6 > > orig: [1x1 struct] > > > > and output from ft_read_data > > > > [338x651x6] that being channels by samples by number of stimulus > > averaged epochs. To proceed, ideally I'd like to compute a > > grandaverage for each condition, visualize them in a multiplot, and > > carry out sensor level stats. To be able to do this I understand I > > need the output from ft_timelockanalysis, how do I arrange my data > as > > such? I am assuming it is already in that state. Thanks for your > > time. > > > > -Kambiz. > > ------------------------------------------------------------- > > Kambiz Tavabi PhD > > Biomedical Imaging Laboratory > > The Children's Hospital of Philadelphia > > 34th Street and Civic Center Boulevard > > Philadelphia, Pa. 19104 > > Tel: 267.426.0302 > > email: tavabik at email.chop.edu > > ------------------------------------------------------------- > > _______________________________________________ > > 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 a.stolk at fcdonders.ru.nl Sat Jun 11 09:26:58 2011 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Sat, 11 Jun 2011 09:26:58 +0200 (CEST) Subject: [FieldTrip] working with neuromag data In-Reply-To: Message-ID: <621524636.372728.1307777218636.JavaMail.root@sculptor.zimbra.ru.nl> Dear Kambiz, Does your data.avg contain NaNs or real numbers? In the latter case; do they fall in the plotting range as specified by your cfg.ylim? Yours, Arjen ----- "Kambiz Tavabi" schreef: > Van: "Kambiz Tavabi" > Aan: "Email discussion list for the FieldTrip project" > Verzonden: Vrijdag 10 juni 2011 18:59:03 > Onderwerp: Re: [FieldTrip] working with neuromag data > > As per advise from Arjen, I was able to use following steps > 1) ft_preprocessing on your stimulus averaged epoch data. This should > give you a data structure with 6 trials (which are actually the > averages per condition). > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat > this so you end up with 6 timelocked structures representing the 6 > different conditions. > to create individual condition averaged ft data structures which I can > visualize using ft_topoplotER(cfg,data) > data: > avg: [338x651 double] > var: [338x651 double] > fsample: 1000 > time: [1x651 double] > dof: [338x651 double] > label: {338x1 cell} > dimord: 'chan_time' > grad: [1x1 struct] > cfg: [1x1 struct] > however when i use; > cfg = []; > cfg.showlabels = 'yes'; > cfg.fontsize = 6; > cfg.ylim = [-10e-13 10e-13] > ft_multiplotER(cfg, data); > Fieldtrip chruns through creating the > selection avg along dimension 1 > selection dof along dimension 1 > selection var along dimension 1 > creating layout from data.grad > creating layout for neuromag306 system > > but the resutling figure is an empty figure containing only layout > with ch lables without any data what so ever. Any ideas why this might > be? > > > > -Kambiz. > ------------------------------------------------------------- > Kambiz Tavabi PhD > Biomedical Imaging Laboratory > The Children's Hospital of Philadelphia > 34th Street and Civic Center Boulevard > Philadelphia, Pa. 19104 > Tel: 267.426.0302 > email: tavabik at email.chop.edu > ------------------------------------------------------------- > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > [a.stolk at fcdonders.ru.nl] > Sent: Tuesday, March 29, 2011 4:20 AM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] working with neuromag data > > Dear Kambiz, > > I think I see your point. Your data presumably is already preprocessed > and timelocked (averaged over trials) with neuromag software. I then > take it that you have 6 different conditions which you would like to > plot separately and possibly test at the group level. > > Since the data is already averaged, I'd recommend to do the following > to get your data back on track. > > 1) ft_preprocessing on your stimulus averaged epoch data. This should > give you a data structure with 6 trials (which are actually the > averages per condition). > > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat > this so you end up with 6 timelocked structures representing the 6 > different conditions. > > 3) plot or grandaverage (see tutorials how to proceed as your data now > should be 'ft-friendly'). > > Goodluck, > Arjen > > > > > > > ----- "Kambiz Tavabi" schreef: > > > Van: "Kambiz Tavabi" > > Aan: "Email discussion list for the FieldTrip project" > > > Verzonden: Dinsdag 29 maart 2011 01:10:14 > > Onderwerp: Re: [FieldTrip] working with neuromag data > > > > Dear Arjen - Thanks for your response. Just to clarify the low > level > > functions ft_read_header & ft_read_data are mentioned in the ft > > getting started tutorial. I believe they're recommended to make > sure > > the data is ft friendly. In my case the data is ft friendly. My > data > > is also pre-processed and already 'time-locked'--meaning that I > have > > stimulus averaged epoch data in fif format for all my subjects. My > > question is how to proceed from there? I've been through the pages > you > > refer to but have not been able to piece together my data in such a > > way to proceed with grand-averaging and carrying out stats. > > -Kambiz. > > ------------------------------------------------------------- > > Kambiz Tavabi PhD > > Biomedical Imaging Laboratory > > The Children's Hospital of Philadelphia > > 34th Street and Civic Center Boulevard > > Philadelphia, Pa. 19104 > > Tel: 267.426.0302 > > email: tavabik at email.chop.edu > > ------------------------------------------------------------- > > ________________________________________ > > From: fieldtrip-bounces at donders.ru.nl > > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > > [a.stolk at fcdonders.ru.nl] > > Sent: Monday, March 28, 2011 4:05 PM > > To: Email discussion list for the FieldTrip project > > Subject: Re: [FieldTrip] working with neuromag data > > > > Dear Kambiz, > > > > While you are able to use the 'low level' ft_read_header and > > ft_read_data functions, you should be able to preprocess and > analyze > > your neuromag data using the 'high level' functions such as > > ft_preprocessing (which calls the low level functions mentioned > > above). > > > > How to proceed depends on what you want to do with your data. If > you > > have triggers stored in your dataset that are synchronuous with the > > recorded brain activity, it'd be recommended to start with the > > following tutorial on how to select your trials: > > > > http://fieldtrip.fcdonders.nl/tutorial/preprocessing > > > > Since your experience with FT is still limited as you say, I > believe > > the following text may provide a good overview of what the data, > once > > read in to FT (i.e. matlab) environment, may look like: > > > > http://fieldtrip.fcdonders.nl/walkthrough > > > > Typically, your next steps involve single-subject timelocked > analysis, > > then grand-average and perform statistics at the group level. For > an > > overview of the steps and protocols, see: > > > > http://fieldtrip.fcdonders.nl/tutorial/analysis_protocols > > > > Hope this has helped for a start, > > > > Arjen > > > > > > ----- "Kambiz Tavabi" schreef: > > > > > Van: "Kambiz Tavabi" > > > Aan: "Email discussion list for the FieldTrip project" > > > > > Verzonden: Maandag 28 maart 2011 20:59:36 > > > Onderwerp: [FieldTrip] working with neuromag data > > > > > > Greetings - I have preprocessed/averaged neuromag data for a > group > > of > > > subjects that I'd like to visualize, compute grandaverage and > carry > > > out sensor level statistics on. The only help I managed to find > on > > the > > > Fieldtrip site/list Re: neurmag data concerns getting started > e.g., > > > with ft_read_header and ft_read_data. In my case these programs > > work > > > fine meaning that I can proceed with further analysis. > > > On a side, in my limited experience with FT, a major problem I > run > > > into frequently is that there is no clear suggestion(s) on how to > > > proceed with data that is not raw. I understand it is impossible > to > > > cover all analysis scenarios, but it is often the case that > working > > > with CTF, or in particular Elekta system, the data is likely to > be > > in > > > a post-preprocessed phase. Everytime I've tried to work with ft, > It > > > seems to me that if I don't start with square one in fieldtrip, > it > > is > > > difficult to figure out how to use downstream programs to work on > > the > > > data. > > > That said, in my case I have the output from ft_read_header: > > > > > > label: {338x1 cell} > > > nChans: 338 > > > Fs: 1000 > > > grad: [1x1 struct] > > > unit: {1x338 cell} > > > nSamples: 651 > > > nSamplesPre: 100 > > > nTrials: 6 > > > orig: [1x1 struct] > > > > > > and output from ft_read_data > > > > > > [338x651x6] that being channels by samples by number of stimulus > > > averaged epochs. To proceed, ideally I'd like to compute a > > > grandaverage for each condition, visualize them in a multiplot, > and > > > carry out sensor level stats. To be able to do this I understand > I > > > need the output from ft_timelockanalysis, how do I arrange my > data > > as > > > such? I am assuming it is already in that state. Thanks for your > > > time. > > > > > > -Kambiz. > > > ------------------------------------------------------------- > > > Kambiz Tavabi PhD > > > Biomedical Imaging Laboratory > > > The Children's Hospital of Philadelphia > > > 34th Street and Civic Center Boulevard > > > Philadelphia, Pa. 19104 > > > Tel: 267.426.0302 > > > email: tavabik at email.chop.edu > > > ------------------------------------------------------------- > > > _______________________________________________ > > > 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 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Sun Jun 12 10:40:48 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Sun, 12 Jun 2011 10:40:48 +0200 Subject: [FieldTrip] (no subject) In-Reply-To: <00ed01cc277e$170492c0$450db840$@dimitriadis@donders.ru.nl> References: <213089.20008.qm@web45503.mail.sp1.yahoo.com> <550011EB-7B66-40F1-87BB-77974ED41D1B@donders.ru.nl> <00ed01cc277e$170492c0$450db840$@dimitriadis@donders.ru.nl> Message-ID: <4DF47B90.1020400@donders.ru.nl> Hi George, first of all, I just changed the code after I read your mail - but I doubt that this fixes your problem. Anyway, what version of Matlab are you using that causes a comma to break your code? In a lot of fieldtrip functions, we are using if(z), x=y; end; Did this not work for some Matlab versions? If this was the case, you could not use ft_multiplotER, for example, because ft_plot_vector does have a lot of these if-clauses. Are you sure it is this comma and not something else that breaks your code? Please excuse my skepticism :) Best, Jörn On 6/10/2011 4:52 PM, George Dimitriadis wrote: > Hello guys, > > In ft_plot_topo.m at line 69 you say if isempty(tag), tag=''; > Could you please turn the comma into a ; because it breaks my code. > > Thanks > > _______________________________________________ > 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 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 Kapitelweg 29 NL-6525 EN Nijmegen The Netherlands From cmuehl at gmail.com Sun Jun 12 17:56:49 2011 From: cmuehl at gmail.com (Christian Muehl) Date: Sun, 12 Jun 2011 17:56:49 +0200 Subject: [FieldTrip] Final Call for Papers: Affective BCI Workshop, Memphis, USA Message-ID: ** Final Call for Papers ** 2nd Workshop on Affective Brain-Computer Interfaces (aBCI) Workshop at ACII 2011 (October 9-12), Memphis, USA, October 9, 2011 Apologies for multiple postings http://hmi.ewi.utwente.nl/abci2011 http://www.acii2011.org The second workshop on affective brain-computer interfaces will explore the advantages and limitations of using neuro-physiological signals as a modality for the automatic recognition of affective and cognitive states, and the possibilities of using this information about the user state in innovative and adaptive applications. The goal is to bring researchers from the communities of brain computer interfacing, affective computing, neuro-ergonomics, affective and cognitive neuroscience together to present state-of-the-art progress and visions on the various overlaps between those disciplines. Recent research in brain-computer interfaces (BCI) shows that brain activity can be used as an active/voluntary, or passive/involuntary control modality in man-machine interaction. While active BCI paradigms have received a lot of attention in recent years, research on passive approaches to BCI still desperately needs concerted activity. However, it has been shown more than once that brain activations can carry information about the affective and cognitive state of a subject, and that the interaction between humans and machines can be aided by the recognition of those user states. To achieve robust passive BCIs, efforts from applied and basic sciences have to be combined. On the one hand, applied fields such as affective computing aim at the development of applications that adapt to changes in the user states and thereby enrich the interaction, leading to a more natural and effective usability. On the other hand, basic research in neuroscience advances our understanding of the neural processes associated with emotions. Furthermore, similar advancements are being made for more cognitive mental states, for example, attention, fatigue, and work load, which strongly interact with affective states. Topics of interest include, but are not limited to: * emotion elicitation and data collection for affective BCI * detection of affective and cognitive states with BCI and other modalities * adaptive interfaces and affective BCI Invited Talk: 'Brain Dynamics of Affective Engagement' by Scott Makeig, SCCN, University of California at San Diego, USA The workshop will be held in conjunction with the 4th International conference on Affective Computing and Intelligent Interaction (ACII2011) at the FedEx Institute of Technology at the University of Memphis, TN. Submission Instructions * The papers should feature original empirical work, theoretical work, or a well defendable but arguable position of the authors (i.e., not submitted, in submission, or submitted to another conference or journal while in review). * Papers will be published in the proceedings of ACII 2011 by Springer. Papers should not exceed 10 pages and should be formatted according to the Springer LNCS formatting guidelines http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0. * Papers must be submitted as PDF through the EasyChair conference system, which can be accessed through the workshop web site and the ACII conference website. * For further information, contact abci at cs.utwente.nl Important Dates: 15th of June: Workshop papers due 1st of July: Notification of Acceptance 18th of July: Camera-ready papers due 9th of October: Workshop Programme Chairs: * Anton Nijholt, Universiteit Twente, The Netherlands * Brendan Allison, TU Graz, Austria * Stephen Dunne, Starlab Barcelona, Spain * Dirk Heylen, University of Twente, The Netherlands Local Organizer: * Christian Mühl, University of Twente, The Netherlands Programme Committee: * Egon L. van den Broek, University of Twente, The Netherlands * Touradj Ebrahimi, EPFL, Lausanne, Switzerland * Peter Desain, Radboud University Nijmegen, The Netherlands * Jan B.F. van Erp, TNO Human Factors, Soesterberg, The Netherlands * Stephen Fairclough, John Moores University, Liverpool, UK * Gary Garcia Molina, Philips Research, Eindhoven, The Netherlands * Audrey Girouard, Queen's University, Kingston, Canada * Jonghwa Kim, University of Augsburg, Germany * Brent Lance, Army Research Laboratory/TNB, Aberdeen Proving Ground, USA * Robert Leeb, University of Lausanne, Switzerland * Scott Makeig, University of California at San Diego, USA * Femke Nijboer, University of Twente, The Netherlands * Ioannis Patras, Queen Mary University, London, UK * Thierry Pun, University of Geneva, Switzerland * Tanja Schultz, Karlsruhe Institute of Technology (KIT), Germany * Olga Sourina, NanYang Technological University, Singapore * Thomas J. Sullivan, NeuroSky, San Jose, USA * Thorsten Zander, Graz University of Technology, Austria From michael.wibral at web.de Mon Jun 13 14:20:33 2011 From: michael.wibral at web.de (Michael Wibral) Date: Mon, 13 Jun 2011 14:20:33 +0200 (CEST) Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis Message-ID: <826564097.1273685.1307967633954.JavaMail.fmail@mwmweb071> Dear Elena, we do not use neuromag data. So I cannot say anything wrt to neuromag data. On theoretical grounds, the problem is that both sensor types have highly varying SNR from brain location to brain location. While SNR gets worse with depth for both sensor types, this happens more rapidly with the gradiometers. For example for a deep source that means: Gradiometers have little true signal but standard noise, since their leadfields are small, the inverse of their leadfield is big and noise contributions to your voxels are high, for magnetometers its sligtly different. So if one naively uses both types in one inversion noise will often be dominated by gradiometers and signal by magnetometers. For shallow sources its reverse , the noise will be dominated by the high noise of the magnetometers and the signal comes from the gradiometers, so again things will be matched unfortunately. i guess this creates the relatively homogenic power distribution you observe (unless there's a bug in the code or the analysis setup - see below). For some background you might want to have a look at: Commonalities and differences among vectorized beamformers in electromagnetic source imaging. Huang MX et al, Brain Topogr. Do handle this two things are necessary: 1. Compute the beamformer filters for data that have baseline and task combined. searate filter computation will almost certainly create problems. 2. To localize activity use the statistics function not some simple difference measure or relative power picture. For the reasons above, this might still not work. In this case the best workaround would be a weighted average with different, leadfield dependend weights for each voxel and modality. A simpler possibility might be simple averaging (this might work for your case, since source look very similar for the two modalities). Michael ------------------------------------------------------------ Von: "Elena Orekhova" Gesendet: 09.06.2011 22:48:34 An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Michael, I still have not resolved this problem and do not know whether  is specific for my data(or program bag) or the other Neuromag users also had it. Do you use Neuromag? Elena ------------------------------------------------------------ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Thursday, June 09, 2011 5:06 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis     Hi Elena, disregard my last email, I overlooked the att. Michael ------------------------------------------------------------ Von: "Elena Orekhova" Gesendet: Jun 2, 2011 8:03:16 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Verdana"; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear Michael,   I did normalize the data (sourcepst.avg.nai=sourcepst.avg.pow./sourcepre.avg.pow) as it was suggested in the tutorial.   I used the same scales in all plots for comparison purposes. If  automatic scaling is used the result for MAG+GRA does not look any better (see attachment).   >What you could do as a workaround is to average the separate results with a weighting per voxel and  that >is corresponding to the squared norms of the leadfields for the respective modalities for a given voxel , this >would guarantee equal amounts of backprojected noise from both modalities (if I'm not mistaken).   Thank you for your suggestion.  I may use it as a last resort.  Hopefully, there is still a way to get more optimal solution using both GRA and MAG in the same analysis...     Elena ------------------------------------------------------------ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Elena Orekhova [Elena.Orekhova at neuro.gu.se] Sent: Thursday, June 02, 2011 6:22 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis     BODY {direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;} Dear Michael,   I have tried to multiply the leadfield by -1 as you suggested:   for i = 1 : size (grid.leadfield, 2)     grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); end   This had no effect on the 'lcmv' output. I attached the pictures for ‘GRA only, ’MAG only’ and ‘GRA + MAG’   In this experiment I measured evoked field in response to  the unilateral (left) click. The source is expected to be in the right superior temporal cortex.  This is the case  for  ‘GRA only' and ’MAG only’ datasets. The combined sensors give meaningless result.   Elena   ------------------------------------------------------------ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Wednesday, June 01, 2011 4:04 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis     Dear Elena, could you give the following a try: invert (*-1) the leadfileds for one of the two sensor types. Let me know what happens. I would also be interested in taking a look at the results - maybe you could sent images off-list: Michael.Wibral web.de. Michael ------------------------------------------------------------ Von: "Elena Orekhova" Gesendet: Jun 1, 2011 12:23:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "Arial"; }@font-face { font-family: "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: Times; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear  fieldtrippers, This message is mainly for Neuromag users.   When I do  'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. If I combine the two types of sensors without weighting, the result is meaningless. Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements.  Does anybody know how to deal with this problem?     Elena     From tobias.staudigl at uni-konstanz.de Mon Jun 13 15:02:55 2011 From: tobias.staudigl at uni-konstanz.de (Tobias Staudigl) Date: Mon, 13 Jun 2011 15:02:55 +0200 Subject: [FieldTrip] granger causality In-Reply-To: <01F5D123-C4D5-42B2-9D93-CC3B4E86BD66@donders.ru.nl> References: <4DF1F52B.3000406@uni-konstanz.de> <01F5D123-C4D5-42B2-9D93-CC3B4E86BD66@donders.ru.nl> Message-ID: <4DF60A7F.9060505@uni-konstanz.de> Thanks a lot for your answer, Jan-Mathijs , what "other confounding quantity" were you thinking of concerning the shuffling across conditions? There is another question i have: Is there a way to estimate the order of the mvar-model in fieldtrip, or would one do it as implemented in the bsmart toolbox? The bsmart toolbox uses the Akaike Information Criterion to find the right order parameter. However, this criterion sometimes seems to have trouble finding a reasonable model-order. Does anybody know a toolbox that uses other criterions, e.g., Bayesian Information Criterion? And, what is a "reasonable range of the model-order"? Is there any convention or standard? E.g., I m thinking of something like: "This order is too small/big to be meaningful in this particular frequency band / for this particular connectivity measure." Any advice, ideas or literature suggestions welcome! Thank you very much, tobi Am 10.06.2011 13:00, schrieb jan-mathijs schoffelen: > Hi Tobias, > >> >> Q 1: >> If I understood correctly, the grangerspectrum >> (granger.grangerspctrm) gives me values for the granger-causality in >> a matrix [nChannel, nChannel, Freqs]. >> Does [1,2,:] give me the granger-causality of Channel1 predicting >> Channel2, or the other way round? >> > > The FieldTrip convention is indeed (1,2,:) relates to 1->2 > >> Q2: >> The plotting function gives me an error: >> >> ft_connectivityplot(cfg, granger) >> >> ??? Error using ==> seloverdim at 36 >> cannot select over multiple dimensions at the same time >> >> Error in ==> ft_selectdata at 528 >> if selectchan, data = seloverdim(data, 'chan', selchan, fb); end >> >> Error in ==> ft_connectivityplot at 79 >> data = ft_selectdata(data, 'channel', cfg.channel); > > Please update your fieldtrip version. There is a fix (dated 22-04) > that should take care of this > >> Q3: >> How do i statistically validate the measures i get fromthe >> granger-analysis? >> Is there some recommended statistical test? >> Is it correct to do bootstrapping / permutation testing? >> What I could do on my data is shuffle the trials across conditions, >> compute granger causality on the shuffeld data, and compair this >> distribution with the value i get from the data. > > This is a very relevant issue. From what you describe it seems as if > you want to compare across conditions. The shuffling across conditions > is what we do as well, although it remains open to debate how > meaningful it is to compare granger causality indices across > conditions. And, also, if you are able to reject your null-hypothesis, > whether your decision to reject it is actually due to the actual > granger causality being different, or by some other confounding quantity. > > Best wishes, > > Jan-Mathijs > > >> Maybe, somebody is experienced in using granger and could help me out! >> Any advice appreciated! >> >> Thanks a lot! >> tobi >> >> >> I used the following ft_functions according to the online tutorial: >> >> %% MVAR >> cfg = []; >> cfg.order = 2; >> cfg.toolbox = 'bsmart'; >> mdata = ft_mvaranalysis(cfg, data); >> >> %% transfer function >> cfg = []; >> cfg.method = 'mvar'; >> mfreq = ft_freqanalysis(cfg, mdata); >> >> %% granger >> cfg = []; >> cfg.method = 'granger'; >> granger = ft_connectivityanalysis(cfg, mfreq); >> >> %% >> cfg = []; >> cfg.zparam = 'grangerspctrm'; >> %cfg.channel = 'all'; >> ft_connectivityplot(cfg, granger); >> >> -- >> Tobias Staudigl >> Fachbereich Psychologie - ZPR >> Postfach ZPR >> 78457 Konstanz >> ZPR, Haus 12 >> Tel.: +49 (0)7531 / 88 - 5703 >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Tobias Staudigl Fachbereich Psychologie - ZPR Postfach ZPR 78457 Konstanz ZPR, Haus 12 Tel.: +49 (0)7531 / 88 - 5703 From Elena.Orekhova at neuro.gu.se Mon Jun 13 16:31:35 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Mon, 13 Jun 2011 14:31:35 +0000 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <826564097.1273685.1307967633954.JavaMail.fmail@mwmweb071> References: <826564097.1273685.1307967633954.JavaMail.fmail@mwmweb071> Message-ID: <32CC77C0C8A7AD4B9410934642608E1F1333583E@exchccr1.neuro.gu.se> Dear Michael, Thank you for your explanations. As I understand, there is no routine way of handling combined gradiometers and magnetometers in Fieldtrip. I feel that the easiest way will be to average, as you have suggested, or to take a subset of the sensors (GRA or MAG). Elena ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Monday, June 13, 2011 2:20 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Elena, we do not use neuromag data. So I cannot say anything wrt to neuromag data. On theoretical grounds, the problem is that both sensor types have highly varying SNR from brain location to brain location. While SNR gets worse with depth for both sensor types, this happens more rapidly with the gradiometers. For example for a deep source that means: Gradiometers have little true signal but standard noise, since their leadfields are small, the inverse of their leadfield is big and noise contributions to your voxels are high, for magnetometers its sligtly different. So if one naively uses both types in one inversion noise will often be dominated by gradiometers and signal by magnetometers. For shallow sources its reverse , the noise will be dominated by the high noise of the magnetometers and the signal comes from the gradiometers, so again things will be matched unfortunately. i guess this creates the relatively homogenic power distribution you observe (unless there's a bug in the code or the analysis setup - see below). For some background you might want to have a look at: Commonalities and differences among vectorized beamformers in electromagnetic source imaging. Huang MX et al, Brain Topogr. Do handle this two things are necessary: 1. Compute the beamformer filters for data that have baseline and task combined. searate filter computation will almost certainly create problems. 2. To localize activity use the statistics function not some simple difference measure or relative power picture. For the reasons above, this might still not work. In this case the best workaround would be a weighted average with different, leadfield dependend weights for each voxel and modality. A simpler possibility might be simple averaging (this might work for your case, since source look very similar for the two modalities). Michael ------------------------------------------------------------ Von: "Elena Orekhova" Gesendet: 09.06.2011 22:48:34 An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Michael, I still have not resolved this problem and do not know whether is specific for my data(or program bag) or the other Neuromag users also had it. Do you use Neuromag? Elena ------------------------------------------------------------ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Thursday, June 09, 2011 5:06 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Hi Elena, disregard my last email, I overlooked the att. Michael ------------------------------------------------------------ Von: "Elena Orekhova" Gesendet: Jun 2, 2011 8:03:16 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Verdana"; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear Michael, I did normalize the data (sourcepst.avg.nai=sourcepst.avg.pow./sourcepre.avg.pow) as it was suggested in the tutorial. I used the same scales in all plots for comparison purposes. If automatic scaling is used the result for MAG+GRA does not look any better (see attachment). >What you could do as a workaround is to average the separate results with a weighting per voxel and that >is corresponding to the squared norms of the leadfields for the respective modalities for a given voxel , this >would guarantee equal amounts of backprojected noise from both modalities (if I'm not mistaken). Thank you for your suggestion. I may use it as a last resort. Hopefully, there is still a way to get more optimal solution using both GRA and MAG in the same analysis... Elena ------------------------------------------------------------ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Elena Orekhova [Elena.Orekhova at neuro.gu.se] Sent: Thursday, June 02, 2011 6:22 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis BODY {direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;} Dear Michael, I have tried to multiply the leadfield by -1 as you suggested: for i = 1 : size (grid.leadfield, 2) grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); end This had no effect on the 'lcmv' output. I attached the pictures for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ In this experiment I measured evoked field in response to the unilateral (left) click. The source is expected to be in the right superior temporal cortex. This is the case for ‘GRA only' and ’MAG only’ datasets. The combined sensors give meaningless result. Elena ------------------------------------------------------------ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Wednesday, June 01, 2011 4:04 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Elena, could you give the following a try: invert (*-1) the leadfileds for one of the two sensor types. Let me know what happens. I would also be interested in taking a look at the results - maybe you could sent images off-list: Michael.Wibral web.de. Michael ------------------------------------------------------------ Von: "Elena Orekhova" Gesendet: Jun 1, 2011 12:23:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "Arial"; }@font-face { font-family: "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: Times; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear fieldtrippers, This message is mainly for Neuromag users. When I do 'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. If I combine the two types of sensors without weighting, the result is meaningless. Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements. Does anybody know how to deal with this problem? Elena _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From TAVABIK at email.chop.edu Mon Jun 13 20:50:39 2011 From: TAVABIK at email.chop.edu (Tavabi, Kambiz) Date: Mon, 13 Jun 2011 14:50:39 -0400 Subject: [FieldTrip] working with neuromag data In-Reply-To: <621524636.372728.1307777218636.JavaMail.root@sculptor.zimbra.ru.nl> References: <621524636.372728.1307777218636.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Dear Arjen, The data.avt I am using to plot with ft_multiplotER is infact real numbers, quite small numbers on the order of x.xxxe-15, but I still get no visualization using cfg.ylim(min(data.avg), max(data.avg) or extremely small numbers eg., cfg.ylim [-3e-50 3e-50]. Conversely, ft_topoplotER seems to work just fine with the exception of a couple of warnings: 1- some points fall outside the outline, please consider using another layout >ft_plot_topo line 112 and ft_topoplotER line 719 2- Duplicate x-y data points detected: using average of the z values >ft_plot_topo line 144 and ft_topoplotER line 719. What does this warning mean? Regards, Kambiz -----Original Message----- From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. Sent: Saturday, June 11, 2011 3:27 AM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] working with neuromag data Dear Kambiz, Does your data.avg contain NaNs or real numbers? In the latter case; do they fall in the plotting range as specified by your cfg.ylim? Yours, Arjen ----- "Kambiz Tavabi" schreef: > Van: "Kambiz Tavabi" > Aan: "Email discussion list for the FieldTrip project" > Verzonden: Vrijdag 10 juni 2011 18:59:03 > Onderwerp: Re: [FieldTrip] working with neuromag data > > As per advise from Arjen, I was able to use following steps > 1) ft_preprocessing on your stimulus averaged epoch data. This should > give you a data structure with 6 trials (which are actually the > averages per condition). > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat > this so you end up with 6 timelocked structures representing the 6 > different conditions. > to create individual condition averaged ft data structures which I can > visualize using ft_topoplotER(cfg,data) > data: > avg: [338x651 double] > var: [338x651 double] > fsample: 1000 > time: [1x651 double] > dof: [338x651 double] > label: {338x1 cell} > dimord: 'chan_time' > grad: [1x1 struct] > cfg: [1x1 struct] > however when i use; > cfg = []; > cfg.showlabels = 'yes'; > cfg.fontsize = 6; > cfg.ylim = [-10e-13 10e-13] > ft_multiplotER(cfg, data); > Fieldtrip chruns through creating the > selection avg along dimension 1 > selection dof along dimension 1 > selection var along dimension 1 > creating layout from data.grad > creating layout for neuromag306 system > > but the resutling figure is an empty figure containing only layout > with ch lables without any data what so ever. Any ideas why this might > be? > > > > -Kambiz. > ------------------------------------------------------------- > Kambiz Tavabi PhD > Biomedical Imaging Laboratory > The Children's Hospital of Philadelphia > 34th Street and Civic Center Boulevard > Philadelphia, Pa. 19104 > Tel: 267.426.0302 > email: tavabik at email.chop.edu > ------------------------------------------------------------- > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > [a.stolk at fcdonders.ru.nl] > Sent: Tuesday, March 29, 2011 4:20 AM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] working with neuromag data > > Dear Kambiz, > > I think I see your point. Your data presumably is already preprocessed > and timelocked (averaged over trials) with neuromag software. I then > take it that you have 6 different conditions which you would like to > plot separately and possibly test at the group level. > > Since the data is already averaged, I'd recommend to do the following > to get your data back on track. > > 1) ft_preprocessing on your stimulus averaged epoch data. This should > give you a data structure with 6 trials (which are actually the > averages per condition). > > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat > this so you end up with 6 timelocked structures representing the 6 > different conditions. > > 3) plot or grandaverage (see tutorials how to proceed as your data now > should be 'ft-friendly'). > > Goodluck, > Arjen > > > > > > > ----- "Kambiz Tavabi" schreef: > > > Van: "Kambiz Tavabi" > > Aan: "Email discussion list for the FieldTrip project" > > > Verzonden: Dinsdag 29 maart 2011 01:10:14 > > Onderwerp: Re: [FieldTrip] working with neuromag data > > > > Dear Arjen - Thanks for your response. Just to clarify the low > level > > functions ft_read_header & ft_read_data are mentioned in the ft > > getting started tutorial. I believe they're recommended to make > sure > > the data is ft friendly. In my case the data is ft friendly. My > data > > is also pre-processed and already 'time-locked'--meaning that I > have > > stimulus averaged epoch data in fif format for all my subjects. My > > question is how to proceed from there? I've been through the pages > you > > refer to but have not been able to piece together my data in such a > > way to proceed with grand-averaging and carrying out stats. > > -Kambiz. > > ------------------------------------------------------------- > > Kambiz Tavabi PhD > > Biomedical Imaging Laboratory > > The Children's Hospital of Philadelphia > > 34th Street and Civic Center Boulevard > > Philadelphia, Pa. 19104 > > Tel: 267.426.0302 > > email: tavabik at email.chop.edu > > ------------------------------------------------------------- > > ________________________________________ > > From: fieldtrip-bounces at donders.ru.nl > > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > > [a.stolk at fcdonders.ru.nl] > > Sent: Monday, March 28, 2011 4:05 PM > > To: Email discussion list for the FieldTrip project > > Subject: Re: [FieldTrip] working with neuromag data > > > > Dear Kambiz, > > > > While you are able to use the 'low level' ft_read_header and > > ft_read_data functions, you should be able to preprocess and > analyze > > your neuromag data using the 'high level' functions such as > > ft_preprocessing (which calls the low level functions mentioned > > above). > > > > How to proceed depends on what you want to do with your data. If > you > > have triggers stored in your dataset that are synchronuous with the > > recorded brain activity, it'd be recommended to start with the > > following tutorial on how to select your trials: > > > > http://fieldtrip.fcdonders.nl/tutorial/preprocessing > > > > Since your experience with FT is still limited as you say, I > believe > > the following text may provide a good overview of what the data, > once > > read in to FT (i.e. matlab) environment, may look like: > > > > http://fieldtrip.fcdonders.nl/walkthrough > > > > Typically, your next steps involve single-subject timelocked > analysis, > > then grand-average and perform statistics at the group level. For > an > > overview of the steps and protocols, see: > > > > http://fieldtrip.fcdonders.nl/tutorial/analysis_protocols > > > > Hope this has helped for a start, > > > > Arjen > > > > > > ----- "Kambiz Tavabi" schreef: > > > > > Van: "Kambiz Tavabi" > > > Aan: "Email discussion list for the FieldTrip project" > > > > > Verzonden: Maandag 28 maart 2011 20:59:36 > > > Onderwerp: [FieldTrip] working with neuromag data > > > > > > Greetings - I have preprocessed/averaged neuromag data for a > group > > of > > > subjects that I'd like to visualize, compute grandaverage and > carry > > > out sensor level statistics on. The only help I managed to find > on > > the > > > Fieldtrip site/list Re: neurmag data concerns getting started > e.g., > > > with ft_read_header and ft_read_data. In my case these programs > > work > > > fine meaning that I can proceed with further analysis. > > > On a side, in my limited experience with FT, a major problem I > run > > > into frequently is that there is no clear suggestion(s) on how to > > > proceed with data that is not raw. I understand it is impossible > to > > > cover all analysis scenarios, but it is often the case that > working > > > with CTF, or in particular Elekta system, the data is likely to > be > > in > > > a post-preprocessed phase. Everytime I've tried to work with ft, > It > > > seems to me that if I don't start with square one in fieldtrip, > it > > is > > > difficult to figure out how to use downstream programs to work on > > the > > > data. > > > That said, in my case I have the output from ft_read_header: > > > > > > label: {338x1 cell} > > > nChans: 338 > > > Fs: 1000 > > > grad: [1x1 struct] > > > unit: {1x338 cell} > > > nSamples: 651 > > > nSamplesPre: 100 > > > nTrials: 6 > > > orig: [1x1 struct] > > > > > > and output from ft_read_data > > > > > > [338x651x6] that being channels by samples by number of stimulus > > > averaged epochs. To proceed, ideally I'd like to compute a > > > grandaverage for each condition, visualize them in a multiplot, > and > > > carry out sensor level stats. To be able to do this I understand > I > > > need the output from ft_timelockanalysis, how do I arrange my > data > > as > > > such? I am assuming it is already in that state. Thanks for your > > > time. > > > > > > -Kambiz. > > > ------------------------------------------------------------- > > > Kambiz Tavabi PhD > > > Biomedical Imaging Laboratory > > > The Children's Hospital of Philadelphia > > > 34th Street and Civic Center Boulevard > > > Philadelphia, Pa. 19104 > > > Tel: 267.426.0302 > > > email: tavabik at email.chop.edu > > > ------------------------------------------------------------- > > > _______________________________________________ > > > 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 > > _______________________________________________ > 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 marcel.heers at googlemail.com Mon Jun 13 23:48:04 2011 From: marcel.heers at googlemail.com (Marcel Heers) Date: Mon, 13 Jun 2011 23:48:04 +0200 Subject: [FieldTrip] courses In-Reply-To: <5B0A148A-D4F0-454F-B60B-E47ECCA47E75@donders.ru.nl> References: <32CC77C0C8A7AD4B9410934642608E1F03ECAF47@exchccr1.neuro.gu.se> <5B0A148A-D4F0-454F-B60B-E47ECCA47E75@donders.ru.nl> Message-ID: Dear Robert, might there be a chance for external person to participate in the fieldtrip course in Paris at the end of the year? Best regards, Marcel 2011/6/9 Robert Oostenveld : > Dear Elena > > For 2011 there are no courses planned any more in Nijmege, which are open to > external participants (there will be a course for local studens in the > Donders Graduate School in the autumn). The next course in Nijmegen will be > the MEG Toolkit course, which most likely will be somewhere in the spring of > 2012. > > For 2011 we are currently considering a course in Paris at the end of this > year. I believe that Stefan and Saskia are considering to do another course > in New York later this year, although I don't know any details for the New > York plans. > > At the upcoming HBM meeting in Quebec there will be an educational course in > which FieldTrip and the other open source academic toolboxes will play a > (relatively small) role. Although I don't think it is efficient to travel to > Quebec just for this part, it might be interesting for you to attend if you > are attending the HBM conference anyway. See > http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3437 > and for the program one of the last pages of > http://www.humanbrainmapping.org/files/2011MeetingFiles/Descriptions/HBM%202011%20Educational%20Program.pdf > > Please note that we are open to invitations for presenting the FieldTrip > course at external sites. This year we have already been in Tuebingen, St > Louis, and New York, and if there is an interesting venue, an enthousiastic > local organizer and funding can be arranged to cover the expenses, most > likely some experienced users/developers from Nijmegen can be found or > appointed to present a 2,5 day course at the external site. > > best regards, > Robert > > > > On 7 Jun 2011, at 12:53, Elena Orekhova wrote: > >> Dear FieldTrip gurus, >> >> Are you planning  any FieldTrip courses for the users in the nearest >> future? >> >> Elena >> >> _______________________________________________ >> 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 > -- Dr. Marcel Heers, M.D. Fischenbergstr. 10 D-58455 Witten phone: +49-2302-2034057 From jan.schoffelen at donders.ru.nl Wed Jun 15 15:51:01 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 15 Jun 2011 15:51:01 +0200 Subject: [FieldTrip] functionality change of ft_prepare_sourcemodel Message-ID: <0A5873EA-0666-4EDD-9AAB-13CA8EDA12FC@donders.ru.nl> Dear all, We implemented a slight change in the default behaviour of ft_prepare_sourcemodel. This is a fieldtrip function (often not called directly by you), which creates a specified source model for inverse reconstruction. Typically, this is a 3D regular grid, or a 2D mesh of the cortical sheet. The function is typically called with additional input arguments, specifying geometric objects, such as a volume conductor model of the head, or a description of the sensor-array. To make a long story short, before you had the option to specify cfg.sourceunits and cfg.mriunits. Cfg.sourceunits refers to the metrical unit of the dipole positions, and this defaulted (if you didn't explicitly specify it) to 'cm'. As of yet, it will default to the metrical units in the input data, i.e. the units of the sensor-array (if provided), or the units of the volume conductor of the head. For example, for neuromag and 4d- neuroimaging users the default will now be a grid with 'm' as a unit. Cfg.mriunits is as of now deprecated, and was used to specify the units of the (optional) input anatomical or segmented mri. Nowadays, these structures explicitly contain a unit, so that can be easily recovered from the data. We will build in explicit checks on the units in which different geometric objects are defined (many of those are already in place, e.g. ensuring same units for volume conductor model of the head and sensor positions) in the near future. For now, if you want to have explicitly the same behavior as before, you need to specify cfg.sourceunits to be 'cm'. Best wishes, Jan-Mathijs Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From cmuehl at gmail.com Thu Jun 16 18:22:02 2011 From: cmuehl at gmail.com (Christian Muehl) Date: Thu, 16 Jun 2011 18:22:02 +0200 Subject: [FieldTrip] Extended Deadline: Affective BCI Workshop, Memphis, USA Message-ID: ** Final Call for Papers - Extended Deadline ** 2nd Workshop on Affective Brain-Computer Interfaces (aBCI) Workshop at ACII 2011 (October 9-12), Memphis, USA, October 9, 2011 Apologies for multiple postings http://hmi.ewi.utwente.nl/abci2011 http://www.acii2011.org The second workshop on affective brain-computer interfaces will explore the advantages and limitations of using neuro-physiological signals as a modality for the automatic recognition of affective and cognitive states, and the possibilities of using this information about the user state in innovative and adaptive applications. The goal is to bring researchers from the communities of brain computer interfacing, affective computing, neuro-ergonomics, affective and cognitive neuroscience together to present state-of-the-art progress and visions on the various overlaps between those disciplines. Recent research in brain-computer interfaces (BCI) shows that brain activity can be used as an active/voluntary, or passive/involuntary control modality in man-machine interaction. While active BCI paradigms have received a lot of attention in recent years, research on passive approaches to BCI still desperately needs concerted activity. However, it has been shown more than once that brain activations can carry information about the affective and cognitive state of a subject, and that the interaction between humans and machines can be aided by the recognition of those user states. To achieve robust passive BCIs, efforts from applied and basic sciences have to be combined. On the one hand, applied fields such as affective computing aim at the development of applications that adapt to changes in the user states and thereby enrich the interaction, leading to a more natural and effective usability. On the other hand, basic research in neuroscience advances our understanding of the neural processes associated with emotions. Furthermore, similar advancements are being made for more cognitive mental states, for example, attention, fatigue, and work load, which strongly interact with affective states. Topics of interest include, but are not limited to: * emotion elicitation and data collection for affective BCI * detection of affective and cognitive states with BCI and other modalities * adaptive interfaces and affective BCI Invited Talk: 'Brain Dynamics of Affective Engagement' by Scott Makeig, SCCN, University of California at San Diego, USA The workshop will be held in conjunction with the 4th International conference on Affective Computing and Intelligent Interaction (ACII2011) at the FedEx Institute of Technology at the University of Memphis, TN. Submission Instructions * The papers should feature original empirical work, theoretical work, or a well defendable but arguable position of the authors (i.e., not submitted, in submission, or submitted to another conference or journal while in review). * Papers will be published in the proceedings of ACII 2011 by Springer. Papers should not exceed 10 pages and should be formatted according to the Springer LNCS formatting guidelines http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0. * Papers must be submitted as PDF through the EasyChair conference system, which can be accessed through the workshop web site and the ACII conference website. * For further information, contact abci at cs.utwente.nl Important Dates: 22nd of June: Workshop papers due 7th of July: Notification of Acceptance 24th of July: Camera-ready papers due 9th of October: Workshop Programme Chairs: * Anton Nijholt, Universiteit Twente, The Netherlands * Brendan Allison, TU Graz, Austria * Stephen Dunne, Starlab Barcelona, Spain * Dirk Heylen, University of Twente, The Netherlands Local Organizer: * Christian Mühl, University of Twente, The Netherlands Programme Committee: * Egon L. van den Broek, University of Twente, The Netherlands * Touradj Ebrahimi, EPFL, Lausanne, Switzerland * Peter Desain, Radboud University Nijmegen, The Netherlands * Jan B.F. van Erp, TNO Human Factors, Soesterberg, The Netherlands * Stephen Fairclough, John Moores University, Liverpool, UK * Gary Garcia Molina, Philips Research, Eindhoven, The Netherlands * Audrey Girouard, Queen's University, Kingston, Canada * Jonghwa Kim, University of Augsburg, Germany * Brent Lance, Army Research Laboratory/TNB, Aberdeen Proving Ground, USA * Robert Leeb, University of Lausanne, Switzerland * Scott Makeig, University of California at San Diego, USA * Femke Nijboer, University of Twente, The Netherlands * Ioannis Patras, Queen Mary University, London, UK * Thierry Pun, University of Geneva, Switzerland * Tanja Schultz, Karlsruhe Institute of Technology (KIT), Germany * Olga Sourina, NanYang Technological University, Singapore * Thomas J. Sullivan, NeuroSky, San Jose, USA * Thorsten Zander, Graz University of Technology, Austria From TAVABIK at email.chop.edu Thu Jun 16 18:31:54 2011 From: TAVABIK at email.chop.edu (Tavabi, Kambiz) Date: Thu, 16 Jun 2011 12:31:54 -0400 Subject: [FieldTrip] working with neuromag data In-Reply-To: <621524636.372728.1307777218636.JavaMail.root@sculptor.zimbra.ru.nl> References: , <621524636.372728.1307777218636.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Dear Arjen, The data.avg I am using to plot with ft_multiplotER is infact real numbers, quite small numbers on the order of x.xxxe-15, but I still get no visualization using cfg.ylim(min(data.avg), max(data.avg) or extremely small numbers eg., cfg.ylim [-3e-50 3e-50]. Conversely, ft_topoplotER seems to work just fine with the exception of a couple of warnings: 1- some points fall outside the outline, please consider using another layout >ft_plot_topo line 112 and ft_topoplotER line 719 2- Duplicate x-y data points detected: using average of the z values >ft_plot_topo line 144 and ft_topoplotER line 719. What does this warning mean? >From what I understand the ft_multiplotER step is necessary to carry out sensor level analysis of the data? As I mentioned previously, the grand average data structure does not contain the proper layout information that is in the timelock structure. Is this purposefully done, or am I doing something wrong here? Regards, -Kambiz. ------------------------------------------------------------- Kambiz Tavabi PhD Biomedical Imaging Laboratory The Children's Hospital of Philadelphia 34th Street and Civic Center Boulevard Philadelphia, Pa. 19104 Tel: 267.426.0302 email: tavabik at email.chop.edu ------------------------------------------------------------- ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. [a.stolk at fcdonders.ru.nl] Sent: Saturday, June 11, 2011 3:26 AM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] working with neuromag data Dear Kambiz, Does your data.avg contain NaNs or real numbers? In the latter case; do they fall in the plotting range as specified by your cfg.ylim? Yours, Arjen ----- "Kambiz Tavabi" schreef: > Van: "Kambiz Tavabi" > Aan: "Email discussion list for the FieldTrip project" > Verzonden: Vrijdag 10 juni 2011 18:59:03 > Onderwerp: Re: [FieldTrip] working with neuromag data > > As per advise from Arjen, I was able to use following steps > 1) ft_preprocessing on your stimulus averaged epoch data. This should > give you a data structure with 6 trials (which are actually the > averages per condition). > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat > this so you end up with 6 timelocked structures representing the 6 > different conditions. > to create individual condition averaged ft data structures which I can > visualize using ft_topoplotER(cfg,data) > data: > avg: [338x651 double] > var: [338x651 double] > fsample: 1000 > time: [1x651 double] > dof: [338x651 double] > label: {338x1 cell} > dimord: 'chan_time' > grad: [1x1 struct] > cfg: [1x1 struct] > however when i use; > cfg = []; > cfg.showlabels = 'yes'; > cfg.fontsize = 6; > cfg.ylim = [-10e-13 10e-13] > ft_multiplotER(cfg, data); > Fieldtrip chruns through creating the > selection avg along dimension 1 > selection dof along dimension 1 > selection var along dimension 1 > creating layout from data.grad > creating layout for neuromag306 system > > but the resutling figure is an empty figure containing only layout > with ch lables without any data what so ever. Any ideas why this might > be? > > > > -Kambiz. > ------------------------------------------------------------- > Kambiz Tavabi PhD > Biomedical Imaging Laboratory > The Children's Hospital of Philadelphia > 34th Street and Civic Center Boulevard > Philadelphia, Pa. 19104 > Tel: 267.426.0302 > email: tavabik at email.chop.edu > ------------------------------------------------------------- > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > [a.stolk at fcdonders.ru.nl] > Sent: Tuesday, March 29, 2011 4:20 AM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] working with neuromag data > > Dear Kambiz, > > I think I see your point. Your data presumably is already preprocessed > and timelocked (averaged over trials) with neuromag software. I then > take it that you have 6 different conditions which you would like to > plot separately and possibly test at the group level. > > Since the data is already averaged, I'd recommend to do the following > to get your data back on track. > > 1) ft_preprocessing on your stimulus averaged epoch data. This should > give you a data structure with 6 trials (which are actually the > averages per condition). > > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat > this so you end up with 6 timelocked structures representing the 6 > different conditions. > > 3) plot or grandaverage (see tutorials how to proceed as your data now > should be 'ft-friendly'). > > Goodluck, > Arjen > > > > > > > ----- "Kambiz Tavabi" schreef: > > > Van: "Kambiz Tavabi" > > Aan: "Email discussion list for the FieldTrip project" > > > Verzonden: Dinsdag 29 maart 2011 01:10:14 > > Onderwerp: Re: [FieldTrip] working with neuromag data > > > > Dear Arjen - Thanks for your response. Just to clarify the low > level > > functions ft_read_header & ft_read_data are mentioned in the ft > > getting started tutorial. I believe they're recommended to make > sure > > the data is ft friendly. In my case the data is ft friendly. My > data > > is also pre-processed and already 'time-locked'--meaning that I > have > > stimulus averaged epoch data in fif format for all my subjects. My > > question is how to proceed from there? I've been through the pages > you > > refer to but have not been able to piece together my data in such a > > way to proceed with grand-averaging and carrying out stats. > > -Kambiz. > > ------------------------------------------------------------- > > Kambiz Tavabi PhD > > Biomedical Imaging Laboratory > > The Children's Hospital of Philadelphia > > 34th Street and Civic Center Boulevard > > Philadelphia, Pa. 19104 > > Tel: 267.426.0302 > > email: tavabik at email.chop.edu > > ------------------------------------------------------------- > > ________________________________________ > > From: fieldtrip-bounces at donders.ru.nl > > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > > [a.stolk at fcdonders.ru.nl] > > Sent: Monday, March 28, 2011 4:05 PM > > To: Email discussion list for the FieldTrip project > > Subject: Re: [FieldTrip] working with neuromag data > > > > Dear Kambiz, > > > > While you are able to use the 'low level' ft_read_header and > > ft_read_data functions, you should be able to preprocess and > analyze > > your neuromag data using the 'high level' functions such as > > ft_preprocessing (which calls the low level functions mentioned > > above). > > > > How to proceed depends on what you want to do with your data. If > you > > have triggers stored in your dataset that are synchronuous with the > > recorded brain activity, it'd be recommended to start with the > > following tutorial on how to select your trials: > > > > http://fieldtrip.fcdonders.nl/tutorial/preprocessing > > > > Since your experience with FT is still limited as you say, I > believe > > the following text may provide a good overview of what the data, > once > > read in to FT (i.e. matlab) environment, may look like: > > > > http://fieldtrip.fcdonders.nl/walkthrough > > > > Typically, your next steps involve single-subject timelocked > analysis, > > then grand-average and perform statistics at the group level. For > an > > overview of the steps and protocols, see: > > > > http://fieldtrip.fcdonders.nl/tutorial/analysis_protocols > > > > Hope this has helped for a start, > > > > Arjen > > > > > > ----- "Kambiz Tavabi" schreef: > > > > > Van: "Kambiz Tavabi" > > > Aan: "Email discussion list for the FieldTrip project" > > > > > Verzonden: Maandag 28 maart 2011 20:59:36 > > > Onderwerp: [FieldTrip] working with neuromag data > > > > > > Greetings - I have preprocessed/averaged neuromag data for a > group > > of > > > subjects that I'd like to visualize, compute grandaverage and > carry > > > out sensor level statistics on. The only help I managed to find > on > > the > > > Fieldtrip site/list Re: neurmag data concerns getting started > e.g., > > > with ft_read_header and ft_read_data. In my case these programs > > work > > > fine meaning that I can proceed with further analysis. > > > On a side, in my limited experience with FT, a major problem I > run > > > into frequently is that there is no clear suggestion(s) on how to > > > proceed with data that is not raw. I understand it is impossible > to > > > cover all analysis scenarios, but it is often the case that > working > > > with CTF, or in particular Elekta system, the data is likely to > be > > in > > > a post-preprocessed phase. Everytime I've tried to work with ft, > It > > > seems to me that if I don't start with square one in fieldtrip, > it > > is > > > difficult to figure out how to use downstream programs to work on > > the > > > data. > > > That said, in my case I have the output from ft_read_header: > > > > > > label: {338x1 cell} > > > nChans: 338 > > > Fs: 1000 > > > grad: [1x1 struct] > > > unit: {1x338 cell} > > > nSamples: 651 > > > nSamplesPre: 100 > > > nTrials: 6 > > > orig: [1x1 struct] > > > > > > and output from ft_read_data > > > > > > [338x651x6] that being channels by samples by number of stimulus > > > averaged epochs. To proceed, ideally I'd like to compute a > > > grandaverage for each condition, visualize them in a multiplot, > and > > > carry out sensor level stats. To be able to do this I understand > I > > > need the output from ft_timelockanalysis, how do I arrange my > data > > as > > > such? I am assuming it is already in that state. Thanks for your > > > time. > > > > > > -Kambiz. > > > ------------------------------------------------------------- > > > Kambiz Tavabi PhD > > > Biomedical Imaging Laboratory > > > The Children's Hospital of Philadelphia > > > 34th Street and Civic Center Boulevard > > > Philadelphia, Pa. 19104 > > > Tel: 267.426.0302 > > > email: tavabik at email.chop.edu > > > ------------------------------------------------------------- > > > _______________________________________________ > > > 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 > > _______________________________________________ > 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 fieldtrip at greenant.net Thu Jun 16 18:42:58 2011 From: fieldtrip at greenant.net (frank@greenant.net) Date: Fri, 17 Jun 2011 02:42:58 +1000 Subject: [FieldTrip] Using ICA to filter data In-Reply-To: References: Message-ID: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> I am trying to use fieldtrip to filter EOG data obtained in an MRI. I want to be able to spot the saccades in the samples and ideally measure their onset at the end of each trial. As you may guess, it's quite noisy and it's broad spectrum noise, despite pre-filtering. Ideally, I would like to isolate the component that corresponds to the MRI interference and then filter this out. I have managed to import the data and can run ft_componentanalysis but it fails with: runica() - data size (1,30720) too small My data is single channel, 40 epochs, each of 6 seconds (time locked to stim onset but not saccade onset) Is there a different method I should be using? I have posted some sample data and the current script (which reads in the data and runs preprocessing) to the following urls: http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat http://greenant.net/temp/EOG_analysis.m From batrod at gmail.com Thu Jun 16 18:48:07 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Thu, 16 Jun 2011 11:48:07 -0500 Subject: [FieldTrip] Using ICA to filter data In-Reply-To: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> Message-ID: To summarize, the ICA will decompose your signal into as many components as Electrodes. Therefore, trying to decompose only one source is useless. Did you use a full net of electrodes into your MRI machine or only EOG electrodes? Hope this helps, Rodolphe N. On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net wrote: > I am trying to use fieldtrip to filter EOG data obtained in an MRI. > I want to be able to spot the saccades in the samples and ideally measure > their onset at the > end of each trial. > > As you may guess, it's quite noisy and it's broad spectrum noise, despite > pre-filtering. > > Ideally, I would like to isolate the component that corresponds to the MRI > interference > and then filter this out. > > I have managed to import the data and can run ft_componentanalysis > but it fails with: > > runica() - data size (1,30720) too small > > My data is single channel, 40 epochs, each of 6 seconds (time locked to > stim onset but not saccade onset) > Is there a different method I should be using? > > I have posted some sample data and the current script (which reads in the > data and runs preprocessing) to the following urls: > > http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat > http://greenant.net/temp/EOG_analysis.m > _______________________________________________ > 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 fieldtrip at greenant.net Thu Jun 16 20:16:45 2011 From: fieldtrip at greenant.net (frank@greenant.net) Date: Fri, 17 Jun 2011 04:16:45 +1000 Subject: [FieldTrip] Using ICA to filter data In-Reply-To: References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> Message-ID: It's a bit of a unique experiment, we're trying to use an ECG machine to acquire EOG, so it's only a single output channel. i guess what I need is a temporal ICA rather than a spatial one... On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: > To summarize, the ICA will decompose your signal into as many components as Electrodes. > Therefore, trying to decompose only one source is useless. > Did you use a full net of electrodes into your MRI machine or only EOG electrodes? > > Hope this helps, > > Rodolphe N. > > On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net wrote: > I am trying to use fieldtrip to filter EOG data obtained in an MRI. > I want to be able to spot the saccades in the samples and ideally measure their onset at the > end of each trial. > > As you may guess, it's quite noisy and it's broad spectrum noise, despite pre-filtering. > > Ideally, I would like to isolate the component that corresponds to the MRI interference > and then filter this out. > > I have managed to import the data and can run ft_componentanalysis > but it fails with: > > runica() - data size (1,30720) too small > > My data is single channel, 40 epochs, each of 6 seconds (time locked to stim onset but not saccade onset) > Is there a different method I should be using? > > I have posted some sample data and the current script (which reads in the > data and runs preprocessing) to the following urls: > > http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat > http://greenant.net/temp/EOG_analysis.m > _______________________________________________ > 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 a.stolk at fcdonders.ru.nl Thu Jun 16 20:33:38 2011 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Thu, 16 Jun 2011 20:33:38 +0200 (CEST) Subject: [FieldTrip] working with neuromag data In-Reply-To: <1394883530.423835.1308249012378.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <1699057884.423853.1308249218140.JavaMail.root@sculptor.zimbra.ru.nl> Dear Kambiz, To answer your first question, I do not know what this error when calling ft_topoplotER means. Secondly, ft_multiplotTFR is a visualization step of the data and not an analysis step. It is not necessary to call this function before proceeding, but giving that it works far from what you'd expect, it tells us something's wrong. :) At your third question; what do you mean with layout information? Information on the gradiometer and magnetometer definitions? Keep in mind that when creating a grand-average, you cannot effectively average these. Ok, for a plan de campagne; are you using the most recent version of FT? If so, could you send me your data in a .mat file? Please send it to my e-mail address and not the FT list. Yours, Arjen Are you using the most recent version of FT? ----- "Kambiz Tavabi" schreef: > Van: "Kambiz Tavabi" > Aan: "Email discussion list for the FieldTrip project" > Verzonden: Donderdag 16 juni 2011 18:31:54 > Onderwerp: Re: [FieldTrip] working with neuromag data > > Dear Arjen, > The data.avg I am using to plot with ft_multiplotER is infact real > numbers, quite small numbers on the order of x.xxxe-15, but I still > get no visualization using cfg.ylim(min(data.avg), max(data.avg) or > extremely small numbers eg., cfg.ylim [-3e-50 3e-50]. Conversely, > ft_topoplotER seems to work just fine with the exception of a couple > of warnings: > 1- some points fall outside the outline, please consider using another > layout >ft_plot_topo line 112 and ft_topoplotER line 719 > 2- Duplicate x-y data points detected: using average of the z values > >ft_plot_topo line 144 and ft_topoplotER line 719. What does this > warning mean? > > >From what I understand the ft_multiplotER step is necessary to carry > out sensor level analysis of the data? > > As I mentioned previously, the grand average data structure does not > contain the proper layout information that is in the timelock > structure. Is this purposefully done, or am I doing something wrong > here? > > Regards, > > -Kambiz. > ------------------------------------------------------------- > Kambiz Tavabi PhD > Biomedical Imaging Laboratory > The Children's Hospital of Philadelphia > 34th Street and Civic Center Boulevard > Philadelphia, Pa. 19104 > Tel: 267.426.0302 > email: tavabik at email.chop.edu > ------------------------------------------------------------- > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > [a.stolk at fcdonders.ru.nl] > Sent: Saturday, June 11, 2011 3:26 AM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] working with neuromag data > > Dear Kambiz, > > Does your data.avg contain NaNs or real numbers? In the latter case; > do they fall in the plotting range as specified by your cfg.ylim? > > Yours, > Arjen > > ----- "Kambiz Tavabi" schreef: > > > Van: "Kambiz Tavabi" > > Aan: "Email discussion list for the FieldTrip project" > > > Verzonden: Vrijdag 10 juni 2011 18:59:03 > > Onderwerp: Re: [FieldTrip] working with neuromag data > > > > As per advise from Arjen, I was able to use following steps > > 1) ft_preprocessing on your stimulus averaged epoch data. This > should > > give you a data structure with 6 trials (which are actually the > > averages per condition). > > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And > repeat > > this so you end up with 6 timelocked structures representing the 6 > > different conditions. > > to create individual condition averaged ft data structures which I > can > > visualize using ft_topoplotER(cfg,data) > > data: > > avg: [338x651 double] > > var: [338x651 double] > > fsample: 1000 > > time: [1x651 double] > > dof: [338x651 double] > > label: {338x1 cell} > > dimord: 'chan_time' > > grad: [1x1 struct] > > cfg: [1x1 struct] > > however when i use; > > cfg = []; > > cfg.showlabels = 'yes'; > > cfg.fontsize = 6; > > cfg.ylim = [-10e-13 10e-13] > > ft_multiplotER(cfg, data); > > Fieldtrip chruns through creating the > > selection avg along dimension 1 > > selection dof along dimension 1 > > selection var along dimension 1 > > creating layout from data.grad > > creating layout for neuromag306 system > > > > but the resutling figure is an empty figure containing only layout > > with ch lables without any data what so ever. Any ideas why this > might > > be? > > > > > > > > -Kambiz. > > ------------------------------------------------------------- > > Kambiz Tavabi PhD > > Biomedical Imaging Laboratory > > The Children's Hospital of Philadelphia > > 34th Street and Civic Center Boulevard > > Philadelphia, Pa. 19104 > > Tel: 267.426.0302 > > email: tavabik at email.chop.edu > > ------------------------------------------------------------- > > ________________________________________ > > From: fieldtrip-bounces at donders.ru.nl > > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > > [a.stolk at fcdonders.ru.nl] > > Sent: Tuesday, March 29, 2011 4:20 AM > > To: Email discussion list for the FieldTrip project > > Subject: Re: [FieldTrip] working with neuromag data > > > > Dear Kambiz, > > > > I think I see your point. Your data presumably is already > preprocessed > > and timelocked (averaged over trials) with neuromag software. I > then > > take it that you have 6 different conditions which you would like > to > > plot separately and possibly test at the group level. > > > > Since the data is already averaged, I'd recommend to do the > following > > to get your data back on track. > > > > 1) ft_preprocessing on your stimulus averaged epoch data. This > should > > give you a data structure with 6 trials (which are actually the > > averages per condition). > > > > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And > repeat > > this so you end up with 6 timelocked structures representing the 6 > > different conditions. > > > > 3) plot or grandaverage (see tutorials how to proceed as your data > now > > should be 'ft-friendly'). > > > > Goodluck, > > Arjen > > > > > > > > > > > > > > ----- "Kambiz Tavabi" schreef: > > > > > Van: "Kambiz Tavabi" > > > Aan: "Email discussion list for the FieldTrip project" > > > > > Verzonden: Dinsdag 29 maart 2011 01:10:14 > > > Onderwerp: Re: [FieldTrip] working with neuromag data > > > > > > Dear Arjen - Thanks for your response. Just to clarify the low > > level > > > functions ft_read_header & ft_read_data are mentioned in the ft > > > getting started tutorial. I believe they're recommended to make > > sure > > > the data is ft friendly. In my case the data is ft friendly. My > > data > > > is also pre-processed and already 'time-locked'--meaning that I > > have > > > stimulus averaged epoch data in fif format for all my subjects. > My > > > question is how to proceed from there? I've been through the > pages > > you > > > refer to but have not been able to piece together my data in such > a > > > way to proceed with grand-averaging and carrying out stats. > > > -Kambiz. > > > ------------------------------------------------------------- > > > Kambiz Tavabi PhD > > > Biomedical Imaging Laboratory > > > The Children's Hospital of Philadelphia > > > 34th Street and Civic Center Boulevard > > > Philadelphia, Pa. 19104 > > > Tel: 267.426.0302 > > > email: tavabik at email.chop.edu > > > ------------------------------------------------------------- > > > ________________________________________ > > > From: fieldtrip-bounces at donders.ru.nl > > > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > > > [a.stolk at fcdonders.ru.nl] > > > Sent: Monday, March 28, 2011 4:05 PM > > > To: Email discussion list for the FieldTrip project > > > Subject: Re: [FieldTrip] working with neuromag data > > > > > > Dear Kambiz, > > > > > > While you are able to use the 'low level' ft_read_header and > > > ft_read_data functions, you should be able to preprocess and > > analyze > > > your neuromag data using the 'high level' functions such as > > > ft_preprocessing (which calls the low level functions mentioned > > > above). > > > > > > How to proceed depends on what you want to do with your data. If > > you > > > have triggers stored in your dataset that are synchronuous with > the > > > recorded brain activity, it'd be recommended to start with the > > > following tutorial on how to select your trials: > > > > > > http://fieldtrip.fcdonders.nl/tutorial/preprocessing > > > > > > Since your experience with FT is still limited as you say, I > > believe > > > the following text may provide a good overview of what the data, > > once > > > read in to FT (i.e. matlab) environment, may look like: > > > > > > http://fieldtrip.fcdonders.nl/walkthrough > > > > > > Typically, your next steps involve single-subject timelocked > > analysis, > > > then grand-average and perform statistics at the group level. For > > an > > > overview of the steps and protocols, see: > > > > > > http://fieldtrip.fcdonders.nl/tutorial/analysis_protocols > > > > > > Hope this has helped for a start, > > > > > > Arjen > > > > > > > > > ----- "Kambiz Tavabi" schreef: > > > > > > > Van: "Kambiz Tavabi" > > > > Aan: "Email discussion list for the FieldTrip project" > > > > > > > Verzonden: Maandag 28 maart 2011 20:59:36 > > > > Onderwerp: [FieldTrip] working with neuromag data > > > > > > > > Greetings - I have preprocessed/averaged neuromag data for a > > group > > > of > > > > subjects that I'd like to visualize, compute grandaverage and > > carry > > > > out sensor level statistics on. The only help I managed to find > > on > > > the > > > > Fieldtrip site/list Re: neurmag data concerns getting started > > e.g., > > > > with ft_read_header and ft_read_data. In my case these programs > > > work > > > > fine meaning that I can proceed with further analysis. > > > > On a side, in my limited experience with FT, a major problem I > > run > > > > into frequently is that there is no clear suggestion(s) on how > to > > > > proceed with data that is not raw. I understand it is > impossible > > to > > > > cover all analysis scenarios, but it is often the case that > > working > > > > with CTF, or in particular Elekta system, the data is likely to > > be > > > in > > > > a post-preprocessed phase. Everytime I've tried to work with > ft, > > It > > > > seems to me that if I don't start with square one in fieldtrip, > > it > > > is > > > > difficult to figure out how to use downstream programs to work > on > > > the > > > > data. > > > > That said, in my case I have the output from ft_read_header: > > > > > > > > label: {338x1 cell} > > > > nChans: 338 > > > > Fs: 1000 > > > > grad: [1x1 struct] > > > > unit: {1x338 cell} > > > > nSamples: 651 > > > > nSamplesPre: 100 > > > > nTrials: 6 > > > > orig: [1x1 struct] > > > > > > > > and output from ft_read_data > > > > > > > > [338x651x6] that being channels by samples by number of > stimulus > > > > averaged epochs. To proceed, ideally I'd like to compute a > > > > grandaverage for each condition, visualize them in a multiplot, > > and > > > > carry out sensor level stats. To be able to do this I > understand > > I > > > > need the output from ft_timelockanalysis, how do I arrange my > > data > > > as > > > > such? I am assuming it is already in that state. Thanks for > your > > > > time. > > > > > > > > -Kambiz. > > > > ------------------------------------------------------------- > > > > Kambiz Tavabi PhD > > > > Biomedical Imaging Laboratory > > > > The Children's Hospital of Philadelphia > > > > 34th Street and Civic Center Boulevard > > > > Philadelphia, Pa. 19104 > > > > Tel: 267.426.0302 > > > > email: tavabik at email.chop.edu > > > > ------------------------------------------------------------- > > > > _______________________________________________ > > > > 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 > > > > _______________________________________________ > > 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 bibi.raquel at gmail.com Thu Jun 16 21:38:31 2011 From: bibi.raquel at gmail.com (Raquel Bibi) Date: Thu, 16 Jun 2011 15:38:31 -0400 Subject: [FieldTrip] Reading data from ASA 4 Message-ID: Dear Fieldtrippers, I am trying to read in ASA 4 files that were saved as an EEGProbe .cnt file. I am using Windows 7 64bit and Matlab 2010. Although I've downloaded the newest files from ANT, I an unable to read the proper MEX files. Is there something special I must do in order for Matlab to invoke the MEX file. I believe the files from ANT have already been compiled. Since I am unfamiliar with MEX files and our new EEG system, any information would be greatly appreciated. Currently, get errors due to the fact that the MEX file are not being used. Thanks, Raquel -------------- next part -------------- An HTML attachment was scrubbed... URL: From batrod at gmail.com Fri Jun 17 00:37:45 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Thu, 16 Jun 2011 17:37:45 -0500 Subject: [FieldTrip] Using ICA to filter data In-Reply-To: References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> Message-ID: Im still afraid that the power of this analysis will be very low. Maybe you can try an ICA on your fMRI data and try to correlate each component with your EOG timecourse. Rodolphe N. On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net wrote: > It's a bit of a unique experiment, we're trying to use an ECG machine > to acquire EOG, so it's only a single output channel. > > i guess what I need is a temporal ICA rather than a spatial one... > > On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: > > To summarize, the ICA will decompose your signal into as many components as > Electrodes. > Therefore, trying to decompose only one source is useless. > Did you use a full net of electrodes into your MRI machine or only EOG > electrodes? > > Hope this helps, > > Rodolphe N. > > On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net < > fieldtrip at greenant.net> wrote: > >> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >> I want to be able to spot the saccades in the samples and ideally measure >> their onset at the >> end of each trial. >> >> As you may guess, it's quite noisy and it's broad spectrum noise, despite >> pre-filtering. >> >> Ideally, I would like to isolate the component that corresponds to the MRI >> interference >> and then filter this out. >> >> I have managed to import the data and can run ft_componentanalysis >> but it fails with: >> >> runica() - data size (1,30720) too small >> >> My data is single channel, 40 epochs, each of 6 seconds (time locked to >> stim onset but not saccade onset) >> Is there a different method I should be using? >> >> I have posted some sample data and the current script (which reads in the >> data and runs preprocessing) to the following urls: >> >> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >> http://greenant.net/temp/EOG_analysis.m >> _______________________________________________ >> 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 smoratti at psi.ucm.es Fri Jun 17 09:01:45 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Fri, 17 Jun 2011 09:01:45 +0200 Subject: [FieldTrip] Problems with Neuromag Data after SSS In-Reply-To: References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> Message-ID: <76A4F15A-0795-44E8-8658-AA73CAA45CD9@psi.ucm.es> Hello everybody, I had no problems reading Neuromag data, but when I want to read data treated with SSS I get the following error: ??? Error using ==> fiff_read_tag at 232 Cannot handle other than dense or sparse matrices yet Error in ==> fiff_open at 80 tag = fiff_read_tag(fid,dirpos); Error in ==> fiff_read_meas_info at 82 [ fid, tree ] = fiff_open(source); Error in ==> ft_read_header at 1049 orig = fiff_read_meas_info(filename); Error in ==> mytrialfun_Neuromag_face at 3 hdr = ft_read_header(cfg.dataset); Error in ==> ft_definetrial at 139 trl = feval(cfg.trialfun, cfg); Any idea, what I could do? Best, Stephan El 17/06/2011, a las 0:37, Rodolphe Nenert escribió: > Im still afraid that the power of this analysis will be very low. > Maybe you can try an ICA on your fMRI data and try to correlate each > component with your EOG timecourse. > > Rodolphe N. > > On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net > wrote: > It's a bit of a unique experiment, we're trying to use an ECG machine > to acquire EOG, so it's only a single output channel. > > i guess what I need is a temporal ICA rather than a spatial one... > > On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: > >> To summarize, the ICA will decompose your signal into as many >> components as Electrodes. >> Therefore, trying to decompose only one source is useless. >> Did you use a full net of electrodes into your MRI machine or only >> EOG electrodes? >> >> Hope this helps, >> >> Rodolphe N. >> >> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net > > wrote: >> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >> I want to be able to spot the saccades in the samples and ideally >> measure their onset at the >> end of each trial. >> >> As you may guess, it's quite noisy and it's broad spectrum noise, >> despite pre-filtering. >> >> Ideally, I would like to isolate the component that corresponds to >> the MRI interference >> and then filter this out. >> >> I have managed to import the data and can run ft_componentanalysis >> but it fails with: >> >> runica() - data size (1,30720) too small >> >> My data is single channel, 40 epochs, each of 6 seconds (time >> locked to stim onset but not saccade onset) >> Is there a different method I should be using? >> >> I have posted some sample data and the current script (which reads >> in the >> data and runs preprocessing) to the following urls: >> >> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >> http://greenant.net/temp/EOG_analysis.m >> _______________________________________________ >> 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 ________________________________________________________ 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 lhunt at fmrib.ox.ac.uk Fri Jun 17 09:28:27 2011 From: lhunt at fmrib.ox.ac.uk (Laurence Hunt) Date: Fri, 17 Jun 2011 08:28:27 +0100 Subject: [FieldTrip] Problems with Neuromag Data after SSS In-Reply-To: <76A4F15A-0795-44E8-8658-AA73CAA45CD9@psi.ucm.es> References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> <76A4F15A-0795-44E8-8658-AA73CAA45CD9@psi.ucm.es> Message-ID: <32F04EF7-8D0F-4C73-9C3D-11AB66BF8E81@fmrib.ox.ac.uk> Hi Stephan, Did you do anything else to the data besides applying SSS? I use SSS on all my data and haven't encountered this problem before. Does it apply to all your datasets or just one specific file? Laurence =========================================== Laurence Hunt, DPhil Student Centre for Functional MRI of the Brain (FMRIB), University of Oxford lhunt at fmrib.ox.ac.uk Phone: (+44)1865-(2)22738 =========================================== On 17 Jun 2011, at 08:01, Stephan Moratti wrote: > Hello everybody, > > I had no problems reading Neuromag data, but when I want to read data treated with SSS I get the following error: > > ??? Error using ==> fiff_read_tag at 232 > Cannot handle other than dense or sparse matrices yet > > Error in ==> fiff_open at 80 > tag = fiff_read_tag(fid,dirpos); > > Error in ==> fiff_read_meas_info at 82 > [ fid, tree ] = fiff_open(source); > > Error in ==> ft_read_header at 1049 > orig = fiff_read_meas_info(filename); > > Error in ==> mytrialfun_Neuromag_face at 3 > hdr = ft_read_header(cfg.dataset); > > Error in ==> ft_definetrial at 139 > trl = feval(cfg.trialfun, cfg); > > Any idea, what I could do? > > Best, > > Stephan > > > El 17/06/2011, a las 0:37, Rodolphe Nenert escribió: > >> Im still afraid that the power of this analysis will be very low. >> Maybe you can try an ICA on your fMRI data and try to correlate each component with your EOG timecourse. >> >> Rodolphe N. >> >> On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net wrote: >> It's a bit of a unique experiment, we're trying to use an ECG machine >> to acquire EOG, so it's only a single output channel. >> >> i guess what I need is a temporal ICA rather than a spatial one... >> >> On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: >> >>> To summarize, the ICA will decompose your signal into as many components as Electrodes. >>> Therefore, trying to decompose only one source is useless. >>> Did you use a full net of electrodes into your MRI machine or only EOG electrodes? >>> >>> Hope this helps, >>> >>> Rodolphe N. >>> >>> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net wrote: >>> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >>> I want to be able to spot the saccades in the samples and ideally measure their onset at the >>> end of each trial. >>> >>> As you may guess, it's quite noisy and it's broad spectrum noise, despite pre-filtering. >>> >>> Ideally, I would like to isolate the component that corresponds to the MRI interference >>> and then filter this out. >>> >>> I have managed to import the data and can run ft_componentanalysis >>> but it fails with: >>> >>> runica() - data size (1,30720) too small >>> >>> My data is single channel, 40 epochs, each of 6 seconds (time locked to stim onset but not saccade onset) >>> Is there a different method I should be using? >>> >>> I have posted some sample data and the current script (which reads in the >>> data and runs preprocessing) to the following urls: >>> >>> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >>> http://greenant.net/temp/EOG_analysis.m >>> _______________________________________________ >>> 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 > > > ________________________________________________________ > 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 > > > _______________________________________________ > 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 sherrykhan78 at gmail.com Sat Jun 18 00:28:14 2011 From: sherrykhan78 at gmail.com (Sheraz Khan) Date: Fri, 17 Jun 2011 18:28:14 -0400 Subject: [FieldTrip] Suitable value of cfg.wcm_weight Message-ID: Hello everyone. I am new to fieldtrip, and using "cluster based statistics", I am using "cfg.clusterstatistics=wcm" as my option. Can any experience field-tripper suggest suitable value of* "cfg.wcm_weight"*, Thanks Sheraz On Fri, Jun 17, 2011 at 3:01 AM, Stephan Moratti wrote: > Hello everybody, > > I had no problems reading Neuromag data, but when I want to read data > treated with SSS I get the following error: > > ??? Error using ==> fiff_read_tag at 232 > Cannot handle other than dense or sparse matrices yet > > Error in ==> fiff_open at 80 > tag = fiff_read_tag(fid,dirpos); > > Error in ==> fiff_read_meas_info at 82 > [ fid, tree ] = fiff_open(source); > > Error in ==> ft_read_header at 1049 > orig = fiff_read_meas_info(filename); > > Error in ==> mytrialfun_Neuromag_face at 3 > hdr = ft_read_header(cfg.dataset); > > Error in ==> ft_definetrial at 139 > trl = feval(cfg.trialfun, cfg); > > Any idea, what I could do? > > Best, > > Stephan > > > El 17/06/2011, a las 0:37, Rodolphe Nenert escribió: > > Im still afraid that the power of this analysis will be very low. > Maybe you can try an ICA on your fMRI data and try to correlate each > component with your EOG timecourse. > > Rodolphe N. > > On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net < > fieldtrip at greenant.net> wrote: > >> It's a bit of a unique experiment, we're trying to use an ECG machine >> to acquire EOG, so it's only a single output channel. >> >> i guess what I need is a temporal ICA rather than a spatial one... >> >> On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: >> >> To summarize, the ICA will decompose your signal into as many components >> as Electrodes. >> Therefore, trying to decompose only one source is useless. >> Did you use a full net of electrodes into your MRI machine or only EOG >> electrodes? >> >> Hope this helps, >> >> Rodolphe N. >> >> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net < >> fieldtrip at greenant.net> wrote: >> >>> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >>> I want to be able to spot the saccades in the samples and ideally measure >>> their onset at the >>> end of each trial. >>> >>> As you may guess, it's quite noisy and it's broad spectrum noise, despite >>> pre-filtering. >>> >>> Ideally, I would like to isolate the component that corresponds to the >>> MRI interference >>> and then filter this out. >>> >>> I have managed to import the data and can run ft_componentanalysis >>> but it fails with: >>> >>> runica() - data size (1,30720) too small >>> >>> My data is single channel, 40 epochs, each of 6 seconds (time locked to >>> stim onset but not saccade onset) >>> Is there a different method I should be using? >>> >>> I have posted some sample data and the current script (which reads in the >>> data and runs preprocessing) to the following urls: >>> >>> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >>> http://greenant.net/temp/EOG_analysis.m >>> _______________________________________________ >>> 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 > > > > ________________________________________________________ > 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 > > > > _______________________________________________ > 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 fieldtrip at greenant.net Sat Jun 18 08:56:57 2011 From: fieldtrip at greenant.net (frank@greenant.net) Date: Sat, 18 Jun 2011 16:56:57 +1000 Subject: [FieldTrip] Using ICA to filter data In-Reply-To: References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> Message-ID: <17D1903D-8B16-4CA7-8581-7D6221A57E59@greenant.net> My apologies, I think I may have been a bit unclear about the aims of collecting the data. We're aiming to measure saccadic onset from the signal on a per-trial basis. I was hoping to isolate the MRI noise "component" and subtract this from the EOG signal component to give a cleaner EOG signal. Can the ICA module be applied in the temporal domain in this fashion? There are 40 single session trials of 6 seconds each, I would have thought that'd be enough data to give it a try. Also open to any suggestions as to other adaptive filter techniques.... Thanks On 17/06/2011, at 8:37 AM, Rodolphe Nenert wrote: > Im still afraid that the power of this analysis will be very low. > Maybe you can try an ICA on your fMRI data and try to correlate each component with your EOG timecourse. > > Rodolphe N. > > On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net wrote: > It's a bit of a unique experiment, we're trying to use an ECG machine > to acquire EOG, so it's only a single output channel. > > i guess what I need is a temporal ICA rather than a spatial one... > > On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: > >> To summarize, the ICA will decompose your signal into as many components as Electrodes. >> Therefore, trying to decompose only one source is useless. >> Did you use a full net of electrodes into your MRI machine or only EOG electrodes? >> >> Hope this helps, >> >> Rodolphe N. >> >> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net wrote: >> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >> I want to be able to spot the saccades in the samples and ideally measure their onset at the >> end of each trial. >> >> As you may guess, it's quite noisy and it's broad spectrum noise, despite pre-filtering. >> >> Ideally, I would like to isolate the component that corresponds to the MRI interference >> and then filter this out. >> >> I have managed to import the data and can run ft_componentanalysis >> but it fails with: >> >> runica() - data size (1,30720) too small >> >> My data is single channel, 40 epochs, each of 6 seconds (time locked to stim onset but not saccade onset) >> Is there a different method I should be using? >> >> I have posted some sample data and the current script (which reads in the >> data and runs preprocessing) to the following urls: >> >> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >> http://greenant.net/temp/EOG_analysis.m >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From manuel.mercier at einstein.yu.edu Sat Jun 18 11:09:55 2011 From: manuel.mercier at einstein.yu.edu (Manuel Mercier) Date: Sat, 18 Jun 2011 05:09:55 -0400 Subject: [FieldTrip] wavelet analysis Message-ID: <6ac7ddd3f73a325534c24be6edd039d2.squirrel@netmail.aecom.yu.edu> Dear Field-trippers I recently ran some time frequency analysis using the wavelet method. I was surprise to see that whereas I asked for a step of 1Hz, it was not the case every alternate step (for foi=2:1:10 ; I got [2 3.2 4 5.2 6 7.2 8 9.2 10]), and it was also the case when I changed the toi (2.5, 1.5 with constant trials length of 2.5 sec and sampling freq 1000Hz). I found a kind of explanation following the faq (http://fieldtrip.fcdonders.nl/faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_wavelet_formerly_wltconvol_in_ft_freqanalyis). Still it is not clear to me why this refers to Fourier transform. >From my (none specialist) point of view it is possible to produce a wavelet of any size (Hz;Dt). It is clear that there is some limitations based on the duration of the epochs and the number of time points. But in the present case it shouldn't be a problem, is it? Would be please if someone can help me with this issue. Thanks in advance Manuel From yossiarzouan at ucla.edu Sat Jun 18 17:37:27 2011 From: yossiarzouan at ucla.edu (Yossi Arzouan) Date: Sat, 18 Jun 2011 18:37:27 +0300 Subject: [FieldTrip] influences between the regions In-Reply-To: <1324085935.896862.1306654007541.JavaMail.fmail@mwmweb084> References: <1324085935.896862.1306654007541.JavaMail.fmail@mwmweb084> Message-ID: Dear Aka if that is still relevant maybe our lately published paper on connectivity using Complexity System approach can be a starting point : http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0019345 Big Words, Halved Brains and Small Worlds: Complex Brain Networks of Figurative Language Comprehension Best Wishes Yossi On Sun, May 29, 2011 at 10:26 AM, Michael Wibral wrote: > Dear Aka, > > there is a connectivity Toolbox in fieldtrip, isn't there? > At least I know there was something under development so maybe someone on > the list can help out. > > If that doesn't help or if you are specifically interested in information > transfer you might also try the transfer entropy toolbox 'TRENTOOL' ( > www.trentool.de). > > Michael > > > ------------------------------ > *Von:* "Aka Demon" > *Gesendet:* May 27, 2011 10:43:11 AM > *An:* fieldtrip at donders.ru.nl > *Betreff:* [FieldTrip] influences between the regions > > > Dear experts > > After analyzing memory experiment EEG/MEG and source localization data, i > figured out that there is little I can say about the interactions between > the activated regions as I don’t have any information about the connection > between the activated areas. > > So I was wondering if there are some useful works/tools that I can use to > explorer the influences between the regions (such as information transfer > from one region to the other). > > Thanks a lot > > Aka > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- ____________________________________________________________ Yossi Arzouan, PhD Postdoctoral Fellow at UCLA (Zaidel Lab.) and Haifa Univ (Breznitz and Karni Labs) Cell : 972-54-4446645; Skype : yossi_arzouan www : http://www.complexity-research.org/user/yossiarzouan http://faculty.biu.ac.il/~goldsa/index.html http://www.zaidellab.org/ http://ejsafra.haifa.ac.il/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Sun Jun 19 17:20:41 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Sun, 19 Jun 2011 17:20:41 +0200 Subject: [FieldTrip] Problems with Neuromag Data after SSS In-Reply-To: <32F04EF7-8D0F-4C73-9C3D-11AB66BF8E81@fmrib.ox.ac.uk> References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> <76A4F15A-0795-44E8-8658-AA73CAA45CD9@psi.ucm.es> <32F04EF7-8D0F-4C73-9C3D-11AB66BF8E81@fmrib.ox.ac.uk> Message-ID: Hi Lauren, Thanks for your reply. Yes I had it with 6 data sets where SSS was applied. I had them copied from the HP workstation to our server and from there to my Mac. Could it be a little and big endian thing provoked by moving the files from different platforms? Stephan El 17/06/2011, a las 9:28, Laurence Hunt escribió: > Hi Stephan, > > Did you do anything else to the data besides applying SSS? I use SSS > on all my data and haven't encountered this problem before. Does it > apply to all your datasets or just one specific file? > > Laurence > > =========================================== > Laurence Hunt, DPhil Student > Centre for Functional MRI of the Brain (FMRIB), > University of Oxford > lhunt at fmrib.ox.ac.uk > Phone: (+44)1865-(2)22738 > =========================================== > > On 17 Jun 2011, at 08:01, Stephan Moratti wrote: > >> Hello everybody, >> >> I had no problems reading Neuromag data, but when I want to read >> data treated with SSS I get the following error: >> >> ??? Error using ==> fiff_read_tag at 232 >> Cannot handle other than dense or sparse matrices yet >> >> Error in ==> fiff_open at 80 >> tag = fiff_read_tag(fid,dirpos); >> >> Error in ==> fiff_read_meas_info at 82 >> [ fid, tree ] = fiff_open(source); >> >> Error in ==> ft_read_header at 1049 >> orig = fiff_read_meas_info(filename); >> >> Error in ==> mytrialfun_Neuromag_face at 3 >> hdr = ft_read_header(cfg.dataset); >> >> Error in ==> ft_definetrial at 139 >> trl = feval(cfg.trialfun, cfg); >> >> Any idea, what I could do? >> >> Best, >> >> Stephan >> >> >> El 17/06/2011, a las 0:37, Rodolphe Nenert escribió: >> >>> Im still afraid that the power of this analysis will be very low. >>> Maybe you can try an ICA on your fMRI data and try to correlate >>> each component with your EOG timecourse. >>> >>> Rodolphe N. >>> >>> On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net >> > wrote: >>> It's a bit of a unique experiment, we're trying to use an ECG >>> machine >>> to acquire EOG, so it's only a single output channel. >>> >>> i guess what I need is a temporal ICA rather than a spatial one... >>> >>> On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: >>> >>>> To summarize, the ICA will decompose your signal into as many >>>> components as Electrodes. >>>> Therefore, trying to decompose only one source is useless. >>>> Did you use a full net of electrodes into your MRI machine or >>>> only EOG electrodes? >>>> >>>> Hope this helps, >>>> >>>> Rodolphe N. >>>> >>>> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net >>> > wrote: >>>> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >>>> I want to be able to spot the saccades in the samples and ideally >>>> measure their onset at the >>>> end of each trial. >>>> >>>> As you may guess, it's quite noisy and it's broad spectrum noise, >>>> despite pre-filtering. >>>> >>>> Ideally, I would like to isolate the component that corresponds >>>> to the MRI interference >>>> and then filter this out. >>>> >>>> I have managed to import the data and can run ft_componentanalysis >>>> but it fails with: >>>> >>>> runica() - data size (1,30720) too small >>>> >>>> My data is single channel, 40 epochs, each of 6 seconds (time >>>> locked to stim onset but not saccade onset) >>>> Is there a different method I should be using? >>>> >>>> I have posted some sample data and the current script (which >>>> reads in the >>>> data and runs preprocessing) to the following urls: >>>> >>>> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >>>> http://greenant.net/temp/EOG_analysis.m >>>> _______________________________________________ >>>> 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 >> >> >> ________________________________________________________ >> 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 >> >> >> _______________________________________________ >> 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 ________________________________________________________ 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 v.litvak at ion.ucl.ac.uk Sun Jun 19 21:08:45 2011 From: v.litvak at ion.ucl.ac.uk (Vladimir Litvak) Date: Sun, 19 Jun 2011 20:08:45 +0100 Subject: [FieldTrip] Problems with Neuromag Data after SSS In-Reply-To: References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> <76A4F15A-0795-44E8-8658-AA73CAA45CD9@psi.ucm.es> <32F04EF7-8D0F-4C73-9C3D-11AB66BF8E81@fmrib.ox.ac.uk> Message-ID: Dear Stephan, It might be that or that you transferred the files as ascii in FTP rather than binary. I've seen this error before and showed the file to Matti Hamalainen. He said the file was corrupted. Best, Vladimir On Sun, Jun 19, 2011 at 4:20 PM, Stephan Moratti wrote: > Hi Lauren, > Thanks for your reply. Yes I had it with 6 data sets where SSS was applied. > I had them copied from the HP workstation to our server and from there to my > Mac. Could it be a little and big endian thing provoked by moving the files > from different platforms? > Stephan > El 17/06/2011, a las 9:28, Laurence Hunt escribió: > > Hi Stephan, > Did you do anything else to the data besides applying SSS? I use SSS on all > my data and haven't encountered this problem before. Does it apply to all > your datasets or just one specific file? > Laurence > =========================================== > Laurence Hunt, DPhil Student >  Centre for Functional MRI of the Brain (FMRIB), > University of Oxford > lhunt at fmrib.ox.ac.uk > Phone: (+44)1865-(2)22738 > =========================================== > On 17 Jun 2011, at 08:01, Stephan Moratti wrote: > > Hello everybody, > I had no problems reading Neuromag data, but when I want to read data > treated with SSS I get the following error: > ??? Error using ==> fiff_read_tag at 232 > Cannot handle other than dense or sparse matrices yet > Error in ==> fiff_open at 80 >     tag = fiff_read_tag(fid,dirpos); > Error in ==> fiff_read_meas_info at 82 >     [ fid, tree ] = fiff_open(source); > Error in ==> ft_read_header at 1049 >     orig = fiff_read_meas_info(filename); > Error in ==> mytrialfun_Neuromag_face at 3 > hdr = ft_read_header(cfg.dataset); > Error in ==> ft_definetrial at 139 >     trl   = feval(cfg.trialfun, cfg); > Any idea, what I could do? > Best, > Stephan > > El 17/06/2011, a las 0:37, Rodolphe Nenert escribió: > > Im still afraid that the power of this analysis will be very low. > Maybe you can try an ICA on your fMRI data and try to correlate each > component with your EOG timecourse. > Rodolphe N. > > On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net > wrote: >> >> It's a bit of a unique experiment, we're trying to use an ECG machine >> to acquire EOG, so it's only a single output channel. >> i guess what I need is a temporal ICA rather than a spatial one... >> On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: >> >> To summarize, the ICA will decompose your signal into as many components >> as Electrodes. >> Therefore, trying to decompose only one source is useless. >> Did you use a full net of electrodes into your MRI machine or only EOG >> electrodes? >> Hope this helps, >> Rodolphe N. >> >> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net >> wrote: >>> >>> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >>> I want to be able to spot the saccades in the samples and ideally measure >>> their onset at the >>> end of each trial. >>> >>> As you may guess, it's quite noisy and it's broad spectrum noise, despite >>> pre-filtering. >>> >>> Ideally, I would like to isolate the component that corresponds to the >>> MRI interference >>> and then filter this out. >>> >>> I have managed to import the data and can run ft_componentanalysis >>> but it fails with: >>> >>> runica() - data size (1,30720) too small >>> >>> My data is single channel, 40 epochs, each of 6 seconds (time locked to >>> stim onset but not saccade onset) >>> Is there a different method I should be using? >>> >>> I have posted some sample data and the current script (which reads in the >>> data and runs preprocessing) to the following urls: >>> >>> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >>> http://greenant.net/temp/EOG_analysis.m >>> _______________________________________________ >>> 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 > > ________________________________________________________ > 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 > > > _______________________________________________ > 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 > > ________________________________________________________ > 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 > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From lhunt at fmrib.ox.ac.uk Mon Jun 20 00:04:46 2011 From: lhunt at fmrib.ox.ac.uk (Laurence Hunt) Date: Sun, 19 Jun 2011 23:04:46 +0100 Subject: [FieldTrip] Problems with Neuromag Data after SSS In-Reply-To: References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> <76A4F15A-0795-44E8-8658-AA73CAA45CD9@psi.ucm.es> <32F04EF7-8D0F-4C73-9C3D-11AB66BF8E81@fmrib.ox.ac.uk> Message-ID: <9C063DE1-06F4-461D-9EE4-094F439CDDE8@fmrib.ox.ac.uk> p.s. If this is the problem, try copying using scp from the mac command line, using Terminal - this has always worked for me ok. The files are big endian but this shouldn't be affected by copying to a mac. Laurence On 19 Jun 2011, at 20:08, Vladimir Litvak wrote: > Dear Stephan, > > It might be that or that you transferred the files as ascii in FTP > rather than binary. I've seen this error before and showed the file to > Matti Hamalainen. He said the file was corrupted. > > Best, > > Vladimir > > On Sun, Jun 19, 2011 at 4:20 PM, Stephan Moratti wrote: >> Hi Lauren, >> Thanks for your reply. Yes I had it with 6 data sets where SSS was applied. >> I had them copied from the HP workstation to our server and from there to my >> Mac. Could it be a little and big endian thing provoked by moving the files >> from different platforms? >> Stephan >> El 17/06/2011, a las 9:28, Laurence Hunt escribió: >> >> Hi Stephan, >> Did you do anything else to the data besides applying SSS? I use SSS on all >> my data and haven't encountered this problem before. Does it apply to all >> your datasets or just one specific file? >> Laurence >> =========================================== >> Laurence Hunt, DPhil Student >> Centre for Functional MRI of the Brain (FMRIB), >> University of Oxford >> lhunt at fmrib.ox.ac.uk >> Phone: (+44)1865-(2)22738 >> =========================================== >> On 17 Jun 2011, at 08:01, Stephan Moratti wrote: >> >> Hello everybody, >> I had no problems reading Neuromag data, but when I want to read data >> treated with SSS I get the following error: >> ??? Error using ==> fiff_read_tag at 232 >> Cannot handle other than dense or sparse matrices yet >> Error in ==> fiff_open at 80 >> tag = fiff_read_tag(fid,dirpos); >> Error in ==> fiff_read_meas_info at 82 >> [ fid, tree ] = fiff_open(source); >> Error in ==> ft_read_header at 1049 >> orig = fiff_read_meas_info(filename); >> Error in ==> mytrialfun_Neuromag_face at 3 >> hdr = ft_read_header(cfg.dataset); >> Error in ==> ft_definetrial at 139 >> trl = feval(cfg.trialfun, cfg); >> Any idea, what I could do? >> Best, >> Stephan >> >> El 17/06/2011, a las 0:37, Rodolphe Nenert escribió: >> >> Im still afraid that the power of this analysis will be very low. >> Maybe you can try an ICA on your fMRI data and try to correlate each >> component with your EOG timecourse. >> Rodolphe N. >> >> On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net >> wrote: >>> >>> It's a bit of a unique experiment, we're trying to use an ECG machine >>> to acquire EOG, so it's only a single output channel. >>> i guess what I need is a temporal ICA rather than a spatial one... >>> On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: >>> >>> To summarize, the ICA will decompose your signal into as many components >>> as Electrodes. >>> Therefore, trying to decompose only one source is useless. >>> Did you use a full net of electrodes into your MRI machine or only EOG >>> electrodes? >>> Hope this helps, >>> Rodolphe N. >>> >>> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net >>> wrote: >>>> >>>> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >>>> I want to be able to spot the saccades in the samples and ideally measure >>>> their onset at the >>>> end of each trial. >>>> >>>> As you may guess, it's quite noisy and it's broad spectrum noise, despite >>>> pre-filtering. >>>> >>>> Ideally, I would like to isolate the component that corresponds to the >>>> MRI interference >>>> and then filter this out. >>>> >>>> I have managed to import the data and can run ft_componentanalysis >>>> but it fails with: >>>> >>>> runica() - data size (1,30720) too small >>>> >>>> My data is single channel, 40 epochs, each of 6 seconds (time locked to >>>> stim onset but not saccade onset) >>>> Is there a different method I should be using? >>>> >>>> I have posted some sample data and the current script (which reads in the >>>> data and runs preprocessing) to the following urls: >>>> >>>> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >>>> http://greenant.net/temp/EOG_analysis.m >>>> _______________________________________________ >>>> 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 >> >> ________________________________________________________ >> 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 >> >> >> _______________________________________________ >> 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 >> >> ________________________________________________________ >> 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 >> >> >> >> _______________________________________________ >> 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 smoratti at psi.ucm.es Mon Jun 20 08:26:46 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Mon, 20 Jun 2011 08:26:46 +0200 Subject: [FieldTrip] Problems with Neuromag Data after SSS In-Reply-To: References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> <76A4F15A-0795-44E8-8658-AA73CAA45CD9@psi.ucm.es> <32F04EF7-8D0F-4C73-9C3D-11AB66BF8E81@fmrib.ox.ac.uk> Message-ID: Dear Vladimir, Thanks for this hint. I will check this! Best, Stephan El 19/06/2011, a las 21:08, Vladimir Litvak escribió: > Dear Stephan, > > It might be that or that you transferred the files as ascii in FTP > rather than binary. I've seen this error before and showed the file to > Matti Hamalainen. He said the file was corrupted. > > Best, > > Vladimir > > On Sun, Jun 19, 2011 at 4:20 PM, Stephan Moratti > wrote: >> Hi Lauren, >> Thanks for your reply. Yes I had it with 6 data sets where SSS was >> applied. >> I had them copied from the HP workstation to our server and from >> there to my >> Mac. Could it be a little and big endian thing provoked by moving >> the files >> from different platforms? >> Stephan >> El 17/06/2011, a las 9:28, Laurence Hunt escribió: >> >> Hi Stephan, >> Did you do anything else to the data besides applying SSS? I use >> SSS on all >> my data and haven't encountered this problem before. Does it apply >> to all >> your datasets or just one specific file? >> Laurence >> =========================================== >> Laurence Hunt, DPhil Student >> Centre for Functional MRI of the Brain (FMRIB), >> University of Oxford >> lhunt at fmrib.ox.ac.uk >> Phone: (+44)1865-(2)22738 >> =========================================== >> On 17 Jun 2011, at 08:01, Stephan Moratti wrote: >> >> Hello everybody, >> I had no problems reading Neuromag data, but when I want to read data >> treated with SSS I get the following error: >> ??? Error using ==> fiff_read_tag at 232 >> Cannot handle other than dense or sparse matrices yet >> Error in ==> fiff_open at 80 >> tag = fiff_read_tag(fid,dirpos); >> Error in ==> fiff_read_meas_info at 82 >> [ fid, tree ] = fiff_open(source); >> Error in ==> ft_read_header at 1049 >> orig = fiff_read_meas_info(filename); >> Error in ==> mytrialfun_Neuromag_face at 3 >> hdr = ft_read_header(cfg.dataset); >> Error in ==> ft_definetrial at 139 >> trl = feval(cfg.trialfun, cfg); >> Any idea, what I could do? >> Best, >> Stephan >> >> El 17/06/2011, a las 0:37, Rodolphe Nenert escribió: >> >> Im still afraid that the power of this analysis will be very low. >> Maybe you can try an ICA on your fMRI data and try to correlate each >> component with your EOG timecourse. >> Rodolphe N. >> >> On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net > > >> wrote: >>> >>> It's a bit of a unique experiment, we're trying to use an ECG >>> machine >>> to acquire EOG, so it's only a single output channel. >>> i guess what I need is a temporal ICA rather than a spatial one... >>> On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: >>> >>> To summarize, the ICA will decompose your signal into as many >>> components >>> as Electrodes. >>> Therefore, trying to decompose only one source is useless. >>> Did you use a full net of electrodes into your MRI machine or only >>> EOG >>> electrodes? >>> Hope this helps, >>> Rodolphe N. >>> >>> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net >>> wrote: >>>> >>>> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >>>> I want to be able to spot the saccades in the samples and ideally >>>> measure >>>> their onset at the >>>> end of each trial. >>>> >>>> As you may guess, it's quite noisy and it's broad spectrum noise, >>>> despite >>>> pre-filtering. >>>> >>>> Ideally, I would like to isolate the component that corresponds >>>> to the >>>> MRI interference >>>> and then filter this out. >>>> >>>> I have managed to import the data and can run ft_componentanalysis >>>> but it fails with: >>>> >>>> runica() - data size (1,30720) too small >>>> >>>> My data is single channel, 40 epochs, each of 6 seconds (time >>>> locked to >>>> stim onset but not saccade onset) >>>> Is there a different method I should be using? >>>> >>>> I have posted some sample data and the current script (which >>>> reads in the >>>> data and runs preprocessing) to the following urls: >>>> >>>> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >>>> http://greenant.net/temp/EOG_analysis.m >>>> _______________________________________________ >>>> 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 >> >> ________________________________________________________ >> 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 >> >> >> _______________________________________________ >> 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 >> >> ________________________________________________________ >> 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 >> >> >> >> _______________________________________________ >> 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 ________________________________________________________ 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 a.wollbrink at uni-muenster.de Mon Jun 20 14:45:54 2011 From: a.wollbrink at uni-muenster.de (Andreas Wollbrink) Date: Mon, 20 Jun 2011 14:45:54 +0200 Subject: [FieldTrip] concatenating data to a single trial data set Message-ID: <4DFF4102.3020101@uni-muenster.de> Dear all, in order not to run into a RAM memory overload when performing an ICA on MEG data I subdivided the raw data into several equally long segments (chops) using ft_preprocessing with varying cfg.trl settings. After applying ft_componentanalysis to each of these chops I removed some (bad) components and backprojected the data to seperate data matrices using the following code: cfg = []; cfg.component = badCompVec; % to be removed component(s) dataCorr = ft_rejectcomponent(cfg, compData); Finally I like to concatenate these data to a continuous (single trial) data matrix in order to compare it with the original raw data set and perform the further timelock analysis on it. I tried using ft_appenddata for this issue. Doing so one gets a multi trial data matrix which I could not convert to single trial continuous data matrix using e.g. ft_redefinetrial. I would appreciate any help in how to solve this problem. Thanks in advance. Andreas Wollbrink -- ====================================================================== Andreas Wollbrink, Biomedical Engineer Institute for Biomagnetism and Biosignalanalysis Muenster University Hospital Malmedyweg 15 phone: +49-(0)251-83-52546 D-48149 Muenster mobil: +49-(0)160-98527553 Germany fax: +49-(0)251-83-56874 e-Mail: a.wollbrink at uni-muenster.de ====================================================================== From eelke.spaak at donders.ru.nl Mon Jun 20 15:35:14 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 20 Jun 2011 15:35:14 +0200 Subject: [FieldTrip] concatenating data to a single trial data set In-Reply-To: <4DFF4102.3020101@uni-muenster.de> References: <4DFF4102.3020101@uni-muenster.de> Message-ID: Dear Andreas, The way I concatenate data is just 'manually', so without the intervention of FieldTrip. To do this, you will have to concatenate the arrays in both the data.trial and the data.time cell array. In pseudocode: initialize matrix data_concat of size channels X total time points initialize matrix time_concat of size 1 X total time points loop over data.trial and data.time (have the same size) data_concat(:,appropriate time indices) = data.trial{k}(:,:); time_concat(1,appropriate time indices) = data.time{k}(:); end loop data.trial = data_concat; data.time = time_concat; That should do the trick. I would have provided actual code, were it not that I am doing something slightly different from what you are asking. I hope this helps! Best, Eelke 2011/6/20 Andreas Wollbrink : > Dear all, > > in order not to run into a RAM memory overload when performing an ICA on MEG > data I subdivided the raw data into several equally long segments (chops) > using ft_preprocessing with varying cfg.trl settings. > After applying ft_componentanalysis to each of these chops I removed some > (bad) components and backprojected the data to seperate data matrices using > the following code: > > cfg = []; > cfg.component = badCompVec; % to be removed component(s) > dataCorr = ft_rejectcomponent(cfg, compData); > > > Finally I like to concatenate these data to a continuous (single trial) data > matrix in order to compare it with the original raw data set and perform the > further timelock analysis on it. > > I tried using ft_appenddata for this issue. Doing so one gets a multi trial > data matrix which I could not convert to single trial continuous data matrix > using e.g. ft_redefinetrial. > > I would appreciate any help in how to solve this problem. > > Thanks in advance. > > Andreas Wollbrink > -- > > > ====================================================================== > >  Andreas Wollbrink, Biomedical Engineer > >  Institute for Biomagnetism and Biosignalanalysis >  Muenster University Hospital > >  Malmedyweg 15         phone:   +49-(0)251-83-52546 >  D-48149 Muenster      mobil:   +49-(0)160-98527553 >  Germany               fax:     +49-(0)251-83-56874 >                        e-Mail: a.wollbrink at uni-muenster.de > > ====================================================================== > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From nathanweisz at mac.com Mon Jun 20 17:15:50 2011 From: nathanweisz at mac.com (Nathan Weisz) Date: Mon, 20 Jun 2011 17:15:50 +0200 Subject: [FieldTrip] concatenating data to a single trial data set In-Reply-To: References: <4DFF4102.3020101@uni-muenster.de> Message-ID: hi andreas, perhaps i misunderstood something. but your RAM worries concern the ICA computation? then after running your ICA & getting the components, why don't you just read the raw data again with the option as continuous data (cfg.continuous i think). then apply the components to the single-trial raw data and finally reject the bad components. less efficient than elkes solution, rather the lazy one :-) cheers, n On 20.06.2011, at 15:35, Eelke Spaak wrote: > Dear Andreas, > > The way I concatenate data is just 'manually', so without the > intervention of FieldTrip. To do this, you will have to concatenate > the arrays in both the data.trial and the data.time cell array. > > In pseudocode: > > initialize matrix data_concat of size channels X total time points > initialize matrix time_concat of size 1 X total time points > > loop over data.trial and data.time (have the same size) > data_concat(:,appropriate time indices) = data.trial{k}(:,:); > time_concat(1,appropriate time indices) = data.time{k}(:); > end loop > > data.trial = data_concat; > data.time = time_concat; > > That should do the trick. I would have provided actual code, were it > not that I am doing something slightly different from what you are > asking. > > I hope this helps! > > Best, > Eelke > > 2011/6/20 Andreas Wollbrink : >> Dear all, >> >> in order not to run into a RAM memory overload when performing an ICA on MEG >> data I subdivided the raw data into several equally long segments (chops) >> using ft_preprocessing with varying cfg.trl settings. >> After applying ft_componentanalysis to each of these chops I removed some >> (bad) components and backprojected the data to seperate data matrices using >> the following code: >> >> cfg = []; >> cfg.component = badCompVec; % to be removed component(s) >> dataCorr = ft_rejectcomponent(cfg, compData); >> >> >> Finally I like to concatenate these data to a continuous (single trial) data >> matrix in order to compare it with the original raw data set and perform the >> further timelock analysis on it. >> >> I tried using ft_appenddata for this issue. Doing so one gets a multi trial >> data matrix which I could not convert to single trial continuous data matrix >> using e.g. ft_redefinetrial. >> >> I would appreciate any help in how to solve this problem. >> >> Thanks in advance. >> >> Andreas Wollbrink >> -- >> >> >> ====================================================================== >> >> Andreas Wollbrink, Biomedical Engineer >> >> Institute for Biomagnetism and Biosignalanalysis >> Muenster University Hospital >> >> Malmedyweg 15 phone: +49-(0)251-83-52546 >> D-48149 Muenster mobil: +49-(0)160-98527553 >> Germany fax: +49-(0)251-83-56874 >> e-Mail: a.wollbrink at uni-muenster.de >> >> ====================================================================== >> _______________________________________________ >> 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 jan.schoffelen at donders.ru.nl Tue Jun 21 09:08:34 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 21 Jun 2011 09:08:34 +0200 Subject: [FieldTrip] wavelet analysis In-Reply-To: <6ac7ddd3f73a325534c24be6edd039d2.squirrel@netmail.aecom.yu.edu> References: <6ac7ddd3f73a325534c24be6edd039d2.squirrel@netmail.aecom.yu.edu> Message-ID: <9B183DFC-CD62-489D-9F0B-C2292AFFAF1A@donders.ru.nl> Dear Manuel, Thanks for your message. I gave the faq a good read, and I agree that the answer can be made a bit more clear. I updated the faqs you mentioned and hope that this explains the issue better. Let me know if it is still not clear. Best wishes, Jan-Mathijs On Jun 18, 2011, at 11:09 AM, Manuel Mercier wrote: > Dear Field-trippers > I recently ran some time frequency analysis using the wavelet method. > I was surprise to see that whereas I asked for a step of 1Hz, it was > not > the case every alternate step (for foi=2:1:10 ; I got [2 3.2 4 5.2 6 > 7.2 8 > 9.2 10]), and it was also the case when I changed the toi (2.5, 1.5 > with > constant trials length of 2.5 sec and sampling freq 1000Hz). > I found a kind of explanation following the faq > (http://fieldtrip.fcdonders.nl/faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_wavelet_formerly_wltconvol_in_ft_freqanalyis > ). > Still it is not clear to me why this refers to Fourier transform. >> From my (none specialist) point of view it is possible to produce a > wavelet of any size (Hz;Dt). > It is clear that there is some limitations based on the duration of > the > epochs and the number of time points. But in the present case it > shouldn't > be a problem, is it? > Would be please if someone can help me with this issue. > Thanks in advance > > Manuel > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From a.wollbrink at uni-muenster.de Tue Jun 21 10:05:19 2011 From: a.wollbrink at uni-muenster.de (Andreas Wollbrink) Date: Tue, 21 Jun 2011 10:05:19 +0200 Subject: [FieldTrip] concatenating data to a single trial data set In-Reply-To: References: <4DFF4102.3020101@uni-muenster.de> Message-ID: <4E0050BF.80008@uni-muenster.de> Dear Eelke, dear Nathan, thanks for your help on a way to concatenate the data. In the end I successfully used a mixture of both approaches you suggested. Best, Andreas On 06/20/11 15:35, Eelke Spaak wrote: > Dear Andreas, > > The way I concatenate data is just 'manually', so without the > intervention of FieldTrip. To do this, you will have to concatenate > the arrays in both the data.trial and the data.time cell array. > > In pseudocode: > > initialize matrix data_concat of size channels X total time points > initialize matrix time_concat of size 1 X total time points > > loop over data.trial and data.time (have the same size) > data_concat(:,appropriate time indices) = data.trial{k}(:,:); > time_concat(1,appropriate time indices) = data.time{k}(:); > end loop > > data.trial = data_concat; > data.time = time_concat; > > That should do the trick. I would have provided actual code, were it > not that I am doing something slightly different from what you are > asking. > > I hope this helps! > > Best, > Eelke > > 2011/6/20 Andreas Wollbrink: >> Dear all, >> >> in order not to run into a RAM memory overload when performing an ICA on MEG >> data I subdivided the raw data into several equally long segments (chops) >> using ft_preprocessing with varying cfg.trl settings. >> After applying ft_componentanalysis to each of these chops I removed some >> (bad) components and backprojected the data to seperate data matrices using >> the following code: >> >> cfg = []; >> cfg.component = badCompVec; % to be removed component(s) >> dataCorr = ft_rejectcomponent(cfg, compData); >> >> >> Finally I like to concatenate these data to a continuous (single trial) data >> matrix in order to compare it with the original raw data set and perform the >> further timelock analysis on it. >> >> I tried using ft_appenddata for this issue. Doing so one gets a multi trial >> data matrix which I could not convert to single trial continuous data matrix >> using e.g. ft_redefinetrial. >> >> I would appreciate any help in how to solve this problem. >> >> Thanks in advance. >> >> Andreas Wollbrink >> -- >> >> >> ====================================================================== >> >> Andreas Wollbrink, Biomedical Engineer >> >> Institute for Biomagnetism and Biosignalanalysis >> Muenster University Hospital >> >> Malmedyweg 15 phone: +49-(0)251-83-52546 >> D-48149 Muenster mobil: +49-(0)160-98527553 >> Germany fax: +49-(0)251-83-56874 >> e-Mail: a.wollbrink at uni-muenster.de >> >> ====================================================================== >> _______________________________________________ >> 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 -- ====================================================================== Andreas Wollbrink, Biomedical Engineer Institute for Biomagnetism and Biosignalanalysis Muenster University Hospital Malmedyweg 15 phone: +49-(0)251-83-52546 D-48149 Muenster mobil: +49-(0)160-98527553 Germany fax: +49-(0)251-83-56874 e-Mail: a.wollbrink at uni-muenster.de ====================================================================== From drivolta81 at gmail.com Tue Jun 21 15:24:31 2011 From: drivolta81 at gmail.com (Davide Rivolta) Date: Tue, 21 Jun 2011 15:24:31 +0200 Subject: [FieldTrip] downsampling MEG data Message-ID: Dear fieldtrippers, I have recorded some MEG data with a sampling rate of 6000 Hz. I would need to downsample it to 600 Hz. What is the best way to do it? It something I have to do in the preprocessing I guess. Any advice would be really appreciated, Thanks, Davide -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Tue Jun 21 15:29:59 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 21 Jun 2011 15:29:59 +0200 Subject: [FieldTrip] downsampling MEG data In-Reply-To: References: Message-ID: Dear Davide, Have a look at the ft_resampledata function: http://fieldtrip.fcdonders.nl/reference/ft_resampledata Best, Eelke 2011/6/21 Davide Rivolta : > Dear fieldtrippers, > > I have recorded some MEG data with a sampling rate of 6000 Hz. > I would need to downsample it to 600 Hz. > > What is the best way to do it? > > It something I have to do in the preprocessing I guess. > > Any advice would be really appreciated, > > Thanks, > > Davide > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From batrod at gmail.com Tue Jun 21 15:37:54 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Tue, 21 Jun 2011 08:37:54 -0500 Subject: [FieldTrip] downsampling MEG data In-Reply-To: References: Message-ID: Dear Davide, the function ft_resampledata should do that perfectly ! :) On Tue, Jun 21, 2011 at 8:24 AM, Davide Rivolta wrote: > Dear fieldtrippers, > > I have recorded some MEG data with a sampling rate of 6000 Hz. > I would need to downsample it to 600 Hz. > > What is the best way to do it? > > It something I have to do in the preprocessing I guess. > > Any advice would be really appreciated, > > Thanks, > > Davide > > _______________________________________________ > 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 Jun 21 16:08:21 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 21 Jun 2011 16:08:21 +0200 Subject: [FieldTrip] Publications using FieldTrip: add your own! Message-ID: Dear Fieldtrippers, We have revamped the list of publications using FieldTrip on our wiki website. I wrote a plugin for Dokuwiki, enabling the wiki to parse BibTeX code (see http://www.bibtex.org/ if you don't know what this is). This allows all of you to easily add your publications using FieldTrip to our wiki, improving the visibility of both FieldTrip and your papers. The list is quite extensive already, but we explicitly invite all of you to browse through it and add anything we might have missed. Editing the page is done by going to Page tools (top left, above the site menu) --> Edit this page. If you are not familiar with BibTeX syntax, it is probably easiest to just look at what is already there and use that as an example. Note that the list will be automatically sorted by year and by first author, so you can just insert new entries wherever you like. Visit http://fieldtrip.fcdonders.nl/publications to see the new page. Best, Eelke From johanna.zumer at donders.ru.nl Tue Jun 21 16:56:20 2011 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Tue, 21 Jun 2011 16:56:20 +0200 Subject: [FieldTrip] code change in ft_compute_leadfield.m Message-ID: Dear FieldTrip users, I've made a small change to ft_compute_leadfield (available in tonight's release) regarding how the 'reducerank' option is handled, if multiple dipole locations are entered all at once into ft_compute_leadfield.m. This will *not* affect the vast majority of users, since usually ft_compute_leadfield is called by higher FT functions and not directly by users. For example, it will not affect you if you create a leadfield either by calling ft_prepare_leadfield or by letting ft_sourceanalysis compute the leadfield for you (regardless of your 'reducedrank' option), since these higher level FT functions call ft_compute_leadfield in a for-loop over dipole location (and _not_ multiple dipole locations at once). For completeness, here's a list of (rare) cases when it will affect your results: 1) If you call ft_compute_leadfield directly with Nx3 dipoles (N>1) and reducerank='yes' (or =2) 2) If you use a refdip in beamformer_DICS or beamformer_PCC, or a supdip in beamformer_PCC, of *more than 1 dipole location* at a time (Nx3 refdip or subdip, where N>1), AND you specified reducerank='yes' (or =2) in any of these cases. 3) Default behaviour of calling ft_dipolefitting will not change. However if you call dipole_fit directly with more than one dipole AND reducerank='yes' (or =2). Please let me know if this isn't clear. Best, Johanna -------------- next part -------------- An HTML attachment was scrubbed... URL: From BelluscB at ninds.nih.gov Tue Jun 21 23:24:16 2011 From: BelluscB at ninds.nih.gov (Belluscio, Beth (NIH/NINDS) [E]) Date: Tue, 21 Jun 2011 17:24:16 -0400 Subject: [FieldTrip] define events for ft_definetrial Message-ID: <794DFDD3C128EF44AC49ADC58FD0090C04F09E165B@NIHMLBX10.nih.gov> HI all- I use CFT data sets in which I use a trigger channel to define various stimuli (usually called stim1, stim2, stim3). Each stim repeats several times (120) during the data file. The time points corresponding to each stim are catalogued in the MarkerFile.mrk file. I would like to use these markers to define trials around each stim. I used to do this with the following set of commands: cfg = []; cfg.dataset = 'TS1.ds'; cfg.trialdef.eventtype = 'stim1'; cfg.trialdef.prestim = 0.1; cfg.trialdef.posstim = 3.0; cfg = ft_definetrial(cfg) Now when I do this I get the following error messages: readCTFds: Data set error: size of meg4 files(s) 0 bytes (from dir command) 1126080000 (from res4 file) ??? Attempt to reference field of non-structure array. Error in ==> trialfun_general at 111 For i=find(strcmp(cfg.trialdef.eventtype, {event.types})) Error in==> ft_definetrial at 126 [trl, event] = feval(cfg.trialfun, cfg) Is this a problem with the way I am defining the events? How can I use these markers within the data file to specify events in fieldtrip? Thanks, Beth Belluscio MD-PhD Clinical Fellow Human Motor Control Section NINDS, NIH 301-402-3495 -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at fcdonders.ru.nl Wed Jun 22 08:12:48 2011 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Wed, 22 Jun 2011 08:12:48 +0200 (CEST) Subject: [FieldTrip] define events for ft_definetrial In-Reply-To: <794DFDD3C128EF44AC49ADC58FD0090C04F09E165B@NIHMLBX10.nih.gov> Message-ID: <49300862.469268.1308723168601.JavaMail.root@sculptor.zimbra.ru.nl> Hi Beth, Just wondering. Did you copy those lines from your script? If so, please try cfg.trialdef.poststim = 3.0; (notice the t). Yours, Arjen ----- "Beth Belluscio (NIH/NINDS) [E]" schreef: > Van: "Beth Belluscio (NIH/NINDS) [E]" > Aan: "fieldtrip at donders.ru.nl" > Verzonden: Dinsdag 21 juni 2011 23:24:16 > Onderwerp: [FieldTrip] define events for ft_definetrial > > > HI all-   I use CFT data sets in which I use a trigger channel to define various stimuli (usually called stim1, stim2, stim3).  Each stim repeats several times (120) during the data file.  The time points corresponding to each stim are catalogued in the MarkerFile.mrk file.  I would like to use these markers to define trials around each stim.  I used to do this with the following set of commands:                 cfg = [];                 cfg.dataset = ‘TS1.ds’;                 cfg.trialdef.eventtype = ‘stim1’;                 cfg.trialdef.prestim = 0.1;                 cfg.trialdef.posstim = 3.0;                 cfg = ft_definetrial(cfg) Now when I do this I get the following error messages:                 readCTFds: Data set error:  size of meg4 files(s)                                 0 bytes (from dir command)                                 1126080000 (from res4 file)                 ??? Attempt to reference field of non-structure array.                 Error in è trialfun_general at 111                 For i=find(strcmp(cfg.trialdef.eventtype, {event.types}))                                 Error in è ft_definetrial at 126                 [trl, event] = feval(cfg.trialfun, cfg) Is this a problem with the way I am defining the events?  How can I use these markers within the data file to specify events in fieldtrip? Thanks, Beth Belluscio MD-PhD Clinical Fellow Human Motor Control Section NINDS, NIH 301-402-3495 > _______________________________________________ > 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 Jun 22 08:59:04 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 22 Jun 2011 08:59:04 +0200 Subject: [FieldTrip] define events for ft_definetrial In-Reply-To: <794DFDD3C128EF44AC49ADC58FD0090C04F09E165B@NIHMLBX10.nih.gov> References: <794DFDD3C128EF44AC49ADC58FD0090C04F09E165B@NIHMLBX10.nih.gov> Message-ID: <4D29A1F9-957B-41E4-8CBC-582BF0AD25D6@donders.ru.nl> Dear Beth, It could be that your dataset is corrupt. > readCTFds: Data set error: size of meg4 files(s) > 0 bytes (from dir command) > 1126080000 (from res4 file) This is namely a low level reading error. It then percolates to the next step, where > > ??? Attempt to reference field of non-structure array. which is most likely caused by FieldTrip not having been successful in creating an event structure. > > Error in è trialfun_general at 111 > For i=find(strcmp(cfg.trialdef.eventtype, > {event.types})) > > Error inè ft_definetrial at 126 > [trl, event] = feval(cfg.trialfun, cfg) > > Is this a problem with the way I am defining the events? How can I > use these markers within the data file to specify events in fieldtrip? Does this pertain to this particular dataset? Best Jan-Mathijs PS: please update to a more recent version of FieldTrip: the content of the line number in which the errer occurs does not coincide with my version > > Thanks, > > Beth Belluscio MD-PhD > Clinical Fellow > Human Motor Control Section > NINDS, NIH > 301-402-3495 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From lulswinnik at gmail.com Thu Jun 23 12:30:35 2011 From: lulswinnik at gmail.com (Ekaterina Vinnik) Date: Thu, 23 Jun 2011 11:30:35 +0100 Subject: [FieldTrip] Champalimaud Neuroscience Symposium announcement; early registration deadline 30 of June Message-ID: The Champalimaud Neuroscience Symposium will bring together researchers from around the world who are interested in solving the puzzle of the brain. The Programme includes 30 distinguished speakers (including Gyorgy Buzsaki, Antonio Damasio, Jim DiCarlo, Ranulfo Romo, Erin Schuman and Haim Sompolinsky) and poster sessions. The Symposium will take place at the Champalimaud Centre for the Unknown on the waterfront in central Lisbon, Portugal. We are looking forward to a lively and stimulating scientific meeting, and we hope that you will join us. more information at http://symposium.neuro.fchampalimaud.org/ http://www.facebook.com/event.php?eid=191246457589517 The early registration deadline is 30 of June (150/300 euro fee), though abstracts are not due till 31 of August. Travel grants available! Join us in Lisbon, All the best, Ekaterina -- Ekaterina Vinnik, MD, PhD Behavioural neuroscience lab, Champalimaud Neuroscience, Lisbon, Portugal +351918951392 lulswinnik at gmail.com From ekanal at cmu.edu Fri Jun 24 16:21:47 2011 From: ekanal at cmu.edu (Kanal Eliezer) Date: Fri, 24 Jun 2011 10:21:47 -0400 Subject: [FieldTrip] plot ave + variance Message-ID: Hello fieldtrip - Is there a simple way to plot a timelock average along with confidence intervals? I simply want to see how much the data varied across trials. The structure returned by the ft_timelock function contains a `var` element, but the data it contains is many order of magnitude smaller than that in the `ave` element. Thanks - Elli -------------------- Eliezer Kanal, Ph.D. Postdoctoral Fellow Center for the Neural Basis of Cognition Carnegie Mellon University 4400 Fifth Ave, Suite 110A Pittsburgh PA 15213 P: 412-268-4115 F: 412-268-5060 From akiko at nyu.edu Fri Jun 24 17:42:20 2011 From: akiko at nyu.edu (Akiko Ikkai) Date: Fri, 24 Jun 2011 11:42:20 -0400 Subject: [FieldTrip] ft_sourceanalysis & ft_sourceinterpolate Message-ID: Hi, I'm working on beamformer with MEG data, and having trouble making ft_sourceanalysis and/or ft_sourceinterpolate work. It appears that anatomical MRI and source data do not align, although anatomical MRI ("mri_aligned") and the result of ft_prepare_singleshell ("vol_cm") are both aligned with MEG helmet. Is there any way I could verify that the output of ft_sourceanalysis is not distorted (i.e. same space as input)? I'm using fieldtrip-20110525 version. Thanks in advance! Akiko Below is my code: 1. compute the common filter cfg = []; cfg.grad = data_common.grad; % data_common = baseline + left + right cfg.grid.xgrid = -15:0.5:15; cfg.grid.ygrid = -15:0.5:15; cfg.grid.zgrid = -15:0.5:15; cfg.inwardshift = -2; cfg.vol = vol_cm; % this is from segmented "mri_aligned" cfg.channel = {'all'}; cfg.reducerank = 2; cfg.frequency = 10; cfg.method = 'dics'; cfg.projectnoise = 'yes'; cfg.keepfilter = 'yes'; cfg.feedback = 'no'; cfg.realfilter = 'yes'; cfg.lambda = '0.005%'; source_common = ft_sourceanalysis(cfg, freq_common) 2. compute the spatial filter for one of the conditions (using grid & filter from the step 1) cfg = []; cfg.grad = data_common.grad; cfg.grid.pos = source_common.pos; % using grid & filter from the common filter cfg.grid.filter = source_common.avg.filter; cfg.vol = vol_cm; cfg.channel = {'all'}; cfg.reducerank = 2; cfg.frequency = 10; cfg.method = 'dics'; cfg.projectnoise = 'yes'; cfg.keepfilter = 'no'; cfg.feedback = 'no'; cfg.realfilter = 'yes'; cfg.lambda = '0.005%'; source_left = ft_sourceanalysis(cfg, freq_stiml); source_left.unit = 'cm'; source_left.dim = source_common.dim; 3. calculate difference source_left_bl = source_left; source_left_bl.avg.pow = source_left_bl.avg.pow ./ source_common.avg.pow; 4. interpolate source to anatomical MRI space cfg = []; cfg.method = 'linear'; source_left_bl_int = ft_sourceinterpolate(cfg, source_left_bl,mri_aligned); -------------- next part -------------- An HTML attachment was scrubbed... URL: From ekanal at cmu.edu Fri Jun 24 21:17:42 2011 From: ekanal at cmu.edu (Kanal Eliezer) Date: Fri, 24 Jun 2011 15:17:42 -0400 Subject: [FieldTrip] plot ave + variance In-Reply-To: <31844_1308925377_p5OEMuo1011583_B732C6AD-E522-4B28-8D7A-0660CF0520A8@cmu.edu> References: <31844_1308925377_p5OEMuo1011583_B732C6AD-E522-4B28-8D7A-0660CF0520A8@cmu.edu> Message-ID: I apologize; I wasn't thinking. stdev = var^2. Elli On Jun 24, 2011, at 10:21 AM, Kanal Eliezer wrote: > Hello fieldtrip - > > Is there a simple way to plot a timelock average along with confidence intervals? I simply want to see how much the data varied across trials. The structure returned by the ft_timelock function contains a `var` element, but the data it contains is many order of magnitude smaller than that in the `ave` element. Thanks - > > Elli > > > -------------------- > Eliezer Kanal, Ph.D. > Postdoctoral Fellow > Center for the Neural Basis of Cognition > Carnegie Mellon University > 4400 Fifth Ave, Suite 110A > Pittsburgh PA 15213 > P: 412-268-4115 > F: 412-268-5060 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From paul_c at gmx.de Mon Jun 27 10:11:51 2011 From: paul_c at gmx.de (Paul Czienskowski) Date: Mon, 27 Jun 2011 10:11:51 +0200 Subject: [FieldTrip] Brainvision renamer tool In-Reply-To: References: <31844_1308925377_p5OEMuo1011583_B732C6AD-E522-4B28-8D7A-0660CF0520A8@cmu.edu> Message-ID: <4E083B47.4070008@gmx.de> Dear all, I wrote a small brainvision renamer tool based on RegEx patters which I needed to make the filenames of my EEG-Recordings more consistent. If anyone is interested in, check out http://code.google.com/p/eeg-renamer/ Cheers, Paul -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 From Hanneke.vanDijk at med.uni-duesseldorf.de Mon Jun 27 10:38:03 2011 From: Hanneke.vanDijk at med.uni-duesseldorf.de (Hanneke.vanDijk at med.uni-duesseldorf.de) Date: Mon, 27 Jun 2011 10:38:03 +0200 Subject: [FieldTrip] ft_databrowser Message-ID: <72E993C35FB11743B79FF9286E5B6D8B029F8B2A@Mail2-UKD.VMED.UKD> Dear FT-ers, I have discovered ft_databrowser a few weeks ago (maybe abit late ;-))! Thanks so much for implementing this, I like it. I am setting up a small presentation about artifact rejection using FT and decided to use the tutorial data (Subject01.ds) to generate some examples. When I use the raw dataset and cfg.continuous = 'yes', it runs fine but after preprocessing (as in the online tutorial; and cfg.continuous = 'no') I run into this problem: cfg = ft_databrowser(cfg,dataFIC); the input is raw data with 152 channels and 87 trials redrawing with viewmode butterfly fetching data... done fetching artifacts... done preprocessing data... done plotting data... ??? Reference to non-existent field 'hlim'. Error in ==> ft_databrowser>redraw_cb at 1003 eventtim = (eventtim - opt.hlim(1)) / (opt.hlim(2) - opt.hlim(1)); % convert to value relative to box, i.e. from 0 to 1 Error in ==> ft_databrowser at 434 redraw_cb(h); 'opt' indeed does not contain 'hlim' and also no 'hpos' which is asked for a line later. I think it originates in the input given into the function guidata. I hope you can help me! Groetjes Hanneke __________________________________________ Dr. Hanneke van Dijk http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNe urowiss/Team/HannekevanDijk/page.html Institute for Clinical Neuroscience, Heinrich Heine Universitaet Duesseldorf, Germany Hanneke.vanDijk at med.uni-duesseldorf.de Tel. +49 (0) 211 81 13074 __________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Tue Jun 28 09:19:13 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 28 Jun 2011 09:19:13 +0200 Subject: [FieldTrip] ft_databrowser In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8B029F8B2A@Mail2-UKD.VMED.UKD> References: <72E993C35FB11743B79FF9286E5B6D8B029F8B2A@Mail2-UKD.VMED.UKD> Message-ID: <4E098071.6010502@donders.ru.nl> Dear Hanneke, Thanks for reporting this. We are currently working on improving the databrowser in terms of code readability, which also includes removing some bugs. We will also deal with this one, if not already done (I will check) Best, Jörn On 6/27/2011 10:38 AM, Hanneke.vanDijk at med.uni-duesseldorf.de wrote: > > Dear FT-ers, > > I have discovered ft_databrowser a few weeks ago (maybe abit late > ;-))! Thanks so much for implementing this, I like it. > > I am setting up a small presentation about artifact rejection using FT > and decided to use the tutorial data (Subject01.ds) to generate some > examples. When I use the raw dataset and cfg.continuous = 'yes', it > runs fine but after preprocessing (as in the online tutorial; and > cfg.continuous = 'no') I run into this problem: > > cfg = ft_databrowser(cfg,dataFIC); > > the input is raw data with 152 channels and 87 trials > > redrawing with viewmode butterfly > > fetching data... done > > fetching artifacts... done > > preprocessing data... done > > plotting data... ??? Reference to non-existent field 'hlim'. > > Error in ==> ft_databrowser>redraw_cb at 1003 > > eventtim = (eventtim - opt.hlim(1)) / (opt.hlim(2) - > opt.hlim(1)); % convert to value relative to > > box, i.e. from 0 to 1 > > Error in ==> ft_databrowser at 434 > > redraw_cb(h); > > 'opt' indeed does not contain 'hlim' and also no 'hpos' which is asked > for a line later. I think it originates in the input given into the > function guidata. > > I hope you can help me! > > Groetjes Hanneke > > __________________________________________ > > Dr. Hanneke van Dijk > > http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html > > Institute for Clinical Neuroscience, > > Heinrich Heine Universitaet Duesseldorf, Germany > > Hanneke.vanDijk at med.uni-duesseldorf.de > > > Tel. +49 (0) 211 81 13074 > > __________________________________________ > > > _______________________________________________ > 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 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 suforraxi at gmail.com Tue Jun 28 14:46:28 2011 From: suforraxi at gmail.com (Matteo Demuru) Date: Tue, 28 Jun 2011 14:46:28 +0200 Subject: [FieldTrip] WPLI statistic, permutation like test?? Message-ID: Hi, I have a couple of questions about using the WPLI index to assess the phase on my MEG data. The experiment consists of recordings during a mental calculation task: I have 30 sec in which each subject performed continuously an arithmetic operation. It seems to me that WPLI index required more than one trial in order to be computed. Am I right? (Is this necessary in order to reduce volume conduction problems?) I could divide my 30 sec in 5 sec-trials to create my trials, but I was wandering if this could be a misuse of the WPLI, i.e. WPLI is not appropriate for my experiment. I am also interested in assessing the significance of WPLI index, I would like to gauge the significance per se of my WPLI values. The idea is to calculate the WPLI distribution under the null hypothesis (not phase coupling) for each pair of channels in this way: Example to assess the significance of WPLI value for ch1 vs ch2 1) Calculate the WPLI for ch1 and ch2, this would be the observed WPLI (WPLI_observed) 2) Randomly permute the ch2 time series 3) Calculate the WPLI for ch1 and ch2 (WPLI_i) 4) Repeat step 2 and 3 (for instance 100 times) in order to create the WPLI_i distribution 5) Calculate the proportion ( # (WPLI_i > WPLI_observed) / # (WPLI_i ) ) of WPLI_i which are greater than the WPLI_observed, if this proportion is < 0.05 I could say that the WPLI_observed represents a significant degree of phase, otherwise not. Does it make sense or is it not the right approach? Let suppose this is a correct approach, I have two other questions: First, usually when I compute the WPLI value between two channels I obtain a number of WPLI values according to the cross-spectrum times (one WPLI for each sliding window), in the steps above I am assuming to compute the average WPLI_observed and the average WPLI_i for each step. Does this raise any problems? Second, is it a problem using the same random permutations employed to obtain ch1-ch2 (WPLI_i distribution) to calculate also the ch1-ch3 (WPLI_i distribution). This is just an implementatiion question. I would like to know if I could shuffle the time series of other channels in one step (i.e. for ch1 something like data.trial{other_than_ch1,perm}), and finally extract just the column relative to ch1 from WPLI matrix. thanks Matteo -------------- next part -------------- An HTML attachment was scrubbed... URL: From dimitri.bayle at inserm.fr Tue Jun 28 15:14:43 2011 From: dimitri.bayle at inserm.fr (Dimitri BAYLE) Date: Tue, 28 Jun 2011 15:14:43 +0200 Subject: [FieldTrip] DICS conditions comparison Message-ID: <4E09D3C3.6050906@inserm.fr> Dear Fieldtrip-users, I have a general question about source analysis comparison. I want to compare visual alpha deactivation between 2 conditions (A and B), both containing a baseline (pre) interval and a poststimulus interval, and both showing a strong occipital visual deactivation when comparing the relative contrast ((preA-postA)/preA). To compare A and B, should i calculated a common filter for the baseline and another one for the poststimulus interval, or used the same filter (calculated on which interval)? After applying the filter to all individuals trials (pre and post stimulus), is it better to 1) average alls trials, then calculated the relative contrast for A and for B ((pre-post)/pre)), and substract A and B relative contrast to reveal the difference or 2) calculated the relative contrast for each individuals trials, then average all relatives contrast per conditions (A and B), and substract A and B? Thanks for your help Dimitri From michael.wibral at web.de Tue Jun 28 20:34:28 2011 From: michael.wibral at web.de (Michael Wibral) Date: Tue, 28 Jun 2011 20:34:28 +0200 (CEST) Subject: [FieldTrip] WPLI statistic, permutation like test?? Message-ID: <7105645.2302309.1309286068611.JavaMail.fmail@mwmweb088> An HTML attachment was scrubbed... URL: From suforraxi at gmail.com Wed Jun 29 10:01:15 2011 From: suforraxi at gmail.com (Matteo Demuru) Date: Wed, 29 Jun 2011 10:01:15 +0200 Subject: [FieldTrip] WPLI statistic, permutation like test?? In-Reply-To: <7105645.2302309.1309286068611.JavaMail.fmail@mwmweb088> References: <7105645.2302309.1309286068611.JavaMail.fmail@mwmweb088> Message-ID: Hi Micheal, It seems to me that if you shuffle the trials and then compute the WPLI, the result is the same as if you do not shuffle. For example I have tried compute the WPLI on my trials and then switch trial{1} with trial{2} and the obtained WPLI is the same. Matteo On Tue, Jun 28, 2011 at 8:34 PM, Michael Wibral wrote: > Hi Matteo, > > I am not an expert on the WPLI measures, but to me it seems that in doing > > > "2) Randomly permute the ch2 time series" > > you're destroying a lot of ch2's properties (ie.g. it's spectrum will get a > lot of high ferquencies this way) and this will typically lead to false > positives. This is why permutation tests for connectivity measures typically > shuffle trials (i.e. permute data in a very controlled way, keeping the > intrinsic structure of the data). > > Michael > > > ------------------------------ > *Von:* "Matteo Demuru" > *Gesendet:* Jun 28, 2011 2:46:28 PM > *An:* fieldtrip at donders.ru.nl > *Betreff:* [FieldTrip] WPLI statistic, permutation like test?? > > > Hi, > > I have a couple of questions about using the WPLI index to assess the phase > on my MEG data. > > The experiment consists of recordings during a mental calculation task: I > have 30 sec in which each subject performed continuously an arithmetic > operation. > > It seems to me that WPLI index required more than one trial in order to be > computed. Am I right? (Is this necessary in order to reduce volume > conduction problems?) > I could divide my 30 sec in 5 sec-trials to create my trials, but I was > wandering if this could be a misuse of the WPLI, i.e. WPLI is not > appropriate for my experiment. > > I am also interested in assessing the significance of WPLI index, I would > like to gauge the significance per se of my WPLI values. > The idea is to calculate the WPLI distribution under the null hypothesis > (not phase coupling) for each pair of channels in this way: > > Example to assess the significance of WPLI value for ch1 vs ch2 > > 1) Calculate the WPLI for ch1 and ch2, this would be the observed WPLI > (WPLI_observed) > > 2) Randomly permute the ch2 time series > > 3) Calculate the WPLI for ch1 and ch2 (WPLI_i) > > 4) Repeat step 2 and 3 (for instance 100 times) in order to create the WPLI_i > distribution > > 5) Calculate the proportion ( # (WPLI_i > WPLI_observed) / # (WPLI_i ) ) > of WPLI_i which are greater than the WPLI_observed, if this proportion > is < 0.05 I could say that the WPLI_observed represents a significant > degree of phase, otherwise not. > > Does it make sense or is it not the right approach? > > Let suppose this is a correct approach, I have two other questions: > > First, usually when I compute the WPLI value between two channels I obtain > a number of WPLI values according to the cross-spectrum times (one WPLI for > each sliding window), in the steps above I am assuming to compute the > average WPLI_observed and the average WPLI_i for each step. Does this > raise any problems? > > Second, is it a problem using the same random permutations employed to > obtain ch1-ch2 (WPLI_i distribution) to calculate also the ch1-ch3 (WPLI_i distribution). > This is just an implementatiion question. I would like to know if I could > shuffle the time series of other channels in one step (i.e. for ch1 > something like data.trial{other_than_ch1,perm}), and finally extract just > the column relative to ch1 from WPLI matrix. > > thanks > > Matteo > > > > > > > > > > _______________________________________________ > 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 michael.wibral at web.de Wed Jun 29 17:35:29 2011 From: michael.wibral at web.de (Michael Wibral) Date: Wed, 29 Jun 2011 17:35:29 +0200 (CEST) Subject: [FieldTrip] WPLI statistic, permutation like test?? Message-ID: <786760757.45247.1309361729100.JavaMail.fmail@mwmweb077> An HTML attachment was scrubbed... URL: From paul_c at gmx.de Wed Jun 29 20:54:06 2011 From: paul_c at gmx.de (Paul Czienskowski) Date: Wed, 29 Jun 2011 20:54:06 +0200 Subject: [FieldTrip] ft_databrowser problems and questions Message-ID: <4E0B74CE.3050306@gmx.de> Dear all, I'm trying to plot ICA components with the ft_databrowser function. First of all the topoplots seem to look not like I'm used to. The topoplots I've seen this far filled out the whole circle and not only the rectangle it fills here (see attachment). Second one is, that sometimes, the functions starts to plot unselected components overlaying the selected components. Additionally there is a Question I have. I marked artifacts in the original data (with the ft_databrowser function) and hoped, they would be shown in the ft_databrowser too, when I'm plotting the components. Is there any (easy) way to accomplish this? Cheers, Paul -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 -------------- next part -------------- A non-text attachment was scrubbed... Name: 1to8.png Type: image/png Size: 38959 bytes Desc: not available URL: From megjim1 at gmail.com Thu Jun 30 08:05:08 2011 From: megjim1 at gmail.com (Jim Li) Date: Thu, 30 Jun 2011 01:05:08 -0500 Subject: [FieldTrip] channelrepair issue Message-ID: Dear all, We have 4D's WH3600 MEG system (248 channels) and we found the ----------------- cfg = []; cfg.dataset = 'e,rfhp0.1Hz'; cfg.trialdef.eventtype = 'TRIGGER'; cfg.trialdef.eventvalue = 320; cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 1; cfg = ft_definetrial(cfg); cfg.blc = 'yes'; cfg.blcwindow = [-1 0]; cfg.channel = {'MEG'}; raw_DATA = ft_preprocessing(cfg); raw_DATA.grad = ft_convert_units(raw_DATA.grad, 'cm') cfg = []; cfg.badchannel = {'A234'}; [raw_DATA] = ft_channelrepair(cfg, raw_DATA) the input is raw data with 248 channels and 201 trials repairing channel A234 using neighbour A121 using neighbour A143 using neighbour A154 using neighbour A173 using neighbour A224 using neighbour A8 using neighbour A91 repairing bad channels for trial 1 repairing bad channels for trial 2 repairing bad channels for trial 3 ... ------------------------------------ But channels like A121 and A143 are far away from the bad channel A234. How can they be used as neighbours (i.e. within 4cm, the default value for cfg.neighbourdist) for this bad channel? Any suggestions? Thanks a lot. Jim -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Jun 30 08:50:25 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 30 Jun 2011 08:50:25 +0200 Subject: [FieldTrip] channelrepair issue In-Reply-To: References: Message-ID: Hi Jim, where exactly are they located with respect to the bad channel? Best, Jan-Mathijs On Jun 30, 2011, at 8:05 AM, Jim Li wrote: > Dear all, > > We have 4D's WH3600 MEG system (248 channels) and we found the > ----------------- > cfg = []; > > cfg.dataset = > > 'e,rfhp0.1Hz'; > cfg.trialdef.eventtype = 'TRIGGER'; > > cfg.trialdef.eventvalue = 320; > > cfg.trialdef.prestim = 1; > > cfg.trialdef.poststim = 1 > > ; > cfg = ft_definetrial(cfg); > > cfg.blc = > > 'yes'; > cfg.blcwindow = [-1 0]; > > cfg.channel = {'MEG'}; > > raw_DATA = ft_preprocessing(cfg); > > raw_DATA.grad = ft_convert_units(raw_DATA.grad, 'cm') > > > cfg = []; > cfg.badchannel = {'A234'}; > [raw_DATA] = ft_channelrepair(cfg, raw_DATA) > the input is raw data with 248 channels and 201 trials > repairing channel A234 > using neighbour A121 > using neighbour A143 > using neighbour A154 > using neighbour A173 > using neighbour A224 > using neighbour A8 > using neighbour A91 > repairing bad channels for trial 1 > repairing bad channels for trial 2 > repairing bad channels for trial 3 > ... > ------------------------------------ > > But channels like A121 and A143 are far away from the bad channel > A234. How can they be used as neighbours (i.e. within 4cm, the > default value for cfg.neighbourdist) for this bad channel? > > Any suggestions? > > Thanks a lot. > > Jim > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Thu Jun 30 09:45:57 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 30 Jun 2011 09:45:57 +0200 Subject: [FieldTrip] ft_databrowser problems and questions In-Reply-To: <4E0B74CE.3050306@gmx.de> References: <4E0B74CE.3050306@gmx.de> Message-ID: <4E0C29B5.8060201@donders.ru.nl> Dear Paul, the topoplot bug you get should have been resolved in some newer FieldTrip version, I can remember this one and resolved it a while ago. The overlaying plotting is simply caused because you click too fast. The function plots the individual topos- and time courses. Any callback from one of the buttons does not interrupt this plotting, meaning that it will clear the axes, continue plotting the topos- and time courses if this was not already finished and then start plotting the new topos- and time courses. This will be resolved in a newer version (see below). About the third question: In the current implementation, this is not possible. However, we just started restructuring the code for the databrowser, and in my opinion it should be ready to be made public. In the new implementation, you can annotate and see annotated artifacts in component viewmode. I will keep you up to date on this. Best, Jörn ThisOn 6/29/2011 8:54 PM, Paul Czienskowski wrote: > Dear all, > > I'm trying to plot ICA components with the ft_databrowser function. > First of all the topoplots seem to look not like I'm used to. The > topoplots I've seen this far filled out the whole circle and not only > the rectangle it fills here (see attachment). Second one is, that > sometimes, the functions starts to plot unselected components > overlaying the selected components. > Additionally there is a Question I have. I marked artifacts in the > original data (with the ft_databrowser function) and hoped, they would > be shown in the ft_databrowser too, when I'm plotting the components. > Is there any (easy) way to accomplish this? > > Cheers, > Paul > > > > > _______________________________________________ > 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 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 odidodi at hotmail.com Thu Jun 30 11:04:55 2011 From: odidodi at hotmail.com (odelia nakar) Date: Thu, 30 Jun 2011 09:04:55 +0000 Subject: [FieldTrip] channelrepair issue In-Reply-To: References: Message-ID: Hi Jim, Try : cfg.neighbourdist = 0.03; I found it good for my data. (When you run the function the channels that repaired your data is displayed in the command window). Good luck! Odelia. Date: Thu, 30 Jun 2011 01:05:08 -0500 From: megjim1 at gmail.com To: fieldtrip at donders.ru.nl Subject: [FieldTrip] channelrepair issue Dear all, We have 4D's WH3600 MEG system (248 channels) and we found the ----------------- cfg = []; cfg.dataset = 'e,rfhp0.1Hz'; cfg.trialdef.eventtype = 'TRIGGER'; cfg.trialdef.eventvalue = 320; cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 1; cfg = ft_definetrial(cfg); cfg.blc = 'yes'; cfg.blcwindow = [-1 0]; cfg.channel = {'MEG'}; raw_DATA = ft_preprocessing(cfg); raw_DATA.grad = ft_convert_units(raw_DATA.grad, 'cm') cfg = []; cfg.badchannel = {'A234'}; [raw_DATA] = ft_channelrepair(cfg, raw_DATA) the input is raw data with 248 channels and 201 trials repairing channel A234 using neighbour A121 using neighbour A143 using neighbour A154 using neighbour A173 using neighbour A224 using neighbour A8 using neighbour A91 repairing bad channels for trial 1 repairing bad channels for trial 2 repairing bad channels for trial 3 ... ------------------------------------ But channels like A121 and A143 are far away from the bad channel A234. How can they be used as neighbours (i.e. within 4cm, the default value for cfg.neighbourdist) for this bad channel? Any suggestions? Thanks a lot. Jim _______________________________________________ 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 megjim1 at gmail.com Thu Jun 30 17:39:23 2011 From: megjim1 at gmail.com (Jim Li) Date: Thu, 30 Jun 2011 10:39:23 -0500 Subject: [FieldTrip] channelrepair issue In-Reply-To: References: Message-ID: Hi Jan-Mathijs, >From Fieldtrip data structure I saw that the coordinate of A234 is [ -7.2133 9.1712 5.7117]. And it's [14.4320 -0.0683 0.4437] for A121. All these are in "cm". So the distance between the two channels are 24.1172cm. I checked 4D's orignial file and found the channel coordinates to agree with what I read from Fieldtrip. So I'm wondering how those coils 24.1172cm apart can be considered neighbours (within 4cms). Thanks a lot, Jim On Thu, Jun 30, 2011 at 1:50 AM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Hi Jim, where exactly are they located with respect to the bad channel? > > Best, > > Jan-Mathijs > > > On Jun 30, 2011, at 8:05 AM, Jim Li wrote: > > Dear all, > > We have 4D's WH3600 MEG system (248 channels) and we found the > ----------------- > > cfg = []; > > cfg.dataset = > 'e,rfhp0.1Hz'; > > cfg.trialdef.eventtype = 'TRIGGER'; > > cfg.trialdef.eventvalue = 320; > > cfg.trialdef.prestim = 1; > > cfg.trialdef.poststim = 1 > ; > > cfg = ft_definetrial(cfg); > > cfg.blc = > 'yes'; > > cfg.blcwindow = [-1 0]; > > cfg.channel = {'MEG'}; > > raw_DATA = ft_preprocessing(cfg); > > raw_DATA.grad = ft_convert_units(raw_DATA.grad, 'cm') > > cfg = []; > cfg.badchannel = {'A234'}; > [raw_DATA] = ft_channelrepair(cfg, raw_DATA) > the input is raw data with 248 channels and 201 trials > repairing channel A234 > using neighbour A121 > using neighbour A143 > using neighbour A154 > using neighbour A173 > using neighbour A224 > using neighbour A8 > using neighbour A91 > repairing bad channels for trial 1 > repairing bad channels for trial 2 > repairing bad channels for trial 3 > ... > ------------------------------------ > > But channels like A121 and A143 are far away from the bad channel A234. How > can they be used as neighbours (i.e. within 4cm, the default value for > cfg.neighbourdist) for this bad channel? > > Any suggestions? > > Thanks a lot. > > Jim > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > > _______________________________________________ > 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 odidodi at hotmail.com Wed Jun 1 09:10:30 2011 From: odidodi at hotmail.com (odelia nakar) Date: Wed, 1 Jun 2011 07:10:30 +0000 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>, <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl>, , , <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com>, , <4DDB5A14.3090102@uni-oldenburg.de>, <34CEBDBD-7738-403D-A563-4A6FDBD83C04@mac.com>, , Message-ID: Hi all, Thank you all for the discussion. I'm sorry I response only now, I went on a vacation... I actually didn't want to run the ICA on trials with blinks, rather on all trials, but to remove the component only for trials with a blink. Your critics concern my idea as well, since if I have any kind of correlation between condition and blink I might yield a difference that does not exist between conditions... Considering your suggestion, Mahesh, unfortunately I don't have EOG recording for this experiment. Thanks again for the discussion, Odelia. Date: Fri, 27 May 2011 00:32:01 -0400 From: mahesh.casiraghi at gmail.com To: yuvharpaz at gmail.com; fieldtrip at donders.ru.nl Subject: Re: [FieldTrip] ICA+frqanalysis questions Dear Yuval and discussion group, it seems to me that what you are proposing is getting close to what proposed by the hybrid approach of regica described here: Manousos A. Klados, Christos Papadelis, Christoph Braun, Panagiotis D. Bamidis, REG-ICA: A hybrid methodology combining Blind Source Separation and regression techniques for the rejection of ocular artifacts, Biomedical Signal Processing and Control, In Press, Corrected Proof, Available online 16 March 2011, ISSN 1746-8094, DOI: 10.1016/j.bspc.2011.02.001. They suggest to selectively run regression based AR only on those components which correlate with EOG signals. This makes sense to me and I have been trying to experiment that on some old data, although with no clear conclusions yet. It may be worth a try for Odelia: Anybody out there with some insights for this - or maybe a similar - approach? Cheers, Mahesh Mahesh M. CasiraghiPhD candidate - Cognitive Sciences Roberto Dell'Acqua Lab, University of PadovaPierre Jolicoeur Lab, Univesité de Montréal mahesh.casiraghi at umontreal.ca I have the conviction that when Physiology will be far enough advanced, the poet, the philosopher, and the physiologist will all understand each other. Claude Bernard On Thu, May 26, 2011 at 11:40 PM, Yuval Harpaz wrote: Dear discussion groupDid anybody consider smoothing or filtering the component trace before rejecting it? it seems that the added noise to no-blink trials is in a frequency higher than that typical to blinks. what if we evaluate the component weight, creating a trace for the eyeblink component for every trial, then bandpass filter the blink trace , say 0.1-25Hz, and only then remove the component from the data? yuval On 27 May 2011 06:16, Joseph Dien wrote: Stefan, just to be clear, I don't think any of us were saying not to use ICA to correct blinks. David was just saying that there are potential concerns when one only applies the ICA to the blink trials rather than to all the trials. I myself use EEGlab's infomax implementation in the automatic eyeblink correction tool of my EP Toolkit (http://sourceforge.net/projects/erppcatoolkit/). Now that said, I should add a little more nuance to my response. One of the things I observed (or rather, that Tim Curran pointed out to me) is that when you apply ICA to remove eyeblink artifacts in this manner, it can actually substantially increase the noise level in the data, so for the trials without eyeblinks it can have a considerable cost. So in order to balance the cost/benefit ratio, what I did was to include a trial by trial criterion that the putative eyeblink factors would only be removed if doing so reduced the overall variance of the trial. This approach does still have some potential for causing the concerns that David raises but not as much as only applying the ICA to blink trials since it does end up getting applied to non-blink trials too. This does mean that one should be cautious about any apparent effects in the artifact corrected data that are centered around the eyes (that have a blink topography) but that goes without saying in any case. So anyway, I agree, it's not perfect but seems to be the best available option. Cheers! Joe On May 24, 2011, at 3:11 AM, Stefan Debener wrote: Hi Odelia, I have a slightly different opinion here. It is certainly true that any filter has the tendency to distort data (with distortion I mean that data consists of a mixture of some wanted, true signal and some unwanted signal, and that the removal of the unwanted part of the signal is neither complete nor specific). In our lab we regularly use ICA for artefact removal (and more), and the benefit/gain is clearly are much larger than the distortion. In fact there are a number of examples out showing that currently only ICA (or related tools) can recover the study of (a substantial fraction of the wanted) EEG signal (but again, it is NOT a perfect tool at all), in particular in cases where other means of SNR enhancement don't work well (averaging, spectral analysis). I am happy to provide references if you are interested... For the evaluation of outcome it would be reasonable to not evaluate the ERP alone, as this could be misleading. Better evaluate the sensitivity and specificity of an eye blink attentuation approach on the single trial (and single subject) level, this will give you good insight. And it is worth keeping in mind that the preprocessing of the data (among other issues, like the quality of the recording and so on) largely determines the quality of the output (for some introduction you may look up chapter 3.1 in Ullsperger & Debener, 2010, Simultaneous EEG and FMRI, Oxford University Press). Just by a different preprocessing ICA output could vary between crap and excellent unmixing. Thus a poor ICA eye blink attenuation would make me a bit suspicious... Best, Stefan Am 5/24/11 4:00 AM, schrieb Alexander J. Shackman: And for a related perspective, see McMenamin, B. W., Shackman, A. J., Greischar, L. L. & Davidson, R. J. (2011). Electromyogenic artifacts and electroencephalographic inferences revisited, Neuroimage, 54, 4-9. http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf On Mon, May 23, 2011 at 8:07 PM, Joseph Dien wrote: I agree with David's reasoning. You may find the following article to be of help as well in understanding the issues involved: Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of simulated ERPs: Promax versus Infomax rotations. Human Brain Mapping, 28(8), 742-763. Cheers! Joe On May 23, 2011, at 11:57 AM, David Groppe wrote: Hi Odelia, When you use ICA (or any other spatial filter) to correct for EEG artifacts, you're going to distort your data some by removing true EEG activity in addition to the artifact (for an explanation, see: http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). So to minimize distortion, it would be better not to apply ICA artifact correction to artifact-free data. However, if the frequency of the artifact differs across experimental conditions, it could confound your analysis. For example, I suspect people blink more often to targets in an oddball experiment than standards. Thus if you apply ICA only to blinky trials, you could find a difference between the EEG response to standards and targets that simply reflects the fact ICA removed more EEG activity in the target trials (i.e., it wouldn't reflect a true difference in neural processing). hope this helps, -David On Mon, May 23, 2011 at 1:44 AM, odelia nakar wrote: Hi all, I'm troubled by the fact that when I use ICA for blinks\eyes movements removal, I remove the relevant components also from trials that do not contain blinks\eyes movements. In order to avoid this bias we thought to combine the data before ICA ("data" structure) with the data after ICA ("dataica" structure), only in specific trials, as follows: datall=dataica; datall.trial=data.trial; datall.time=data.time; blinks=[2 4 5 8 bla bla 156]; for ind=1:length(blinks) datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; end To my first question: I just wanted to check that there is no problem with that, or any reason not to use it. Another issue- I use motor learning task, and I'm trying to understand what happens through the process, in terms of power-frequency changes through the process. How would you recommend that I'd use the ft_freqanalysis function? What method to use (or what do I need to consider when choosing the method field)? Thanks a lot, Odelia. _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- David Groppe, Ph.D. Postdoctoral Researcher Kutaslab Dept. of Cognitive Science University of California, San Diego http://www.cogsci.ucsd.edu/~dgroppe/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------------------------------------------------------------------------- Joseph Dien E-mail: jdien07 at mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://homepage.mac.com/jdien07/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Alexander J. Shackman, Ph.D. Wisconsin Psychiatric Institute & Clinics and Department of Psychology University of Wisconsin-Madison 1202 West Johnson Street Madison, Wisconsin 53706 Telephone: +1 (608) 358-5025 Fax: +1 (608) 265-2875 Email: shackman at wisc.edu http://psyphz.psych.wisc.edu/~shackman _______________________________________________ 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 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Y.Harpaz a link to the BIU MEG lab: http://faculty.biu.ac.il/~goldsa/index.html "Many were increasingly of the opinion that they'd all made a big mistake in coming down from the trees in the first place. And some said that even the trees had been a bad move, and that no one should ever have left the oceans". Douglas Adams _______________________________________________ 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 suforraxi at gmail.com Wed Jun 1 11:23:54 2011 From: suforraxi at gmail.com (Matteo Demuru) Date: Wed, 1 Jun 2011 11:23:54 +0200 Subject: [FieldTrip] WPLI question Message-ID: Hi, I have question about the WPLI: I would like to know why it can have either positive or negative value? It seems to me that it could be due from the relation (lagging or leading) between two signals, but I am not sure. Taking the absolute value of the WPLI is it a way to preserve the 'synchronization infomation' discardig which signal is leading or lagging? Thanks Matteo -------------- next part -------------- An HTML attachment was scrubbed... URL: From martinvinck at gmail.com Wed Jun 1 12:07:17 2011 From: martinvinck at gmail.com (Martin Vinck) Date: Wed, 1 Jun 2011 12:07:17 +0200 Subject: [FieldTrip] WPLI question In-Reply-To: References: Message-ID: <345B36F9-D0E3-43F4-8B7B-25333BB5681E@gmail.com> Hi Mateo, As it is computed in ft_connectivity_wpli it preserves the information about the sign, i.e. whether the average imaginary component of the cross-spectrum is positive or negative. That is, it estimates the average imaginary component of the cross-spectrum divided by the average magnitude of this imaginary component. By taking the absolute value over the output one gets a measure of the strength of the interaction,- WPLI as it is defined in the paper, by taking the sign one gets a measure of the direction of the interaction. The debiased WPLI estimator gets negative however as a consequence of the debiasing method - different issue. Best, Martin. From Elena.Orekhova at neuro.gu.se Wed Jun 1 12:23:29 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Wed, 1 Jun 2011 10:23:29 +0000 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECA991@exchccr1.neuro.gu.se> Dear fieldtrippers, This message is mainly for Neuromag users. When I do 'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. If I combine the two types of sensors without weighting, the result is meaningless. Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements. Does anybody know how to deal with this problem? Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.wibral at web.de Wed Jun 1 16:04:46 2011 From: michael.wibral at web.de (Michael Wibral) Date: Wed, 1 Jun 2011 16:04:46 +0200 (CEST) Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis Message-ID: <1960081272.1639684.1306937086986.JavaMail.fmail@mwmweb084> An HTML attachment was scrubbed... URL: From zechuan_he at hotmail.com Wed Jun 1 15:35:07 2011 From: zechuan_he at hotmail.com (Zeddy He) Date: Wed, 1 Jun 2011 11:35:07 -0200 Subject: [FieldTrip] Emotiv headset realtime capture In-Reply-To: References: Message-ID: Hi Valentin, I am not entirely sure exactly what part of the process you're not sure about. I'm new to fieldtrip as well and I have never heard of emotiv until today. I have, however, been playing around with FieldTrip's realtime acquisition part for the last couple of weeks(acq2ft, AcqBuffer), and maybe able to offer some pointers in getting it set up on your system. It seems that to use emotive2ft, you would have to compile it first, call upon it in matlab before starting your emotive software, and then start the emotiv software. I am not exactly sure what can read the bufferdata, though ft_realtime_signalviewer as well as viewer.exe may be good functions/programs to start off with. If you're using acq2ft or Acqbuffer already for realtime acquistion from another CTF device, you could try running one of those first either by standalone or their MATLAB equivilent functions, and then run emotiv2ft in matlab without any passed in parameters(unless you didn't decide to put the buffer on localhost:1972). You also might be able to just let the function create it's own buffer by giving it a new port, and then draw from that port seperately later on. Some troubles I've ran into while using FieldTrip's realtime functions include: shmget() errors on linux systems firewall blocking port number type in-compatibility and perhaps a couple others I can't recall at the moment. If you think I might be capable of assisting you, let me know and I'll see if I can give you additional details. Regards Zeddy > From: valentin.umbach at hu-berlin.de > Date: Tue, 31 May 2011 18:51:17 +0200 > To: fieldtrip at donders.ru.nl > Subject: [FieldTrip] Emotiv headset realtime capture > > Hi, I'm new to FieldTrip and I'm interested in using it to capture > realtime data from the Emotiv headset using this interface: > http://fieldtrip.fcdonders.nl/development/realtime/emotiv > I'm not clear about how to make calls to this interface from within > Matlab. Also, I would like to know if it's possible to access not just > the raw EEG, but also the API output of the detection libraries > (Affectiv Suite...). > Any help is greatly appreciated! > > Best, Valentin > > -- > Dipl.-Psych. Valentin J. Umbach > Institut für Psychologie > Humboldt-Universität zu Berlin > Rudower Chaussee 18 > 12489 Berlin > Tel. +49 30 2093 9438 > E-Mail: valentin.umbach at hu-berlin.de > > _______________________________________________ > 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 michael.wibral at web.de Thu Jun 2 13:18:04 2011 From: michael.wibral at web.de (michael.wibral at web.de) Date: Thu, 2 Jun 2011 13:18:04 +0200 (CEST) Subject: [FieldTrip] Poblem with options for ft_volumesegment Message-ID: <511684614.2148844.1307013484440.JavaMail.fmail@mwmweb077> An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Jun 2 13:26:45 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 2 Jun 2011 13:26:45 +0200 Subject: [FieldTrip] Poblem with options for ft_volumesegment In-Reply-To: <511684614.2148844.1307013484440.JavaMail.fmail@mwmweb077> References: <511684614.2148844.1307013484440.JavaMail.fmail@mwmweb077> Message-ID: Dear Michael, Thanks for reporting this; we'll look into it. Best, JM On Jun 2, 2011, at 1:18 PM, michael.wibral at web.de wrote: > Dear FT'ers, > > Davide Rivolta posted a problem with ft_volumesegment a while ago. > We have meanwhile solved this problem. > > There is (FT from may 31st) a problem with the handling of the > > cfg.smooth > > option. > > It's default is 'no', according to the function HELP. > However in line 434 of ft_volumesegment, this option is put into a > numerical array - this makes sense for a smoothing value. Also if no > specification is given at all, then a NaN is inserted into the > array. However if "no" is set explicitely then ft_getopt tries to > insert the string 'no' into the array which leads to an error. Below > is a script that is running and the error is once again detailed in > the commets. > In my opinion this could be fixed by simply updating te function HELP. > > Michael > > %%Brain segmentation – MRI > > > mri = ft_read_mri('NPD18_V2.mri'); > > cfg = []; > > cfg.spmversion = 'spm8'; > > cfg.output = 'tpm'; > > cfg.template = 'T1.nii'; > > cfg.units = 'mm'; > > cfg.write = 'no'; > > cfg.coordsys = 'ctf'; > > cfg.downsample = 2; > > cfg.smooth = NaN; % works. option 'no' as recommended (!) in > the function HELP throws an > > % error because ft_getopt > on line 434 of ft_volumesegment > > % tries to put a string of > length two into an array that is for numbers > > % leaving out this option > also worked, but some > > % people might try to use > this option > > segmentedmri = ft_volumesegment(cfg, mri); > > save ('segmentedmri'); > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Thu Jun 2 18:22:03 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Thu, 2 Jun 2011 16:22:03 +0000 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <1960081272.1639684.1306937086986.JavaMail.fmail@mwmweb084> References: <1960081272.1639684.1306937086986.JavaMail.fmail@mwmweb084> Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECAB58@exchccr1.neuro.gu.se> Dear Michael, I have tried to multiply the leadfield by -1 as you suggested: for i = 1 : size (grid.leadfield, 2) grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); end This had no effect on the 'lcmv' output. I attached the pictures for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ In this experiment I measured evoked field in response to the unilateral (left) click. The source is expected to be in the right superior temporal cortex. This is the case for ‘GRA only' and ’MAG only’ datasets. The combined sensors give meaningless result. Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Wednesday, June 01, 2011 4:04 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Elena, could you give the following a try: invert (*-1) the leadfileds for one of the two sensor types. Let me know what happens. I would also be interested in taking a look at the results - maybe you could sent images off-list: Michael.Wibral web.de. Michael ________________________________ Von: "Elena Orekhova" Gesendet: Jun 1, 2011 12:23:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "Arial"; }@font-face { font-family: "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: Times; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear fieldtrippers, This message is mainly for Neuromag users. When I do 'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. If I combine the two types of sensors without weighting, the result is meaningless. Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements. Does anybody know how to deal with this problem? Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: lcmv_St1_gra_1p2-1p5.jpg Type: image/jpeg Size: 22987 bytes Desc: lcmv_St1_gra_1p2-1p5.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: lcmv_St1_mag_1p2-1p5.jpg Type: image/jpeg Size: 22978 bytes Desc: lcmv_St1_mag_1p2-1p5.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: lcmv_St1_mag+gra_1p2-1p5.jpg Type: image/jpeg Size: 22576 bytes Desc: lcmv_St1_mag+gra_1p2-1p5.jpg URL: From michael.wibral at web.de Thu Jun 2 19:20:07 2011 From: michael.wibral at web.de (Michael Wibral) Date: Thu, 2 Jun 2011 19:20:07 +0200 (CEST) Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis Message-ID: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Thu Jun 2 20:03:16 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Thu, 2 Jun 2011 18:03:16 +0000 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F03ECAB58@exchccr1.neuro.gu.se> References: <1960081272.1639684.1306937086986.JavaMail.fmail@mwmweb084>, <32CC77C0C8A7AD4B9410934642608E1F03ECAB58@exchccr1.neuro.gu.se> Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECAB81@exchccr1.neuro.gu.se> Dear Michael, I did normalize the data (sourcepst.avg.nai=sourcepst.avg.pow./sourcepre.avg.pow) as it was suggested in the tutorial. I used the same scales in all plots for comparison purposes. If automatic scaling is used the result for MAG+GRA does not look any better (see attachment). >What you could do as a workaround is to average the separate results with a weighting per voxel and that >is corresponding to the squared norms of the leadfields for the respective modalities for a given voxel , this >would guarantee equal amounts of backprojected noise from both modalities (if I'm not mistaken). Thank you for your suggestion. I may use it as a last resort. Hopefully, there is still a way to get more optimal solution using both GRA and MAG in the same analysis... Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Elena Orekhova [Elena.Orekhova at neuro.gu.se] Sent: Thursday, June 02, 2011 6:22 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Michael, I have tried to multiply the leadfield by -1 as you suggested: for i = 1 : size (grid.leadfield, 2) grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); end This had no effect on the 'lcmv' output. I attached the pictures for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ In this experiment I measured evoked field in response to the unilateral (left) click. The source is expected to be in the right superior temporal cortex. This is the case for ‘GRA only' and ’MAG only’ datasets. The combined sensors give meaningless result. Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Wednesday, June 01, 2011 4:04 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Elena, could you give the following a try: invert (*-1) the leadfileds for one of the two sensor types. Let me know what happens. I would also be interested in taking a look at the results - maybe you could sent images off-list: Michael.Wibral web.de. Michael ________________________________ Von: "Elena Orekhova" Gesendet: Jun 1, 2011 12:23:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "Arial"; }@font-face { font-family: "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: Times; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear fieldtrippers, This message is mainly for Neuromag users. When I do 'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. If I combine the two types of sensors without weighting, the result is meaningless. Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements. Does anybody know how to deal with this problem? Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: lcmv_St1_mag+gra_autoscale.jpg Type: image/jpeg Size: 22257 bytes Desc: lcmv_St1_mag+gra_autoscale.jpg URL: From smoratti at psi.ucm.es Fri Jun 3 11:00:18 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Fri, 03 Jun 2011 11:00:18 +0200 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> References: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> Message-ID: <722801BA-5C22-4A69-8F87-18C1C54A7F00@psi.ucm.es> Hi Michael y Elena, I am following your discussion with great interest as I have just started to work with Neuromag data. As FT uses the MNE toolbox to read the data I assume that the SSP vectors are applied to the data during reading the data. However, the SSP vectors are stored in "data.hdr.orig.projs". However, when I go on with averaging in the ERF from timelockanalysis I cannot find this info. So my question is, does FT apply the SSP vectors later on also to the leadfield when calculating it? I assume that not, as the SSP vectors are not passed on further. How can I apply the SSP vectors to the leadfield to get correct results? Best and thanks, STephan El 02/06/2011, a las 19:20, Michael Wibral escribió: > Hi Elena, > > I assume that you were well aware of the difficulties in beamforming evoked activty and baseline normalisation and these things, your results really look that way. I mus say I am quite puzzled by the results - could it be a color scaling problem in the plot? I think this mmay be a problem because most of your plot is a peak power, only a tiny corner seems to be in a low-amplitude range. > > What you could do as a workaround is to average the separate results with a weighting per voxel and that is corresponding to the squared norms of the leadfields for the respective modalities for a given voxel , this would guarantee equal amounts of backprojected noise from both modalities (if I'm not mistaken). > > Michael > PS: I am away for a couple of days, but after that, I'll be happy to resume this discussion. > > > Von: "Elena Orekhova" > Gesendet: Jun 2, 2011 6:22:03 PM > An: "Email discussion list for the FieldTrip project" > Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis > > @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } > Dear Michael, > > > I have tried to multiply the leadfield by -1 as you suggested: > > > for i = 1 : size (grid.leadfield, 2) > > grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); > > end > > > This had no effect on the 'lcmv' output. I attached the pictures for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ > > > In this experiment I measured evoked field in response to the unilateral (left) click. > > The source is expected to be in the right superior temporal cortex. This is the case for ‘GRA only' and ’MAG only’ datasets. The combined sensors give meaningless result. > > > Elena > > > From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] > Sent: Wednesday, June 01, 2011 4:04 PM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis > > > Dear Elena, > > could you give the following a try: invert (*-1) the leadfileds for one of the two sensor types. Let me know what happens. > I would also be interested in taking a look at the results - maybe you could sent images off-list: Michael.Wibral web.de. > > Michael > > > > Von: "Elena Orekhova" > Gesendet: Jun 1, 2011 12:23:29 PM > An: "fieldtrip at donders.ru.nl" > Betreff: [FieldTrip] combining magnetometers and planad gradiometers for analysis > > @font-face { font-family: "Arial"; }@font-face { font-family: "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: Times; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } > Dear fieldtrippers, > > This message is mainly for Neuromag users. > > > When I do 'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. > > If I combine the two types of sensors without weighting, the result is meaningless. > > Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements. Does anybody know how to deal with this problem? > > > > Elena > > > > _______________________________________________ > 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 jan.schoffelen at donders.ru.nl Fri Jun 3 13:11:02 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 3 Jun 2011 13:11:02 +0200 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <722801BA-5C22-4A69-8F87-18C1C54A7F00@psi.ucm.es> References: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> <722801BA-5C22-4A69-8F87-18C1C54A7F00@psi.ucm.es> Message-ID: <77A55ECC-5A84-4839-9093-75FA499D3D31@donders.ru.nl> Hi Stephan et al, Any balancing coefficients (e.g. the digital weights for the bti- system, or ctf's 3d order gradient coefficients) are only applied to the leadfield if they end up in the data.grad.tra matrix. These .tra matrices will be compiled when reading the data header, by functions like XXX2grad (in fileio/private: ctf2grad, bti2grad, fif2grad). You can check whether it is constructed using hdr.orig.projs. If not, it may be worthwile to implement I guess. Best, JM On Jun 3, 2011, at 11:00 AM, Stephan Moratti wrote: > Hi Michael y Elena, > > I am following your discussion with great interest as I have just > started to work with Neuromag data. As FT uses the MNE toolbox to > read the data I assume that the SSP vectors are applied to the data > during reading the data. However, the SSP vectors are stored in > "data.hdr.orig.projs". However, when I go on with averaging in the > ERF from timelockanalysis I cannot find this info. So my question > is, does FT apply the SSP vectors later on also to the leadfield > when calculating it? I assume that not, as the SSP vectors are not > passed on further. How can I apply the SSP vectors to the leadfield > to get correct results? > > Best and thanks, > > STephan > > El 02/06/2011, a las 19:20, Michael Wibral escribió: > >> Hi Elena, >> >> I assume that you were well aware of the difficulties in >> beamforming evoked activty and baseline normalisation and these >> things, your results really look that way. I mus say I am quite >> puzzled by the results - could it be a color scaling problem in the >> plot? I think this mmay be a problem because most of your plot is a >> peak power, only a tiny corner seems to be in a low-amplitude range. >> >> What you could do as a workaround is to average the separate >> results with a weighting per voxel and that is corresponding to >> the squared norms of the leadfields for the respective modalities >> for a given voxel , this would guarantee equal amounts of >> backprojected noise from both modalities (if I'm not mistaken). >> >> Michael >> PS: I am away for a couple of days, but after that, I'll be happy >> to resume this discussion. >> >> >> Von: "Elena Orekhova" >> Gesendet: Jun 2, 2011 6:22:03 PM >> An: "Email discussion list for the FieldTrip project" > > >> Betreff: Re: [FieldTrip] combining magnetometers and planad >> gradiometers for analysis >> >> @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face >> { font-family: "Cambria Math"; }@font-face { font-family: >> "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal, >> li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: >> 12pt; font-family: Cambria; }.MsoChpDefault { font-family: >> Cambria; }div.WordSection1 { page: WordSection1; } >> Dear Michael, >> >> >> I have tried to multiply the leadfield by -1 as you suggested: >> >> >> for i = 1 : size (grid.leadfield, 2) >> >> grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); >> >> end >> >> >> This had no effect on the 'lcmv' output. I attached the pictures >> for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ >> >> >> In this experiment I measured evoked field in response to the >> unilateral (left) click. >> >> The source is expected to be in the right superior temporal >> cortex. This is the case for ‘GRA only' and ’MAG only’ datasets. >> The combined sensors give meaningless result. >> >> >> Elena >> >> >> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl >> ] on behalf of Michael Wibral [michael.wibral at web.de] >> Sent: Wednesday, June 01, 2011 4:04 PM >> To: Email discussion list for the FieldTrip project >> Subject: Re: [FieldTrip] combining magnetometers and planad >> gradiometers for analysis >> >> >> Dear Elena, >> >> could you give the following a try: invert (*-1) the leadfileds for >> one of the two sensor types. Let me know what happens. >> I would also be interested in taking a look at the results - maybe >> you could sent images off-list: Michael.Wibral web.de. >> >> Michael >> >> >> >> Von: "Elena Orekhova" >> Gesendet: Jun 1, 2011 12:23:29 PM >> An: "fieldtrip at donders.ru.nl" >> Betreff: [FieldTrip] combining magnetometers and planad >> gradiometers for analysis >> >> @font-face { font-family: "Arial"; }@font-face { font-family: >> "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D >> "; }@font-face { font-family: "Cambria Math"; }@font-face { font- >> family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal >> { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: >> Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; >> font-family: Times; }.MsoChpDefault { font-family: >> Cambria; }div.WordSection1 { page: WordSection1; } >> Dear fieldtrippers, >> >> This message is mainly for Neuromag users. >> >> >> When I do 'lcmv' beamforming analysis separately on planar >> gradiometers or magnetometers, I get quite meaningful results. >> >> If I combine the two types of sensors without weighting, the result >> is meaningless. >> >> Apparently, the algorithm does not take care of different scales >> and units of the GRA and MAG measurements. Does anybody know how >> to deal with this problem? >> >> >> >> Elena >> >> >> >> _______________________________________________ >> 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 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Fri Jun 3 14:25:46 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Fri, 3 Jun 2011 12:25:46 +0000 Subject: [FieldTrip] cfg.method = 'sam' Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECAC4F@exchccr1.neuro.gu.se> Dear colleagues, Sorry, I posted much on the list recent time. I want to figure out howto run SAM analysis on my data. When I run 'lcmv' beamformer on my averaged dataset it works fine: cfg = []; cfg.grad = hdr.grad; cfg.method = 'lcmv'; cfg.grid = grid; cfg.vol = vol_cm; cfg.reducerank=2; cfg.keepfilter = 'yes' cfg.channel = MAG; %MAG = {'MEG0721', 'MEG0731',... } source = ft_sourceanalysis(cfg, tlckavg); When I do the same with cfg.method = 'lcmv' option, I get the error: ***************************** ??? Undefined function or method 'beamformer_sam' for input arguments of type 'struct'. Error in ==> sourceanalysis at 1158 dip(i) = beamformer_sam(grid, sens, vol, squeeze(avg(i,:,:)), squeeze(Cy(i,:,:)), optarg{:}); Error in ==> ft_sourceanalysis at 11 [varargout{1:nargout}] = funhandle(varargin{:}); Does anybody know how to make the ‘SAM’ option to work? Does anybody used cfg.method = 'lcmv' option in the Fieldtrip??? Regards, Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Fri Jun 3 14:57:47 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Fri, 3 Jun 2011 12:57:47 +0000 Subject: [FieldTrip] cfg.method = 'sam' Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECAC6B@exchccr1.neuro.gu.se> Dear colleagues, Sorry, I posted much on the list recent time. I want to figure out how to run SAM analysis on my data. When I run 'lcmv' beamformer on my averaged dataset it works fine: cfg = []; cfg.grad = hdr.grad; cfg.method = 'lcmv'; cfg.grid = grid; cfg.vol = vol_cm; cfg.reducerank=2; cfg.keepfilter = 'yes' cfg.channel = MAG; %MAG = {'MEG0721', 'MEG0731',... } source = ft_sourceanalysis(cfg, tlckavg); When I do the same with cfg.method = 'sam' option, I get the error: ***************************** ??? Undefined function or method 'beamformer_sam' for input arguments of type 'struct'. Error in ==> sourceanalysis at 1158 dip(i) = beamformer_sam(grid, sens, vol, squeeze(avg(i,:,:)), squeeze(Cy(i,:,:)), optarg{:}); Error in ==> ft_sourceanalysis at 11 [varargout{1:nargout}] = funhandle(varargin{:}); Does anybody know how to make the ‘SAM’ option to work? Does anybody used cfg.method = 'sam' option in the Fieldtrip??? Regards, Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Fri Jun 3 15:08:53 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Fri, 03 Jun 2011 15:08:53 +0200 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <77A55ECC-5A84-4839-9093-75FA499D3D31@donders.ru.nl> References: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> <722801BA-5C22-4A69-8F87-18C1C54A7F00@psi.ucm.es> <77A55ECC-5A84-4839-9093-75FA499D3D31@donders.ru.nl> Message-ID: <32BF5576-A020-41A6-AF11-0879E03067FD@psi.ucm.es> Hi Jan-Mathijs, I had just a look at fif2grad.m and it seems to me that the information of hdr.orig.projs is not used to construct the .tra field. It only codes for magnetometers 1 and for the two gradiometers 1 and -1 (to get the difference). Going through the code I found out that FT uses mne2grad.m rather than fif2grad.m. But mne2grad.m does not use the info in hdr.orig.projs. Thus, it seems the information does not go into grad.tra. (So I guess the topographies and leadfields will not be correct when SSP vectors are used). Best, Stephan El 03/06/2011, a las 13:11, jan-mathijs schoffelen escribió: > Hi Stephan et al, > > Any balancing coefficients (e.g. the digital weights for the bti-system, or ctf's 3d order gradient coefficients) are only applied to the leadfield if they end up in the data.grad.tra matrix. These .tra matrices will be compiled when reading the data header, by functions like XXX2grad (in fileio/private: ctf2grad, bti2grad, fif2grad). > You can check whether it is constructed using hdr.orig.projs. > If not, it may be worthwile to implement I guess. > > Best, > > JM > > > > On Jun 3, 2011, at 11:00 AM, Stephan Moratti wrote: > >> Hi Michael y Elena, >> >> I am following your discussion with great interest as I have just started to work with Neuromag data. As FT uses the MNE toolbox to read the data I assume that the SSP vectors are applied to the data during reading the data. However, the SSP vectors are stored in "data.hdr.orig.projs". However, when I go on with averaging in the ERF from timelockanalysis I cannot find this info. So my question is, does FT apply the SSP vectors later on also to the leadfield when calculating it? I assume that not, as the SSP vectors are not passed on further. How can I apply the SSP vectors to the leadfield to get correct results? >> >> Best and thanks, >> >> STephan >> >> El 02/06/2011, a las 19:20, Michael Wibral escribió: >> >>> Hi Elena, >>> >>> I assume that you were well aware of the difficulties in beamforming evoked activty and baseline normalisation and these things, your results really look that way. I mus say I am quite puzzled by the results - could it be a color scaling problem in the plot? I think this mmay be a problem because most of your plot is a peak power, only a tiny corner seems to be in a low-amplitude range. >>> >>> What you could do as a workaround is to average the separate results with a weighting per voxel and that is corresponding to the squared norms of the leadfields for the respective modalities for a given voxel , this would guarantee equal amounts of backprojected noise from both modalities (if I'm not mistaken). >>> >>> Michael >>> PS: I am away for a couple of days, but after that, I'll be happy to resume this discussion. >>> >>> >>> Von: "Elena Orekhova" >>> Gesendet: Jun 2, 2011 6:22:03 PM >>> An: "Email discussion list for the FieldTrip project" >>> Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis >>> >>> @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } >>> Dear Michael, >>> >>> >>> I have tried to multiply the leadfield by -1 as you suggested: >>> >>> >>> for i = 1 : size (grid.leadfield, 2) >>> >>> grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); >>> >>> end >>> >>> >>> This had no effect on the 'lcmv' output. I attached the pictures for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ >>> >>> >>> In this experiment I measured evoked field in response to the unilateral (left) click. >>> >>> The source is expected to be in the right superior temporal cortex. This is the case for ‘GRA only' and ’MAG only’ datasets. The combined sensors give meaningless result. >>> >>> >>> Elena >>> >>> >>> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] >>> Sent: Wednesday, June 01, 2011 4:04 PM >>> To: Email discussion list for the FieldTrip project >>> Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis >>> >>> >>> Dear Elena, >>> >>> could you give the following a try: invert (*-1) the leadfileds for one of the two sensor types. Let me know what happens. >>> I would also be interested in taking a look at the results - maybe you could sent images off-list: Michael.Wibral web.de. >>> >>> Michael >>> >>> >>> >>> Von: "Elena Orekhova" >>> Gesendet: Jun 1, 2011 12:23:29 PM >>> An: "fieldtrip at donders.ru.nl" >>> Betreff: [FieldTrip] combining magnetometers and planad gradiometers for analysis >>> >>> @font-face { font-family: "Arial"; }@font-face { font-family: "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: Times; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } >>> Dear fieldtrippers, >>> >>> This message is mainly for Neuromag users. >>> >>> >>> When I do 'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. >>> >>> If I combine the two types of sensors without weighting, the result is meaningless. >>> >>> Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements. Does anybody know how to deal with this problem? >>> >>> >>> >>> Elena >>> >>> >>> >>> _______________________________________________ >>> 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 >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > _______________________________________________ > 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 jan.schoffelen at donders.ru.nl Fri Jun 3 15:22:10 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 3 Jun 2011 15:22:10 +0200 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <32BF5576-A020-41A6-AF11-0879E03067FD@psi.ucm.es> References: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> <722801BA-5C22-4A69-8F87-18C1C54A7F00@psi.ucm.es> <77A55ECC-5A84-4839-9093-75FA499D3D31@donders.ru.nl> <32BF5576-A020-41A6-AF11-0879E03067FD@psi.ucm.es> Message-ID: <9A770E4F-6106-4136-BADB-5BBCBE84862D@donders.ru.nl> Dear Stephan, Ah, you're right. I forgot about the mne2grad... Sorry. Regarding the SSP vectors I forgot to mention that of course the sensor data needs to have the SSP vectors incorporated as well, if such info is to be applied to the leadfields too? Either the data on disk is already balanced, or the coefficients need to be applied after reading in the unbalanced data. I don't know enough about the elekta- software/mne-software to know what is happening to the data when the ssp vectors are computed, but once we know enough details it should be straightforward to build it into fieldtrip. Best, JM On Jun 3, 2011, at 3:08 PM, Stephan Moratti wrote: > Hi Jan-Mathijs, > > I had just a look at fif2grad.m and it seems to me that the > information of hdr.orig.projs is not used to construct the .tra > field. It only codes for magnetometers 1 and for the two > gradiometers 1 and -1 (to get the difference). Going through the > code I found out that FT uses mne2grad.m rather than fif2grad.m. But > mne2grad.m does not use the info in hdr.orig.projs. Thus, it seems > the information does not go into grad.tra. (So I guess the > topographies and leadfields will not be correct when SSP vectors are > used). > > Best, > > Stephan > > El 03/06/2011, a las 13:11, jan-mathijs schoffelen escribió: > >> Hi Stephan et al, >> >> Any balancing coefficients (e.g. the digital weights for the bti- >> system, or ctf's 3d order gradient coefficients) are only applied >> to the leadfield if they end up in the data.grad.tra matrix. >> These .tra matrices will be compiled when reading the data header, >> by functions like XXX2grad (in fileio/private: ctf2grad, bti2grad, >> fif2grad). >> You can check whether it is constructed using hdr.orig.projs. >> If not, it may be worthwile to implement I guess. >> >> Best, >> >> JM >> >> >> >> On Jun 3, 2011, at 11:00 AM, Stephan Moratti wrote: >> >>> Hi Michael y Elena, >>> >>> I am following your discussion with great interest as I have just >>> started to work with Neuromag data. As FT uses the MNE toolbox to >>> read the data I assume that the SSP vectors are applied to the >>> data during reading the data. However, the SSP vectors are stored >>> in "data.hdr.orig.projs". However, when I go on with averaging in >>> the ERF from timelockanalysis I cannot find this info. So my >>> question is, does FT apply the SSP vectors later on also to the >>> leadfield when calculating it? I assume that not, as the SSP >>> vectors are not passed on further. How can I apply the SSP vectors >>> to the leadfield to get correct results? >>> >>> Best and thanks, >>> >>> STephan >>> >>> El 02/06/2011, a las 19:20, Michael Wibral escribió: >>> >>>> Hi Elena, >>>> >>>> I assume that you were well aware of the difficulties in >>>> beamforming evoked activty and baseline normalisation and these >>>> things, your results really look that way. I mus say I am quite >>>> puzzled by the results - could it be a color scaling problem in >>>> the plot? I think this mmay be a problem because most of your >>>> plot is a peak power, only a tiny corner seems to be in a low- >>>> amplitude range. >>>> >>>> What you could do as a workaround is to average the separate >>>> results with a weighting per voxel and that is corresponding to >>>> the squared norms of the leadfields for the respective modalities >>>> for a given voxel , this would guarantee equal amounts of >>>> backprojected noise from both modalities (if I'm not mistaken). >>>> >>>> Michael >>>> PS: I am away for a couple of days, but after that, I'll be happy >>>> to resume this discussion. >>>> >>>> >>>> Von: "Elena Orekhova" >>>> Gesendet: Jun 2, 2011 6:22:03 PM >>>> An: "Email discussion list for the FieldTrip project" >>> > >>>> Betreff: Re: [FieldTrip] combining magnetometers and planad >>>> gradiometers for analysis >>>> >>>> @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face >>>> { font-family: "Cambria Math"; }@font-face { font-family: >>>> "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal, >>>> li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font- >>>> size: 12pt; font-family: Cambria; }.MsoChpDefault { font-family: >>>> Cambria; }div.WordSection1 { page: WordSection1; } >>>> Dear Michael, >>>> >>>> >>>> I have tried to multiply the leadfield by -1 as you suggested: >>>> >>>> >>>> for i = 1 : size (grid.leadfield, 2) >>>> >>>> grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i} >>>> (3:3:306, :); >>>> >>>> end >>>> >>>> >>>> This had no effect on the 'lcmv' output. I attached the pictures >>>> for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ >>>> >>>> >>>> In this experiment I measured evoked field in response to the >>>> unilateral (left) click. >>>> >>>> The source is expected to be in the right superior temporal >>>> cortex. This is the case for ‘GRA only' and ’MAG only’ >>>> datasets. The combined sensors give meaningless result. >>>> >>>> >>>> Elena >>>> >>>> >>>> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl >>>> ] on behalf of Michael Wibral [michael.wibral at web.de] >>>> Sent: Wednesday, June 01, 2011 4:04 PM >>>> To: Email discussion list for the FieldTrip project >>>> Subject: Re: [FieldTrip] combining magnetometers and planad >>>> gradiometers for analysis >>>> >>>> >>>> Dear Elena, >>>> >>>> could you give the following a try: invert (*-1) the leadfileds >>>> for one of the two sensor types. Let me know what happens. >>>> I would also be interested in taking a look at the results - >>>> maybe you could sent images off-list: Michael.Wibral web.de. >>>> >>>> Michael >>>> >>>> >>>> >>>> Von: "Elena Orekhova" >>>> Gesendet: Jun 1, 2011 12:23:29 PM >>>> An: "fieldtrip at donders.ru.nl" >>>> Betreff: [FieldTrip] combining magnetometers and planad >>>> gradiometers for analysis >>>> >>>> @font-face { font-family: "Arial"; }@font-face { font-family: >>>> "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D >>>> "; }@font-face { font-family: "Cambria Math"; }@font-face { font- >>>> family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal >>>> { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: >>>> Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: >>>> 10pt; font-family: Times; }.MsoChpDefault { font-family: >>>> Cambria; }div.WordSection1 { page: WordSection1; } >>>> Dear fieldtrippers, >>>> >>>> This message is mainly for Neuromag users. >>>> >>>> >>>> When I do 'lcmv' beamforming analysis separately on planar >>>> gradiometers or magnetometers, I get quite meaningful results. >>>> >>>> If I combine the two types of sensors without weighting, the >>>> result is meaningless. >>>> >>>> Apparently, the algorithm does not take care of different scales >>>> and units of the GRA and MAG measurements. Does anybody know how >>>> to deal with this problem? >>>> >>>> >>>> >>>> Elena >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> Dr. J.M. (Jan-Mathijs) Schoffelen >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> J.Schoffelen at donders.ru.nl >> Telephone: 0031-24-3614793 >> >> _______________________________________________ >> 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 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri Jun 3 15:23:34 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 3 Jun 2011 15:23:34 +0200 Subject: [FieldTrip] cfg.method = 'sam' In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F03ECAC6B@exchccr1.neuro.gu.se> References: <32CC77C0C8A7AD4B9410934642608E1F03ECAC6B@exchccr1.neuro.gu.se> Message-ID: Hi Elena, At some point we had an implementation for sam in FieldTrip. Apparently, this has been taken out of the release version. I don't know whether this was on purpose, or whether there was a good reason to do so. The reason you get an error is that the function is missing. We will look into the missing function issue. For the time being, you could try lcmv, which is very similar to sam. Best, Jan-Mathijs On Jun 3, 2011, at 2:57 PM, Elena Orekhova wrote: > Dear colleagues, > Sorry, I posted much on the list recent time. I want to figure out > how to run SAM analysis on my data. > > When I run 'lcmv' beamformer on my averaged dataset it works fine: > cfg = []; > cfg.grad = hdr.grad; > cfg.method = 'lcmv'; > cfg.grid = grid; > cfg.vol = vol_cm; > cfg.reducerank=2; > cfg.keepfilter = 'yes' > cfg.channel = MAG; %MAG = {'MEG0721', 'MEG0731',... } > source = ft_sourceanalysis(cfg, tlckavg); > > > When I do the same with cfg.method = 'sam' option, > I get the error: > ***************************** > ??? Undefined function or method 'beamformer_sam' for input > arguments of type 'struct'. > > Error in ==> sourceanalysis at 1158 > dip(i) = beamformer_sam(grid, sens, vol, squeeze(avg(i,:,:)), > squeeze(Cy(i,:,:)), > optarg{:}); > > Error in ==> ft_sourceanalysis at 11 > [varargout{1:nargout}] = funhandle(varargin{:}); > > Does anybody know how to make the ‘SAM’ option to work? > Does anybody used cfg.method = 'sam' option in the Fieldtrip??? > > Regards, > Elena > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at inria.fr Fri Jun 3 15:30:25 2011 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Fri, 3 Jun 2011 09:30:25 -0400 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <9A770E4F-6106-4136-BADB-5BBCBE84862D@donders.ru.nl> References: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> <722801BA-5C22-4A69-8F87-18C1C54A7F00@psi.ucm.es> <77A55ECC-5A84-4839-9093-75FA499D3D31@donders.ru.nl> <32BF5576-A020-41A6-AF11-0879E03067FD@psi.ucm.es> <9A770E4F-6106-4136-BADB-5BBCBE84862D@donders.ru.nl> Message-ID: Hi everyone, > I don't know enough about the elekta-software/mne-software to know what is > happening to the data when the ssp vectors are computed, but once we know > enough details it should be straightforward to build it into fieldtrip. SSP vectors are stored in fif files and applied to data only if requested. In a typical MNE workflow, the SSP vectors are no directly applied to the raw file (avoid data duplication on disk) but rather to the noise covariance matrix and consequently in the whitening matrix. When computing an inverse solution, the whitening matrix is used on the data and the lead field, hence taking into account the SSP vectors. Hope this helps. -- Alexandre Gramfort, PhD gramfort at nmr.mgh.harvard.edu Dept. of Radiology MGH Martinos Center / Harvard Medical School http://www-sop.inria.fr/members/Alexandre.Gramfort/ From smoratti at psi.ucm.es Fri Jun 3 16:06:28 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Fri, 03 Jun 2011 16:06:28 +0200 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: References: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> <722801BA-5C22-4A69-8F87-18C1C54A7F00@psi.ucm.es> <77A55ECC-5A84-4839-9093-75FA499D3D31@donders.ru.nl> <32BF5576-A020-41A6-AF11-0879E03067FD@psi.ucm.es> <9A770E4F-6106-4136-BADB-5BBCBE84862D@donders.ru.nl> Message-ID: Hi everyone, Thanks Alexandre for the info. I went a little bit through the FT code and it seems that it reads the raw data without applying the SSP vectors on the data (raw.proj is empty!!). I saw in mne_ex_read_raw.m that you have to activate the projectors and then get the proj matrix with mne_make_projector_info .m It is a chan by chan matrix. So adding the proj matrix to the raw structure I understand that by using fiff_read_raw_segment .m I get the data filtered by the SSP vectors. So now my stupid? question: If I just multiply the grad.tra matrix by the proj matrix, this would fix everything (plotting topos and leadfield calculation???) best, Stephan El 03/06/2011, a las 15:30, Alexandre Gramfort escribió: > Hi everyone, > >> I don't know enough about the elekta-software/mne-software to know what is >> happening to the data when the ssp vectors are computed, but once we know >> enough details it should be straightforward to build it into fieldtrip. > > SSP vectors are stored in fif files and applied to data only if requested. > > In a typical MNE workflow, the SSP vectors are no directly applied to the raw > file (avoid data duplication on disk) but rather to the noise covariance matrix > and consequently in the whitening matrix. When computing an inverse solution, > the whitening matrix is used on the data and the lead field, hence taking > into account the SSP vectors. > > Hope this helps. > > -- > Alexandre Gramfort, PhD > gramfort at nmr.mgh.harvard.edu > Dept. of Radiology MGH Martinos Center / Harvard Medical School > http://www-sop.inria.fr/members/Alexandre.Gramfort/ > _______________________________________________ > 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 sylvana.schister at utah.edu Fri Jun 3 19:09:21 2011 From: sylvana.schister at utah.edu (Sylvana) Date: Fri, 03 Jun 2011 11:09:21 -0600 Subject: [FieldTrip] Question about layout for Neuromag data Message-ID: <1307120961.4481.1.camel@weston-desktop> Greetings - I have preprocessed and computed TF analysis on a set of neuromag data that I will like to visualize using ft_multiplotTFR. I found out that the function crashes when I try to plot the data. After trying to understand the source of the problem and comparing my analysis to the ones explained in the different tutorials, I found out that the layout produced for these data contains fields 'lay.width' and 'lay.height' that are zero vectors. These vectors are used in ft_multiplotTFR to define the axes of the different plots. Has anyone encountered this problem before? Any clue how to overcome it? I am a just getting familiar with FT and although I have read and followed the tutorials, I wouldn't exclude the possibility that I am doing something wrong. I will appreciate any help you can offer. Have a great day! Sylvana From michael.wibral at web.de Fri Jun 3 23:05:05 2011 From: michael.wibral at web.de (michael.wibral at web.de) Date: Fri, 3 Jun 2011 23:05:05 +0200 (CEST) Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis Message-ID: <533029427.749303.1307135105021.JavaMail.www-data@mwebmailfe05.dlan.cinetic.de> dear neuromag / fieldtrip community, just a small question so I can keep up with the dsicussion: I thought that (t)SSS would nor project in a classical sense, i.e. for activities from inside the head leadfields would not have to be corrected? at least this I have read on the neuromeg list. So in most respcts the data should be treated just like rawdata - with standard coil positions after the motion correction ? maybe someone can shed more light on this? michael -----Ursprüngliche Nachricht----- Von: "Alexandre Gramfort" Gesendet: 03.06.11 15:30:25 An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis >Hi everyone, > > > I don't know enough about the elekta-software/mne-software to know what is > > happening to the data when the ssp vectors are computed, but once we know > > enough details it should be straightforward to build it into fieldtrip. > > SSP vectors are stored in fif files and applied to data only if requested. > > In a typical MNE workflow, the SSP vectors are no directly applied to the raw > file (avoid data duplication on disk) but rather to the noise covariance matrix > and consequently in the whitening matrix. When computing an inverse solution, > the whitening matrix is used on the data and the lead field, hence taking > into account the SSP vectors. > > Hope this helps. > > -- > Alexandre Gramfort, PhD > gramfort at nmr.mgh.harvard.edu > Dept. of Radiology MGH Martinos Center / Harvard Medical School > http://www-sop.inria.fr/members/Alexandre.Gramfort/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: From tony.w.wilson at gmail.com Sat Jun 4 00:09:08 2011 From: tony.w.wilson at gmail.com (Tony W. Wilson) Date: Fri, 3 Jun 2011 17:09:08 -0500 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <533029427.749303.1307135105021.JavaMail.www-data@mwebmailfe05.dlan.cinetic.de> References: <533029427.749303.1307135105021.JavaMail.www-data@mwebmailfe05.dlan.cinetic.de> Message-ID: Dear Michael, everyone, I believe you are correct. Most Neuromag sites have SSP vectors computed for data acquisitions; some groups occasionally recompute these per subject. These acquisition SSP vectors are stored in the fif file, but not applied w/o user intervention. In addition, I believe the tag relating to these vectors is removed from the fif file if you apply (t)SSS (through Maxfilter). However, I am not totally certain because I have never tried to apply these SSP vectors after applying SSS. Regardless, during analysis I treat the motion corrected t(SSS) output files just like raw data files. ... It is also worth noting here that one can compute new sets of SSP vectors in the MNE software (not directly related to the data acquisition vectors) and save these with the fif file for later use. I am not sure if these SSP vectors can be used outside of the MNE software. Tony On Fri, Jun 3, 2011 at 4:05 PM, wrote: > dear neuromag / fieldtrip community, > > just a small question so I can keep up with the dsicussion: > I thought that (t)SSS would nor project in a classical sense, i.e. for > activities from inside the head leadfields would not have to be corrected? > at least this I have read on the neuromeg list. So in most respcts the data > should be treated just like rawdata - with standard coil positions after the > motion correction ? > > maybe someone can shed more light on this? > > michael > > -----Ursprüngliche Nachricht----- > Von: "Alexandre Gramfort" > Gesendet: 03.06.11 15:30:25 > An: "Email discussion list for the FieldTrip project" < > fieldtrip at donders.ru.nl> > Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers > for analysis > > >Hi everyone, > > > > > I don't know enough about the elekta-software/mne-software to know what > is > > > happening to the data when the ssp vectors are computed, but once we > know > > > enough details it should be straightforward to build it into fieldtrip. > > > > SSP vectors are stored in fif files and applied to data only if > requested. > > > > In a typical MNE workflow, the SSP vectors are no directly applied to the > raw > > file (avoid data duplication on disk) but rather to the noise covariance > matrix > > and consequently in the whitening matrix. When computing an inverse > solution, > > the whitening matrix is used on the data and the lead field, hence taking > > into account the SSP vectors. > > > > Hope this helps. > > > > -- > > Alexandre Gramfort, PhD > > gramfort at nmr.mgh.harvard.edu > > Dept. of Radiology MGH Martinos Center / Harvard Medical School > > http://www-sop.inria.fr/members/Alexandre.Gramfort/ > > _______________________________________________ > > 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 smoratti at psi.ucm.es Sat Jun 4 11:54:55 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Sat, 04 Jun 2011 11:54:55 +0200 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: References: <533029427.749303.1307135105021.JavaMail.www-data@mwebmailfe05.dlan.cinetic.de> Message-ID: <60211D3C-5BDA-49AE-8F17-B83594F7DB09@psi.ucm.es> Dear everyone, It would be cool to have the possibility to choose if one wants to apply the SSP vectors or not. Some sites use them, others use SSS or tSSS, depends how noisy your environment is. I think it is good that the data is read in raw format and that the SSP vectors are not applied as default, but it would be great to have the possibility to do so. What do you think? Stephan El 04/06/2011, a las 0:09, Tony W. Wilson escribió: > Dear Michael, everyone, > I believe you are correct. Most Neuromag sites have SSP vectors > computed for data acquisitions; some groups occasionally recompute > these per subject. These acquisition SSP vectors are stored in the > fif file, but not applied w/o user intervention. In addition, I > believe the tag relating to these vectors is removed from the fif > file if you apply (t)SSS (through Maxfilter). However, I am not > totally certain because I have never tried to apply these SSP > vectors after applying SSS. Regardless, during analysis I treat the > motion corrected t(SSS) output files just like raw data files. ... > It is also worth noting here that one can compute new sets of SSP > vectors in the MNE software (not directly related to the data > acquisition vectors) and save these with the fif file for later > use. I am not sure if these SSP vectors can be used outside of the > MNE software. > > Tony > > On Fri, Jun 3, 2011 at 4:05 PM, wrote: > dear neuromag / fieldtrip community, > > just a small question so I can keep up with the dsicussion: > I thought that (t)SSS would nor project in a classical sense, i.e. > for activities from inside the head leadfields would not have to be > corrected? at least this I have read on the neuromeg list. So in > most respcts the data should be treated just like rawdata - with > standard coil positions after the motion correction ? > > maybe someone can shed more light on this? > > michael > > -----Ursprüngliche Nachricht----- > Von: "Alexandre Gramfort" > Gesendet: 03.06.11 15:30:25 > An: "Email discussion list for the FieldTrip project" > > Betreff: Re: [FieldTrip] combining magnetometers and planad > gradiometers for analysis > > >Hi everyone, > > > > > I don't know enough about the elekta-software/mne-software to > know what is > > > happening to the data when the ssp vectors are computed, but > once we know > > > enough details it should be straightforward to build it into > fieldtrip. > > > > SSP vectors are stored in fif files and applied to data only if > requested. > > > > In a typical MNE workflow, the SSP vectors are no directly applied > to the raw > > file (avoid data duplication on disk) but rather to the noise > covariance matrix > > and consequently in the whitening matrix. When computing an > inverse solution, > > the whitening matrix is used on the data and the lead field, hence > taking > > into account the SSP vectors. > > > > Hope this helps. > > > > -- > > Alexandre Gramfort, PhD > > gramfort at nmr.mgh.harvard.edu > > Dept. of Radiology MGH Martinos Center / Harvard Medical School > > http://www-sop.inria.fr/members/Alexandre.Gramfort/ > > _______________________________________________ > > 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 ________________________________________________________ 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 Mon Jun 6 12:37:53 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Mon, 06 Jun 2011 12:37:53 +0200 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: References: <533029427.749303.1307135105021.JavaMail.www-data@mwebmailfe05.dlan.cinetic.de> Message-ID: <6B0B1BCA-8D99-4123-93CA-830E7E4D07B8@psi.ucm.es> Dear all, Looking at the MNE toolbox code, I think the following could be done to get the SSP projection if wanted: %% do SSP projection on data %%%% added by stephan moratti to do SSP for k = 1:length(data.hdr.orig.projs) data.hdr.orig.projs(k).active = true; end fprintf(1,'%d projection items activated\n',length(data.hdr.orig.projs)); [proj,nproj] = mne_make_projector_info(data.hdr.orig); data.hdr.orig.raw.proj = proj; % now apply to data for i = 1:length(data.trial) data.trial{i} = proj*data.trial{i}; end However, I am not sure how to put them into the grad.tra field. Best, Stephan El 04/06/2011, a las 00:09, Tony W. Wilson escribió: > Dear Michael, everyone, > I believe you are correct. Most Neuromag sites have SSP vectors computed for data acquisitions; some groups occasionally recompute these per subject. These acquisition SSP vectors are stored in the fif file, but not applied w/o user intervention. In addition, I believe the tag relating to these vectors is removed from the fif file if you apply (t)SSS (through Maxfilter). However, I am not totally certain because I have never tried to apply these SSP vectors after applying SSS. Regardless, during analysis I treat the motion corrected t(SSS) output files just like raw data files. ... It is also worth noting here that one can compute new sets of SSP vectors in the MNE software (not directly related to the data acquisition vectors) and save these with the fif file for later use. I am not sure if these SSP vectors can be used outside of the MNE software. > > Tony > > On Fri, Jun 3, 2011 at 4:05 PM, wrote: > dear neuromag / fieldtrip community, > > just a small question so I can keep up with the dsicussion: > I thought that (t)SSS would nor project in a classical sense, i.e. for activities from inside the head leadfields would not have to be corrected? at least this I have read on the neuromeg list. So in most respcts the data should be treated just like rawdata - with standard coil positions after the motion correction ? > > maybe someone can shed more light on this? > > michael > > -----Ursprüngliche Nachricht----- > Von: "Alexandre Gramfort" > Gesendet: 03.06.11 15:30:25 > An: "Email discussion list for the FieldTrip project" > Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis > > >Hi everyone, > > > > > I don't know enough about the elekta-software/mne-software to know what is > > > happening to the data when the ssp vectors are computed, but once we know > > > enough details it should be straightforward to build it into fieldtrip. > > > > SSP vectors are stored in fif files and applied to data only if requested. > > > > In a typical MNE workflow, the SSP vectors are no directly applied to the raw > > file (avoid data duplication on disk) but rather to the noise covariance matrix > > and consequently in the whitening matrix. When computing an inverse solution, > > the whitening matrix is used on the data and the lead field, hence taking > > into account the SSP vectors. > > > > Hope this helps. > > > > -- > > Alexandre Gramfort, PhD > > gramfort at nmr.mgh.harvard.edu > > Dept. of Radiology MGH Martinos Center / Harvard Medical School > > http://www-sop.inria.fr/members/Alexandre.Gramfort/ > > _______________________________________________ > > 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 ________________________________________________________ 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 valentin.umbach at hu-berlin.de Mon Jun 6 14:18:51 2011 From: valentin.umbach at hu-berlin.de (Valentin J. Umbach) Date: Mon, 6 Jun 2011 14:18:51 +0200 Subject: [FieldTrip] Emotiv headset realtime capture Message-ID: Hi Zeddy, thanks alot for your reply. FieldTrip comes with a precompiled version of emotiv2ft.exe. However, I can't get this to connect with my hardware. I've been trying to change some code in emotiv2ft.cc, but I couldn't compile it using mingw (as suggested here: http://fieldtrip.fcdonders.nl/development/realtime/emotiv). If you haven't worked with the Emotiv headset, this might be too specific. I wonder who wrote the interface to FieldTrip - someone must have connected the two before... Best, Valentin - Zitierten Text ausblenden - > > Message: 4 > Date: Wed, 1 Jun 2011 11:35:07 -0200 > From: Zeddy He > To: > Subject: Re: [FieldTrip] Emotiv headset realtime capture > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > > Hi Valentin, > > I am not entirely sure exactly what part of the process you're not sure about. I'm new to fieldtrip as well and I have never heard of emotiv until today. I have, however, been playing around with FieldTrip's realtime acquisition part for the last couple of weeks(acq2ft, AcqBuffer), and maybe able to offer some pointers in getting it set up on your system. > It seems that to use emotive2ft, you would have to compile it first, call upon it in matlab before starting your emotive software, and then start the emotiv software. I am not exactly sure what can read the bufferdata, though ft_realtime_signalviewer as well as viewer.exe may be good functions/programs to start off with. > If you're using acq2ft or Acqbuffer already for realtime acquistion from another CTF device, you could try running one of those first either by standalone or their MATLAB equivilent functions, and then run emotiv2ft in matlab without any passed in parameters(unless you didn't decide to put the buffer on localhost:1972). You also might be able to just let the function create it's own buffer by giving it a new port, and then draw from that port seperately later on. > Some troubles I've ran into while using FieldTrip's realtime functions include: > shmget() errors on linux systems > firewall blocking port > number type in-compatibility > and perhaps a couple others I can't recall at the moment. > > If you think I might be capable of assisting you, let me know and I'll see if I can give you additional details. > > Regards > > Zeddy > > >> From: valentin.umbach at hu-berlin.de >> Date: Tue, 31 May 2011 18:51:17 +0200 >> To: fieldtrip at donders.ru.nl >> Subject: [FieldTrip] Emotiv headset realtime capture >> >> Hi, I'm new to FieldTrip and I'm interested in using it to capture >> realtime data from the Emotiv headset using this interface: >> http://fieldtrip.fcdonders.nl/development/realtime/emotiv >> I'm not clear about how to make calls to this interface from within >> Matlab. Also, I would like to know if it's possible to access not just >> the raw EEG, but also the API output of the detection libraries >> (Affectiv Suite...). >> Any help is greatly appreciated! >> >> Best, Valentin >> >> -- >> Dipl.-Psych. Valentin J. Umbach >> Institut f?r Psychologie >> Humboldt-Universit?t zu Berlin >> Rudower Chaussee 18 >> 12489 Berlin >> Tel. +49 30 2093 9438 >> E-Mail: valentin.umbach at hu-berlin.de >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From n.a.kloosterman at uva.nl Mon Jun 6 15:28:41 2011 From: n.a.kloosterman at uva.nl (Kloosterman, Niels) Date: Mon, 6 Jun 2011 13:28:41 +0000 Subject: [FieldTrip] Problem passing arguments to peerslave command line executable Message-ID: Dear Fieldtrippers, Although I have succesfully used the command-line ./peerslave.glnxa64 to launch slaves for parallel analysis of my batch jobs, I am somehow not able to pass arguments to the command, for example ./peerslave.glnxa64 --number 8, to launch 8 slaves at once. Could anybody tell me what’s going on? When I execute without arguments this line pops up: peerslave[9705]: peerinit: niels at gb-r35n18.irc.sara.nl, id = 4020038417 All seems fine: the master is indeed able to send jobs to the slave. No other information is printed to the shell when it gets a job or whatever (is this normal?). Now when I try to run the --help I get this: niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./peerslave.glnxa64 --help peerslave[9753]: peerinit: niels at gb-r35n18.irc.sara.nl, id = 2887682376 parser: cannot open file --help peerslave[9753]: cannot read the configuration file And when I try to do --number 8: niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./peerslave.glnxa64 --number 8 peerslave[9759]: peerinit: niels at gb-r35n18.irc.sara.nl, id = 3997336815 ./peerslave.glnxa64: unrecognized option '--number' peerslave[9759]: invalid command line options I have recompiled the peerslave.glnxa64 by editing the Makefile and using make, but the problem stays. I am using MATLAB 2011a on a 64 bit linux node with 8 cores on a grid computer, which I access using ssh –X. Any ideas would be appreciated! Best, Niels Kloosterman -- Niels A. Kloosterman MSc.| PhD student | University of Amsterdam | Cognitive Neuroscience Group | Dept. of Psychology | Roetersstraat 15, A614 | 1018 WB Amsterdam | Tel: +31 20 525 6847 -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Mon Jun 6 20:32:07 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 6 Jun 2011 20:32:07 +0200 Subject: [FieldTrip] Emotiv headset realtime capture In-Reply-To: References: Message-ID: Dear Valentin The interface was implemented by Stefan Klanke here at the Donders for the BrainGain project, but he is not working with us any more. He has been testing it and it worked for him. I don't have an emotiv headset myself, but think that Ali Bahramisharif (CC), one of our colleagues, is in possession of the headset that Stefan used for testing. I checked the fieldtrip/realtime/acquisition/emotiv/emotiv2ft.cc source code, and from what I see it it requires additional software from emotiv that is not included with the fieldtrip release. See http://emotiv.com/developer/SDK/UserManual.pdf and specifically chapter 5. If that emotiv software developers kit is missing from your computer, you'll be getting errors that the compiler cannot find the edk.h, EmoStateDLL.h and/or edkErrorCode.h header files. It might also be that you need import libraries on your compile path. Please have a look in fieldtrip/realtime/acquisition/emotiv/Makefile for some further instructions. Hope this helps. If not, Ali (CC) might be able to provide some additional information. best, Robert On 6 Jun 2011, at 14:18, Valentin J. Umbach wrote: > Hi Zeddy, > > thanks alot for your reply. > FieldTrip comes with a precompiled version of emotiv2ft.exe. However, > I can't get this to connect with my hardware. I've been trying to > change some code in emotiv2ft.cc, but I couldn't compile it using > mingw (as suggested here: > http://fieldtrip.fcdonders.nl/development/realtime/emotiv). > If you haven't worked with the Emotiv headset, this might be too > specific. I wonder who wrote the interface to FieldTrip - someone must > have connected the two before... > > Best, Valentin > - Zitierten Text ausblenden - > >> >> Message: 4 >> Date: Wed, 1 Jun 2011 11:35:07 -0200 >> From: Zeddy He >> To: >> Subject: Re: [FieldTrip] Emotiv headset realtime capture >> Message-ID: >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Hi Valentin, >> >> I am not entirely sure exactly what part of the process you're not sure about. I'm new to fieldtrip as well and I have never heard of emotiv until today. I have, however, been playing around with FieldTrip's realtime acquisition part for the last couple of weeks(acq2ft, AcqBuffer), and maybe able to offer some pointers in getting it set up on your system. >> It seems that to use emotive2ft, you would have to compile it first, call upon it in matlab before starting your emotive software, and then start the emotiv software. I am not exactly sure what can read the bufferdata, though ft_realtime_signalviewer as well as viewer.exe may be good functions/programs to start off with. >> If you're using acq2ft or Acqbuffer already for realtime acquistion from another CTF device, you could try running one of those first either by standalone or their MATLAB equivilent functions, and then run emotiv2ft in matlab without any passed in parameters(unless you didn't decide to put the buffer on localhost:1972). You also might be able to just let the function create it's own buffer by giving it a new port, and then draw from that port seperately later on. >> Some troubles I've ran into while using FieldTrip's realtime functions include: >> shmget() errors on linux systems >> firewall blocking port >> number type in-compatibility >> and perhaps a couple others I can't recall at the moment. >> >> If you think I might be capable of assisting you, let me know and I'll see if I can give you additional details. >> >> Regards >> >> Zeddy >> >> >>> From: valentin.umbach at hu-berlin.de >>> Date: Tue, 31 May 2011 18:51:17 +0200 >>> To: fieldtrip at donders.ru.nl >>> Subject: [FieldTrip] Emotiv headset realtime capture >>> >>> Hi, I'm new to FieldTrip and I'm interested in using it to capture >>> realtime data from the Emotiv headset using this interface: >>> http://fieldtrip.fcdonders.nl/development/realtime/emotiv >>> I'm not clear about how to make calls to this interface from within >>> Matlab. Also, I would like to know if it's possible to access not just >>> the raw EEG, but also the API output of the detection libraries >>> (Affectiv Suite...). >>> Any help is greatly appreciated! >>> >>> Best, Valentin >>> >>> -- >>> Dipl.-Psych. Valentin J. Umbach >>> Institut f?r Psychologie >>> Humboldt-Universit?t zu Berlin >>> Rudower Chaussee 18 >>> 12489 Berlin >>> Tel. +49 30 2093 9438 >>> E-Mail: valentin.umbach at hu-berlin.de >>> >>> _______________________________________________ >>> 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 r.oostenveld at donders.ru.nl Mon Jun 6 20:39:18 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 6 Jun 2011 20:39:18 +0200 Subject: [FieldTrip] cfg.method = 'sam' In-Reply-To: References: <32CC77C0C8A7AD4B9410934642608E1F03ECAC6B@exchccr1.neuro.gu.se> Message-ID: Dear Elena The SAM implementation was contributed some time ago by Gareth Barnes, but apaprently went missing in the release version. I found the missing files in an older versionand just added them to the latest release version(*). Note that I did not test them for some time and also did not test them right now. It might be that you'll get follow up problems. If so, better report them on bugzilla.fcdonders.nl and not on the email list. best regards, Robert PS (*) please download the FT version of this evening, which will include the beamformer_sam function which you need for cfg.method='sam' in ft_sourceanalysis. On 3 Jun 2011, at 15:23, jan-mathijs schoffelen wrote: > Hi Elena, > > At some point we had an implementation for sam in FieldTrip. Apparently, this has been taken out of the release version. I don't know whether this was on purpose, or whether there was a good reason to do so. > The reason you get an error is that the function is missing. We will look into the missing function issue. > For the time being, you could try lcmv, which is very similar to sam. > > Best, > > Jan-Mathijs > > > On Jun 3, 2011, at 2:57 PM, Elena Orekhova wrote: > >> Dear colleagues, >> Sorry, I posted much on the list recent time. I want to figure out how to run SAM analysis on my data. >> >> When I run 'lcmv' beamformer on my averaged dataset it works fine: >> cfg = []; >> cfg.grad = hdr.grad; >> cfg.method = 'lcmv'; >> cfg.grid = grid; >> cfg.vol = vol_cm; >> cfg.reducerank=2; >> cfg.keepfilter = 'yes' >> cfg.channel = MAG; %MAG = {'MEG0721', 'MEG0731',... } >> source = ft_sourceanalysis(cfg, tlckavg); >> >> >> When I do the same with cfg.method = 'sam' option, >> I get the error: >> ***************************** >> ??? Undefined function or method 'beamformer_sam' for input arguments of type 'struct'. >> >> Error in ==> sourceanalysis at 1158 >> dip(i) = beamformer_sam(grid, sens, vol, squeeze(avg(i,:,:)), squeeze(Cy(i,:,:)), >> optarg{:}); >> >> Error in ==> ft_sourceanalysis at 11 >> [varargout{1:nargout}] = funhandle(varargin{:}); >> >> Does anybody know how to make the ‘SAM’ option to work? >> Does anybody used cfg.method = 'sam' option in the Fieldtrip??? >> >> Regards, >> Elena >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > _______________________________________________ > 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 r.oostenveld at donders.ru.nl Mon Jun 6 21:18:53 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 6 Jun 2011 21:18:53 +0200 Subject: [FieldTrip] questions about realtime buffer In-Reply-To: References: Message-ID: Dear Amelie > I’m implementing a realtime buffer in C++ pretty much like in “demo_combined” : my application creates a buffer server and an acquisition client. > I encountered a first problem when trying to close the buffer server cleanly, but with some small changes in tcpsocket.c and tcpserver.c, I think I solved the problem. > If these modifications can be useful for other users and do not create other problems, I will share them. If you have changes that don't break the ANSI-C compilation then I am certainly happy to include them in our version. Please go to http://bugzilla.fcdonders.nl and submit a bug/request in which you attach the updated files. > I encounter now a new problem : what if there are several acquisition clients ? > I tried to create several couples “buffer-server + acquisition client” in different threads in my application, but it does not work at all, because of global variables (I suppose). > It seems that one buffer server can not manage several acquisition clients, but I’m not sure of this point. > Did anyone encounter this problem (or solve it) ? > Or do anyone have an idea ? You are right about the global variables. The buffer is implemented using multithreading and to ensure that incoming data (Write) does not interfere with outgoing (read) data a mutex (http://en.wikipedia.org/wiki/Mutual_exclusion) is set. That mutex is shared throughout the code so that all pieces of code are aware of when they are allowed to change the buffer content. Having multiple buffers would require multiple mutexes and multiple (separately identifyable) memory segments for the actual data. That would require a lot of changes to the code. You can run multiple buffers on the same computer, but you would have to start them separately and they would have to have different TCP ports. The application you are writing could write different aspects to the different TCP ports. You can use fieldtrip/realtime/general/buffer.exe, which in fact is a compiled version of fieldtrip/realtime/buffer/test/demo_buffer. Note that you would use it as buffer.exe localhost 2340 buffer.exe localhost 2341 buffer.exe localhost 2342 buffer.exe localhost 2343 to start 4 buffers on ports 2340-2343. The "localhost" argument is not used, but still appears to be required according to the demo_buffer.c source code. Of course it is cumbersome to have to start the 4 seperate processes on top of your own application. On unix-like computers you should be able to write a single application that at the beginning forks into a parent and child, where the parent continues as your application and where the child (which is then a separate process) can start the buffer. You can fork multiple times, to have multiple buffers (one per child). best Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: From batrod at gmail.com Tue Jun 7 00:51:20 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Mon, 6 Jun 2011 17:51:20 -0500 Subject: [FieldTrip] Weird trialfun_general error Message-ID: Dear fieldtrippers, i just noticed and found the origin of a weird error obtained with the trialfun_general function, i thought it could be useful to send it here. I use the ft_definetrial function on a file obtained using the merge function in EEGlab. Apparently, this function is adding some triggers with the value 'boundary' in the new file, indicating the old frontier between the dataset that have been merged. The funny part is that the trialfun_general() function in fieltrip is using the intersect() matlab function to match event values. Moreover, im using 27 different event values to indicate point of interest (112,114,116,122,etc...) All of my event values dont create any problems except the value 114 because intersect('boundary',114) = 114 whereas it gives an empty result with any other of my values... Therefore, for that particular event value, there was a dimension mismatch between trl and val in trialfun_general. I just removed events with 'boundary' values and it worked. Best regards, Rodolphe Nenert, Ph.D. -------------- next part -------------- An HTML attachment was scrubbed... URL: From johemart at gmail.com Tue Jun 7 01:36:51 2011 From: johemart at gmail.com (=?ISO-8859-1?Q?Johann_Heinz_Mart=EDnez_Huartos?=) Date: Tue, 7 Jun 2011 01:36:51 +0200 Subject: [FieldTrip] Reference to non-existent field 'statistic' !????? Message-ID: Hello dear fieldtrip guys. Im new using this toolbox and i dont understand why is happened this error that i think it must be easy to solve but I have tryed and nothing happend. The thing is that im following (step by step) the tutorial for multivariableanalysis from fieldtrip wiki using the data that web link offer us. But when I run the command: stat = ft_timelockstatistics(cfg,tleft,tright); there are appear those errors: ??? Reference to non-existent field 'statistic'. Error in ==> prepare_design at 67 if any(strcmp(cfg.statistic,{'indepsamplesT','indepsamplesregrT','indepsamplesZcoh','indepsamplesF'})) Error in ==> statistics_wrapper at 249 [cfg] = prepare_design(cfg); Error in ==> ft_timelockstatistics at 123 [stat, cfg] = statistics_wrapper(cfg, varargin{:}); Error in ==> JohannTestFieldtrip at 45 stat = ft_timelockstatistics(cfg,tleft,tright); and i Dunno what can i do... Im using Matlab (R2011a) and the (fieldtrip-20110603). I have been looking for the documentation and i coundt find out how to fix it. Is it probably the matlab version very new? Which would be the last matlab version available using for? Thanks -- Atentamente: Johann Martínez. -------------- next part -------------- An HTML attachment was scrubbed... URL: From n.a.kloosterman at uva.nl Tue Jun 7 10:33:39 2011 From: n.a.kloosterman at uva.nl (Kloosterman, Niels) Date: Tue, 7 Jun 2011 08:33:39 +0000 Subject: [FieldTrip] Problem passing arguments to peerslave command line executable Message-ID: Dear Fieldtrippers, Although I have succesfully used the command-line ./peerslave.glnxa64 to launch slaves for parallel analysis of my batch jobs, I am somehow not able to pass arguments to the command, for example ./peerslave.glnxa64 --number 8, to launch 8 slaves at once. Could anybody tell me what’s going on? When I execute without arguments this line pops up: niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./peerslave.glnxa64 peerslave[9705]: peerinit: niels at gb-r35n18.irc.sara.nl, id = 4020038417 All seems fine: the master is indeed able to send jobs to the slave. No other information is printed to the shell when it gets a job or whatever (is this normal?). Now when I try to run the --help I get this: niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./peerslave.glnxa64 --help peerslave[9753]: peerinit: niels at gb-r35n18.irc.sara.nl, id = 2887682376 parser: cannot open file --help peerslave[9753]: cannot read the configuration file And when I try to do --number 8: niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./peerslave.glnxa64 --number 8 peerslave[9759]: peerinit: niels at gb-r35n18.irc.sara.nl, id = 3997336815 ./peerslave.glnxa64: unrecognized option '--number' peerslave[9759]: invalid command line options I have recompiled the peerslave.glnxa64 by editing the Makefile and using make, but the problem persists. I am using MATLAB 2011a on a 64 bit linux node with 8 cores, which I access interactively using ssh –X. Any ideas would be appreciated! Best, Niels Kloosterman -- Niels A. Kloosterman MSc.| PhD student | University of Amsterdam | Cognitive Neuroscience Group | Dept. of Psychology | Roetersstraat 15, A614 | 1018 WB Amsterdam | Tel: +31 20 525 6847 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Tue Jun 7 12:53:24 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Tue, 7 Jun 2011 10:53:24 +0000 Subject: [FieldTrip] courses Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECAF47@exchccr1.neuro.gu.se> Dear FieldTrip gurus, Are you planning any FieldTrip courses for the users in the nearest future? Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From valentin.umbach at hu-berlin.de Tue Jun 7 13:47:18 2011 From: valentin.umbach at hu-berlin.de (Valentin J. Umbach) Date: Tue, 7 Jun 2011 13:47:18 +0200 Subject: [FieldTrip] fieldtrip Digest, Vol 7, Issue 13 In-Reply-To: References: Message-ID: Dear Robert, thank you for your helpful information. The Problem seems to be that I only have the "Developer" version of the headset (and the accompanying SDK), whereas the one used in the interface is the "Researcher" version (or above). The DLL (and header files) supplied in my SDK lacks some of the functions used in emotiv2ft. So I either have to upgrade my SDK or rewrite the interface to only use my functionality (at this point I'm not interested in the "raw" EEG, but rather the output of Emotiv's own "EmoEngine" - this should work with my version). Best, Valentin > Message: 1 > Date: Mon, 6 Jun 2011 20:32:07 +0200 > From: Robert Oostenveld > To: Email discussion list for the FieldTrip project >         > Cc: Ali Bahramisharif > Subject: Re: [FieldTrip] Emotiv headset realtime capture > Message-ID: > Content-Type: text/plain; charset=us-ascii > > Dear Valentin > > The interface was implemented by Stefan Klanke here at the Donders for the BrainGain project, but he is not  working with us any more. He has been testing it and it worked for him. I don't have an emotiv headset myself, but think that Ali Bahramisharif (CC), one of our colleagues, is in possession of the headset that Stefan used for testing. > > I checked the fieldtrip/realtime/acquisition/emotiv/emotiv2ft.cc source code, and from what I see it it requires additional software from emotiv that is not included with the fieldtrip release. See http://emotiv.com/developer/SDK/UserManual.pdf and specifically chapter 5. If that emotiv software developers kit is missing from your computer, you'll be getting errors that the compiler cannot find the edk.h, EmoStateDLL.h and/or edkErrorCode.h header files. It might also be that you need import libraries on your compile path. Please have a look in fieldtrip/realtime/acquisition/emotiv/Makefile for some further instructions. > > Hope this helps. If not, Ali (CC) might be able to provide some additional information. > > best, > Robert From bornalikundu at gmail.com Tue Jun 7 22:01:46 2011 From: bornalikundu at gmail.com (Bornali Kundu) Date: Tue, 7 Jun 2011 15:01:46 -0500 Subject: [FieldTrip] Test interactions for multi-level factors Message-ID: Greetings, We are interested in testing the main effects and interactions between 2 factors that have more than 2 levels (a 2x4 within subjects design) using the cluster-based permutation test for either time domain or time-frequency domain data. Has anyone done this using Fieldtrip scripts? There is only one such contrast for a 2x2 design thus the interaction effects can be tested using a t test on design cell differences. However, for a factor with more levels, is there a way to perhaps specify contrasts to test the full effect of the interaction? Would setting cfg.contrastcoefs to something work? Otherwise, is there a way to specify this in cfg.design? Thanks so much for your time, Bornali Kundu -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at donders.ru.nl Wed Jun 8 14:54:48 2011 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Wed, 8 Jun 2011 14:54:48 +0200 Subject: [FieldTrip] Reference to non-existent field 'statistic' !????? In-Reply-To: References: Message-ID: Dear Johann, The function prepare_design should not be called by statistics_wrapper in this specific case, since the cfg.design is specified in this tutorial example. cfg.design = [ones(size(tleft.trial,1),1); 2*ones(size(tright.trial,1),1)]; Be sure to specifically add the multivariate directory and subdirectories to your path for this example, otherwise it will crash complaining of not finding other functions (for example ft_mv_standardizer.m) Best, Johanna On 7 June 2011 01:36, Johann Heinz Martínez Huartos wrote: > Hello dear fieldtrip guys. > > Im new using this toolbox and i dont understand why is happened this error > that i think it must be easy to solve but I have tryed and nothing happend. > The thing is that im following (step by step) the tutorial for > multivariableanalysis from fieldtrip wiki using the data that web link offer > us. But when I run the command: > > stat = ft_timelockstatistics(cfg,tleft,tright); > > there are appear those errors: > > ??? Reference to non-existent field 'statistic'. > > Error in ==> prepare_design at 67 > if > any(strcmp(cfg.statistic,{'indepsamplesT','indepsamplesregrT','indepsamplesZcoh','indepsamplesF'})) > > Error in ==> statistics_wrapper at 249 > [cfg] = prepare_design(cfg); > > Error in ==> ft_timelockstatistics at 123 > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > Error in ==> JohannTestFieldtrip at 45 > stat = ft_timelockstatistics(cfg,tleft,tright); > > and i Dunno what can i do... > > Im using Matlab (R2011a) and the (fieldtrip-20110603). I have been looking > for the documentation and i coundt find out how to fix it. > > Is it probably the matlab version very new? > Which would be the last matlab version available using for? > > Thanks > > > -- > Atentamente: > Johann Martínez. > > _______________________________________________ > 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 johemart at gmail.com Wed Jun 8 22:14:18 2011 From: johemart at gmail.com (=?ISO-8859-1?Q?Johann_Heinz_Mart=EDnez_Huartos?=) Date: Wed, 8 Jun 2011 22:14:18 +0200 Subject: [FieldTrip] Reference to non-existent field 'statistic' !????? In-Reply-To: References: Message-ID: Hello dear. Thnks a lot for your comments. I was very useful, eventually i was added all the fieldtrip directory including its subdirectories in order to avoid future problems and at the end it was succesfully instaled in my Matlab R2011b version. Best. Johann. On 8 June 2011 14:54, Johanna Zumer wrote: > Dear Johann, > > The function prepare_design should not be called by statistics_wrapper in > this specific case, since the cfg.design is specified in this tutorial > example. > > cfg.design = [ones(size(tleft.trial,1),1); 2*ones(size(tright.trial,1),1)]; > > > Be sure to specifically add the multivariate directory and subdirectories > to your path for this example, otherwise it will crash complaining of not > finding other functions (for example ft_mv_standardizer.m) > > Best, > Johanna > > > On 7 June 2011 01:36, Johann Heinz Martínez Huartos wrote: > >> Hello dear fieldtrip guys. >> >> Im new using this toolbox and i dont understand why is happened this error >> that i think it must be easy to solve but I have tryed and nothing happend. >> The thing is that im following (step by step) the tutorial for >> multivariableanalysis from fieldtrip wiki using the data that web link offer >> us. But when I run the command: >> >> stat = ft_timelockstatistics(cfg,tleft,tright); >> >> there are appear those errors: >> >> ??? Reference to non-existent field 'statistic'. >> >> Error in ==> prepare_design at 67 >> if >> any(strcmp(cfg.statistic,{'indepsamplesT','indepsamplesregrT','indepsamplesZcoh','indepsamplesF'})) >> >> Error in ==> statistics_wrapper at 249 >> [cfg] = prepare_design(cfg); >> >> Error in ==> ft_timelockstatistics at 123 >> [stat, cfg] = statistics_wrapper(cfg, varargin{:}); >> >> Error in ==> JohannTestFieldtrip at 45 >> stat = ft_timelockstatistics(cfg,tleft,tright); >> >> and i Dunno what can i do... >> >> Im using Matlab (R2011a) and the (fieldtrip-20110603). I have been looking >> for the documentation and i coundt find out how to fix it. >> >> Is it probably the matlab version very new? >> Which would be the last matlab version available using for? >> >> Thanks >> >> >> -- >> Atentamente: >> Johann Martínez. >> >> _______________________________________________ >> 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 > -- Atentamente: Johann Martínez. M.Sc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From amelie.serpollet at cea.fr Thu Jun 9 10:52:42 2011 From: amelie.serpollet at cea.fr (=?iso-8859-1?Q?SERPOLLET_Am=E9lie_228173?=) Date: Thu, 9 Jun 2011 10:52:42 +0200 Subject: [FieldTrip] questions about realtime buffer In-Reply-To: References: Message-ID: Dear Robert, Thank you for your answer. I was trying to run several buffers in the same process, but running them in different processes as you describe it seems to be very easier. The modifications I did to close the buffer cleanly make possible to run a new buffer after closing one, in the same process. Maybe it is not necessary if buffers are created in different processes, but they are few modifications and I find it is still convenient, so I submit it. Best regards Amélie ________________________________ De : Robert Oostenveld [mailto:r.oostenveld at donders.ru.nl] Envoyé : lundi 6 juin 2011 21:19 À : Email discussion list for the FieldTrip project Cc : SERPOLLET Amélie 228173 Objet : Re: [FieldTrip] questions about realtime buffer Dear Amelie I'm implementing a realtime buffer in C++ pretty much like in "demo_combined" : my application creates a buffer server and an acquisition client. I encountered a first problem when trying to close the buffer server cleanly, but with some small changes in tcpsocket.c and tcpserver.c, I think I solved the problem. If these modifications can be useful for other users and do not create other problems, I will share them. If you have changes that don't break the ANSI-C compilation then I am certainly happy to include them in our version. Please go to http://bugzilla.fcdonders.nl and submit a bug/request in which you attach the updated files. I encounter now a new problem : what if there are several acquisition clients ? I tried to create several couples "buffer-server + acquisition client" in different threads in my application, but it does not work at all, because of global variables (I suppose). It seems that one buffer server can not manage several acquisition clients, but I'm not sure of this point. Did anyone encounter this problem (or solve it) ? Or do anyone have an idea ? You are right about the global variables. The buffer is implemented using multithreading and to ensure that incoming data (Write) does not interfere with outgoing (read) data a mutex (http://en.wikipedia.org/wiki/Mutual_exclusion) is set. That mutex is shared throughout the code so that all pieces of code are aware of when they are allowed to change the buffer content. Having multiple buffers would require multiple mutexes and multiple (separately identifyable) memory segments for the actual data. That would require a lot of changes to the code. You can run multiple buffers on the same computer, but you would have to start them separately and they would have to have different TCP ports. The application you are writing could write different aspects to the different TCP ports. You can use fieldtrip/realtime/general/buffer.exe, which in fact is a compiled version of fieldtrip/realtime/buffer/test/demo_buffer. Note that you would use it as buffer.exe localhost 2340 buffer.exe localhost 2341 buffer.exe localhost 2342 buffer.exe localhost 2343 to start 4 buffers on ports 2340-2343. The "localhost" argument is not used, but still appears to be required according to the demo_buffer.c source code. Of course it is cumbersome to have to start the 4 seperate processes on top of your own application. On unix-like computers you should be able to write a single application that at the beginning forks into a parent and child, where the parent continues as your application and where the child (which is then a separate process) can start the buffer. You can fork multiple times, to have multiple buffers (one per child). best Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Jun 9 15:19:14 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 9 Jun 2011 15:19:14 +0200 Subject: [FieldTrip] courses In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F03ECAF47@exchccr1.neuro.gu.se> References: <32CC77C0C8A7AD4B9410934642608E1F03ECAF47@exchccr1.neuro.gu.se> Message-ID: <5B0A148A-D4F0-454F-B60B-E47ECCA47E75@donders.ru.nl> Dear Elena For 2011 there are no courses planned any more in Nijmege, which are open to external participants (there will be a course for local studens in the Donders Graduate School in the autumn). The next course in Nijmegen will be the MEG Toolkit course, which most likely will be somewhere in the spring of 2012. For 2011 we are currently considering a course in Paris at the end of this year. I believe that Stefan and Saskia are considering to do another course in New York later this year, although I don't know any details for the New York plans. At the upcoming HBM meeting in Quebec there will be an educational course in which FieldTrip and the other open source academic toolboxes will play a (relatively small) role. Although I don't think it is efficient to travel to Quebec just for this part, it might be interesting for you to attend if you are attending the HBM conference anyway. See http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3437 and for the program one of the last pages of http://www.humanbrainmapping.org/files/2011MeetingFiles/Descriptions/HBM%202011%20Educational%20Program.pdf Please note that we are open to invitations for presenting the FieldTrip course at external sites. This year we have already been in Tuebingen, St Louis, and New York, and if there is an interesting venue, an enthousiastic local organizer and funding can be arranged to cover the expenses, most likely some experienced users/developers from Nijmegen can be found or appointed to present a 2,5 day course at the external site. best regards, Robert On 7 Jun 2011, at 12:53, Elena Orekhova wrote: > Dear FieldTrip gurus, > > Are you planning any FieldTrip courses for the users in the nearest > future? > > Elena > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From r.oostenveld at donders.ru.nl Thu Jun 9 17:02:38 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 9 Jun 2011 17:02:38 +0200 Subject: [FieldTrip] Problem passing arguments to peerslave command line executable In-Reply-To: References: Message-ID: <33AD75FB-959A-4F3B-AD5B-1ABBD9F2C1DE@donders.ru.nl> Hi Niels On 7 Jun 2011, at 10:33, Kloosterman, Niels wrote: > Although I have succesfully used the command-line ./ > peerslave.glnxa64 to launch slaves for parallel analysis of my batch > jobs, I am somehow not able to pass arguments to the command, for > example ./peerslave.glnxa64 --number 8, to launch 8 slaves at once. > Could anybody tell me what’s going on? I'll give it a try. > When I execute without arguments this line pops up: > > niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./ > peerslave.glnxa64 > peerslave[9705]: peerinit: niels at gb-r35n18.irc.sara.nl, id = > 4020038417 > > All seems fine: the master is indeed able to send jobs to the slave. > No other information is printed to the shell when it gets a job or > whatever (is this normal?). Yes, that is normal. Since we are running the peerslaves at the Donders on our ~50 node cluster on the background, the default (compiled) behaviour is to use the syslog facility. If I were to start them from a cronjob, I would either get very lengthy mails (which cron sends if the process finishes), or not get any information (when I redirect the output to /dev/null). To keep track of all processes on all nodes, we use a syslog server. The peerslave messages are all sent to a single syslog server where I can track them all in /var/log/ peerslave.log Note however that if you recompile, you can change this. Have a look at this section in peer.h #if SYSLOG == 0 #define PANIC(format, ...) {exit(-1);} #define DEBUG(level, format, ...) { } #elif SYSLOG == 1 #define PANIC(format, ...) {syslog(LOG_ERR, format, ## __VA_ARGS__); exit(-1);} #define DEBUG(level, format, ...) {syslog(level, format, ## __VA_ARGS__);} #elif SYSLOG == 2 #define PANIC(format, ...) {fprintf(stderr, format"\n", ## __VA_ARGS__); exit(-1);} #define DEBUG(level, format, ...) {fprintf(stderr, format"\n", ## __VA_ARGS__);} #elif SYSLOG == 3 #define PANIC(format, ...) {mexPrintf(format"\n", ## __VA_ARGS__); exit(-1);} #define DEBUG(level, format, ...) {if (level<=syslog_level) mexPrintf(format"\n", ## __VA_ARGS__);} #endif At compile time you can specify whether the output goes to syslog (1), stderr (2) or whether mexPrintf shoudl be used (for the mex file, 3). Probably you'll want to add -DSYSLOG=2 to the compile flags. Furthermore note that the syslog level is used to control how much info is given. That is controlled with the --verbose=number option on the peerslave command line. > Now when I try to run the --help I get this: > > niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./ > peerslave.glnxa64 --help > peerslave[9753]: peerinit: niels at gb-r35n18.irc.sara.nl, id = > 2887682376 > parser: cannot open file --help > peerslave[9753]: cannot read the configuration file Hmm, this is not good. It appears that it misinterprets the cmd line option. > And when I try to do --number 8: > > niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./ > peerslave.glnxa64 --number 8 > peerslave[9759]: peerinit: niels at gb-r35n18.irc.sara.nl, id = > 3997336815 > ./peerslave.glnxa64: unrecognized option '--number' > peerslave[9759]: invalid command line options Again here the cmd line option is misinterpreted. This one I can reproduce roboos at mentat258> ../bin/peerslave.glnxa64 --number 8 peerslave[14690]: peerinit: roboos at mentat258.dccn.nl, id = 2375758516 ../bin/peerslave.glnxa64: unrecognized option `--number' peerslave[14690]: invalid command line options I'll file a bug for it. For the meantime, I suggest you look into the configuration files. That is also how we are using them at the Donders, you can find an example below. best Robert ------------------------ cut here ------------------------ # has 12GB of RAM, one CPU and 4 cores # Intel(R) Xeon(R) CPU W3530 @ 2.80GHz [peer] matlab=/opt/cluster/matlab2010b -nodisplay -singleCompThread timavail=86399 smartcpu=1 smartmem=1 udsserver=1 [peer] matlab=/opt/cluster/matlab2010b -nodisplay -singleCompThread timavail=3599 smartcpu=1 smartmem=1 udsserver=1 [peer] matlab=/opt/cluster/matlab2010b -nodisplay -singleCompThread timavail=3599 smartcpu=1 smartmem=1 udsserver=1 [peer] matlab=/opt/cluster/matlab2010b -nodisplay -singleCompThread timavail=599 smartcpu=1 smartmem=1 udsserver=1 ------------------------ cut here ------------------------ From michael.wibral at web.de Thu Jun 9 17:05:49 2011 From: michael.wibral at web.de (Michael Wibral) Date: Thu, 9 Jun 2011 17:05:49 +0200 (CEST) Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis Message-ID: <327769233.351093.1307631949517.JavaMail.fmail@mwmweb082> An HTML attachment was scrubbed... URL: From michael.wibral at web.de Thu Jun 9 17:06:47 2011 From: michael.wibral at web.de (Michael Wibral) Date: Thu, 9 Jun 2011 17:06:47 +0200 (CEST) Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis Message-ID: <619181926.351452.1307632007849.JavaMail.fmail@mwmweb082> An HTML attachment was scrubbed... URL: From johan.bergmann at yahoo.com Thu Jun 9 20:35:54 2011 From: johan.bergmann at yahoo.com (Johan Bergmann) Date: Thu, 9 Jun 2011 11:35:54 -0700 (PDT) Subject: [FieldTrip] Converting time stamps into NCS. Message-ID: <213089.20008.qm@web45503.mail.sp1.yahoo.com> Hello, I have a .mat file containing a single column of voltage values which i wish to convert to the ncs file format. I cannot seem to achieve this, please can someone show me a usage example. Cheers, Johan. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Thu Jun 9 22:48:34 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Thu, 9 Jun 2011 20:48:34 +0000 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <619181926.351452.1307632007849.JavaMail.fmail@mwmweb082> References: <619181926.351452.1307632007849.JavaMail.fmail@mwmweb082> Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECB515@exchccr1.neuro.gu.se> Dear Michael, I still have not resolved this problem and do not know whether is specific for my data(or program bag) or the other Neuromag users also had it. Do you use Neuromag? Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Thursday, June 09, 2011 5:06 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Hi Elena, disregard my last email, I overlooked the att. Michael ________________________________ Von: "Elena Orekhova" Gesendet: Jun 2, 2011 8:03:16 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Verdana"; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear Michael, I did normalize the data (sourcepst.avg.nai=sourcepst.avg.pow./sourcepre.avg.pow) as it was suggested in the tutorial. I used the same scales in all plots for comparison purposes. If automatic scaling is used the result for MAG+GRA does not look any better (see attachment). >What you could do as a workaround is to average the separate results with a weighting per voxel and that >is corresponding to the squared norms of the leadfields for the respective modalities for a given voxel , this >would guarantee equal amounts of backprojected noise from both modalities (if I'm not mistaken). Thank you for your suggestion. I may use it as a last resort. Hopefully, there is still a way to get more optimal solution using both GRA and MAG in the same analysis... Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Elena Orekhova [Elena.Orekhova at neuro.gu.se] Sent: Thursday, June 02, 2011 6:22 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis BODY {direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;} Dear Michael, I have tried to multiply the leadfield by -1 as you suggested: for i = 1 : size (grid.leadfield, 2) grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); end This had no effect on the 'lcmv' output. I attached the pictures for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ In this experiment I measured evoked field in response to the unilateral (left) click. The source is expected to be in the right superior temporal cortex. This is the case for ‘GRA only' and ’MAG only’ datasets. The combined sensors give meaningless result. Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Wednesday, June 01, 2011 4:04 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Elena, could you give the following a try: invert (*-1) the leadfileds for one of the two sensor types. Let me know what happens. I would also be interested in taking a look at the results - maybe you could sent images off-list: Michael.Wibral web.de. Michael ________________________________ Von: "Elena Orekhova" Gesendet: Jun 1, 2011 12:23:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "Arial"; }@font-face { font-family: "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: Times; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear fieldtrippers, This message is mainly for Neuromag users. When I do 'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. If I combine the two types of sensors without weighting, the result is meaningless. Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements. Does anybody know how to deal with this problem? Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri Jun 10 09:45:30 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 10 Jun 2011 09:45:30 +0200 Subject: [FieldTrip] Converting time stamps into NCS. In-Reply-To: <213089.20008.qm@web45503.mail.sp1.yahoo.com> References: <213089.20008.qm@web45503.mail.sp1.yahoo.com> Message-ID: <550011EB-7B66-40F1-87BB-77974ED41D1B@donders.ru.nl> Dear Johan You can use ft_write_data(FILENAME, DAT, 'header', HDR, 'dataformat', 'neuralynx_ncs') where you have to provide the filename, the data (as 1*Nsamples matrix) and the header (i.e. everything in upper case in the example). For the header you have to provide a matlab structure such as the one that is returned by ft_read_header returns when you read an original neuralynx ncs file. I suggest that you look into the ft_write_data function at line 529 for further details. best Robert On 9 Jun 2011, at 20:35, Johan Bergmann wrote: > Hello, > > I have a .mat file containing a single column of voltage values > which i wish to convert to the ncs file format. I cannot seem to > achieve this, please can someone show me a usage example. > > Cheers, > > Johan. > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From johan.bergmann at yahoo.com Fri Jun 10 12:39:37 2011 From: johan.bergmann at yahoo.com (Johan Bergmann) Date: Fri, 10 Jun 2011 03:39:37 -0700 (PDT) Subject: [FieldTrip] Converting time stamps into NCS. In-Reply-To: <550011EB-7B66-40F1-87BB-77974ED41D1B@donders.ru.nl> References: <213089.20008.qm@web45503.mail.sp1.yahoo.com> <550011EB-7B66-40F1-87BB-77974ED41D1B@donders.ru.nl> Message-ID: <629642.35556.qm@web45515.mail.sp1.yahoo.com> Dear Robert, Thanks for your response. I have taken a look at the code in ft_write_data. My original file was not from a .ncs file format it was from a .mcd file format, scaled in micro volts and a continuous recording. So, i have a "900x1 double" voltage values as a variable called "data" in Matlab. I call: ft_write_data(new_file.ncs, data, '?', ? , 'matlab', '?') ft_write_data(FILENAME, DAT, 'header', HDR, 'dataformat', 'neuralynx_ncs') sorry for the simplistic question. Thanks, Johan. ________________________________ From: Robert Oostenveld To: Email discussion list for the FieldTrip project Sent: Fri, June 10, 2011 8:45:30 AM Subject: Re: [FieldTrip] Converting time stamps into NCS. Dear Johan You can use ft_write_data(FILENAME, DAT, 'header', HDR, 'dataformat', 'neuralynx_ncs') where you have to provide the filename, the data (as 1*Nsamples matrix) and the header (i.e. everything in upper case in the example). For the header you have to provide a matlab structure such as the one that is returned by ft_read_header returns when you read an original neuralynx ncs file. I suggest that you look into the ft_write_data function at line 529 for further details. best Robert On 9 Jun 2011, at 20:35, Johan Bergmann wrote: > Hello, > > I have a .mat file containing a single column of voltage values which i wish to >convert to the ncs file format. I cannot seem to achieve this, please can >someone show me a usage example. > > Cheers, > > Johan. > _______________________________________________ > 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 tobias.staudigl at uni-konstanz.de Fri Jun 10 12:42:51 2011 From: tobias.staudigl at uni-konstanz.de (Tobias Staudigl) Date: Fri, 10 Jun 2011 12:42:51 +0200 Subject: [FieldTrip] granger causality Message-ID: <4DF1F52B.3000406@uni-konstanz.de> Dear all, I am trying to make sense out of a granger-causality analysis i did using ft-functions. I have two condition in which i already identified a sig. difference in plv. now i would like to know the directionality of the coupling in one of the conditions. To this end, I use granger causality as implemented in fieldtrip (see below for details). At the moment, i have 3 questions. (As i am not very familiar with using fieldtrip, i may have missed something obvious). Q 1: If I understood correctly, the grangerspectrum (granger.grangerspctrm) gives me values for the granger-causality in a matrix [nChannel, nChannel, Freqs]. Does [1,2,:] give me the granger-causality of Channel1 predicting Channel2, or the other way round? Q2: The plotting function gives me an error: ft_connectivityplot(cfg, granger) ??? Error using ==> seloverdim at 36 cannot select over multiple dimensions at the same time Error in ==> ft_selectdata at 528 if selectchan, data = seloverdim(data, 'chan', selchan, fb); end Error in ==> ft_connectivityplot at 79 data = ft_selectdata(data, 'channel', cfg.channel); Q3: How do i statistically validate the measures i get fromthe granger-analysis? Is there some recommended statistical test? Is it correct to do bootstrapping / permutation testing? What I could do on my data is shuffle the trials across conditions, compute granger causality on the shuffeld data, and compair this distribution with the value i get from the data. Maybe, somebody is experienced in using granger and could help me out! Any advice appreciated! Thanks a lot! tobi I used the following ft_functions according to the online tutorial: %% MVAR cfg = []; cfg.order = 2; cfg.toolbox = 'bsmart'; mdata = ft_mvaranalysis(cfg, data); %% transfer function cfg = []; cfg.method = 'mvar'; mfreq = ft_freqanalysis(cfg, mdata); %% granger cfg = []; cfg.method = 'granger'; granger = ft_connectivityanalysis(cfg, mfreq); %% cfg = []; cfg.zparam = 'grangerspctrm'; %cfg.channel = 'all'; ft_connectivityplot(cfg, granger); -- Tobias Staudigl Fachbereich Psychologie - ZPR Postfach ZPR 78457 Konstanz ZPR, Haus 12 Tel.: +49 (0)7531 / 88 - 5703 From jan.schoffelen at donders.ru.nl Fri Jun 10 13:00:12 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 10 Jun 2011 13:00:12 +0200 Subject: [FieldTrip] granger causality In-Reply-To: <4DF1F52B.3000406@uni-konstanz.de> References: <4DF1F52B.3000406@uni-konstanz.de> Message-ID: <01F5D123-C4D5-42B2-9D93-CC3B4E86BD66@donders.ru.nl> Hi Tobias, > > Q 1: > If I understood correctly, the grangerspectrum > (granger.grangerspctrm) gives me values for the granger-causality in > a matrix [nChannel, nChannel, Freqs]. > Does [1,2,:] give me the granger-causality of Channel1 predicting > Channel2, or the other way round? > The FieldTrip convention is indeed (1,2,:) relates to 1->2 > Q2: > The plotting function gives me an error: > > ft_connectivityplot(cfg, granger) > > ??? Error using ==> seloverdim at 36 > cannot select over multiple dimensions at the same time > > Error in ==> ft_selectdata at 528 > if selectchan, data = seloverdim(data, 'chan', selchan, fb); end > > Error in ==> ft_connectivityplot at 79 > data = ft_selectdata(data, 'channel', cfg.channel); Please update your fieldtrip version. There is a fix (dated 22-04) that should take care of this > Q3: > How do i statistically validate the measures i get fromthe granger- > analysis? > Is there some recommended statistical test? > Is it correct to do bootstrapping / permutation testing? > What I could do on my data is shuffle the trials across conditions, > compute granger causality on the shuffeld data, and compair this > distribution with the value i get from the data. This is a very relevant issue. From what you describe it seems as if you want to compare across conditions. The shuffling across conditions is what we do as well, although it remains open to debate how meaningful it is to compare granger causality indices across conditions. And, also, if you are able to reject your null-hypothesis, whether your decision to reject it is actually due to the actual granger causality being different, or by some other confounding quantity. Best wishes, Jan-Mathijs > Maybe, somebody is experienced in using granger and could help me out! > Any advice appreciated! > > Thanks a lot! > tobi > > > I used the following ft_functions according to the online tutorial: > > %% MVAR > cfg = []; > cfg.order = 2; > cfg.toolbox = 'bsmart'; > mdata = ft_mvaranalysis(cfg, data); > > %% transfer function > cfg = []; > cfg.method = 'mvar'; > mfreq = ft_freqanalysis(cfg, mdata); > > %% granger > cfg = []; > cfg.method = 'granger'; > granger = ft_connectivityanalysis(cfg, mfreq); > > %% > cfg = []; > cfg.zparam = 'grangerspctrm'; > %cfg.channel = 'all'; > ft_connectivityplot(cfg, granger); > > -- > Tobias Staudigl > Fachbereich Psychologie - ZPR > Postfach ZPR > 78457 Konstanz > ZPR, Haus 12 > Tel.: +49 (0)7531 / 88 - 5703 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From jan.schoffelen at donders.ru.nl Fri Jun 10 13:01:58 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 10 Jun 2011 13:01:58 +0200 Subject: [FieldTrip] Weird trialfun_general error In-Reply-To: References: Message-ID: <59055861-365E-4FD7-A85C-C57C2FF430C4@donders.ru.nl> Hi Rodolphe, This is a funny bug. It goes wrong in trialfun_general when the intersect() tries to compare a string (event(i).vale being 'boundary') with a list of numbers (your event values). This leads in your case to unwanted behavior, and I can imagine that this will cause problems elsewhere too. We'll look into it and fix it. Thanks for the notification. Best, Jan-Mathijs On Jun 7, 2011, at 12:51 AM, Rodolphe Nenert wrote: > Dear fieldtrippers, > > i just noticed and found the origin of a weird error obtained with > the trialfun_general function, i thought it could be useful to send > it here. > I use the ft_definetrial function on a file obtained using the merge > function in EEGlab. Apparently, this function is adding some > triggers with the value 'boundary' in the new file, indicating the > old frontier between the dataset that have been merged. > The funny part is that the trialfun_general() function in fieltrip > is using the intersect() matlab function to match event values. > Moreover, im using 27 different event values to indicate point of > interest (112,114,116,122,etc...) > All of my event values dont create any problems except the value > 114 because intersect('boundary',114) = 114 whereas it gives an > empty result with any other of my values... > Therefore, for that particular event value, there was a dimension > mismatch between trl and val in trialfun_general. > > I just removed events with 'boundary' values and it worked. > > Best regards, > > Rodolphe Nenert, Ph.D. > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From g.dimitriadis at donders.ru.nl Fri Jun 10 16:52:54 2011 From: g.dimitriadis at donders.ru.nl (George Dimitriadis) Date: Fri, 10 Jun 2011 16:52:54 +0200 Subject: [FieldTrip] (no subject) In-Reply-To: <550011EB-7B66-40F1-87BB-77974ED41D1B@donders.ru.nl> References: <213089.20008.qm@web45503.mail.sp1.yahoo.com> <550011EB-7B66-40F1-87BB-77974ED41D1B@donders.ru.nl> Message-ID: <00ed01cc277e$170492c0$450db840$@dimitriadis@donders.ru.nl> Hello guys, In ft_plot_topo.m at line 69 you say if isempty(tag), tag=''; Could you please turn the comma into a ; because it breaks my code. Thanks From TAVABIK at email.chop.edu Fri Jun 10 18:59:03 2011 From: TAVABIK at email.chop.edu (Tavabi, Kambiz) Date: Fri, 10 Jun 2011 12:59:03 -0400 Subject: [FieldTrip] working with neuromag data In-Reply-To: <887659131.308634.1301386835573.JavaMail.root@sculptor.zimbra.ru.nl> References: <717208384.308488.1301386421578.JavaMail.root@sculptor.zimbra.ru.nl>, <887659131.308634.1301386835573.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: As per advise from Arjen, I was able to use following steps 1) ft_preprocessing on your stimulus averaged epoch data. This should give you a data structure with 6 trials (which are actually the averages per condition). 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat this so you end up with 6 timelocked structures representing the 6 different conditions. to create individual condition averaged ft data structures which I can visualize using ft_topoplotER(cfg,data) data: avg: [338x651 double] var: [338x651 double] fsample: 1000 time: [1x651 double] dof: [338x651 double] label: {338x1 cell} dimord: 'chan_time' grad: [1x1 struct] cfg: [1x1 struct] however when i use; cfg = []; cfg.showlabels = 'yes'; cfg.fontsize = 6; cfg.ylim = [-10e-13 10e-13] ft_multiplotER(cfg, data); Fieldtrip chruns through creating the selection avg along dimension 1 selection dof along dimension 1 selection var along dimension 1 creating layout from data.grad creating layout for neuromag306 system but the resutling figure is an empty figure containing only layout with ch lables without any data what so ever. Any ideas why this might be? -Kambiz. ------------------------------------------------------------- Kambiz Tavabi PhD Biomedical Imaging Laboratory The Children's Hospital of Philadelphia 34th Street and Civic Center Boulevard Philadelphia, Pa. 19104 Tel: 267.426.0302 email: tavabik at email.chop.edu ------------------------------------------------------------- ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. [a.stolk at fcdonders.ru.nl] Sent: Tuesday, March 29, 2011 4:20 AM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] working with neuromag data Dear Kambiz, I think I see your point. Your data presumably is already preprocessed and timelocked (averaged over trials) with neuromag software. I then take it that you have 6 different conditions which you would like to plot separately and possibly test at the group level. Since the data is already averaged, I'd recommend to do the following to get your data back on track. 1) ft_preprocessing on your stimulus averaged epoch data. This should give you a data structure with 6 trials (which are actually the averages per condition). 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat this so you end up with 6 timelocked structures representing the 6 different conditions. 3) plot or grandaverage (see tutorials how to proceed as your data now should be 'ft-friendly'). Goodluck, Arjen ----- "Kambiz Tavabi" schreef: > Van: "Kambiz Tavabi" > Aan: "Email discussion list for the FieldTrip project" > Verzonden: Dinsdag 29 maart 2011 01:10:14 > Onderwerp: Re: [FieldTrip] working with neuromag data > > Dear Arjen - Thanks for your response. Just to clarify the low level > functions ft_read_header & ft_read_data are mentioned in the ft > getting started tutorial. I believe they're recommended to make sure > the data is ft friendly. In my case the data is ft friendly. My data > is also pre-processed and already 'time-locked'--meaning that I have > stimulus averaged epoch data in fif format for all my subjects. My > question is how to proceed from there? I've been through the pages you > refer to but have not been able to piece together my data in such a > way to proceed with grand-averaging and carrying out stats. > -Kambiz. > ------------------------------------------------------------- > Kambiz Tavabi PhD > Biomedical Imaging Laboratory > The Children's Hospital of Philadelphia > 34th Street and Civic Center Boulevard > Philadelphia, Pa. 19104 > Tel: 267.426.0302 > email: tavabik at email.chop.edu > ------------------------------------------------------------- > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > [a.stolk at fcdonders.ru.nl] > Sent: Monday, March 28, 2011 4:05 PM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] working with neuromag data > > Dear Kambiz, > > While you are able to use the 'low level' ft_read_header and > ft_read_data functions, you should be able to preprocess and analyze > your neuromag data using the 'high level' functions such as > ft_preprocessing (which calls the low level functions mentioned > above). > > How to proceed depends on what you want to do with your data. If you > have triggers stored in your dataset that are synchronuous with the > recorded brain activity, it'd be recommended to start with the > following tutorial on how to select your trials: > > http://fieldtrip.fcdonders.nl/tutorial/preprocessing > > Since your experience with FT is still limited as you say, I believe > the following text may provide a good overview of what the data, once > read in to FT (i.e. matlab) environment, may look like: > > http://fieldtrip.fcdonders.nl/walkthrough > > Typically, your next steps involve single-subject timelocked analysis, > then grand-average and perform statistics at the group level. For an > overview of the steps and protocols, see: > > http://fieldtrip.fcdonders.nl/tutorial/analysis_protocols > > Hope this has helped for a start, > > Arjen > > > ----- "Kambiz Tavabi" schreef: > > > Van: "Kambiz Tavabi" > > Aan: "Email discussion list for the FieldTrip project" > > > Verzonden: Maandag 28 maart 2011 20:59:36 > > Onderwerp: [FieldTrip] working with neuromag data > > > > Greetings - I have preprocessed/averaged neuromag data for a group > of > > subjects that I'd like to visualize, compute grandaverage and carry > > out sensor level statistics on. The only help I managed to find on > the > > Fieldtrip site/list Re: neurmag data concerns getting started e.g., > > with ft_read_header and ft_read_data. In my case these programs > work > > fine meaning that I can proceed with further analysis. > > On a side, in my limited experience with FT, a major problem I run > > into frequently is that there is no clear suggestion(s) on how to > > proceed with data that is not raw. I understand it is impossible to > > cover all analysis scenarios, but it is often the case that working > > with CTF, or in particular Elekta system, the data is likely to be > in > > a post-preprocessed phase. Everytime I've tried to work with ft, It > > seems to me that if I don't start with square one in fieldtrip, it > is > > difficult to figure out how to use downstream programs to work on > the > > data. > > That said, in my case I have the output from ft_read_header: > > > > label: {338x1 cell} > > nChans: 338 > > Fs: 1000 > > grad: [1x1 struct] > > unit: {1x338 cell} > > nSamples: 651 > > nSamplesPre: 100 > > nTrials: 6 > > orig: [1x1 struct] > > > > and output from ft_read_data > > > > [338x651x6] that being channels by samples by number of stimulus > > averaged epochs. To proceed, ideally I'd like to compute a > > grandaverage for each condition, visualize them in a multiplot, and > > carry out sensor level stats. To be able to do this I understand I > > need the output from ft_timelockanalysis, how do I arrange my data > as > > such? I am assuming it is already in that state. Thanks for your > > time. > > > > -Kambiz. > > ------------------------------------------------------------- > > Kambiz Tavabi PhD > > Biomedical Imaging Laboratory > > The Children's Hospital of Philadelphia > > 34th Street and Civic Center Boulevard > > Philadelphia, Pa. 19104 > > Tel: 267.426.0302 > > email: tavabik at email.chop.edu > > ------------------------------------------------------------- > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- A non-text attachment was scrubbed... Name: multiplot.jpg Type: image/jpeg Size: 47066 bytes Desc: multiplot.jpg URL: From TAVABIK at email.chop.edu Fri Jun 10 20:21:30 2011 From: TAVABIK at email.chop.edu (Tavabi, Kambiz) Date: Fri, 10 Jun 2011 14:21:30 -0400 Subject: [FieldTrip] working with neuromag data In-Reply-To: References: <717208384.308488.1301386421578.JavaMail.root@sculptor.zimbra.ru.nl>, <887659131.308634.1301386835573.JavaMail.root@sculptor.zimbra.ru.nl>, Message-ID: As per advise from Arjen, I was able to use following steps 1) ft_preprocessing on your stimulus averaged epoch data. This should give you a data structure with 6 trials (which are actually the averages per condition). 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat this so you end up with 6 timelocked structures representing the 6 different conditions. to create individual condition averaged ft data structures which I can visualize using ft_topoplotER(cfg,data) data: avg: [338x651 double] var: [338x651 double] fsample: 1000 time: [1x651 double] dof: [338x651 double] label: {338x1 cell} dimord: 'chan_time' grad: [1x1 struct] cfg: [1x1 struct] however when i use; cfg = []; cfg.showlabels = 'yes'; cfg.fontsize = 6; cfg.ylim = [-10e-13 10e-13] ft_multiplotER(cfg, data); Fieldtrip chruns through creating the selection avg along dimension 1 selection dof along dimension 1 selection var along dimension 1 creating layout from data.grad creating layout for neuromag306 system but the resutling figure is an empty figure containing only layout with ch lables without any data what so ever. Any ideas why this might be? Following up my question on plotting: Why would the granaverge structure lose the channel layout information instead of carrying it over from the Timelock structure? ft_topoplotER(cfg,grandavgc1) ??? Error using ==> ft_prepare_layout at 532 no layout detected, please specify cfg.layout Error in ==> ft_topoplotER at 408 lay = ft_prepare_layout(cfg, data); -Kambiz. ------------------------------------------------------------- Kambiz Tavabi PhD Biomedical Imaging Laboratory The Children's Hospital of Philadelphia 34th Street and Civic Center Boulevard Philadelphia, Pa. 19104 Tel: 267.426.0302 email: tavabik at email.chop.edu ------------------------------------------------------------- ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. [a.stolk at fcdonders.ru.nl] Sent: Tuesday, March 29, 2011 4:20 AM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] working with neuromag data Dear Kambiz, I think I see your point. Your data presumably is already preprocessed and timelocked (averaged over trials) with neuromag software. I then take it that you have 6 different conditions which you would like to plot separately and possibly test at the group level. Since the data is already averaged, I'd recommend to do the following to get your data back on track. 1) ft_preprocessing on your stimulus averaged epoch data. This should give you a data structure with 6 trials (which are actually the averages per condition). 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat this so you end up with 6 timelocked structures representing the 6 different conditions. 3) plot or grandaverage (see tutorials how to proceed as your data now should be 'ft-friendly'). Goodluck, Arjen ----- "Kambiz Tavabi" schreef: > Van: "Kambiz Tavabi" > Aan: "Email discussion list for the FieldTrip project" > Verzonden: Dinsdag 29 maart 2011 01:10:14 > Onderwerp: Re: [FieldTrip] working with neuromag data > > Dear Arjen - Thanks for your response. Just to clarify the low level > functions ft_read_header & ft_read_data are mentioned in the ft > getting started tutorial. I believe they're recommended to make sure > the data is ft friendly. In my case the data is ft friendly. My data > is also pre-processed and already 'time-locked'--meaning that I have > stimulus averaged epoch data in fif format for all my subjects. My > question is how to proceed from there? I've been through the pages you > refer to but have not been able to piece together my data in such a > way to proceed with grand-averaging and carrying out stats. > -Kambiz. > ------------------------------------------------------------- > Kambiz Tavabi PhD > Biomedical Imaging Laboratory > The Children's Hospital of Philadelphia > 34th Street and Civic Center Boulevard > Philadelphia, Pa. 19104 > Tel: 267.426.0302 > email: tavabik at email.chop.edu > ------------------------------------------------------------- > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > [a.stolk at fcdonders.ru.nl] > Sent: Monday, March 28, 2011 4:05 PM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] working with neuromag data > > Dear Kambiz, > > While you are able to use the 'low level' ft_read_header and > ft_read_data functions, you should be able to preprocess and analyze > your neuromag data using the 'high level' functions such as > ft_preprocessing (which calls the low level functions mentioned > above). > > How to proceed depends on what you want to do with your data. If you > have triggers stored in your dataset that are synchronuous with the > recorded brain activity, it'd be recommended to start with the > following tutorial on how to select your trials: > > http://fieldtrip.fcdonders.nl/tutorial/preprocessing > > Since your experience with FT is still limited as you say, I believe > the following text may provide a good overview of what the data, once > read in to FT (i.e. matlab) environment, may look like: > > http://fieldtrip.fcdonders.nl/walkthrough > > Typically, your next steps involve single-subject timelocked analysis, > then grand-average and perform statistics at the group level. For an > overview of the steps and protocols, see: > > http://fieldtrip.fcdonders.nl/tutorial/analysis_protocols > > Hope this has helped for a start, > > Arjen > > > ----- "Kambiz Tavabi" schreef: > > > Van: "Kambiz Tavabi" > > Aan: "Email discussion list for the FieldTrip project" > > > Verzonden: Maandag 28 maart 2011 20:59:36 > > Onderwerp: [FieldTrip] working with neuromag data > > > > Greetings - I have preprocessed/averaged neuromag data for a group > of > > subjects that I'd like to visualize, compute grandaverage and carry > > out sensor level statistics on. The only help I managed to find on > the > > Fieldtrip site/list Re: neurmag data concerns getting started e.g., > > with ft_read_header and ft_read_data. In my case these programs > work > > fine meaning that I can proceed with further analysis. > > On a side, in my limited experience with FT, a major problem I run > > into frequently is that there is no clear suggestion(s) on how to > > proceed with data that is not raw. I understand it is impossible to > > cover all analysis scenarios, but it is often the case that working > > with CTF, or in particular Elekta system, the data is likely to be > in > > a post-preprocessed phase. Everytime I've tried to work with ft, It > > seems to me that if I don't start with square one in fieldtrip, it > is > > difficult to figure out how to use downstream programs to work on > the > > data. > > That said, in my case I have the output from ft_read_header: > > > > label: {338x1 cell} > > nChans: 338 > > Fs: 1000 > > grad: [1x1 struct] > > unit: {1x338 cell} > > nSamples: 651 > > nSamplesPre: 100 > > nTrials: 6 > > orig: [1x1 struct] > > > > and output from ft_read_data > > > > [338x651x6] that being channels by samples by number of stimulus > > averaged epochs. To proceed, ideally I'd like to compute a > > grandaverage for each condition, visualize them in a multiplot, and > > carry out sensor level stats. To be able to do this I understand I > > need the output from ft_timelockanalysis, how do I arrange my data > as > > such? I am assuming it is already in that state. Thanks for your > > time. > > > > -Kambiz. > > ------------------------------------------------------------- > > Kambiz Tavabi PhD > > Biomedical Imaging Laboratory > > The Children's Hospital of Philadelphia > > 34th Street and Civic Center Boulevard > > Philadelphia, Pa. 19104 > > Tel: 267.426.0302 > > email: tavabik at email.chop.edu > > ------------------------------------------------------------- > > _______________________________________________ > > 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 a.stolk at fcdonders.ru.nl Sat Jun 11 09:26:58 2011 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Sat, 11 Jun 2011 09:26:58 +0200 (CEST) Subject: [FieldTrip] working with neuromag data In-Reply-To: Message-ID: <621524636.372728.1307777218636.JavaMail.root@sculptor.zimbra.ru.nl> Dear Kambiz, Does your data.avg contain NaNs or real numbers? In the latter case; do they fall in the plotting range as specified by your cfg.ylim? Yours, Arjen ----- "Kambiz Tavabi" schreef: > Van: "Kambiz Tavabi" > Aan: "Email discussion list for the FieldTrip project" > Verzonden: Vrijdag 10 juni 2011 18:59:03 > Onderwerp: Re: [FieldTrip] working with neuromag data > > As per advise from Arjen, I was able to use following steps > 1) ft_preprocessing on your stimulus averaged epoch data. This should > give you a data structure with 6 trials (which are actually the > averages per condition). > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat > this so you end up with 6 timelocked structures representing the 6 > different conditions. > to create individual condition averaged ft data structures which I can > visualize using ft_topoplotER(cfg,data) > data: > avg: [338x651 double] > var: [338x651 double] > fsample: 1000 > time: [1x651 double] > dof: [338x651 double] > label: {338x1 cell} > dimord: 'chan_time' > grad: [1x1 struct] > cfg: [1x1 struct] > however when i use; > cfg = []; > cfg.showlabels = 'yes'; > cfg.fontsize = 6; > cfg.ylim = [-10e-13 10e-13] > ft_multiplotER(cfg, data); > Fieldtrip chruns through creating the > selection avg along dimension 1 > selection dof along dimension 1 > selection var along dimension 1 > creating layout from data.grad > creating layout for neuromag306 system > > but the resutling figure is an empty figure containing only layout > with ch lables without any data what so ever. Any ideas why this might > be? > > > > -Kambiz. > ------------------------------------------------------------- > Kambiz Tavabi PhD > Biomedical Imaging Laboratory > The Children's Hospital of Philadelphia > 34th Street and Civic Center Boulevard > Philadelphia, Pa. 19104 > Tel: 267.426.0302 > email: tavabik at email.chop.edu > ------------------------------------------------------------- > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > [a.stolk at fcdonders.ru.nl] > Sent: Tuesday, March 29, 2011 4:20 AM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] working with neuromag data > > Dear Kambiz, > > I think I see your point. Your data presumably is already preprocessed > and timelocked (averaged over trials) with neuromag software. I then > take it that you have 6 different conditions which you would like to > plot separately and possibly test at the group level. > > Since the data is already averaged, I'd recommend to do the following > to get your data back on track. > > 1) ft_preprocessing on your stimulus averaged epoch data. This should > give you a data structure with 6 trials (which are actually the > averages per condition). > > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat > this so you end up with 6 timelocked structures representing the 6 > different conditions. > > 3) plot or grandaverage (see tutorials how to proceed as your data now > should be 'ft-friendly'). > > Goodluck, > Arjen > > > > > > > ----- "Kambiz Tavabi" schreef: > > > Van: "Kambiz Tavabi" > > Aan: "Email discussion list for the FieldTrip project" > > > Verzonden: Dinsdag 29 maart 2011 01:10:14 > > Onderwerp: Re: [FieldTrip] working with neuromag data > > > > Dear Arjen - Thanks for your response. Just to clarify the low > level > > functions ft_read_header & ft_read_data are mentioned in the ft > > getting started tutorial. I believe they're recommended to make > sure > > the data is ft friendly. In my case the data is ft friendly. My > data > > is also pre-processed and already 'time-locked'--meaning that I > have > > stimulus averaged epoch data in fif format for all my subjects. My > > question is how to proceed from there? I've been through the pages > you > > refer to but have not been able to piece together my data in such a > > way to proceed with grand-averaging and carrying out stats. > > -Kambiz. > > ------------------------------------------------------------- > > Kambiz Tavabi PhD > > Biomedical Imaging Laboratory > > The Children's Hospital of Philadelphia > > 34th Street and Civic Center Boulevard > > Philadelphia, Pa. 19104 > > Tel: 267.426.0302 > > email: tavabik at email.chop.edu > > ------------------------------------------------------------- > > ________________________________________ > > From: fieldtrip-bounces at donders.ru.nl > > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > > [a.stolk at fcdonders.ru.nl] > > Sent: Monday, March 28, 2011 4:05 PM > > To: Email discussion list for the FieldTrip project > > Subject: Re: [FieldTrip] working with neuromag data > > > > Dear Kambiz, > > > > While you are able to use the 'low level' ft_read_header and > > ft_read_data functions, you should be able to preprocess and > analyze > > your neuromag data using the 'high level' functions such as > > ft_preprocessing (which calls the low level functions mentioned > > above). > > > > How to proceed depends on what you want to do with your data. If > you > > have triggers stored in your dataset that are synchronuous with the > > recorded brain activity, it'd be recommended to start with the > > following tutorial on how to select your trials: > > > > http://fieldtrip.fcdonders.nl/tutorial/preprocessing > > > > Since your experience with FT is still limited as you say, I > believe > > the following text may provide a good overview of what the data, > once > > read in to FT (i.e. matlab) environment, may look like: > > > > http://fieldtrip.fcdonders.nl/walkthrough > > > > Typically, your next steps involve single-subject timelocked > analysis, > > then grand-average and perform statistics at the group level. For > an > > overview of the steps and protocols, see: > > > > http://fieldtrip.fcdonders.nl/tutorial/analysis_protocols > > > > Hope this has helped for a start, > > > > Arjen > > > > > > ----- "Kambiz Tavabi" schreef: > > > > > Van: "Kambiz Tavabi" > > > Aan: "Email discussion list for the FieldTrip project" > > > > > Verzonden: Maandag 28 maart 2011 20:59:36 > > > Onderwerp: [FieldTrip] working with neuromag data > > > > > > Greetings - I have preprocessed/averaged neuromag data for a > group > > of > > > subjects that I'd like to visualize, compute grandaverage and > carry > > > out sensor level statistics on. The only help I managed to find > on > > the > > > Fieldtrip site/list Re: neurmag data concerns getting started > e.g., > > > with ft_read_header and ft_read_data. In my case these programs > > work > > > fine meaning that I can proceed with further analysis. > > > On a side, in my limited experience with FT, a major problem I > run > > > into frequently is that there is no clear suggestion(s) on how to > > > proceed with data that is not raw. I understand it is impossible > to > > > cover all analysis scenarios, but it is often the case that > working > > > with CTF, or in particular Elekta system, the data is likely to > be > > in > > > a post-preprocessed phase. Everytime I've tried to work with ft, > It > > > seems to me that if I don't start with square one in fieldtrip, > it > > is > > > difficult to figure out how to use downstream programs to work on > > the > > > data. > > > That said, in my case I have the output from ft_read_header: > > > > > > label: {338x1 cell} > > > nChans: 338 > > > Fs: 1000 > > > grad: [1x1 struct] > > > unit: {1x338 cell} > > > nSamples: 651 > > > nSamplesPre: 100 > > > nTrials: 6 > > > orig: [1x1 struct] > > > > > > and output from ft_read_data > > > > > > [338x651x6] that being channels by samples by number of stimulus > > > averaged epochs. To proceed, ideally I'd like to compute a > > > grandaverage for each condition, visualize them in a multiplot, > and > > > carry out sensor level stats. To be able to do this I understand > I > > > need the output from ft_timelockanalysis, how do I arrange my > data > > as > > > such? I am assuming it is already in that state. Thanks for your > > > time. > > > > > > -Kambiz. > > > ------------------------------------------------------------- > > > Kambiz Tavabi PhD > > > Biomedical Imaging Laboratory > > > The Children's Hospital of Philadelphia > > > 34th Street and Civic Center Boulevard > > > Philadelphia, Pa. 19104 > > > Tel: 267.426.0302 > > > email: tavabik at email.chop.edu > > > ------------------------------------------------------------- > > > _______________________________________________ > > > 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 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Sun Jun 12 10:40:48 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Sun, 12 Jun 2011 10:40:48 +0200 Subject: [FieldTrip] (no subject) In-Reply-To: <00ed01cc277e$170492c0$450db840$@dimitriadis@donders.ru.nl> References: <213089.20008.qm@web45503.mail.sp1.yahoo.com> <550011EB-7B66-40F1-87BB-77974ED41D1B@donders.ru.nl> <00ed01cc277e$170492c0$450db840$@dimitriadis@donders.ru.nl> Message-ID: <4DF47B90.1020400@donders.ru.nl> Hi George, first of all, I just changed the code after I read your mail - but I doubt that this fixes your problem. Anyway, what version of Matlab are you using that causes a comma to break your code? In a lot of fieldtrip functions, we are using if(z), x=y; end; Did this not work for some Matlab versions? If this was the case, you could not use ft_multiplotER, for example, because ft_plot_vector does have a lot of these if-clauses. Are you sure it is this comma and not something else that breaks your code? Please excuse my skepticism :) Best, Jörn On 6/10/2011 4:52 PM, George Dimitriadis wrote: > Hello guys, > > In ft_plot_topo.m at line 69 you say if isempty(tag), tag=''; > Could you please turn the comma into a ; because it breaks my code. > > Thanks > > _______________________________________________ > 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 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 Kapitelweg 29 NL-6525 EN Nijmegen The Netherlands From cmuehl at gmail.com Sun Jun 12 17:56:49 2011 From: cmuehl at gmail.com (Christian Muehl) Date: Sun, 12 Jun 2011 17:56:49 +0200 Subject: [FieldTrip] Final Call for Papers: Affective BCI Workshop, Memphis, USA Message-ID: ** Final Call for Papers ** 2nd Workshop on Affective Brain-Computer Interfaces (aBCI) Workshop at ACII 2011 (October 9-12), Memphis, USA, October 9, 2011 Apologies for multiple postings http://hmi.ewi.utwente.nl/abci2011 http://www.acii2011.org The second workshop on affective brain-computer interfaces will explore the advantages and limitations of using neuro-physiological signals as a modality for the automatic recognition of affective and cognitive states, and the possibilities of using this information about the user state in innovative and adaptive applications. The goal is to bring researchers from the communities of brain computer interfacing, affective computing, neuro-ergonomics, affective and cognitive neuroscience together to present state-of-the-art progress and visions on the various overlaps between those disciplines. Recent research in brain-computer interfaces (BCI) shows that brain activity can be used as an active/voluntary, or passive/involuntary control modality in man-machine interaction. While active BCI paradigms have received a lot of attention in recent years, research on passive approaches to BCI still desperately needs concerted activity. However, it has been shown more than once that brain activations can carry information about the affective and cognitive state of a subject, and that the interaction between humans and machines can be aided by the recognition of those user states. To achieve robust passive BCIs, efforts from applied and basic sciences have to be combined. On the one hand, applied fields such as affective computing aim at the development of applications that adapt to changes in the user states and thereby enrich the interaction, leading to a more natural and effective usability. On the other hand, basic research in neuroscience advances our understanding of the neural processes associated with emotions. Furthermore, similar advancements are being made for more cognitive mental states, for example, attention, fatigue, and work load, which strongly interact with affective states. Topics of interest include, but are not limited to: * emotion elicitation and data collection for affective BCI * detection of affective and cognitive states with BCI and other modalities * adaptive interfaces and affective BCI Invited Talk: 'Brain Dynamics of Affective Engagement' by Scott Makeig, SCCN, University of California at San Diego, USA The workshop will be held in conjunction with the 4th International conference on Affective Computing and Intelligent Interaction (ACII2011) at the FedEx Institute of Technology at the University of Memphis, TN. Submission Instructions * The papers should feature original empirical work, theoretical work, or a well defendable but arguable position of the authors (i.e., not submitted, in submission, or submitted to another conference or journal while in review). * Papers will be published in the proceedings of ACII 2011 by Springer. Papers should not exceed 10 pages and should be formatted according to the Springer LNCS formatting guidelines http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0. * Papers must be submitted as PDF through the EasyChair conference system, which can be accessed through the workshop web site and the ACII conference website. * For further information, contact abci at cs.utwente.nl Important Dates: 15th of June: Workshop papers due 1st of July: Notification of Acceptance 18th of July: Camera-ready papers due 9th of October: Workshop Programme Chairs: * Anton Nijholt, Universiteit Twente, The Netherlands * Brendan Allison, TU Graz, Austria * Stephen Dunne, Starlab Barcelona, Spain * Dirk Heylen, University of Twente, The Netherlands Local Organizer: * Christian Mühl, University of Twente, The Netherlands Programme Committee: * Egon L. van den Broek, University of Twente, The Netherlands * Touradj Ebrahimi, EPFL, Lausanne, Switzerland * Peter Desain, Radboud University Nijmegen, The Netherlands * Jan B.F. van Erp, TNO Human Factors, Soesterberg, The Netherlands * Stephen Fairclough, John Moores University, Liverpool, UK * Gary Garcia Molina, Philips Research, Eindhoven, The Netherlands * Audrey Girouard, Queen's University, Kingston, Canada * Jonghwa Kim, University of Augsburg, Germany * Brent Lance, Army Research Laboratory/TNB, Aberdeen Proving Ground, USA * Robert Leeb, University of Lausanne, Switzerland * Scott Makeig, University of California at San Diego, USA * Femke Nijboer, University of Twente, The Netherlands * Ioannis Patras, Queen Mary University, London, UK * Thierry Pun, University of Geneva, Switzerland * Tanja Schultz, Karlsruhe Institute of Technology (KIT), Germany * Olga Sourina, NanYang Technological University, Singapore * Thomas J. Sullivan, NeuroSky, San Jose, USA * Thorsten Zander, Graz University of Technology, Austria From michael.wibral at web.de Mon Jun 13 14:20:33 2011 From: michael.wibral at web.de (Michael Wibral) Date: Mon, 13 Jun 2011 14:20:33 +0200 (CEST) Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis Message-ID: <826564097.1273685.1307967633954.JavaMail.fmail@mwmweb071> Dear Elena, we do not use neuromag data. So I cannot say anything wrt to neuromag data. On theoretical grounds, the problem is that both sensor types have highly varying SNR from brain location to brain location. While SNR gets worse with depth for both sensor types, this happens more rapidly with the gradiometers. For example for a deep source that means: Gradiometers have little true signal but standard noise, since their leadfields are small, the inverse of their leadfield is big and noise contributions to your voxels are high, for magnetometers its sligtly different. So if one naively uses both types in one inversion noise will often be dominated by gradiometers and signal by magnetometers. For shallow sources its reverse , the noise will be dominated by the high noise of the magnetometers and the signal comes from the gradiometers, so again things will be matched unfortunately. i guess this creates the relatively homogenic power distribution you observe (unless there's a bug in the code or the analysis setup - see below). For some background you might want to have a look at: Commonalities and differences among vectorized beamformers in electromagnetic source imaging. Huang MX et al, Brain Topogr. Do handle this two things are necessary: 1. Compute the beamformer filters for data that have baseline and task combined. searate filter computation will almost certainly create problems. 2. To localize activity use the statistics function not some simple difference measure or relative power picture. For the reasons above, this might still not work. In this case the best workaround would be a weighted average with different, leadfield dependend weights for each voxel and modality. A simpler possibility might be simple averaging (this might work for your case, since source look very similar for the two modalities). Michael ------------------------------------------------------------ Von: "Elena Orekhova" Gesendet: 09.06.2011 22:48:34 An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Michael, I still have not resolved this problem and do not know whether  is specific for my data(or program bag) or the other Neuromag users also had it. Do you use Neuromag? Elena ------------------------------------------------------------ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Thursday, June 09, 2011 5:06 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis     Hi Elena, disregard my last email, I overlooked the att. Michael ------------------------------------------------------------ Von: "Elena Orekhova" Gesendet: Jun 2, 2011 8:03:16 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Verdana"; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear Michael,   I did normalize the data (sourcepst.avg.nai=sourcepst.avg.pow./sourcepre.avg.pow) as it was suggested in the tutorial.   I used the same scales in all plots for comparison purposes. If  automatic scaling is used the result for MAG+GRA does not look any better (see attachment).   >What you could do as a workaround is to average the separate results with a weighting per voxel and  that >is corresponding to the squared norms of the leadfields for the respective modalities for a given voxel , this >would guarantee equal amounts of backprojected noise from both modalities (if I'm not mistaken).   Thank you for your suggestion.  I may use it as a last resort.  Hopefully, there is still a way to get more optimal solution using both GRA and MAG in the same analysis...     Elena ------------------------------------------------------------ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Elena Orekhova [Elena.Orekhova at neuro.gu.se] Sent: Thursday, June 02, 2011 6:22 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis     BODY {direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;} Dear Michael,   I have tried to multiply the leadfield by -1 as you suggested:   for i = 1 : size (grid.leadfield, 2)     grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); end   This had no effect on the 'lcmv' output. I attached the pictures for ‘GRA only, ’MAG only’ and ‘GRA + MAG’   In this experiment I measured evoked field in response to  the unilateral (left) click. The source is expected to be in the right superior temporal cortex.  This is the case  for  ‘GRA only' and ’MAG only’ datasets. The combined sensors give meaningless result.   Elena   ------------------------------------------------------------ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Wednesday, June 01, 2011 4:04 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis     Dear Elena, could you give the following a try: invert (*-1) the leadfileds for one of the two sensor types. Let me know what happens. I would also be interested in taking a look at the results - maybe you could sent images off-list: Michael.Wibral web.de. Michael ------------------------------------------------------------ Von: "Elena Orekhova" Gesendet: Jun 1, 2011 12:23:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "Arial"; }@font-face { font-family: "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: Times; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear  fieldtrippers, This message is mainly for Neuromag users.   When I do  'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. If I combine the two types of sensors without weighting, the result is meaningless. Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements.  Does anybody know how to deal with this problem?     Elena     From tobias.staudigl at uni-konstanz.de Mon Jun 13 15:02:55 2011 From: tobias.staudigl at uni-konstanz.de (Tobias Staudigl) Date: Mon, 13 Jun 2011 15:02:55 +0200 Subject: [FieldTrip] granger causality In-Reply-To: <01F5D123-C4D5-42B2-9D93-CC3B4E86BD66@donders.ru.nl> References: <4DF1F52B.3000406@uni-konstanz.de> <01F5D123-C4D5-42B2-9D93-CC3B4E86BD66@donders.ru.nl> Message-ID: <4DF60A7F.9060505@uni-konstanz.de> Thanks a lot for your answer, Jan-Mathijs , what "other confounding quantity" were you thinking of concerning the shuffling across conditions? There is another question i have: Is there a way to estimate the order of the mvar-model in fieldtrip, or would one do it as implemented in the bsmart toolbox? The bsmart toolbox uses the Akaike Information Criterion to find the right order parameter. However, this criterion sometimes seems to have trouble finding a reasonable model-order. Does anybody know a toolbox that uses other criterions, e.g., Bayesian Information Criterion? And, what is a "reasonable range of the model-order"? Is there any convention or standard? E.g., I m thinking of something like: "This order is too small/big to be meaningful in this particular frequency band / for this particular connectivity measure." Any advice, ideas or literature suggestions welcome! Thank you very much, tobi Am 10.06.2011 13:00, schrieb jan-mathijs schoffelen: > Hi Tobias, > >> >> Q 1: >> If I understood correctly, the grangerspectrum >> (granger.grangerspctrm) gives me values for the granger-causality in >> a matrix [nChannel, nChannel, Freqs]. >> Does [1,2,:] give me the granger-causality of Channel1 predicting >> Channel2, or the other way round? >> > > The FieldTrip convention is indeed (1,2,:) relates to 1->2 > >> Q2: >> The plotting function gives me an error: >> >> ft_connectivityplot(cfg, granger) >> >> ??? Error using ==> seloverdim at 36 >> cannot select over multiple dimensions at the same time >> >> Error in ==> ft_selectdata at 528 >> if selectchan, data = seloverdim(data, 'chan', selchan, fb); end >> >> Error in ==> ft_connectivityplot at 79 >> data = ft_selectdata(data, 'channel', cfg.channel); > > Please update your fieldtrip version. There is a fix (dated 22-04) > that should take care of this > >> Q3: >> How do i statistically validate the measures i get fromthe >> granger-analysis? >> Is there some recommended statistical test? >> Is it correct to do bootstrapping / permutation testing? >> What I could do on my data is shuffle the trials across conditions, >> compute granger causality on the shuffeld data, and compair this >> distribution with the value i get from the data. > > This is a very relevant issue. From what you describe it seems as if > you want to compare across conditions. The shuffling across conditions > is what we do as well, although it remains open to debate how > meaningful it is to compare granger causality indices across > conditions. And, also, if you are able to reject your null-hypothesis, > whether your decision to reject it is actually due to the actual > granger causality being different, or by some other confounding quantity. > > Best wishes, > > Jan-Mathijs > > >> Maybe, somebody is experienced in using granger and could help me out! >> Any advice appreciated! >> >> Thanks a lot! >> tobi >> >> >> I used the following ft_functions according to the online tutorial: >> >> %% MVAR >> cfg = []; >> cfg.order = 2; >> cfg.toolbox = 'bsmart'; >> mdata = ft_mvaranalysis(cfg, data); >> >> %% transfer function >> cfg = []; >> cfg.method = 'mvar'; >> mfreq = ft_freqanalysis(cfg, mdata); >> >> %% granger >> cfg = []; >> cfg.method = 'granger'; >> granger = ft_connectivityanalysis(cfg, mfreq); >> >> %% >> cfg = []; >> cfg.zparam = 'grangerspctrm'; >> %cfg.channel = 'all'; >> ft_connectivityplot(cfg, granger); >> >> -- >> Tobias Staudigl >> Fachbereich Psychologie - ZPR >> Postfach ZPR >> 78457 Konstanz >> ZPR, Haus 12 >> Tel.: +49 (0)7531 / 88 - 5703 >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Tobias Staudigl Fachbereich Psychologie - ZPR Postfach ZPR 78457 Konstanz ZPR, Haus 12 Tel.: +49 (0)7531 / 88 - 5703 From Elena.Orekhova at neuro.gu.se Mon Jun 13 16:31:35 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Mon, 13 Jun 2011 14:31:35 +0000 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <826564097.1273685.1307967633954.JavaMail.fmail@mwmweb071> References: <826564097.1273685.1307967633954.JavaMail.fmail@mwmweb071> Message-ID: <32CC77C0C8A7AD4B9410934642608E1F1333583E@exchccr1.neuro.gu.se> Dear Michael, Thank you for your explanations. As I understand, there is no routine way of handling combined gradiometers and magnetometers in Fieldtrip. I feel that the easiest way will be to average, as you have suggested, or to take a subset of the sensors (GRA or MAG). Elena ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Monday, June 13, 2011 2:20 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Elena, we do not use neuromag data. So I cannot say anything wrt to neuromag data. On theoretical grounds, the problem is that both sensor types have highly varying SNR from brain location to brain location. While SNR gets worse with depth for both sensor types, this happens more rapidly with the gradiometers. For example for a deep source that means: Gradiometers have little true signal but standard noise, since their leadfields are small, the inverse of their leadfield is big and noise contributions to your voxels are high, for magnetometers its sligtly different. So if one naively uses both types in one inversion noise will often be dominated by gradiometers and signal by magnetometers. For shallow sources its reverse , the noise will be dominated by the high noise of the magnetometers and the signal comes from the gradiometers, so again things will be matched unfortunately. i guess this creates the relatively homogenic power distribution you observe (unless there's a bug in the code or the analysis setup - see below). For some background you might want to have a look at: Commonalities and differences among vectorized beamformers in electromagnetic source imaging. Huang MX et al, Brain Topogr. Do handle this two things are necessary: 1. Compute the beamformer filters for data that have baseline and task combined. searate filter computation will almost certainly create problems. 2. To localize activity use the statistics function not some simple difference measure or relative power picture. For the reasons above, this might still not work. In this case the best workaround would be a weighted average with different, leadfield dependend weights for each voxel and modality. A simpler possibility might be simple averaging (this might work for your case, since source look very similar for the two modalities). Michael ------------------------------------------------------------ Von: "Elena Orekhova" Gesendet: 09.06.2011 22:48:34 An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Michael, I still have not resolved this problem and do not know whether is specific for my data(or program bag) or the other Neuromag users also had it. Do you use Neuromag? Elena ------------------------------------------------------------ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Thursday, June 09, 2011 5:06 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Hi Elena, disregard my last email, I overlooked the att. Michael ------------------------------------------------------------ Von: "Elena Orekhova" Gesendet: Jun 2, 2011 8:03:16 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Verdana"; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear Michael, I did normalize the data (sourcepst.avg.nai=sourcepst.avg.pow./sourcepre.avg.pow) as it was suggested in the tutorial. I used the same scales in all plots for comparison purposes. If automatic scaling is used the result for MAG+GRA does not look any better (see attachment). >What you could do as a workaround is to average the separate results with a weighting per voxel and that >is corresponding to the squared norms of the leadfields for the respective modalities for a given voxel , this >would guarantee equal amounts of backprojected noise from both modalities (if I'm not mistaken). Thank you for your suggestion. I may use it as a last resort. Hopefully, there is still a way to get more optimal solution using both GRA and MAG in the same analysis... Elena ------------------------------------------------------------ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Elena Orekhova [Elena.Orekhova at neuro.gu.se] Sent: Thursday, June 02, 2011 6:22 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis BODY {direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;} Dear Michael, I have tried to multiply the leadfield by -1 as you suggested: for i = 1 : size (grid.leadfield, 2) grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); end This had no effect on the 'lcmv' output. I attached the pictures for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ In this experiment I measured evoked field in response to the unilateral (left) click. The source is expected to be in the right superior temporal cortex. This is the case for ‘GRA only' and ’MAG only’ datasets. The combined sensors give meaningless result. Elena ------------------------------------------------------------ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Wednesday, June 01, 2011 4:04 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Elena, could you give the following a try: invert (*-1) the leadfileds for one of the two sensor types. Let me know what happens. I would also be interested in taking a look at the results - maybe you could sent images off-list: Michael.Wibral web.de. Michael ------------------------------------------------------------ Von: "Elena Orekhova" Gesendet: Jun 1, 2011 12:23:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "Arial"; }@font-face { font-family: "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: Times; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear fieldtrippers, This message is mainly for Neuromag users. When I do 'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. If I combine the two types of sensors without weighting, the result is meaningless. Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements. Does anybody know how to deal with this problem? Elena _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From TAVABIK at email.chop.edu Mon Jun 13 20:50:39 2011 From: TAVABIK at email.chop.edu (Tavabi, Kambiz) Date: Mon, 13 Jun 2011 14:50:39 -0400 Subject: [FieldTrip] working with neuromag data In-Reply-To: <621524636.372728.1307777218636.JavaMail.root@sculptor.zimbra.ru.nl> References: <621524636.372728.1307777218636.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Dear Arjen, The data.avt I am using to plot with ft_multiplotER is infact real numbers, quite small numbers on the order of x.xxxe-15, but I still get no visualization using cfg.ylim(min(data.avg), max(data.avg) or extremely small numbers eg., cfg.ylim [-3e-50 3e-50]. Conversely, ft_topoplotER seems to work just fine with the exception of a couple of warnings: 1- some points fall outside the outline, please consider using another layout >ft_plot_topo line 112 and ft_topoplotER line 719 2- Duplicate x-y data points detected: using average of the z values >ft_plot_topo line 144 and ft_topoplotER line 719. What does this warning mean? Regards, Kambiz -----Original Message----- From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. Sent: Saturday, June 11, 2011 3:27 AM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] working with neuromag data Dear Kambiz, Does your data.avg contain NaNs or real numbers? In the latter case; do they fall in the plotting range as specified by your cfg.ylim? Yours, Arjen ----- "Kambiz Tavabi" schreef: > Van: "Kambiz Tavabi" > Aan: "Email discussion list for the FieldTrip project" > Verzonden: Vrijdag 10 juni 2011 18:59:03 > Onderwerp: Re: [FieldTrip] working with neuromag data > > As per advise from Arjen, I was able to use following steps > 1) ft_preprocessing on your stimulus averaged epoch data. This should > give you a data structure with 6 trials (which are actually the > averages per condition). > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat > this so you end up with 6 timelocked structures representing the 6 > different conditions. > to create individual condition averaged ft data structures which I can > visualize using ft_topoplotER(cfg,data) > data: > avg: [338x651 double] > var: [338x651 double] > fsample: 1000 > time: [1x651 double] > dof: [338x651 double] > label: {338x1 cell} > dimord: 'chan_time' > grad: [1x1 struct] > cfg: [1x1 struct] > however when i use; > cfg = []; > cfg.showlabels = 'yes'; > cfg.fontsize = 6; > cfg.ylim = [-10e-13 10e-13] > ft_multiplotER(cfg, data); > Fieldtrip chruns through creating the > selection avg along dimension 1 > selection dof along dimension 1 > selection var along dimension 1 > creating layout from data.grad > creating layout for neuromag306 system > > but the resutling figure is an empty figure containing only layout > with ch lables without any data what so ever. Any ideas why this might > be? > > > > -Kambiz. > ------------------------------------------------------------- > Kambiz Tavabi PhD > Biomedical Imaging Laboratory > The Children's Hospital of Philadelphia > 34th Street and Civic Center Boulevard > Philadelphia, Pa. 19104 > Tel: 267.426.0302 > email: tavabik at email.chop.edu > ------------------------------------------------------------- > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > [a.stolk at fcdonders.ru.nl] > Sent: Tuesday, March 29, 2011 4:20 AM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] working with neuromag data > > Dear Kambiz, > > I think I see your point. Your data presumably is already preprocessed > and timelocked (averaged over trials) with neuromag software. I then > take it that you have 6 different conditions which you would like to > plot separately and possibly test at the group level. > > Since the data is already averaged, I'd recommend to do the following > to get your data back on track. > > 1) ft_preprocessing on your stimulus averaged epoch data. This should > give you a data structure with 6 trials (which are actually the > averages per condition). > > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat > this so you end up with 6 timelocked structures representing the 6 > different conditions. > > 3) plot or grandaverage (see tutorials how to proceed as your data now > should be 'ft-friendly'). > > Goodluck, > Arjen > > > > > > > ----- "Kambiz Tavabi" schreef: > > > Van: "Kambiz Tavabi" > > Aan: "Email discussion list for the FieldTrip project" > > > Verzonden: Dinsdag 29 maart 2011 01:10:14 > > Onderwerp: Re: [FieldTrip] working with neuromag data > > > > Dear Arjen - Thanks for your response. Just to clarify the low > level > > functions ft_read_header & ft_read_data are mentioned in the ft > > getting started tutorial. I believe they're recommended to make > sure > > the data is ft friendly. In my case the data is ft friendly. My > data > > is also pre-processed and already 'time-locked'--meaning that I > have > > stimulus averaged epoch data in fif format for all my subjects. My > > question is how to proceed from there? I've been through the pages > you > > refer to but have not been able to piece together my data in such a > > way to proceed with grand-averaging and carrying out stats. > > -Kambiz. > > ------------------------------------------------------------- > > Kambiz Tavabi PhD > > Biomedical Imaging Laboratory > > The Children's Hospital of Philadelphia > > 34th Street and Civic Center Boulevard > > Philadelphia, Pa. 19104 > > Tel: 267.426.0302 > > email: tavabik at email.chop.edu > > ------------------------------------------------------------- > > ________________________________________ > > From: fieldtrip-bounces at donders.ru.nl > > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > > [a.stolk at fcdonders.ru.nl] > > Sent: Monday, March 28, 2011 4:05 PM > > To: Email discussion list for the FieldTrip project > > Subject: Re: [FieldTrip] working with neuromag data > > > > Dear Kambiz, > > > > While you are able to use the 'low level' ft_read_header and > > ft_read_data functions, you should be able to preprocess and > analyze > > your neuromag data using the 'high level' functions such as > > ft_preprocessing (which calls the low level functions mentioned > > above). > > > > How to proceed depends on what you want to do with your data. If > you > > have triggers stored in your dataset that are synchronuous with the > > recorded brain activity, it'd be recommended to start with the > > following tutorial on how to select your trials: > > > > http://fieldtrip.fcdonders.nl/tutorial/preprocessing > > > > Since your experience with FT is still limited as you say, I > believe > > the following text may provide a good overview of what the data, > once > > read in to FT (i.e. matlab) environment, may look like: > > > > http://fieldtrip.fcdonders.nl/walkthrough > > > > Typically, your next steps involve single-subject timelocked > analysis, > > then grand-average and perform statistics at the group level. For > an > > overview of the steps and protocols, see: > > > > http://fieldtrip.fcdonders.nl/tutorial/analysis_protocols > > > > Hope this has helped for a start, > > > > Arjen > > > > > > ----- "Kambiz Tavabi" schreef: > > > > > Van: "Kambiz Tavabi" > > > Aan: "Email discussion list for the FieldTrip project" > > > > > Verzonden: Maandag 28 maart 2011 20:59:36 > > > Onderwerp: [FieldTrip] working with neuromag data > > > > > > Greetings - I have preprocessed/averaged neuromag data for a > group > > of > > > subjects that I'd like to visualize, compute grandaverage and > carry > > > out sensor level statistics on. The only help I managed to find > on > > the > > > Fieldtrip site/list Re: neurmag data concerns getting started > e.g., > > > with ft_read_header and ft_read_data. In my case these programs > > work > > > fine meaning that I can proceed with further analysis. > > > On a side, in my limited experience with FT, a major problem I > run > > > into frequently is that there is no clear suggestion(s) on how to > > > proceed with data that is not raw. I understand it is impossible > to > > > cover all analysis scenarios, but it is often the case that > working > > > with CTF, or in particular Elekta system, the data is likely to > be > > in > > > a post-preprocessed phase. Everytime I've tried to work with ft, > It > > > seems to me that if I don't start with square one in fieldtrip, > it > > is > > > difficult to figure out how to use downstream programs to work on > > the > > > data. > > > That said, in my case I have the output from ft_read_header: > > > > > > label: {338x1 cell} > > > nChans: 338 > > > Fs: 1000 > > > grad: [1x1 struct] > > > unit: {1x338 cell} > > > nSamples: 651 > > > nSamplesPre: 100 > > > nTrials: 6 > > > orig: [1x1 struct] > > > > > > and output from ft_read_data > > > > > > [338x651x6] that being channels by samples by number of stimulus > > > averaged epochs. To proceed, ideally I'd like to compute a > > > grandaverage for each condition, visualize them in a multiplot, > and > > > carry out sensor level stats. To be able to do this I understand > I > > > need the output from ft_timelockanalysis, how do I arrange my > data > > as > > > such? I am assuming it is already in that state. Thanks for your > > > time. > > > > > > -Kambiz. > > > ------------------------------------------------------------- > > > Kambiz Tavabi PhD > > > Biomedical Imaging Laboratory > > > The Children's Hospital of Philadelphia > > > 34th Street and Civic Center Boulevard > > > Philadelphia, Pa. 19104 > > > Tel: 267.426.0302 > > > email: tavabik at email.chop.edu > > > ------------------------------------------------------------- > > > _______________________________________________ > > > 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 > > _______________________________________________ > 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 marcel.heers at googlemail.com Mon Jun 13 23:48:04 2011 From: marcel.heers at googlemail.com (Marcel Heers) Date: Mon, 13 Jun 2011 23:48:04 +0200 Subject: [FieldTrip] courses In-Reply-To: <5B0A148A-D4F0-454F-B60B-E47ECCA47E75@donders.ru.nl> References: <32CC77C0C8A7AD4B9410934642608E1F03ECAF47@exchccr1.neuro.gu.se> <5B0A148A-D4F0-454F-B60B-E47ECCA47E75@donders.ru.nl> Message-ID: Dear Robert, might there be a chance for external person to participate in the fieldtrip course in Paris at the end of the year? Best regards, Marcel 2011/6/9 Robert Oostenveld : > Dear Elena > > For 2011 there are no courses planned any more in Nijmege, which are open to > external participants (there will be a course for local studens in the > Donders Graduate School in the autumn). The next course in Nijmegen will be > the MEG Toolkit course, which most likely will be somewhere in the spring of > 2012. > > For 2011 we are currently considering a course in Paris at the end of this > year. I believe that Stefan and Saskia are considering to do another course > in New York later this year, although I don't know any details for the New > York plans. > > At the upcoming HBM meeting in Quebec there will be an educational course in > which FieldTrip and the other open source academic toolboxes will play a > (relatively small) role. Although I don't think it is efficient to travel to > Quebec just for this part, it might be interesting for you to attend if you > are attending the HBM conference anyway. See > http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3437 > and for the program one of the last pages of > http://www.humanbrainmapping.org/files/2011MeetingFiles/Descriptions/HBM%202011%20Educational%20Program.pdf > > Please note that we are open to invitations for presenting the FieldTrip > course at external sites. This year we have already been in Tuebingen, St > Louis, and New York, and if there is an interesting venue, an enthousiastic > local organizer and funding can be arranged to cover the expenses, most > likely some experienced users/developers from Nijmegen can be found or > appointed to present a 2,5 day course at the external site. > > best regards, > Robert > > > > On 7 Jun 2011, at 12:53, Elena Orekhova wrote: > >> Dear FieldTrip gurus, >> >> Are you planning  any FieldTrip courses for the users in the nearest >> future? >> >> Elena >> >> _______________________________________________ >> 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 > -- Dr. Marcel Heers, M.D. Fischenbergstr. 10 D-58455 Witten phone: +49-2302-2034057 From jan.schoffelen at donders.ru.nl Wed Jun 15 15:51:01 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 15 Jun 2011 15:51:01 +0200 Subject: [FieldTrip] functionality change of ft_prepare_sourcemodel Message-ID: <0A5873EA-0666-4EDD-9AAB-13CA8EDA12FC@donders.ru.nl> Dear all, We implemented a slight change in the default behaviour of ft_prepare_sourcemodel. This is a fieldtrip function (often not called directly by you), which creates a specified source model for inverse reconstruction. Typically, this is a 3D regular grid, or a 2D mesh of the cortical sheet. The function is typically called with additional input arguments, specifying geometric objects, such as a volume conductor model of the head, or a description of the sensor-array. To make a long story short, before you had the option to specify cfg.sourceunits and cfg.mriunits. Cfg.sourceunits refers to the metrical unit of the dipole positions, and this defaulted (if you didn't explicitly specify it) to 'cm'. As of yet, it will default to the metrical units in the input data, i.e. the units of the sensor-array (if provided), or the units of the volume conductor of the head. For example, for neuromag and 4d- neuroimaging users the default will now be a grid with 'm' as a unit. Cfg.mriunits is as of now deprecated, and was used to specify the units of the (optional) input anatomical or segmented mri. Nowadays, these structures explicitly contain a unit, so that can be easily recovered from the data. We will build in explicit checks on the units in which different geometric objects are defined (many of those are already in place, e.g. ensuring same units for volume conductor model of the head and sensor positions) in the near future. For now, if you want to have explicitly the same behavior as before, you need to specify cfg.sourceunits to be 'cm'. Best wishes, Jan-Mathijs Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From cmuehl at gmail.com Thu Jun 16 18:22:02 2011 From: cmuehl at gmail.com (Christian Muehl) Date: Thu, 16 Jun 2011 18:22:02 +0200 Subject: [FieldTrip] Extended Deadline: Affective BCI Workshop, Memphis, USA Message-ID: ** Final Call for Papers - Extended Deadline ** 2nd Workshop on Affective Brain-Computer Interfaces (aBCI) Workshop at ACII 2011 (October 9-12), Memphis, USA, October 9, 2011 Apologies for multiple postings http://hmi.ewi.utwente.nl/abci2011 http://www.acii2011.org The second workshop on affective brain-computer interfaces will explore the advantages and limitations of using neuro-physiological signals as a modality for the automatic recognition of affective and cognitive states, and the possibilities of using this information about the user state in innovative and adaptive applications. The goal is to bring researchers from the communities of brain computer interfacing, affective computing, neuro-ergonomics, affective and cognitive neuroscience together to present state-of-the-art progress and visions on the various overlaps between those disciplines. Recent research in brain-computer interfaces (BCI) shows that brain activity can be used as an active/voluntary, or passive/involuntary control modality in man-machine interaction. While active BCI paradigms have received a lot of attention in recent years, research on passive approaches to BCI still desperately needs concerted activity. However, it has been shown more than once that brain activations can carry information about the affective and cognitive state of a subject, and that the interaction between humans and machines can be aided by the recognition of those user states. To achieve robust passive BCIs, efforts from applied and basic sciences have to be combined. On the one hand, applied fields such as affective computing aim at the development of applications that adapt to changes in the user states and thereby enrich the interaction, leading to a more natural and effective usability. On the other hand, basic research in neuroscience advances our understanding of the neural processes associated with emotions. Furthermore, similar advancements are being made for more cognitive mental states, for example, attention, fatigue, and work load, which strongly interact with affective states. Topics of interest include, but are not limited to: * emotion elicitation and data collection for affective BCI * detection of affective and cognitive states with BCI and other modalities * adaptive interfaces and affective BCI Invited Talk: 'Brain Dynamics of Affective Engagement' by Scott Makeig, SCCN, University of California at San Diego, USA The workshop will be held in conjunction with the 4th International conference on Affective Computing and Intelligent Interaction (ACII2011) at the FedEx Institute of Technology at the University of Memphis, TN. Submission Instructions * The papers should feature original empirical work, theoretical work, or a well defendable but arguable position of the authors (i.e., not submitted, in submission, or submitted to another conference or journal while in review). * Papers will be published in the proceedings of ACII 2011 by Springer. Papers should not exceed 10 pages and should be formatted according to the Springer LNCS formatting guidelines http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0. * Papers must be submitted as PDF through the EasyChair conference system, which can be accessed through the workshop web site and the ACII conference website. * For further information, contact abci at cs.utwente.nl Important Dates: 22nd of June: Workshop papers due 7th of July: Notification of Acceptance 24th of July: Camera-ready papers due 9th of October: Workshop Programme Chairs: * Anton Nijholt, Universiteit Twente, The Netherlands * Brendan Allison, TU Graz, Austria * Stephen Dunne, Starlab Barcelona, Spain * Dirk Heylen, University of Twente, The Netherlands Local Organizer: * Christian Mühl, University of Twente, The Netherlands Programme Committee: * Egon L. van den Broek, University of Twente, The Netherlands * Touradj Ebrahimi, EPFL, Lausanne, Switzerland * Peter Desain, Radboud University Nijmegen, The Netherlands * Jan B.F. van Erp, TNO Human Factors, Soesterberg, The Netherlands * Stephen Fairclough, John Moores University, Liverpool, UK * Gary Garcia Molina, Philips Research, Eindhoven, The Netherlands * Audrey Girouard, Queen's University, Kingston, Canada * Jonghwa Kim, University of Augsburg, Germany * Brent Lance, Army Research Laboratory/TNB, Aberdeen Proving Ground, USA * Robert Leeb, University of Lausanne, Switzerland * Scott Makeig, University of California at San Diego, USA * Femke Nijboer, University of Twente, The Netherlands * Ioannis Patras, Queen Mary University, London, UK * Thierry Pun, University of Geneva, Switzerland * Tanja Schultz, Karlsruhe Institute of Technology (KIT), Germany * Olga Sourina, NanYang Technological University, Singapore * Thomas J. Sullivan, NeuroSky, San Jose, USA * Thorsten Zander, Graz University of Technology, Austria From TAVABIK at email.chop.edu Thu Jun 16 18:31:54 2011 From: TAVABIK at email.chop.edu (Tavabi, Kambiz) Date: Thu, 16 Jun 2011 12:31:54 -0400 Subject: [FieldTrip] working with neuromag data In-Reply-To: <621524636.372728.1307777218636.JavaMail.root@sculptor.zimbra.ru.nl> References: , <621524636.372728.1307777218636.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Dear Arjen, The data.avg I am using to plot with ft_multiplotER is infact real numbers, quite small numbers on the order of x.xxxe-15, but I still get no visualization using cfg.ylim(min(data.avg), max(data.avg) or extremely small numbers eg., cfg.ylim [-3e-50 3e-50]. Conversely, ft_topoplotER seems to work just fine with the exception of a couple of warnings: 1- some points fall outside the outline, please consider using another layout >ft_plot_topo line 112 and ft_topoplotER line 719 2- Duplicate x-y data points detected: using average of the z values >ft_plot_topo line 144 and ft_topoplotER line 719. What does this warning mean? >From what I understand the ft_multiplotER step is necessary to carry out sensor level analysis of the data? As I mentioned previously, the grand average data structure does not contain the proper layout information that is in the timelock structure. Is this purposefully done, or am I doing something wrong here? Regards, -Kambiz. ------------------------------------------------------------- Kambiz Tavabi PhD Biomedical Imaging Laboratory The Children's Hospital of Philadelphia 34th Street and Civic Center Boulevard Philadelphia, Pa. 19104 Tel: 267.426.0302 email: tavabik at email.chop.edu ------------------------------------------------------------- ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. [a.stolk at fcdonders.ru.nl] Sent: Saturday, June 11, 2011 3:26 AM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] working with neuromag data Dear Kambiz, Does your data.avg contain NaNs or real numbers? In the latter case; do they fall in the plotting range as specified by your cfg.ylim? Yours, Arjen ----- "Kambiz Tavabi" schreef: > Van: "Kambiz Tavabi" > Aan: "Email discussion list for the FieldTrip project" > Verzonden: Vrijdag 10 juni 2011 18:59:03 > Onderwerp: Re: [FieldTrip] working with neuromag data > > As per advise from Arjen, I was able to use following steps > 1) ft_preprocessing on your stimulus averaged epoch data. This should > give you a data structure with 6 trials (which are actually the > averages per condition). > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat > this so you end up with 6 timelocked structures representing the 6 > different conditions. > to create individual condition averaged ft data structures which I can > visualize using ft_topoplotER(cfg,data) > data: > avg: [338x651 double] > var: [338x651 double] > fsample: 1000 > time: [1x651 double] > dof: [338x651 double] > label: {338x1 cell} > dimord: 'chan_time' > grad: [1x1 struct] > cfg: [1x1 struct] > however when i use; > cfg = []; > cfg.showlabels = 'yes'; > cfg.fontsize = 6; > cfg.ylim = [-10e-13 10e-13] > ft_multiplotER(cfg, data); > Fieldtrip chruns through creating the > selection avg along dimension 1 > selection dof along dimension 1 > selection var along dimension 1 > creating layout from data.grad > creating layout for neuromag306 system > > but the resutling figure is an empty figure containing only layout > with ch lables without any data what so ever. Any ideas why this might > be? > > > > -Kambiz. > ------------------------------------------------------------- > Kambiz Tavabi PhD > Biomedical Imaging Laboratory > The Children's Hospital of Philadelphia > 34th Street and Civic Center Boulevard > Philadelphia, Pa. 19104 > Tel: 267.426.0302 > email: tavabik at email.chop.edu > ------------------------------------------------------------- > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > [a.stolk at fcdonders.ru.nl] > Sent: Tuesday, March 29, 2011 4:20 AM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] working with neuromag data > > Dear Kambiz, > > I think I see your point. Your data presumably is already preprocessed > and timelocked (averaged over trials) with neuromag software. I then > take it that you have 6 different conditions which you would like to > plot separately and possibly test at the group level. > > Since the data is already averaged, I'd recommend to do the following > to get your data back on track. > > 1) ft_preprocessing on your stimulus averaged epoch data. This should > give you a data structure with 6 trials (which are actually the > averages per condition). > > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat > this so you end up with 6 timelocked structures representing the 6 > different conditions. > > 3) plot or grandaverage (see tutorials how to proceed as your data now > should be 'ft-friendly'). > > Goodluck, > Arjen > > > > > > > ----- "Kambiz Tavabi" schreef: > > > Van: "Kambiz Tavabi" > > Aan: "Email discussion list for the FieldTrip project" > > > Verzonden: Dinsdag 29 maart 2011 01:10:14 > > Onderwerp: Re: [FieldTrip] working with neuromag data > > > > Dear Arjen - Thanks for your response. Just to clarify the low > level > > functions ft_read_header & ft_read_data are mentioned in the ft > > getting started tutorial. I believe they're recommended to make > sure > > the data is ft friendly. In my case the data is ft friendly. My > data > > is also pre-processed and already 'time-locked'--meaning that I > have > > stimulus averaged epoch data in fif format for all my subjects. My > > question is how to proceed from there? I've been through the pages > you > > refer to but have not been able to piece together my data in such a > > way to proceed with grand-averaging and carrying out stats. > > -Kambiz. > > ------------------------------------------------------------- > > Kambiz Tavabi PhD > > Biomedical Imaging Laboratory > > The Children's Hospital of Philadelphia > > 34th Street and Civic Center Boulevard > > Philadelphia, Pa. 19104 > > Tel: 267.426.0302 > > email: tavabik at email.chop.edu > > ------------------------------------------------------------- > > ________________________________________ > > From: fieldtrip-bounces at donders.ru.nl > > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > > [a.stolk at fcdonders.ru.nl] > > Sent: Monday, March 28, 2011 4:05 PM > > To: Email discussion list for the FieldTrip project > > Subject: Re: [FieldTrip] working with neuromag data > > > > Dear Kambiz, > > > > While you are able to use the 'low level' ft_read_header and > > ft_read_data functions, you should be able to preprocess and > analyze > > your neuromag data using the 'high level' functions such as > > ft_preprocessing (which calls the low level functions mentioned > > above). > > > > How to proceed depends on what you want to do with your data. If > you > > have triggers stored in your dataset that are synchronuous with the > > recorded brain activity, it'd be recommended to start with the > > following tutorial on how to select your trials: > > > > http://fieldtrip.fcdonders.nl/tutorial/preprocessing > > > > Since your experience with FT is still limited as you say, I > believe > > the following text may provide a good overview of what the data, > once > > read in to FT (i.e. matlab) environment, may look like: > > > > http://fieldtrip.fcdonders.nl/walkthrough > > > > Typically, your next steps involve single-subject timelocked > analysis, > > then grand-average and perform statistics at the group level. For > an > > overview of the steps and protocols, see: > > > > http://fieldtrip.fcdonders.nl/tutorial/analysis_protocols > > > > Hope this has helped for a start, > > > > Arjen > > > > > > ----- "Kambiz Tavabi" schreef: > > > > > Van: "Kambiz Tavabi" > > > Aan: "Email discussion list for the FieldTrip project" > > > > > Verzonden: Maandag 28 maart 2011 20:59:36 > > > Onderwerp: [FieldTrip] working with neuromag data > > > > > > Greetings - I have preprocessed/averaged neuromag data for a > group > > of > > > subjects that I'd like to visualize, compute grandaverage and > carry > > > out sensor level statistics on. The only help I managed to find > on > > the > > > Fieldtrip site/list Re: neurmag data concerns getting started > e.g., > > > with ft_read_header and ft_read_data. In my case these programs > > work > > > fine meaning that I can proceed with further analysis. > > > On a side, in my limited experience with FT, a major problem I > run > > > into frequently is that there is no clear suggestion(s) on how to > > > proceed with data that is not raw. I understand it is impossible > to > > > cover all analysis scenarios, but it is often the case that > working > > > with CTF, or in particular Elekta system, the data is likely to > be > > in > > > a post-preprocessed phase. Everytime I've tried to work with ft, > It > > > seems to me that if I don't start with square one in fieldtrip, > it > > is > > > difficult to figure out how to use downstream programs to work on > > the > > > data. > > > That said, in my case I have the output from ft_read_header: > > > > > > label: {338x1 cell} > > > nChans: 338 > > > Fs: 1000 > > > grad: [1x1 struct] > > > unit: {1x338 cell} > > > nSamples: 651 > > > nSamplesPre: 100 > > > nTrials: 6 > > > orig: [1x1 struct] > > > > > > and output from ft_read_data > > > > > > [338x651x6] that being channels by samples by number of stimulus > > > averaged epochs. To proceed, ideally I'd like to compute a > > > grandaverage for each condition, visualize them in a multiplot, > and > > > carry out sensor level stats. To be able to do this I understand > I > > > need the output from ft_timelockanalysis, how do I arrange my > data > > as > > > such? I am assuming it is already in that state. Thanks for your > > > time. > > > > > > -Kambiz. > > > ------------------------------------------------------------- > > > Kambiz Tavabi PhD > > > Biomedical Imaging Laboratory > > > The Children's Hospital of Philadelphia > > > 34th Street and Civic Center Boulevard > > > Philadelphia, Pa. 19104 > > > Tel: 267.426.0302 > > > email: tavabik at email.chop.edu > > > ------------------------------------------------------------- > > > _______________________________________________ > > > 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 > > _______________________________________________ > 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 fieldtrip at greenant.net Thu Jun 16 18:42:58 2011 From: fieldtrip at greenant.net (frank@greenant.net) Date: Fri, 17 Jun 2011 02:42:58 +1000 Subject: [FieldTrip] Using ICA to filter data In-Reply-To: References: Message-ID: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> I am trying to use fieldtrip to filter EOG data obtained in an MRI. I want to be able to spot the saccades in the samples and ideally measure their onset at the end of each trial. As you may guess, it's quite noisy and it's broad spectrum noise, despite pre-filtering. Ideally, I would like to isolate the component that corresponds to the MRI interference and then filter this out. I have managed to import the data and can run ft_componentanalysis but it fails with: runica() - data size (1,30720) too small My data is single channel, 40 epochs, each of 6 seconds (time locked to stim onset but not saccade onset) Is there a different method I should be using? I have posted some sample data and the current script (which reads in the data and runs preprocessing) to the following urls: http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat http://greenant.net/temp/EOG_analysis.m From batrod at gmail.com Thu Jun 16 18:48:07 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Thu, 16 Jun 2011 11:48:07 -0500 Subject: [FieldTrip] Using ICA to filter data In-Reply-To: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> Message-ID: To summarize, the ICA will decompose your signal into as many components as Electrodes. Therefore, trying to decompose only one source is useless. Did you use a full net of electrodes into your MRI machine or only EOG electrodes? Hope this helps, Rodolphe N. On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net wrote: > I am trying to use fieldtrip to filter EOG data obtained in an MRI. > I want to be able to spot the saccades in the samples and ideally measure > their onset at the > end of each trial. > > As you may guess, it's quite noisy and it's broad spectrum noise, despite > pre-filtering. > > Ideally, I would like to isolate the component that corresponds to the MRI > interference > and then filter this out. > > I have managed to import the data and can run ft_componentanalysis > but it fails with: > > runica() - data size (1,30720) too small > > My data is single channel, 40 epochs, each of 6 seconds (time locked to > stim onset but not saccade onset) > Is there a different method I should be using? > > I have posted some sample data and the current script (which reads in the > data and runs preprocessing) to the following urls: > > http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat > http://greenant.net/temp/EOG_analysis.m > _______________________________________________ > 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 fieldtrip at greenant.net Thu Jun 16 20:16:45 2011 From: fieldtrip at greenant.net (frank@greenant.net) Date: Fri, 17 Jun 2011 04:16:45 +1000 Subject: [FieldTrip] Using ICA to filter data In-Reply-To: References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> Message-ID: It's a bit of a unique experiment, we're trying to use an ECG machine to acquire EOG, so it's only a single output channel. i guess what I need is a temporal ICA rather than a spatial one... On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: > To summarize, the ICA will decompose your signal into as many components as Electrodes. > Therefore, trying to decompose only one source is useless. > Did you use a full net of electrodes into your MRI machine or only EOG electrodes? > > Hope this helps, > > Rodolphe N. > > On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net wrote: > I am trying to use fieldtrip to filter EOG data obtained in an MRI. > I want to be able to spot the saccades in the samples and ideally measure their onset at the > end of each trial. > > As you may guess, it's quite noisy and it's broad spectrum noise, despite pre-filtering. > > Ideally, I would like to isolate the component that corresponds to the MRI interference > and then filter this out. > > I have managed to import the data and can run ft_componentanalysis > but it fails with: > > runica() - data size (1,30720) too small > > My data is single channel, 40 epochs, each of 6 seconds (time locked to stim onset but not saccade onset) > Is there a different method I should be using? > > I have posted some sample data and the current script (which reads in the > data and runs preprocessing) to the following urls: > > http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat > http://greenant.net/temp/EOG_analysis.m > _______________________________________________ > 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 a.stolk at fcdonders.ru.nl Thu Jun 16 20:33:38 2011 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Thu, 16 Jun 2011 20:33:38 +0200 (CEST) Subject: [FieldTrip] working with neuromag data In-Reply-To: <1394883530.423835.1308249012378.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <1699057884.423853.1308249218140.JavaMail.root@sculptor.zimbra.ru.nl> Dear Kambiz, To answer your first question, I do not know what this error when calling ft_topoplotER means. Secondly, ft_multiplotTFR is a visualization step of the data and not an analysis step. It is not necessary to call this function before proceeding, but giving that it works far from what you'd expect, it tells us something's wrong. :) At your third question; what do you mean with layout information? Information on the gradiometer and magnetometer definitions? Keep in mind that when creating a grand-average, you cannot effectively average these. Ok, for a plan de campagne; are you using the most recent version of FT? If so, could you send me your data in a .mat file? Please send it to my e-mail address and not the FT list. Yours, Arjen Are you using the most recent version of FT? ----- "Kambiz Tavabi" schreef: > Van: "Kambiz Tavabi" > Aan: "Email discussion list for the FieldTrip project" > Verzonden: Donderdag 16 juni 2011 18:31:54 > Onderwerp: Re: [FieldTrip] working with neuromag data > > Dear Arjen, > The data.avg I am using to plot with ft_multiplotER is infact real > numbers, quite small numbers on the order of x.xxxe-15, but I still > get no visualization using cfg.ylim(min(data.avg), max(data.avg) or > extremely small numbers eg., cfg.ylim [-3e-50 3e-50]. Conversely, > ft_topoplotER seems to work just fine with the exception of a couple > of warnings: > 1- some points fall outside the outline, please consider using another > layout >ft_plot_topo line 112 and ft_topoplotER line 719 > 2- Duplicate x-y data points detected: using average of the z values > >ft_plot_topo line 144 and ft_topoplotER line 719. What does this > warning mean? > > >From what I understand the ft_multiplotER step is necessary to carry > out sensor level analysis of the data? > > As I mentioned previously, the grand average data structure does not > contain the proper layout information that is in the timelock > structure. Is this purposefully done, or am I doing something wrong > here? > > Regards, > > -Kambiz. > ------------------------------------------------------------- > Kambiz Tavabi PhD > Biomedical Imaging Laboratory > The Children's Hospital of Philadelphia > 34th Street and Civic Center Boulevard > Philadelphia, Pa. 19104 > Tel: 267.426.0302 > email: tavabik at email.chop.edu > ------------------------------------------------------------- > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > [a.stolk at fcdonders.ru.nl] > Sent: Saturday, June 11, 2011 3:26 AM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] working with neuromag data > > Dear Kambiz, > > Does your data.avg contain NaNs or real numbers? In the latter case; > do they fall in the plotting range as specified by your cfg.ylim? > > Yours, > Arjen > > ----- "Kambiz Tavabi" schreef: > > > Van: "Kambiz Tavabi" > > Aan: "Email discussion list for the FieldTrip project" > > > Verzonden: Vrijdag 10 juni 2011 18:59:03 > > Onderwerp: Re: [FieldTrip] working with neuromag data > > > > As per advise from Arjen, I was able to use following steps > > 1) ft_preprocessing on your stimulus averaged epoch data. This > should > > give you a data structure with 6 trials (which are actually the > > averages per condition). > > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And > repeat > > this so you end up with 6 timelocked structures representing the 6 > > different conditions. > > to create individual condition averaged ft data structures which I > can > > visualize using ft_topoplotER(cfg,data) > > data: > > avg: [338x651 double] > > var: [338x651 double] > > fsample: 1000 > > time: [1x651 double] > > dof: [338x651 double] > > label: {338x1 cell} > > dimord: 'chan_time' > > grad: [1x1 struct] > > cfg: [1x1 struct] > > however when i use; > > cfg = []; > > cfg.showlabels = 'yes'; > > cfg.fontsize = 6; > > cfg.ylim = [-10e-13 10e-13] > > ft_multiplotER(cfg, data); > > Fieldtrip chruns through creating the > > selection avg along dimension 1 > > selection dof along dimension 1 > > selection var along dimension 1 > > creating layout from data.grad > > creating layout for neuromag306 system > > > > but the resutling figure is an empty figure containing only layout > > with ch lables without any data what so ever. Any ideas why this > might > > be? > > > > > > > > -Kambiz. > > ------------------------------------------------------------- > > Kambiz Tavabi PhD > > Biomedical Imaging Laboratory > > The Children's Hospital of Philadelphia > > 34th Street and Civic Center Boulevard > > Philadelphia, Pa. 19104 > > Tel: 267.426.0302 > > email: tavabik at email.chop.edu > > ------------------------------------------------------------- > > ________________________________________ > > From: fieldtrip-bounces at donders.ru.nl > > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > > [a.stolk at fcdonders.ru.nl] > > Sent: Tuesday, March 29, 2011 4:20 AM > > To: Email discussion list for the FieldTrip project > > Subject: Re: [FieldTrip] working with neuromag data > > > > Dear Kambiz, > > > > I think I see your point. Your data presumably is already > preprocessed > > and timelocked (averaged over trials) with neuromag software. I > then > > take it that you have 6 different conditions which you would like > to > > plot separately and possibly test at the group level. > > > > Since the data is already averaged, I'd recommend to do the > following > > to get your data back on track. > > > > 1) ft_preprocessing on your stimulus averaged epoch data. This > should > > give you a data structure with 6 trials (which are actually the > > averages per condition). > > > > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And > repeat > > this so you end up with 6 timelocked structures representing the 6 > > different conditions. > > > > 3) plot or grandaverage (see tutorials how to proceed as your data > now > > should be 'ft-friendly'). > > > > Goodluck, > > Arjen > > > > > > > > > > > > > > ----- "Kambiz Tavabi" schreef: > > > > > Van: "Kambiz Tavabi" > > > Aan: "Email discussion list for the FieldTrip project" > > > > > Verzonden: Dinsdag 29 maart 2011 01:10:14 > > > Onderwerp: Re: [FieldTrip] working with neuromag data > > > > > > Dear Arjen - Thanks for your response. Just to clarify the low > > level > > > functions ft_read_header & ft_read_data are mentioned in the ft > > > getting started tutorial. I believe they're recommended to make > > sure > > > the data is ft friendly. In my case the data is ft friendly. My > > data > > > is also pre-processed and already 'time-locked'--meaning that I > > have > > > stimulus averaged epoch data in fif format for all my subjects. > My > > > question is how to proceed from there? I've been through the > pages > > you > > > refer to but have not been able to piece together my data in such > a > > > way to proceed with grand-averaging and carrying out stats. > > > -Kambiz. > > > ------------------------------------------------------------- > > > Kambiz Tavabi PhD > > > Biomedical Imaging Laboratory > > > The Children's Hospital of Philadelphia > > > 34th Street and Civic Center Boulevard > > > Philadelphia, Pa. 19104 > > > Tel: 267.426.0302 > > > email: tavabik at email.chop.edu > > > ------------------------------------------------------------- > > > ________________________________________ > > > From: fieldtrip-bounces at donders.ru.nl > > > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > > > [a.stolk at fcdonders.ru.nl] > > > Sent: Monday, March 28, 2011 4:05 PM > > > To: Email discussion list for the FieldTrip project > > > Subject: Re: [FieldTrip] working with neuromag data > > > > > > Dear Kambiz, > > > > > > While you are able to use the 'low level' ft_read_header and > > > ft_read_data functions, you should be able to preprocess and > > analyze > > > your neuromag data using the 'high level' functions such as > > > ft_preprocessing (which calls the low level functions mentioned > > > above). > > > > > > How to proceed depends on what you want to do with your data. If > > you > > > have triggers stored in your dataset that are synchronuous with > the > > > recorded brain activity, it'd be recommended to start with the > > > following tutorial on how to select your trials: > > > > > > http://fieldtrip.fcdonders.nl/tutorial/preprocessing > > > > > > Since your experience with FT is still limited as you say, I > > believe > > > the following text may provide a good overview of what the data, > > once > > > read in to FT (i.e. matlab) environment, may look like: > > > > > > http://fieldtrip.fcdonders.nl/walkthrough > > > > > > Typically, your next steps involve single-subject timelocked > > analysis, > > > then grand-average and perform statistics at the group level. For > > an > > > overview of the steps and protocols, see: > > > > > > http://fieldtrip.fcdonders.nl/tutorial/analysis_protocols > > > > > > Hope this has helped for a start, > > > > > > Arjen > > > > > > > > > ----- "Kambiz Tavabi" schreef: > > > > > > > Van: "Kambiz Tavabi" > > > > Aan: "Email discussion list for the FieldTrip project" > > > > > > > Verzonden: Maandag 28 maart 2011 20:59:36 > > > > Onderwerp: [FieldTrip] working with neuromag data > > > > > > > > Greetings - I have preprocessed/averaged neuromag data for a > > group > > > of > > > > subjects that I'd like to visualize, compute grandaverage and > > carry > > > > out sensor level statistics on. The only help I managed to find > > on > > > the > > > > Fieldtrip site/list Re: neurmag data concerns getting started > > e.g., > > > > with ft_read_header and ft_read_data. In my case these programs > > > work > > > > fine meaning that I can proceed with further analysis. > > > > On a side, in my limited experience with FT, a major problem I > > run > > > > into frequently is that there is no clear suggestion(s) on how > to > > > > proceed with data that is not raw. I understand it is > impossible > > to > > > > cover all analysis scenarios, but it is often the case that > > working > > > > with CTF, or in particular Elekta system, the data is likely to > > be > > > in > > > > a post-preprocessed phase. Everytime I've tried to work with > ft, > > It > > > > seems to me that if I don't start with square one in fieldtrip, > > it > > > is > > > > difficult to figure out how to use downstream programs to work > on > > > the > > > > data. > > > > That said, in my case I have the output from ft_read_header: > > > > > > > > label: {338x1 cell} > > > > nChans: 338 > > > > Fs: 1000 > > > > grad: [1x1 struct] > > > > unit: {1x338 cell} > > > > nSamples: 651 > > > > nSamplesPre: 100 > > > > nTrials: 6 > > > > orig: [1x1 struct] > > > > > > > > and output from ft_read_data > > > > > > > > [338x651x6] that being channels by samples by number of > stimulus > > > > averaged epochs. To proceed, ideally I'd like to compute a > > > > grandaverage for each condition, visualize them in a multiplot, > > and > > > > carry out sensor level stats. To be able to do this I > understand > > I > > > > need the output from ft_timelockanalysis, how do I arrange my > > data > > > as > > > > such? I am assuming it is already in that state. Thanks for > your > > > > time. > > > > > > > > -Kambiz. > > > > ------------------------------------------------------------- > > > > Kambiz Tavabi PhD > > > > Biomedical Imaging Laboratory > > > > The Children's Hospital of Philadelphia > > > > 34th Street and Civic Center Boulevard > > > > Philadelphia, Pa. 19104 > > > > Tel: 267.426.0302 > > > > email: tavabik at email.chop.edu > > > > ------------------------------------------------------------- > > > > _______________________________________________ > > > > 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 > > > > _______________________________________________ > > 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 bibi.raquel at gmail.com Thu Jun 16 21:38:31 2011 From: bibi.raquel at gmail.com (Raquel Bibi) Date: Thu, 16 Jun 2011 15:38:31 -0400 Subject: [FieldTrip] Reading data from ASA 4 Message-ID: Dear Fieldtrippers, I am trying to read in ASA 4 files that were saved as an EEGProbe .cnt file. I am using Windows 7 64bit and Matlab 2010. Although I've downloaded the newest files from ANT, I an unable to read the proper MEX files. Is there something special I must do in order for Matlab to invoke the MEX file. I believe the files from ANT have already been compiled. Since I am unfamiliar with MEX files and our new EEG system, any information would be greatly appreciated. Currently, get errors due to the fact that the MEX file are not being used. Thanks, Raquel -------------- next part -------------- An HTML attachment was scrubbed... URL: From batrod at gmail.com Fri Jun 17 00:37:45 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Thu, 16 Jun 2011 17:37:45 -0500 Subject: [FieldTrip] Using ICA to filter data In-Reply-To: References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> Message-ID: Im still afraid that the power of this analysis will be very low. Maybe you can try an ICA on your fMRI data and try to correlate each component with your EOG timecourse. Rodolphe N. On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net wrote: > It's a bit of a unique experiment, we're trying to use an ECG machine > to acquire EOG, so it's only a single output channel. > > i guess what I need is a temporal ICA rather than a spatial one... > > On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: > > To summarize, the ICA will decompose your signal into as many components as > Electrodes. > Therefore, trying to decompose only one source is useless. > Did you use a full net of electrodes into your MRI machine or only EOG > electrodes? > > Hope this helps, > > Rodolphe N. > > On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net < > fieldtrip at greenant.net> wrote: > >> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >> I want to be able to spot the saccades in the samples and ideally measure >> their onset at the >> end of each trial. >> >> As you may guess, it's quite noisy and it's broad spectrum noise, despite >> pre-filtering. >> >> Ideally, I would like to isolate the component that corresponds to the MRI >> interference >> and then filter this out. >> >> I have managed to import the data and can run ft_componentanalysis >> but it fails with: >> >> runica() - data size (1,30720) too small >> >> My data is single channel, 40 epochs, each of 6 seconds (time locked to >> stim onset but not saccade onset) >> Is there a different method I should be using? >> >> I have posted some sample data and the current script (which reads in the >> data and runs preprocessing) to the following urls: >> >> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >> http://greenant.net/temp/EOG_analysis.m >> _______________________________________________ >> 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 smoratti at psi.ucm.es Fri Jun 17 09:01:45 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Fri, 17 Jun 2011 09:01:45 +0200 Subject: [FieldTrip] Problems with Neuromag Data after SSS In-Reply-To: References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> Message-ID: <76A4F15A-0795-44E8-8658-AA73CAA45CD9@psi.ucm.es> Hello everybody, I had no problems reading Neuromag data, but when I want to read data treated with SSS I get the following error: ??? Error using ==> fiff_read_tag at 232 Cannot handle other than dense or sparse matrices yet Error in ==> fiff_open at 80 tag = fiff_read_tag(fid,dirpos); Error in ==> fiff_read_meas_info at 82 [ fid, tree ] = fiff_open(source); Error in ==> ft_read_header at 1049 orig = fiff_read_meas_info(filename); Error in ==> mytrialfun_Neuromag_face at 3 hdr = ft_read_header(cfg.dataset); Error in ==> ft_definetrial at 139 trl = feval(cfg.trialfun, cfg); Any idea, what I could do? Best, Stephan El 17/06/2011, a las 0:37, Rodolphe Nenert escribió: > Im still afraid that the power of this analysis will be very low. > Maybe you can try an ICA on your fMRI data and try to correlate each > component with your EOG timecourse. > > Rodolphe N. > > On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net > wrote: > It's a bit of a unique experiment, we're trying to use an ECG machine > to acquire EOG, so it's only a single output channel. > > i guess what I need is a temporal ICA rather than a spatial one... > > On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: > >> To summarize, the ICA will decompose your signal into as many >> components as Electrodes. >> Therefore, trying to decompose only one source is useless. >> Did you use a full net of electrodes into your MRI machine or only >> EOG electrodes? >> >> Hope this helps, >> >> Rodolphe N. >> >> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net > > wrote: >> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >> I want to be able to spot the saccades in the samples and ideally >> measure their onset at the >> end of each trial. >> >> As you may guess, it's quite noisy and it's broad spectrum noise, >> despite pre-filtering. >> >> Ideally, I would like to isolate the component that corresponds to >> the MRI interference >> and then filter this out. >> >> I have managed to import the data and can run ft_componentanalysis >> but it fails with: >> >> runica() - data size (1,30720) too small >> >> My data is single channel, 40 epochs, each of 6 seconds (time >> locked to stim onset but not saccade onset) >> Is there a different method I should be using? >> >> I have posted some sample data and the current script (which reads >> in the >> data and runs preprocessing) to the following urls: >> >> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >> http://greenant.net/temp/EOG_analysis.m >> _______________________________________________ >> 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 ________________________________________________________ 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 lhunt at fmrib.ox.ac.uk Fri Jun 17 09:28:27 2011 From: lhunt at fmrib.ox.ac.uk (Laurence Hunt) Date: Fri, 17 Jun 2011 08:28:27 +0100 Subject: [FieldTrip] Problems with Neuromag Data after SSS In-Reply-To: <76A4F15A-0795-44E8-8658-AA73CAA45CD9@psi.ucm.es> References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> <76A4F15A-0795-44E8-8658-AA73CAA45CD9@psi.ucm.es> Message-ID: <32F04EF7-8D0F-4C73-9C3D-11AB66BF8E81@fmrib.ox.ac.uk> Hi Stephan, Did you do anything else to the data besides applying SSS? I use SSS on all my data and haven't encountered this problem before. Does it apply to all your datasets or just one specific file? Laurence =========================================== Laurence Hunt, DPhil Student Centre for Functional MRI of the Brain (FMRIB), University of Oxford lhunt at fmrib.ox.ac.uk Phone: (+44)1865-(2)22738 =========================================== On 17 Jun 2011, at 08:01, Stephan Moratti wrote: > Hello everybody, > > I had no problems reading Neuromag data, but when I want to read data treated with SSS I get the following error: > > ??? Error using ==> fiff_read_tag at 232 > Cannot handle other than dense or sparse matrices yet > > Error in ==> fiff_open at 80 > tag = fiff_read_tag(fid,dirpos); > > Error in ==> fiff_read_meas_info at 82 > [ fid, tree ] = fiff_open(source); > > Error in ==> ft_read_header at 1049 > orig = fiff_read_meas_info(filename); > > Error in ==> mytrialfun_Neuromag_face at 3 > hdr = ft_read_header(cfg.dataset); > > Error in ==> ft_definetrial at 139 > trl = feval(cfg.trialfun, cfg); > > Any idea, what I could do? > > Best, > > Stephan > > > El 17/06/2011, a las 0:37, Rodolphe Nenert escribió: > >> Im still afraid that the power of this analysis will be very low. >> Maybe you can try an ICA on your fMRI data and try to correlate each component with your EOG timecourse. >> >> Rodolphe N. >> >> On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net wrote: >> It's a bit of a unique experiment, we're trying to use an ECG machine >> to acquire EOG, so it's only a single output channel. >> >> i guess what I need is a temporal ICA rather than a spatial one... >> >> On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: >> >>> To summarize, the ICA will decompose your signal into as many components as Electrodes. >>> Therefore, trying to decompose only one source is useless. >>> Did you use a full net of electrodes into your MRI machine or only EOG electrodes? >>> >>> Hope this helps, >>> >>> Rodolphe N. >>> >>> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net wrote: >>> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >>> I want to be able to spot the saccades in the samples and ideally measure their onset at the >>> end of each trial. >>> >>> As you may guess, it's quite noisy and it's broad spectrum noise, despite pre-filtering. >>> >>> Ideally, I would like to isolate the component that corresponds to the MRI interference >>> and then filter this out. >>> >>> I have managed to import the data and can run ft_componentanalysis >>> but it fails with: >>> >>> runica() - data size (1,30720) too small >>> >>> My data is single channel, 40 epochs, each of 6 seconds (time locked to stim onset but not saccade onset) >>> Is there a different method I should be using? >>> >>> I have posted some sample data and the current script (which reads in the >>> data and runs preprocessing) to the following urls: >>> >>> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >>> http://greenant.net/temp/EOG_analysis.m >>> _______________________________________________ >>> 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 > > > ________________________________________________________ > 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 > > > _______________________________________________ > 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 sherrykhan78 at gmail.com Sat Jun 18 00:28:14 2011 From: sherrykhan78 at gmail.com (Sheraz Khan) Date: Fri, 17 Jun 2011 18:28:14 -0400 Subject: [FieldTrip] Suitable value of cfg.wcm_weight Message-ID: Hello everyone. I am new to fieldtrip, and using "cluster based statistics", I am using "cfg.clusterstatistics=wcm" as my option. Can any experience field-tripper suggest suitable value of* "cfg.wcm_weight"*, Thanks Sheraz On Fri, Jun 17, 2011 at 3:01 AM, Stephan Moratti wrote: > Hello everybody, > > I had no problems reading Neuromag data, but when I want to read data > treated with SSS I get the following error: > > ??? Error using ==> fiff_read_tag at 232 > Cannot handle other than dense or sparse matrices yet > > Error in ==> fiff_open at 80 > tag = fiff_read_tag(fid,dirpos); > > Error in ==> fiff_read_meas_info at 82 > [ fid, tree ] = fiff_open(source); > > Error in ==> ft_read_header at 1049 > orig = fiff_read_meas_info(filename); > > Error in ==> mytrialfun_Neuromag_face at 3 > hdr = ft_read_header(cfg.dataset); > > Error in ==> ft_definetrial at 139 > trl = feval(cfg.trialfun, cfg); > > Any idea, what I could do? > > Best, > > Stephan > > > El 17/06/2011, a las 0:37, Rodolphe Nenert escribió: > > Im still afraid that the power of this analysis will be very low. > Maybe you can try an ICA on your fMRI data and try to correlate each > component with your EOG timecourse. > > Rodolphe N. > > On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net < > fieldtrip at greenant.net> wrote: > >> It's a bit of a unique experiment, we're trying to use an ECG machine >> to acquire EOG, so it's only a single output channel. >> >> i guess what I need is a temporal ICA rather than a spatial one... >> >> On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: >> >> To summarize, the ICA will decompose your signal into as many components >> as Electrodes. >> Therefore, trying to decompose only one source is useless. >> Did you use a full net of electrodes into your MRI machine or only EOG >> electrodes? >> >> Hope this helps, >> >> Rodolphe N. >> >> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net < >> fieldtrip at greenant.net> wrote: >> >>> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >>> I want to be able to spot the saccades in the samples and ideally measure >>> their onset at the >>> end of each trial. >>> >>> As you may guess, it's quite noisy and it's broad spectrum noise, despite >>> pre-filtering. >>> >>> Ideally, I would like to isolate the component that corresponds to the >>> MRI interference >>> and then filter this out. >>> >>> I have managed to import the data and can run ft_componentanalysis >>> but it fails with: >>> >>> runica() - data size (1,30720) too small >>> >>> My data is single channel, 40 epochs, each of 6 seconds (time locked to >>> stim onset but not saccade onset) >>> Is there a different method I should be using? >>> >>> I have posted some sample data and the current script (which reads in the >>> data and runs preprocessing) to the following urls: >>> >>> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >>> http://greenant.net/temp/EOG_analysis.m >>> _______________________________________________ >>> 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 > > > > ________________________________________________________ > 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 > > > > _______________________________________________ > 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 fieldtrip at greenant.net Sat Jun 18 08:56:57 2011 From: fieldtrip at greenant.net (frank@greenant.net) Date: Sat, 18 Jun 2011 16:56:57 +1000 Subject: [FieldTrip] Using ICA to filter data In-Reply-To: References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> Message-ID: <17D1903D-8B16-4CA7-8581-7D6221A57E59@greenant.net> My apologies, I think I may have been a bit unclear about the aims of collecting the data. We're aiming to measure saccadic onset from the signal on a per-trial basis. I was hoping to isolate the MRI noise "component" and subtract this from the EOG signal component to give a cleaner EOG signal. Can the ICA module be applied in the temporal domain in this fashion? There are 40 single session trials of 6 seconds each, I would have thought that'd be enough data to give it a try. Also open to any suggestions as to other adaptive filter techniques.... Thanks On 17/06/2011, at 8:37 AM, Rodolphe Nenert wrote: > Im still afraid that the power of this analysis will be very low. > Maybe you can try an ICA on your fMRI data and try to correlate each component with your EOG timecourse. > > Rodolphe N. > > On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net wrote: > It's a bit of a unique experiment, we're trying to use an ECG machine > to acquire EOG, so it's only a single output channel. > > i guess what I need is a temporal ICA rather than a spatial one... > > On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: > >> To summarize, the ICA will decompose your signal into as many components as Electrodes. >> Therefore, trying to decompose only one source is useless. >> Did you use a full net of electrodes into your MRI machine or only EOG electrodes? >> >> Hope this helps, >> >> Rodolphe N. >> >> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net wrote: >> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >> I want to be able to spot the saccades in the samples and ideally measure their onset at the >> end of each trial. >> >> As you may guess, it's quite noisy and it's broad spectrum noise, despite pre-filtering. >> >> Ideally, I would like to isolate the component that corresponds to the MRI interference >> and then filter this out. >> >> I have managed to import the data and can run ft_componentanalysis >> but it fails with: >> >> runica() - data size (1,30720) too small >> >> My data is single channel, 40 epochs, each of 6 seconds (time locked to stim onset but not saccade onset) >> Is there a different method I should be using? >> >> I have posted some sample data and the current script (which reads in the >> data and runs preprocessing) to the following urls: >> >> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >> http://greenant.net/temp/EOG_analysis.m >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From manuel.mercier at einstein.yu.edu Sat Jun 18 11:09:55 2011 From: manuel.mercier at einstein.yu.edu (Manuel Mercier) Date: Sat, 18 Jun 2011 05:09:55 -0400 Subject: [FieldTrip] wavelet analysis Message-ID: <6ac7ddd3f73a325534c24be6edd039d2.squirrel@netmail.aecom.yu.edu> Dear Field-trippers I recently ran some time frequency analysis using the wavelet method. I was surprise to see that whereas I asked for a step of 1Hz, it was not the case every alternate step (for foi=2:1:10 ; I got [2 3.2 4 5.2 6 7.2 8 9.2 10]), and it was also the case when I changed the toi (2.5, 1.5 with constant trials length of 2.5 sec and sampling freq 1000Hz). I found a kind of explanation following the faq (http://fieldtrip.fcdonders.nl/faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_wavelet_formerly_wltconvol_in_ft_freqanalyis). Still it is not clear to me why this refers to Fourier transform. >From my (none specialist) point of view it is possible to produce a wavelet of any size (Hz;Dt). It is clear that there is some limitations based on the duration of the epochs and the number of time points. But in the present case it shouldn't be a problem, is it? Would be please if someone can help me with this issue. Thanks in advance Manuel From yossiarzouan at ucla.edu Sat Jun 18 17:37:27 2011 From: yossiarzouan at ucla.edu (Yossi Arzouan) Date: Sat, 18 Jun 2011 18:37:27 +0300 Subject: [FieldTrip] influences between the regions In-Reply-To: <1324085935.896862.1306654007541.JavaMail.fmail@mwmweb084> References: <1324085935.896862.1306654007541.JavaMail.fmail@mwmweb084> Message-ID: Dear Aka if that is still relevant maybe our lately published paper on connectivity using Complexity System approach can be a starting point : http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0019345 Big Words, Halved Brains and Small Worlds: Complex Brain Networks of Figurative Language Comprehension Best Wishes Yossi On Sun, May 29, 2011 at 10:26 AM, Michael Wibral wrote: > Dear Aka, > > there is a connectivity Toolbox in fieldtrip, isn't there? > At least I know there was something under development so maybe someone on > the list can help out. > > If that doesn't help or if you are specifically interested in information > transfer you might also try the transfer entropy toolbox 'TRENTOOL' ( > www.trentool.de). > > Michael > > > ------------------------------ > *Von:* "Aka Demon" > *Gesendet:* May 27, 2011 10:43:11 AM > *An:* fieldtrip at donders.ru.nl > *Betreff:* [FieldTrip] influences between the regions > > > Dear experts > > After analyzing memory experiment EEG/MEG and source localization data, i > figured out that there is little I can say about the interactions between > the activated regions as I don’t have any information about the connection > between the activated areas. > > So I was wondering if there are some useful works/tools that I can use to > explorer the influences between the regions (such as information transfer > from one region to the other). > > Thanks a lot > > Aka > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- ____________________________________________________________ Yossi Arzouan, PhD Postdoctoral Fellow at UCLA (Zaidel Lab.) and Haifa Univ (Breznitz and Karni Labs) Cell : 972-54-4446645; Skype : yossi_arzouan www : http://www.complexity-research.org/user/yossiarzouan http://faculty.biu.ac.il/~goldsa/index.html http://www.zaidellab.org/ http://ejsafra.haifa.ac.il/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Sun Jun 19 17:20:41 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Sun, 19 Jun 2011 17:20:41 +0200 Subject: [FieldTrip] Problems with Neuromag Data after SSS In-Reply-To: <32F04EF7-8D0F-4C73-9C3D-11AB66BF8E81@fmrib.ox.ac.uk> References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> <76A4F15A-0795-44E8-8658-AA73CAA45CD9@psi.ucm.es> <32F04EF7-8D0F-4C73-9C3D-11AB66BF8E81@fmrib.ox.ac.uk> Message-ID: Hi Lauren, Thanks for your reply. Yes I had it with 6 data sets where SSS was applied. I had them copied from the HP workstation to our server and from there to my Mac. Could it be a little and big endian thing provoked by moving the files from different platforms? Stephan El 17/06/2011, a las 9:28, Laurence Hunt escribió: > Hi Stephan, > > Did you do anything else to the data besides applying SSS? I use SSS > on all my data and haven't encountered this problem before. Does it > apply to all your datasets or just one specific file? > > Laurence > > =========================================== > Laurence Hunt, DPhil Student > Centre for Functional MRI of the Brain (FMRIB), > University of Oxford > lhunt at fmrib.ox.ac.uk > Phone: (+44)1865-(2)22738 > =========================================== > > On 17 Jun 2011, at 08:01, Stephan Moratti wrote: > >> Hello everybody, >> >> I had no problems reading Neuromag data, but when I want to read >> data treated with SSS I get the following error: >> >> ??? Error using ==> fiff_read_tag at 232 >> Cannot handle other than dense or sparse matrices yet >> >> Error in ==> fiff_open at 80 >> tag = fiff_read_tag(fid,dirpos); >> >> Error in ==> fiff_read_meas_info at 82 >> [ fid, tree ] = fiff_open(source); >> >> Error in ==> ft_read_header at 1049 >> orig = fiff_read_meas_info(filename); >> >> Error in ==> mytrialfun_Neuromag_face at 3 >> hdr = ft_read_header(cfg.dataset); >> >> Error in ==> ft_definetrial at 139 >> trl = feval(cfg.trialfun, cfg); >> >> Any idea, what I could do? >> >> Best, >> >> Stephan >> >> >> El 17/06/2011, a las 0:37, Rodolphe Nenert escribió: >> >>> Im still afraid that the power of this analysis will be very low. >>> Maybe you can try an ICA on your fMRI data and try to correlate >>> each component with your EOG timecourse. >>> >>> Rodolphe N. >>> >>> On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net >> > wrote: >>> It's a bit of a unique experiment, we're trying to use an ECG >>> machine >>> to acquire EOG, so it's only a single output channel. >>> >>> i guess what I need is a temporal ICA rather than a spatial one... >>> >>> On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: >>> >>>> To summarize, the ICA will decompose your signal into as many >>>> components as Electrodes. >>>> Therefore, trying to decompose only one source is useless. >>>> Did you use a full net of electrodes into your MRI machine or >>>> only EOG electrodes? >>>> >>>> Hope this helps, >>>> >>>> Rodolphe N. >>>> >>>> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net >>> > wrote: >>>> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >>>> I want to be able to spot the saccades in the samples and ideally >>>> measure their onset at the >>>> end of each trial. >>>> >>>> As you may guess, it's quite noisy and it's broad spectrum noise, >>>> despite pre-filtering. >>>> >>>> Ideally, I would like to isolate the component that corresponds >>>> to the MRI interference >>>> and then filter this out. >>>> >>>> I have managed to import the data and can run ft_componentanalysis >>>> but it fails with: >>>> >>>> runica() - data size (1,30720) too small >>>> >>>> My data is single channel, 40 epochs, each of 6 seconds (time >>>> locked to stim onset but not saccade onset) >>>> Is there a different method I should be using? >>>> >>>> I have posted some sample data and the current script (which >>>> reads in the >>>> data and runs preprocessing) to the following urls: >>>> >>>> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >>>> http://greenant.net/temp/EOG_analysis.m >>>> _______________________________________________ >>>> 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 >> >> >> ________________________________________________________ >> 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 >> >> >> _______________________________________________ >> 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 ________________________________________________________ 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 v.litvak at ion.ucl.ac.uk Sun Jun 19 21:08:45 2011 From: v.litvak at ion.ucl.ac.uk (Vladimir Litvak) Date: Sun, 19 Jun 2011 20:08:45 +0100 Subject: [FieldTrip] Problems with Neuromag Data after SSS In-Reply-To: References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> <76A4F15A-0795-44E8-8658-AA73CAA45CD9@psi.ucm.es> <32F04EF7-8D0F-4C73-9C3D-11AB66BF8E81@fmrib.ox.ac.uk> Message-ID: Dear Stephan, It might be that or that you transferred the files as ascii in FTP rather than binary. I've seen this error before and showed the file to Matti Hamalainen. He said the file was corrupted. Best, Vladimir On Sun, Jun 19, 2011 at 4:20 PM, Stephan Moratti wrote: > Hi Lauren, > Thanks for your reply. Yes I had it with 6 data sets where SSS was applied. > I had them copied from the HP workstation to our server and from there to my > Mac. Could it be a little and big endian thing provoked by moving the files > from different platforms? > Stephan > El 17/06/2011, a las 9:28, Laurence Hunt escribió: > > Hi Stephan, > Did you do anything else to the data besides applying SSS? I use SSS on all > my data and haven't encountered this problem before. Does it apply to all > your datasets or just one specific file? > Laurence > =========================================== > Laurence Hunt, DPhil Student >  Centre for Functional MRI of the Brain (FMRIB), > University of Oxford > lhunt at fmrib.ox.ac.uk > Phone: (+44)1865-(2)22738 > =========================================== > On 17 Jun 2011, at 08:01, Stephan Moratti wrote: > > Hello everybody, > I had no problems reading Neuromag data, but when I want to read data > treated with SSS I get the following error: > ??? Error using ==> fiff_read_tag at 232 > Cannot handle other than dense or sparse matrices yet > Error in ==> fiff_open at 80 >     tag = fiff_read_tag(fid,dirpos); > Error in ==> fiff_read_meas_info at 82 >     [ fid, tree ] = fiff_open(source); > Error in ==> ft_read_header at 1049 >     orig = fiff_read_meas_info(filename); > Error in ==> mytrialfun_Neuromag_face at 3 > hdr = ft_read_header(cfg.dataset); > Error in ==> ft_definetrial at 139 >     trl   = feval(cfg.trialfun, cfg); > Any idea, what I could do? > Best, > Stephan > > El 17/06/2011, a las 0:37, Rodolphe Nenert escribió: > > Im still afraid that the power of this analysis will be very low. > Maybe you can try an ICA on your fMRI data and try to correlate each > component with your EOG timecourse. > Rodolphe N. > > On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net > wrote: >> >> It's a bit of a unique experiment, we're trying to use an ECG machine >> to acquire EOG, so it's only a single output channel. >> i guess what I need is a temporal ICA rather than a spatial one... >> On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: >> >> To summarize, the ICA will decompose your signal into as many components >> as Electrodes. >> Therefore, trying to decompose only one source is useless. >> Did you use a full net of electrodes into your MRI machine or only EOG >> electrodes? >> Hope this helps, >> Rodolphe N. >> >> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net >> wrote: >>> >>> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >>> I want to be able to spot the saccades in the samples and ideally measure >>> their onset at the >>> end of each trial. >>> >>> As you may guess, it's quite noisy and it's broad spectrum noise, despite >>> pre-filtering. >>> >>> Ideally, I would like to isolate the component that corresponds to the >>> MRI interference >>> and then filter this out. >>> >>> I have managed to import the data and can run ft_componentanalysis >>> but it fails with: >>> >>> runica() - data size (1,30720) too small >>> >>> My data is single channel, 40 epochs, each of 6 seconds (time locked to >>> stim onset but not saccade onset) >>> Is there a different method I should be using? >>> >>> I have posted some sample data and the current script (which reads in the >>> data and runs preprocessing) to the following urls: >>> >>> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >>> http://greenant.net/temp/EOG_analysis.m >>> _______________________________________________ >>> 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 > > ________________________________________________________ > 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 > > > _______________________________________________ > 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 > > ________________________________________________________ > 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 > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From lhunt at fmrib.ox.ac.uk Mon Jun 20 00:04:46 2011 From: lhunt at fmrib.ox.ac.uk (Laurence Hunt) Date: Sun, 19 Jun 2011 23:04:46 +0100 Subject: [FieldTrip] Problems with Neuromag Data after SSS In-Reply-To: References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> <76A4F15A-0795-44E8-8658-AA73CAA45CD9@psi.ucm.es> <32F04EF7-8D0F-4C73-9C3D-11AB66BF8E81@fmrib.ox.ac.uk> Message-ID: <9C063DE1-06F4-461D-9EE4-094F439CDDE8@fmrib.ox.ac.uk> p.s. If this is the problem, try copying using scp from the mac command line, using Terminal - this has always worked for me ok. The files are big endian but this shouldn't be affected by copying to a mac. Laurence On 19 Jun 2011, at 20:08, Vladimir Litvak wrote: > Dear Stephan, > > It might be that or that you transferred the files as ascii in FTP > rather than binary. I've seen this error before and showed the file to > Matti Hamalainen. He said the file was corrupted. > > Best, > > Vladimir > > On Sun, Jun 19, 2011 at 4:20 PM, Stephan Moratti wrote: >> Hi Lauren, >> Thanks for your reply. Yes I had it with 6 data sets where SSS was applied. >> I had them copied from the HP workstation to our server and from there to my >> Mac. Could it be a little and big endian thing provoked by moving the files >> from different platforms? >> Stephan >> El 17/06/2011, a las 9:28, Laurence Hunt escribió: >> >> Hi Stephan, >> Did you do anything else to the data besides applying SSS? I use SSS on all >> my data and haven't encountered this problem before. Does it apply to all >> your datasets or just one specific file? >> Laurence >> =========================================== >> Laurence Hunt, DPhil Student >> Centre for Functional MRI of the Brain (FMRIB), >> University of Oxford >> lhunt at fmrib.ox.ac.uk >> Phone: (+44)1865-(2)22738 >> =========================================== >> On 17 Jun 2011, at 08:01, Stephan Moratti wrote: >> >> Hello everybody, >> I had no problems reading Neuromag data, but when I want to read data >> treated with SSS I get the following error: >> ??? Error using ==> fiff_read_tag at 232 >> Cannot handle other than dense or sparse matrices yet >> Error in ==> fiff_open at 80 >> tag = fiff_read_tag(fid,dirpos); >> Error in ==> fiff_read_meas_info at 82 >> [ fid, tree ] = fiff_open(source); >> Error in ==> ft_read_header at 1049 >> orig = fiff_read_meas_info(filename); >> Error in ==> mytrialfun_Neuromag_face at 3 >> hdr = ft_read_header(cfg.dataset); >> Error in ==> ft_definetrial at 139 >> trl = feval(cfg.trialfun, cfg); >> Any idea, what I could do? >> Best, >> Stephan >> >> El 17/06/2011, a las 0:37, Rodolphe Nenert escribió: >> >> Im still afraid that the power of this analysis will be very low. >> Maybe you can try an ICA on your fMRI data and try to correlate each >> component with your EOG timecourse. >> Rodolphe N. >> >> On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net >> wrote: >>> >>> It's a bit of a unique experiment, we're trying to use an ECG machine >>> to acquire EOG, so it's only a single output channel. >>> i guess what I need is a temporal ICA rather than a spatial one... >>> On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: >>> >>> To summarize, the ICA will decompose your signal into as many components >>> as Electrodes. >>> Therefore, trying to decompose only one source is useless. >>> Did you use a full net of electrodes into your MRI machine or only EOG >>> electrodes? >>> Hope this helps, >>> Rodolphe N. >>> >>> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net >>> wrote: >>>> >>>> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >>>> I want to be able to spot the saccades in the samples and ideally measure >>>> their onset at the >>>> end of each trial. >>>> >>>> As you may guess, it's quite noisy and it's broad spectrum noise, despite >>>> pre-filtering. >>>> >>>> Ideally, I would like to isolate the component that corresponds to the >>>> MRI interference >>>> and then filter this out. >>>> >>>> I have managed to import the data and can run ft_componentanalysis >>>> but it fails with: >>>> >>>> runica() - data size (1,30720) too small >>>> >>>> My data is single channel, 40 epochs, each of 6 seconds (time locked to >>>> stim onset but not saccade onset) >>>> Is there a different method I should be using? >>>> >>>> I have posted some sample data and the current script (which reads in the >>>> data and runs preprocessing) to the following urls: >>>> >>>> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >>>> http://greenant.net/temp/EOG_analysis.m >>>> _______________________________________________ >>>> 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 >> >> ________________________________________________________ >> 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 >> >> >> _______________________________________________ >> 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 >> >> ________________________________________________________ >> 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 >> >> >> >> _______________________________________________ >> 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 smoratti at psi.ucm.es Mon Jun 20 08:26:46 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Mon, 20 Jun 2011 08:26:46 +0200 Subject: [FieldTrip] Problems with Neuromag Data after SSS In-Reply-To: References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> <76A4F15A-0795-44E8-8658-AA73CAA45CD9@psi.ucm.es> <32F04EF7-8D0F-4C73-9C3D-11AB66BF8E81@fmrib.ox.ac.uk> Message-ID: Dear Vladimir, Thanks for this hint. I will check this! Best, Stephan El 19/06/2011, a las 21:08, Vladimir Litvak escribió: > Dear Stephan, > > It might be that or that you transferred the files as ascii in FTP > rather than binary. I've seen this error before and showed the file to > Matti Hamalainen. He said the file was corrupted. > > Best, > > Vladimir > > On Sun, Jun 19, 2011 at 4:20 PM, Stephan Moratti > wrote: >> Hi Lauren, >> Thanks for your reply. Yes I had it with 6 data sets where SSS was >> applied. >> I had them copied from the HP workstation to our server and from >> there to my >> Mac. Could it be a little and big endian thing provoked by moving >> the files >> from different platforms? >> Stephan >> El 17/06/2011, a las 9:28, Laurence Hunt escribió: >> >> Hi Stephan, >> Did you do anything else to the data besides applying SSS? I use >> SSS on all >> my data and haven't encountered this problem before. Does it apply >> to all >> your datasets or just one specific file? >> Laurence >> =========================================== >> Laurence Hunt, DPhil Student >> Centre for Functional MRI of the Brain (FMRIB), >> University of Oxford >> lhunt at fmrib.ox.ac.uk >> Phone: (+44)1865-(2)22738 >> =========================================== >> On 17 Jun 2011, at 08:01, Stephan Moratti wrote: >> >> Hello everybody, >> I had no problems reading Neuromag data, but when I want to read data >> treated with SSS I get the following error: >> ??? Error using ==> fiff_read_tag at 232 >> Cannot handle other than dense or sparse matrices yet >> Error in ==> fiff_open at 80 >> tag = fiff_read_tag(fid,dirpos); >> Error in ==> fiff_read_meas_info at 82 >> [ fid, tree ] = fiff_open(source); >> Error in ==> ft_read_header at 1049 >> orig = fiff_read_meas_info(filename); >> Error in ==> mytrialfun_Neuromag_face at 3 >> hdr = ft_read_header(cfg.dataset); >> Error in ==> ft_definetrial at 139 >> trl = feval(cfg.trialfun, cfg); >> Any idea, what I could do? >> Best, >> Stephan >> >> El 17/06/2011, a las 0:37, Rodolphe Nenert escribió: >> >> Im still afraid that the power of this analysis will be very low. >> Maybe you can try an ICA on your fMRI data and try to correlate each >> component with your EOG timecourse. >> Rodolphe N. >> >> On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net > > >> wrote: >>> >>> It's a bit of a unique experiment, we're trying to use an ECG >>> machine >>> to acquire EOG, so it's only a single output channel. >>> i guess what I need is a temporal ICA rather than a spatial one... >>> On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: >>> >>> To summarize, the ICA will decompose your signal into as many >>> components >>> as Electrodes. >>> Therefore, trying to decompose only one source is useless. >>> Did you use a full net of electrodes into your MRI machine or only >>> EOG >>> electrodes? >>> Hope this helps, >>> Rodolphe N. >>> >>> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net >>> wrote: >>>> >>>> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >>>> I want to be able to spot the saccades in the samples and ideally >>>> measure >>>> their onset at the >>>> end of each trial. >>>> >>>> As you may guess, it's quite noisy and it's broad spectrum noise, >>>> despite >>>> pre-filtering. >>>> >>>> Ideally, I would like to isolate the component that corresponds >>>> to the >>>> MRI interference >>>> and then filter this out. >>>> >>>> I have managed to import the data and can run ft_componentanalysis >>>> but it fails with: >>>> >>>> runica() - data size (1,30720) too small >>>> >>>> My data is single channel, 40 epochs, each of 6 seconds (time >>>> locked to >>>> stim onset but not saccade onset) >>>> Is there a different method I should be using? >>>> >>>> I have posted some sample data and the current script (which >>>> reads in the >>>> data and runs preprocessing) to the following urls: >>>> >>>> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >>>> http://greenant.net/temp/EOG_analysis.m >>>> _______________________________________________ >>>> 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 >> >> ________________________________________________________ >> 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 >> >> >> _______________________________________________ >> 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 >> >> ________________________________________________________ >> 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 >> >> >> >> _______________________________________________ >> 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 ________________________________________________________ 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 a.wollbrink at uni-muenster.de Mon Jun 20 14:45:54 2011 From: a.wollbrink at uni-muenster.de (Andreas Wollbrink) Date: Mon, 20 Jun 2011 14:45:54 +0200 Subject: [FieldTrip] concatenating data to a single trial data set Message-ID: <4DFF4102.3020101@uni-muenster.de> Dear all, in order not to run into a RAM memory overload when performing an ICA on MEG data I subdivided the raw data into several equally long segments (chops) using ft_preprocessing with varying cfg.trl settings. After applying ft_componentanalysis to each of these chops I removed some (bad) components and backprojected the data to seperate data matrices using the following code: cfg = []; cfg.component = badCompVec; % to be removed component(s) dataCorr = ft_rejectcomponent(cfg, compData); Finally I like to concatenate these data to a continuous (single trial) data matrix in order to compare it with the original raw data set and perform the further timelock analysis on it. I tried using ft_appenddata for this issue. Doing so one gets a multi trial data matrix which I could not convert to single trial continuous data matrix using e.g. ft_redefinetrial. I would appreciate any help in how to solve this problem. Thanks in advance. Andreas Wollbrink -- ====================================================================== Andreas Wollbrink, Biomedical Engineer Institute for Biomagnetism and Biosignalanalysis Muenster University Hospital Malmedyweg 15 phone: +49-(0)251-83-52546 D-48149 Muenster mobil: +49-(0)160-98527553 Germany fax: +49-(0)251-83-56874 e-Mail: a.wollbrink at uni-muenster.de ====================================================================== From eelke.spaak at donders.ru.nl Mon Jun 20 15:35:14 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 20 Jun 2011 15:35:14 +0200 Subject: [FieldTrip] concatenating data to a single trial data set In-Reply-To: <4DFF4102.3020101@uni-muenster.de> References: <4DFF4102.3020101@uni-muenster.de> Message-ID: Dear Andreas, The way I concatenate data is just 'manually', so without the intervention of FieldTrip. To do this, you will have to concatenate the arrays in both the data.trial and the data.time cell array. In pseudocode: initialize matrix data_concat of size channels X total time points initialize matrix time_concat of size 1 X total time points loop over data.trial and data.time (have the same size) data_concat(:,appropriate time indices) = data.trial{k}(:,:); time_concat(1,appropriate time indices) = data.time{k}(:); end loop data.trial = data_concat; data.time = time_concat; That should do the trick. I would have provided actual code, were it not that I am doing something slightly different from what you are asking. I hope this helps! Best, Eelke 2011/6/20 Andreas Wollbrink : > Dear all, > > in order not to run into a RAM memory overload when performing an ICA on MEG > data I subdivided the raw data into several equally long segments (chops) > using ft_preprocessing with varying cfg.trl settings. > After applying ft_componentanalysis to each of these chops I removed some > (bad) components and backprojected the data to seperate data matrices using > the following code: > > cfg = []; > cfg.component = badCompVec; % to be removed component(s) > dataCorr = ft_rejectcomponent(cfg, compData); > > > Finally I like to concatenate these data to a continuous (single trial) data > matrix in order to compare it with the original raw data set and perform the > further timelock analysis on it. > > I tried using ft_appenddata for this issue. Doing so one gets a multi trial > data matrix which I could not convert to single trial continuous data matrix > using e.g. ft_redefinetrial. > > I would appreciate any help in how to solve this problem. > > Thanks in advance. > > Andreas Wollbrink > -- > > > ====================================================================== > >  Andreas Wollbrink, Biomedical Engineer > >  Institute for Biomagnetism and Biosignalanalysis >  Muenster University Hospital > >  Malmedyweg 15         phone:   +49-(0)251-83-52546 >  D-48149 Muenster      mobil:   +49-(0)160-98527553 >  Germany               fax:     +49-(0)251-83-56874 >                        e-Mail: a.wollbrink at uni-muenster.de > > ====================================================================== > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From nathanweisz at mac.com Mon Jun 20 17:15:50 2011 From: nathanweisz at mac.com (Nathan Weisz) Date: Mon, 20 Jun 2011 17:15:50 +0200 Subject: [FieldTrip] concatenating data to a single trial data set In-Reply-To: References: <4DFF4102.3020101@uni-muenster.de> Message-ID: hi andreas, perhaps i misunderstood something. but your RAM worries concern the ICA computation? then after running your ICA & getting the components, why don't you just read the raw data again with the option as continuous data (cfg.continuous i think). then apply the components to the single-trial raw data and finally reject the bad components. less efficient than elkes solution, rather the lazy one :-) cheers, n On 20.06.2011, at 15:35, Eelke Spaak wrote: > Dear Andreas, > > The way I concatenate data is just 'manually', so without the > intervention of FieldTrip. To do this, you will have to concatenate > the arrays in both the data.trial and the data.time cell array. > > In pseudocode: > > initialize matrix data_concat of size channels X total time points > initialize matrix time_concat of size 1 X total time points > > loop over data.trial and data.time (have the same size) > data_concat(:,appropriate time indices) = data.trial{k}(:,:); > time_concat(1,appropriate time indices) = data.time{k}(:); > end loop > > data.trial = data_concat; > data.time = time_concat; > > That should do the trick. I would have provided actual code, were it > not that I am doing something slightly different from what you are > asking. > > I hope this helps! > > Best, > Eelke > > 2011/6/20 Andreas Wollbrink : >> Dear all, >> >> in order not to run into a RAM memory overload when performing an ICA on MEG >> data I subdivided the raw data into several equally long segments (chops) >> using ft_preprocessing with varying cfg.trl settings. >> After applying ft_componentanalysis to each of these chops I removed some >> (bad) components and backprojected the data to seperate data matrices using >> the following code: >> >> cfg = []; >> cfg.component = badCompVec; % to be removed component(s) >> dataCorr = ft_rejectcomponent(cfg, compData); >> >> >> Finally I like to concatenate these data to a continuous (single trial) data >> matrix in order to compare it with the original raw data set and perform the >> further timelock analysis on it. >> >> I tried using ft_appenddata for this issue. Doing so one gets a multi trial >> data matrix which I could not convert to single trial continuous data matrix >> using e.g. ft_redefinetrial. >> >> I would appreciate any help in how to solve this problem. >> >> Thanks in advance. >> >> Andreas Wollbrink >> -- >> >> >> ====================================================================== >> >> Andreas Wollbrink, Biomedical Engineer >> >> Institute for Biomagnetism and Biosignalanalysis >> Muenster University Hospital >> >> Malmedyweg 15 phone: +49-(0)251-83-52546 >> D-48149 Muenster mobil: +49-(0)160-98527553 >> Germany fax: +49-(0)251-83-56874 >> e-Mail: a.wollbrink at uni-muenster.de >> >> ====================================================================== >> _______________________________________________ >> 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 jan.schoffelen at donders.ru.nl Tue Jun 21 09:08:34 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 21 Jun 2011 09:08:34 +0200 Subject: [FieldTrip] wavelet analysis In-Reply-To: <6ac7ddd3f73a325534c24be6edd039d2.squirrel@netmail.aecom.yu.edu> References: <6ac7ddd3f73a325534c24be6edd039d2.squirrel@netmail.aecom.yu.edu> Message-ID: <9B183DFC-CD62-489D-9F0B-C2292AFFAF1A@donders.ru.nl> Dear Manuel, Thanks for your message. I gave the faq a good read, and I agree that the answer can be made a bit more clear. I updated the faqs you mentioned and hope that this explains the issue better. Let me know if it is still not clear. Best wishes, Jan-Mathijs On Jun 18, 2011, at 11:09 AM, Manuel Mercier wrote: > Dear Field-trippers > I recently ran some time frequency analysis using the wavelet method. > I was surprise to see that whereas I asked for a step of 1Hz, it was > not > the case every alternate step (for foi=2:1:10 ; I got [2 3.2 4 5.2 6 > 7.2 8 > 9.2 10]), and it was also the case when I changed the toi (2.5, 1.5 > with > constant trials length of 2.5 sec and sampling freq 1000Hz). > I found a kind of explanation following the faq > (http://fieldtrip.fcdonders.nl/faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_wavelet_formerly_wltconvol_in_ft_freqanalyis > ). > Still it is not clear to me why this refers to Fourier transform. >> From my (none specialist) point of view it is possible to produce a > wavelet of any size (Hz;Dt). > It is clear that there is some limitations based on the duration of > the > epochs and the number of time points. But in the present case it > shouldn't > be a problem, is it? > Would be please if someone can help me with this issue. > Thanks in advance > > Manuel > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From a.wollbrink at uni-muenster.de Tue Jun 21 10:05:19 2011 From: a.wollbrink at uni-muenster.de (Andreas Wollbrink) Date: Tue, 21 Jun 2011 10:05:19 +0200 Subject: [FieldTrip] concatenating data to a single trial data set In-Reply-To: References: <4DFF4102.3020101@uni-muenster.de> Message-ID: <4E0050BF.80008@uni-muenster.de> Dear Eelke, dear Nathan, thanks for your help on a way to concatenate the data. In the end I successfully used a mixture of both approaches you suggested. Best, Andreas On 06/20/11 15:35, Eelke Spaak wrote: > Dear Andreas, > > The way I concatenate data is just 'manually', so without the > intervention of FieldTrip. To do this, you will have to concatenate > the arrays in both the data.trial and the data.time cell array. > > In pseudocode: > > initialize matrix data_concat of size channels X total time points > initialize matrix time_concat of size 1 X total time points > > loop over data.trial and data.time (have the same size) > data_concat(:,appropriate time indices) = data.trial{k}(:,:); > time_concat(1,appropriate time indices) = data.time{k}(:); > end loop > > data.trial = data_concat; > data.time = time_concat; > > That should do the trick. I would have provided actual code, were it > not that I am doing something slightly different from what you are > asking. > > I hope this helps! > > Best, > Eelke > > 2011/6/20 Andreas Wollbrink: >> Dear all, >> >> in order not to run into a RAM memory overload when performing an ICA on MEG >> data I subdivided the raw data into several equally long segments (chops) >> using ft_preprocessing with varying cfg.trl settings. >> After applying ft_componentanalysis to each of these chops I removed some >> (bad) components and backprojected the data to seperate data matrices using >> the following code: >> >> cfg = []; >> cfg.component = badCompVec; % to be removed component(s) >> dataCorr = ft_rejectcomponent(cfg, compData); >> >> >> Finally I like to concatenate these data to a continuous (single trial) data >> matrix in order to compare it with the original raw data set and perform the >> further timelock analysis on it. >> >> I tried using ft_appenddata for this issue. Doing so one gets a multi trial >> data matrix which I could not convert to single trial continuous data matrix >> using e.g. ft_redefinetrial. >> >> I would appreciate any help in how to solve this problem. >> >> Thanks in advance. >> >> Andreas Wollbrink >> -- >> >> >> ====================================================================== >> >> Andreas Wollbrink, Biomedical Engineer >> >> Institute for Biomagnetism and Biosignalanalysis >> Muenster University Hospital >> >> Malmedyweg 15 phone: +49-(0)251-83-52546 >> D-48149 Muenster mobil: +49-(0)160-98527553 >> Germany fax: +49-(0)251-83-56874 >> e-Mail: a.wollbrink at uni-muenster.de >> >> ====================================================================== >> _______________________________________________ >> 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 -- ====================================================================== Andreas Wollbrink, Biomedical Engineer Institute for Biomagnetism and Biosignalanalysis Muenster University Hospital Malmedyweg 15 phone: +49-(0)251-83-52546 D-48149 Muenster mobil: +49-(0)160-98527553 Germany fax: +49-(0)251-83-56874 e-Mail: a.wollbrink at uni-muenster.de ====================================================================== From drivolta81 at gmail.com Tue Jun 21 15:24:31 2011 From: drivolta81 at gmail.com (Davide Rivolta) Date: Tue, 21 Jun 2011 15:24:31 +0200 Subject: [FieldTrip] downsampling MEG data Message-ID: Dear fieldtrippers, I have recorded some MEG data with a sampling rate of 6000 Hz. I would need to downsample it to 600 Hz. What is the best way to do it? It something I have to do in the preprocessing I guess. Any advice would be really appreciated, Thanks, Davide -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Tue Jun 21 15:29:59 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 21 Jun 2011 15:29:59 +0200 Subject: [FieldTrip] downsampling MEG data In-Reply-To: References: Message-ID: Dear Davide, Have a look at the ft_resampledata function: http://fieldtrip.fcdonders.nl/reference/ft_resampledata Best, Eelke 2011/6/21 Davide Rivolta : > Dear fieldtrippers, > > I have recorded some MEG data with a sampling rate of 6000 Hz. > I would need to downsample it to 600 Hz. > > What is the best way to do it? > > It something I have to do in the preprocessing I guess. > > Any advice would be really appreciated, > > Thanks, > > Davide > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From batrod at gmail.com Tue Jun 21 15:37:54 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Tue, 21 Jun 2011 08:37:54 -0500 Subject: [FieldTrip] downsampling MEG data In-Reply-To: References: Message-ID: Dear Davide, the function ft_resampledata should do that perfectly ! :) On Tue, Jun 21, 2011 at 8:24 AM, Davide Rivolta wrote: > Dear fieldtrippers, > > I have recorded some MEG data with a sampling rate of 6000 Hz. > I would need to downsample it to 600 Hz. > > What is the best way to do it? > > It something I have to do in the preprocessing I guess. > > Any advice would be really appreciated, > > Thanks, > > Davide > > _______________________________________________ > 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 Jun 21 16:08:21 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 21 Jun 2011 16:08:21 +0200 Subject: [FieldTrip] Publications using FieldTrip: add your own! Message-ID: Dear Fieldtrippers, We have revamped the list of publications using FieldTrip on our wiki website. I wrote a plugin for Dokuwiki, enabling the wiki to parse BibTeX code (see http://www.bibtex.org/ if you don't know what this is). This allows all of you to easily add your publications using FieldTrip to our wiki, improving the visibility of both FieldTrip and your papers. The list is quite extensive already, but we explicitly invite all of you to browse through it and add anything we might have missed. Editing the page is done by going to Page tools (top left, above the site menu) --> Edit this page. If you are not familiar with BibTeX syntax, it is probably easiest to just look at what is already there and use that as an example. Note that the list will be automatically sorted by year and by first author, so you can just insert new entries wherever you like. Visit http://fieldtrip.fcdonders.nl/publications to see the new page. Best, Eelke From johanna.zumer at donders.ru.nl Tue Jun 21 16:56:20 2011 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Tue, 21 Jun 2011 16:56:20 +0200 Subject: [FieldTrip] code change in ft_compute_leadfield.m Message-ID: Dear FieldTrip users, I've made a small change to ft_compute_leadfield (available in tonight's release) regarding how the 'reducerank' option is handled, if multiple dipole locations are entered all at once into ft_compute_leadfield.m. This will *not* affect the vast majority of users, since usually ft_compute_leadfield is called by higher FT functions and not directly by users. For example, it will not affect you if you create a leadfield either by calling ft_prepare_leadfield or by letting ft_sourceanalysis compute the leadfield for you (regardless of your 'reducedrank' option), since these higher level FT functions call ft_compute_leadfield in a for-loop over dipole location (and _not_ multiple dipole locations at once). For completeness, here's a list of (rare) cases when it will affect your results: 1) If you call ft_compute_leadfield directly with Nx3 dipoles (N>1) and reducerank='yes' (or =2) 2) If you use a refdip in beamformer_DICS or beamformer_PCC, or a supdip in beamformer_PCC, of *more than 1 dipole location* at a time (Nx3 refdip or subdip, where N>1), AND you specified reducerank='yes' (or =2) in any of these cases. 3) Default behaviour of calling ft_dipolefitting will not change. However if you call dipole_fit directly with more than one dipole AND reducerank='yes' (or =2). Please let me know if this isn't clear. Best, Johanna -------------- next part -------------- An HTML attachment was scrubbed... URL: From BelluscB at ninds.nih.gov Tue Jun 21 23:24:16 2011 From: BelluscB at ninds.nih.gov (Belluscio, Beth (NIH/NINDS) [E]) Date: Tue, 21 Jun 2011 17:24:16 -0400 Subject: [FieldTrip] define events for ft_definetrial Message-ID: <794DFDD3C128EF44AC49ADC58FD0090C04F09E165B@NIHMLBX10.nih.gov> HI all- I use CFT data sets in which I use a trigger channel to define various stimuli (usually called stim1, stim2, stim3). Each stim repeats several times (120) during the data file. The time points corresponding to each stim are catalogued in the MarkerFile.mrk file. I would like to use these markers to define trials around each stim. I used to do this with the following set of commands: cfg = []; cfg.dataset = 'TS1.ds'; cfg.trialdef.eventtype = 'stim1'; cfg.trialdef.prestim = 0.1; cfg.trialdef.posstim = 3.0; cfg = ft_definetrial(cfg) Now when I do this I get the following error messages: readCTFds: Data set error: size of meg4 files(s) 0 bytes (from dir command) 1126080000 (from res4 file) ??? Attempt to reference field of non-structure array. Error in ==> trialfun_general at 111 For i=find(strcmp(cfg.trialdef.eventtype, {event.types})) Error in==> ft_definetrial at 126 [trl, event] = feval(cfg.trialfun, cfg) Is this a problem with the way I am defining the events? How can I use these markers within the data file to specify events in fieldtrip? Thanks, Beth Belluscio MD-PhD Clinical Fellow Human Motor Control Section NINDS, NIH 301-402-3495 -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at fcdonders.ru.nl Wed Jun 22 08:12:48 2011 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Wed, 22 Jun 2011 08:12:48 +0200 (CEST) Subject: [FieldTrip] define events for ft_definetrial In-Reply-To: <794DFDD3C128EF44AC49ADC58FD0090C04F09E165B@NIHMLBX10.nih.gov> Message-ID: <49300862.469268.1308723168601.JavaMail.root@sculptor.zimbra.ru.nl> Hi Beth, Just wondering. Did you copy those lines from your script? If so, please try cfg.trialdef.poststim = 3.0; (notice the t). Yours, Arjen ----- "Beth Belluscio (NIH/NINDS) [E]" schreef: > Van: "Beth Belluscio (NIH/NINDS) [E]" > Aan: "fieldtrip at donders.ru.nl" > Verzonden: Dinsdag 21 juni 2011 23:24:16 > Onderwerp: [FieldTrip] define events for ft_definetrial > > > HI all-   I use CFT data sets in which I use a trigger channel to define various stimuli (usually called stim1, stim2, stim3).  Each stim repeats several times (120) during the data file.  The time points corresponding to each stim are catalogued in the MarkerFile.mrk file.  I would like to use these markers to define trials around each stim.  I used to do this with the following set of commands:                 cfg = [];                 cfg.dataset = ‘TS1.ds’;                 cfg.trialdef.eventtype = ‘stim1’;                 cfg.trialdef.prestim = 0.1;                 cfg.trialdef.posstim = 3.0;                 cfg = ft_definetrial(cfg) Now when I do this I get the following error messages:                 readCTFds: Data set error:  size of meg4 files(s)                                 0 bytes (from dir command)                                 1126080000 (from res4 file)                 ??? Attempt to reference field of non-structure array.                 Error in è trialfun_general at 111                 For i=find(strcmp(cfg.trialdef.eventtype, {event.types}))                                 Error in è ft_definetrial at 126                 [trl, event] = feval(cfg.trialfun, cfg) Is this a problem with the way I am defining the events?  How can I use these markers within the data file to specify events in fieldtrip? Thanks, Beth Belluscio MD-PhD Clinical Fellow Human Motor Control Section NINDS, NIH 301-402-3495 > _______________________________________________ > 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 Jun 22 08:59:04 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 22 Jun 2011 08:59:04 +0200 Subject: [FieldTrip] define events for ft_definetrial In-Reply-To: <794DFDD3C128EF44AC49ADC58FD0090C04F09E165B@NIHMLBX10.nih.gov> References: <794DFDD3C128EF44AC49ADC58FD0090C04F09E165B@NIHMLBX10.nih.gov> Message-ID: <4D29A1F9-957B-41E4-8CBC-582BF0AD25D6@donders.ru.nl> Dear Beth, It could be that your dataset is corrupt. > readCTFds: Data set error: size of meg4 files(s) > 0 bytes (from dir command) > 1126080000 (from res4 file) This is namely a low level reading error. It then percolates to the next step, where > > ??? Attempt to reference field of non-structure array. which is most likely caused by FieldTrip not having been successful in creating an event structure. > > Error in è trialfun_general at 111 > For i=find(strcmp(cfg.trialdef.eventtype, > {event.types})) > > Error inè ft_definetrial at 126 > [trl, event] = feval(cfg.trialfun, cfg) > > Is this a problem with the way I am defining the events? How can I > use these markers within the data file to specify events in fieldtrip? Does this pertain to this particular dataset? Best Jan-Mathijs PS: please update to a more recent version of FieldTrip: the content of the line number in which the errer occurs does not coincide with my version > > Thanks, > > Beth Belluscio MD-PhD > Clinical Fellow > Human Motor Control Section > NINDS, NIH > 301-402-3495 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From lulswinnik at gmail.com Thu Jun 23 12:30:35 2011 From: lulswinnik at gmail.com (Ekaterina Vinnik) Date: Thu, 23 Jun 2011 11:30:35 +0100 Subject: [FieldTrip] Champalimaud Neuroscience Symposium announcement; early registration deadline 30 of June Message-ID: The Champalimaud Neuroscience Symposium will bring together researchers from around the world who are interested in solving the puzzle of the brain. The Programme includes 30 distinguished speakers (including Gyorgy Buzsaki, Antonio Damasio, Jim DiCarlo, Ranulfo Romo, Erin Schuman and Haim Sompolinsky) and poster sessions. The Symposium will take place at the Champalimaud Centre for the Unknown on the waterfront in central Lisbon, Portugal. We are looking forward to a lively and stimulating scientific meeting, and we hope that you will join us. more information at http://symposium.neuro.fchampalimaud.org/ http://www.facebook.com/event.php?eid=191246457589517 The early registration deadline is 30 of June (150/300 euro fee), though abstracts are not due till 31 of August. Travel grants available! Join us in Lisbon, All the best, Ekaterina -- Ekaterina Vinnik, MD, PhD Behavioural neuroscience lab, Champalimaud Neuroscience, Lisbon, Portugal +351918951392 lulswinnik at gmail.com From ekanal at cmu.edu Fri Jun 24 16:21:47 2011 From: ekanal at cmu.edu (Kanal Eliezer) Date: Fri, 24 Jun 2011 10:21:47 -0400 Subject: [FieldTrip] plot ave + variance Message-ID: Hello fieldtrip - Is there a simple way to plot a timelock average along with confidence intervals? I simply want to see how much the data varied across trials. The structure returned by the ft_timelock function contains a `var` element, but the data it contains is many order of magnitude smaller than that in the `ave` element. Thanks - Elli -------------------- Eliezer Kanal, Ph.D. Postdoctoral Fellow Center for the Neural Basis of Cognition Carnegie Mellon University 4400 Fifth Ave, Suite 110A Pittsburgh PA 15213 P: 412-268-4115 F: 412-268-5060 From akiko at nyu.edu Fri Jun 24 17:42:20 2011 From: akiko at nyu.edu (Akiko Ikkai) Date: Fri, 24 Jun 2011 11:42:20 -0400 Subject: [FieldTrip] ft_sourceanalysis & ft_sourceinterpolate Message-ID: Hi, I'm working on beamformer with MEG data, and having trouble making ft_sourceanalysis and/or ft_sourceinterpolate work. It appears that anatomical MRI and source data do not align, although anatomical MRI ("mri_aligned") and the result of ft_prepare_singleshell ("vol_cm") are both aligned with MEG helmet. Is there any way I could verify that the output of ft_sourceanalysis is not distorted (i.e. same space as input)? I'm using fieldtrip-20110525 version. Thanks in advance! Akiko Below is my code: 1. compute the common filter cfg = []; cfg.grad = data_common.grad; % data_common = baseline + left + right cfg.grid.xgrid = -15:0.5:15; cfg.grid.ygrid = -15:0.5:15; cfg.grid.zgrid = -15:0.5:15; cfg.inwardshift = -2; cfg.vol = vol_cm; % this is from segmented "mri_aligned" cfg.channel = {'all'}; cfg.reducerank = 2; cfg.frequency = 10; cfg.method = 'dics'; cfg.projectnoise = 'yes'; cfg.keepfilter = 'yes'; cfg.feedback = 'no'; cfg.realfilter = 'yes'; cfg.lambda = '0.005%'; source_common = ft_sourceanalysis(cfg, freq_common) 2. compute the spatial filter for one of the conditions (using grid & filter from the step 1) cfg = []; cfg.grad = data_common.grad; cfg.grid.pos = source_common.pos; % using grid & filter from the common filter cfg.grid.filter = source_common.avg.filter; cfg.vol = vol_cm; cfg.channel = {'all'}; cfg.reducerank = 2; cfg.frequency = 10; cfg.method = 'dics'; cfg.projectnoise = 'yes'; cfg.keepfilter = 'no'; cfg.feedback = 'no'; cfg.realfilter = 'yes'; cfg.lambda = '0.005%'; source_left = ft_sourceanalysis(cfg, freq_stiml); source_left.unit = 'cm'; source_left.dim = source_common.dim; 3. calculate difference source_left_bl = source_left; source_left_bl.avg.pow = source_left_bl.avg.pow ./ source_common.avg.pow; 4. interpolate source to anatomical MRI space cfg = []; cfg.method = 'linear'; source_left_bl_int = ft_sourceinterpolate(cfg, source_left_bl,mri_aligned); -------------- next part -------------- An HTML attachment was scrubbed... URL: From ekanal at cmu.edu Fri Jun 24 21:17:42 2011 From: ekanal at cmu.edu (Kanal Eliezer) Date: Fri, 24 Jun 2011 15:17:42 -0400 Subject: [FieldTrip] plot ave + variance In-Reply-To: <31844_1308925377_p5OEMuo1011583_B732C6AD-E522-4B28-8D7A-0660CF0520A8@cmu.edu> References: <31844_1308925377_p5OEMuo1011583_B732C6AD-E522-4B28-8D7A-0660CF0520A8@cmu.edu> Message-ID: I apologize; I wasn't thinking. stdev = var^2. Elli On Jun 24, 2011, at 10:21 AM, Kanal Eliezer wrote: > Hello fieldtrip - > > Is there a simple way to plot a timelock average along with confidence intervals? I simply want to see how much the data varied across trials. The structure returned by the ft_timelock function contains a `var` element, but the data it contains is many order of magnitude smaller than that in the `ave` element. Thanks - > > Elli > > > -------------------- > Eliezer Kanal, Ph.D. > Postdoctoral Fellow > Center for the Neural Basis of Cognition > Carnegie Mellon University > 4400 Fifth Ave, Suite 110A > Pittsburgh PA 15213 > P: 412-268-4115 > F: 412-268-5060 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From paul_c at gmx.de Mon Jun 27 10:11:51 2011 From: paul_c at gmx.de (Paul Czienskowski) Date: Mon, 27 Jun 2011 10:11:51 +0200 Subject: [FieldTrip] Brainvision renamer tool In-Reply-To: References: <31844_1308925377_p5OEMuo1011583_B732C6AD-E522-4B28-8D7A-0660CF0520A8@cmu.edu> Message-ID: <4E083B47.4070008@gmx.de> Dear all, I wrote a small brainvision renamer tool based on RegEx patters which I needed to make the filenames of my EEG-Recordings more consistent. If anyone is interested in, check out http://code.google.com/p/eeg-renamer/ Cheers, Paul -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 From Hanneke.vanDijk at med.uni-duesseldorf.de Mon Jun 27 10:38:03 2011 From: Hanneke.vanDijk at med.uni-duesseldorf.de (Hanneke.vanDijk at med.uni-duesseldorf.de) Date: Mon, 27 Jun 2011 10:38:03 +0200 Subject: [FieldTrip] ft_databrowser Message-ID: <72E993C35FB11743B79FF9286E5B6D8B029F8B2A@Mail2-UKD.VMED.UKD> Dear FT-ers, I have discovered ft_databrowser a few weeks ago (maybe abit late ;-))! Thanks so much for implementing this, I like it. I am setting up a small presentation about artifact rejection using FT and decided to use the tutorial data (Subject01.ds) to generate some examples. When I use the raw dataset and cfg.continuous = 'yes', it runs fine but after preprocessing (as in the online tutorial; and cfg.continuous = 'no') I run into this problem: cfg = ft_databrowser(cfg,dataFIC); the input is raw data with 152 channels and 87 trials redrawing with viewmode butterfly fetching data... done fetching artifacts... done preprocessing data... done plotting data... ??? Reference to non-existent field 'hlim'. Error in ==> ft_databrowser>redraw_cb at 1003 eventtim = (eventtim - opt.hlim(1)) / (opt.hlim(2) - opt.hlim(1)); % convert to value relative to box, i.e. from 0 to 1 Error in ==> ft_databrowser at 434 redraw_cb(h); 'opt' indeed does not contain 'hlim' and also no 'hpos' which is asked for a line later. I think it originates in the input given into the function guidata. I hope you can help me! Groetjes Hanneke __________________________________________ Dr. Hanneke van Dijk http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNe urowiss/Team/HannekevanDijk/page.html Institute for Clinical Neuroscience, Heinrich Heine Universitaet Duesseldorf, Germany Hanneke.vanDijk at med.uni-duesseldorf.de Tel. +49 (0) 211 81 13074 __________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Tue Jun 28 09:19:13 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 28 Jun 2011 09:19:13 +0200 Subject: [FieldTrip] ft_databrowser In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8B029F8B2A@Mail2-UKD.VMED.UKD> References: <72E993C35FB11743B79FF9286E5B6D8B029F8B2A@Mail2-UKD.VMED.UKD> Message-ID: <4E098071.6010502@donders.ru.nl> Dear Hanneke, Thanks for reporting this. We are currently working on improving the databrowser in terms of code readability, which also includes removing some bugs. We will also deal with this one, if not already done (I will check) Best, Jörn On 6/27/2011 10:38 AM, Hanneke.vanDijk at med.uni-duesseldorf.de wrote: > > Dear FT-ers, > > I have discovered ft_databrowser a few weeks ago (maybe abit late > ;-))! Thanks so much for implementing this, I like it. > > I am setting up a small presentation about artifact rejection using FT > and decided to use the tutorial data (Subject01.ds) to generate some > examples. When I use the raw dataset and cfg.continuous = 'yes', it > runs fine but after preprocessing (as in the online tutorial; and > cfg.continuous = 'no') I run into this problem: > > cfg = ft_databrowser(cfg,dataFIC); > > the input is raw data with 152 channels and 87 trials > > redrawing with viewmode butterfly > > fetching data... done > > fetching artifacts... done > > preprocessing data... done > > plotting data... ??? Reference to non-existent field 'hlim'. > > Error in ==> ft_databrowser>redraw_cb at 1003 > > eventtim = (eventtim - opt.hlim(1)) / (opt.hlim(2) - > opt.hlim(1)); % convert to value relative to > > box, i.e. from 0 to 1 > > Error in ==> ft_databrowser at 434 > > redraw_cb(h); > > 'opt' indeed does not contain 'hlim' and also no 'hpos' which is asked > for a line later. I think it originates in the input given into the > function guidata. > > I hope you can help me! > > Groetjes Hanneke > > __________________________________________ > > Dr. Hanneke van Dijk > > http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html > > Institute for Clinical Neuroscience, > > Heinrich Heine Universitaet Duesseldorf, Germany > > Hanneke.vanDijk at med.uni-duesseldorf.de > > > Tel. +49 (0) 211 81 13074 > > __________________________________________ > > > _______________________________________________ > 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 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 suforraxi at gmail.com Tue Jun 28 14:46:28 2011 From: suforraxi at gmail.com (Matteo Demuru) Date: Tue, 28 Jun 2011 14:46:28 +0200 Subject: [FieldTrip] WPLI statistic, permutation like test?? Message-ID: Hi, I have a couple of questions about using the WPLI index to assess the phase on my MEG data. The experiment consists of recordings during a mental calculation task: I have 30 sec in which each subject performed continuously an arithmetic operation. It seems to me that WPLI index required more than one trial in order to be computed. Am I right? (Is this necessary in order to reduce volume conduction problems?) I could divide my 30 sec in 5 sec-trials to create my trials, but I was wandering if this could be a misuse of the WPLI, i.e. WPLI is not appropriate for my experiment. I am also interested in assessing the significance of WPLI index, I would like to gauge the significance per se of my WPLI values. The idea is to calculate the WPLI distribution under the null hypothesis (not phase coupling) for each pair of channels in this way: Example to assess the significance of WPLI value for ch1 vs ch2 1) Calculate the WPLI for ch1 and ch2, this would be the observed WPLI (WPLI_observed) 2) Randomly permute the ch2 time series 3) Calculate the WPLI for ch1 and ch2 (WPLI_i) 4) Repeat step 2 and 3 (for instance 100 times) in order to create the WPLI_i distribution 5) Calculate the proportion ( # (WPLI_i > WPLI_observed) / # (WPLI_i ) ) of WPLI_i which are greater than the WPLI_observed, if this proportion is < 0.05 I could say that the WPLI_observed represents a significant degree of phase, otherwise not. Does it make sense or is it not the right approach? Let suppose this is a correct approach, I have two other questions: First, usually when I compute the WPLI value between two channels I obtain a number of WPLI values according to the cross-spectrum times (one WPLI for each sliding window), in the steps above I am assuming to compute the average WPLI_observed and the average WPLI_i for each step. Does this raise any problems? Second, is it a problem using the same random permutations employed to obtain ch1-ch2 (WPLI_i distribution) to calculate also the ch1-ch3 (WPLI_i distribution). This is just an implementatiion question. I would like to know if I could shuffle the time series of other channels in one step (i.e. for ch1 something like data.trial{other_than_ch1,perm}), and finally extract just the column relative to ch1 from WPLI matrix. thanks Matteo -------------- next part -------------- An HTML attachment was scrubbed... URL: From dimitri.bayle at inserm.fr Tue Jun 28 15:14:43 2011 From: dimitri.bayle at inserm.fr (Dimitri BAYLE) Date: Tue, 28 Jun 2011 15:14:43 +0200 Subject: [FieldTrip] DICS conditions comparison Message-ID: <4E09D3C3.6050906@inserm.fr> Dear Fieldtrip-users, I have a general question about source analysis comparison. I want to compare visual alpha deactivation between 2 conditions (A and B), both containing a baseline (pre) interval and a poststimulus interval, and both showing a strong occipital visual deactivation when comparing the relative contrast ((preA-postA)/preA). To compare A and B, should i calculated a common filter for the baseline and another one for the poststimulus interval, or used the same filter (calculated on which interval)? After applying the filter to all individuals trials (pre and post stimulus), is it better to 1) average alls trials, then calculated the relative contrast for A and for B ((pre-post)/pre)), and substract A and B relative contrast to reveal the difference or 2) calculated the relative contrast for each individuals trials, then average all relatives contrast per conditions (A and B), and substract A and B? Thanks for your help Dimitri From michael.wibral at web.de Tue Jun 28 20:34:28 2011 From: michael.wibral at web.de (Michael Wibral) Date: Tue, 28 Jun 2011 20:34:28 +0200 (CEST) Subject: [FieldTrip] WPLI statistic, permutation like test?? Message-ID: <7105645.2302309.1309286068611.JavaMail.fmail@mwmweb088> An HTML attachment was scrubbed... URL: From suforraxi at gmail.com Wed Jun 29 10:01:15 2011 From: suforraxi at gmail.com (Matteo Demuru) Date: Wed, 29 Jun 2011 10:01:15 +0200 Subject: [FieldTrip] WPLI statistic, permutation like test?? In-Reply-To: <7105645.2302309.1309286068611.JavaMail.fmail@mwmweb088> References: <7105645.2302309.1309286068611.JavaMail.fmail@mwmweb088> Message-ID: Hi Micheal, It seems to me that if you shuffle the trials and then compute the WPLI, the result is the same as if you do not shuffle. For example I have tried compute the WPLI on my trials and then switch trial{1} with trial{2} and the obtained WPLI is the same. Matteo On Tue, Jun 28, 2011 at 8:34 PM, Michael Wibral wrote: > Hi Matteo, > > I am not an expert on the WPLI measures, but to me it seems that in doing > > > "2) Randomly permute the ch2 time series" > > you're destroying a lot of ch2's properties (ie.g. it's spectrum will get a > lot of high ferquencies this way) and this will typically lead to false > positives. This is why permutation tests for connectivity measures typically > shuffle trials (i.e. permute data in a very controlled way, keeping the > intrinsic structure of the data). > > Michael > > > ------------------------------ > *Von:* "Matteo Demuru" > *Gesendet:* Jun 28, 2011 2:46:28 PM > *An:* fieldtrip at donders.ru.nl > *Betreff:* [FieldTrip] WPLI statistic, permutation like test?? > > > Hi, > > I have a couple of questions about using the WPLI index to assess the phase > on my MEG data. > > The experiment consists of recordings during a mental calculation task: I > have 30 sec in which each subject performed continuously an arithmetic > operation. > > It seems to me that WPLI index required more than one trial in order to be > computed. Am I right? (Is this necessary in order to reduce volume > conduction problems?) > I could divide my 30 sec in 5 sec-trials to create my trials, but I was > wandering if this could be a misuse of the WPLI, i.e. WPLI is not > appropriate for my experiment. > > I am also interested in assessing the significance of WPLI index, I would > like to gauge the significance per se of my WPLI values. > The idea is to calculate the WPLI distribution under the null hypothesis > (not phase coupling) for each pair of channels in this way: > > Example to assess the significance of WPLI value for ch1 vs ch2 > > 1) Calculate the WPLI for ch1 and ch2, this would be the observed WPLI > (WPLI_observed) > > 2) Randomly permute the ch2 time series > > 3) Calculate the WPLI for ch1 and ch2 (WPLI_i) > > 4) Repeat step 2 and 3 (for instance 100 times) in order to create the WPLI_i > distribution > > 5) Calculate the proportion ( # (WPLI_i > WPLI_observed) / # (WPLI_i ) ) > of WPLI_i which are greater than the WPLI_observed, if this proportion > is < 0.05 I could say that the WPLI_observed represents a significant > degree of phase, otherwise not. > > Does it make sense or is it not the right approach? > > Let suppose this is a correct approach, I have two other questions: > > First, usually when I compute the WPLI value between two channels I obtain > a number of WPLI values according to the cross-spectrum times (one WPLI for > each sliding window), in the steps above I am assuming to compute the > average WPLI_observed and the average WPLI_i for each step. Does this > raise any problems? > > Second, is it a problem using the same random permutations employed to > obtain ch1-ch2 (WPLI_i distribution) to calculate also the ch1-ch3 (WPLI_i distribution). > This is just an implementatiion question. I would like to know if I could > shuffle the time series of other channels in one step (i.e. for ch1 > something like data.trial{other_than_ch1,perm}), and finally extract just > the column relative to ch1 from WPLI matrix. > > thanks > > Matteo > > > > > > > > > > _______________________________________________ > 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 michael.wibral at web.de Wed Jun 29 17:35:29 2011 From: michael.wibral at web.de (Michael Wibral) Date: Wed, 29 Jun 2011 17:35:29 +0200 (CEST) Subject: [FieldTrip] WPLI statistic, permutation like test?? Message-ID: <786760757.45247.1309361729100.JavaMail.fmail@mwmweb077> An HTML attachment was scrubbed... URL: From paul_c at gmx.de Wed Jun 29 20:54:06 2011 From: paul_c at gmx.de (Paul Czienskowski) Date: Wed, 29 Jun 2011 20:54:06 +0200 Subject: [FieldTrip] ft_databrowser problems and questions Message-ID: <4E0B74CE.3050306@gmx.de> Dear all, I'm trying to plot ICA components with the ft_databrowser function. First of all the topoplots seem to look not like I'm used to. The topoplots I've seen this far filled out the whole circle and not only the rectangle it fills here (see attachment). Second one is, that sometimes, the functions starts to plot unselected components overlaying the selected components. Additionally there is a Question I have. I marked artifacts in the original data (with the ft_databrowser function) and hoped, they would be shown in the ft_databrowser too, when I'm plotting the components. Is there any (easy) way to accomplish this? Cheers, Paul -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 -------------- next part -------------- A non-text attachment was scrubbed... Name: 1to8.png Type: image/png Size: 38959 bytes Desc: not available URL: From megjim1 at gmail.com Thu Jun 30 08:05:08 2011 From: megjim1 at gmail.com (Jim Li) Date: Thu, 30 Jun 2011 01:05:08 -0500 Subject: [FieldTrip] channelrepair issue Message-ID: Dear all, We have 4D's WH3600 MEG system (248 channels) and we found the ----------------- cfg = []; cfg.dataset = 'e,rfhp0.1Hz'; cfg.trialdef.eventtype = 'TRIGGER'; cfg.trialdef.eventvalue = 320; cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 1; cfg = ft_definetrial(cfg); cfg.blc = 'yes'; cfg.blcwindow = [-1 0]; cfg.channel = {'MEG'}; raw_DATA = ft_preprocessing(cfg); raw_DATA.grad = ft_convert_units(raw_DATA.grad, 'cm') cfg = []; cfg.badchannel = {'A234'}; [raw_DATA] = ft_channelrepair(cfg, raw_DATA) the input is raw data with 248 channels and 201 trials repairing channel A234 using neighbour A121 using neighbour A143 using neighbour A154 using neighbour A173 using neighbour A224 using neighbour A8 using neighbour A91 repairing bad channels for trial 1 repairing bad channels for trial 2 repairing bad channels for trial 3 ... ------------------------------------ But channels like A121 and A143 are far away from the bad channel A234. How can they be used as neighbours (i.e. within 4cm, the default value for cfg.neighbourdist) for this bad channel? Any suggestions? Thanks a lot. Jim -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Jun 30 08:50:25 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 30 Jun 2011 08:50:25 +0200 Subject: [FieldTrip] channelrepair issue In-Reply-To: References: Message-ID: Hi Jim, where exactly are they located with respect to the bad channel? Best, Jan-Mathijs On Jun 30, 2011, at 8:05 AM, Jim Li wrote: > Dear all, > > We have 4D's WH3600 MEG system (248 channels) and we found the > ----------------- > cfg = []; > > cfg.dataset = > > 'e,rfhp0.1Hz'; > cfg.trialdef.eventtype = 'TRIGGER'; > > cfg.trialdef.eventvalue = 320; > > cfg.trialdef.prestim = 1; > > cfg.trialdef.poststim = 1 > > ; > cfg = ft_definetrial(cfg); > > cfg.blc = > > 'yes'; > cfg.blcwindow = [-1 0]; > > cfg.channel = {'MEG'}; > > raw_DATA = ft_preprocessing(cfg); > > raw_DATA.grad = ft_convert_units(raw_DATA.grad, 'cm') > > > cfg = []; > cfg.badchannel = {'A234'}; > [raw_DATA] = ft_channelrepair(cfg, raw_DATA) > the input is raw data with 248 channels and 201 trials > repairing channel A234 > using neighbour A121 > using neighbour A143 > using neighbour A154 > using neighbour A173 > using neighbour A224 > using neighbour A8 > using neighbour A91 > repairing bad channels for trial 1 > repairing bad channels for trial 2 > repairing bad channels for trial 3 > ... > ------------------------------------ > > But channels like A121 and A143 are far away from the bad channel > A234. How can they be used as neighbours (i.e. within 4cm, the > default value for cfg.neighbourdist) for this bad channel? > > Any suggestions? > > Thanks a lot. > > Jim > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Thu Jun 30 09:45:57 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 30 Jun 2011 09:45:57 +0200 Subject: [FieldTrip] ft_databrowser problems and questions In-Reply-To: <4E0B74CE.3050306@gmx.de> References: <4E0B74CE.3050306@gmx.de> Message-ID: <4E0C29B5.8060201@donders.ru.nl> Dear Paul, the topoplot bug you get should have been resolved in some newer FieldTrip version, I can remember this one and resolved it a while ago. The overlaying plotting is simply caused because you click too fast. The function plots the individual topos- and time courses. Any callback from one of the buttons does not interrupt this plotting, meaning that it will clear the axes, continue plotting the topos- and time courses if this was not already finished and then start plotting the new topos- and time courses. This will be resolved in a newer version (see below). About the third question: In the current implementation, this is not possible. However, we just started restructuring the code for the databrowser, and in my opinion it should be ready to be made public. In the new implementation, you can annotate and see annotated artifacts in component viewmode. I will keep you up to date on this. Best, Jörn ThisOn 6/29/2011 8:54 PM, Paul Czienskowski wrote: > Dear all, > > I'm trying to plot ICA components with the ft_databrowser function. > First of all the topoplots seem to look not like I'm used to. The > topoplots I've seen this far filled out the whole circle and not only > the rectangle it fills here (see attachment). Second one is, that > sometimes, the functions starts to plot unselected components > overlaying the selected components. > Additionally there is a Question I have. I marked artifacts in the > original data (with the ft_databrowser function) and hoped, they would > be shown in the ft_databrowser too, when I'm plotting the components. > Is there any (easy) way to accomplish this? > > Cheers, > Paul > > > > > _______________________________________________ > 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 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 odidodi at hotmail.com Thu Jun 30 11:04:55 2011 From: odidodi at hotmail.com (odelia nakar) Date: Thu, 30 Jun 2011 09:04:55 +0000 Subject: [FieldTrip] channelrepair issue In-Reply-To: References: Message-ID: Hi Jim, Try : cfg.neighbourdist = 0.03; I found it good for my data. (When you run the function the channels that repaired your data is displayed in the command window). Good luck! Odelia. Date: Thu, 30 Jun 2011 01:05:08 -0500 From: megjim1 at gmail.com To: fieldtrip at donders.ru.nl Subject: [FieldTrip] channelrepair issue Dear all, We have 4D's WH3600 MEG system (248 channels) and we found the ----------------- cfg = []; cfg.dataset = 'e,rfhp0.1Hz'; cfg.trialdef.eventtype = 'TRIGGER'; cfg.trialdef.eventvalue = 320; cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 1; cfg = ft_definetrial(cfg); cfg.blc = 'yes'; cfg.blcwindow = [-1 0]; cfg.channel = {'MEG'}; raw_DATA = ft_preprocessing(cfg); raw_DATA.grad = ft_convert_units(raw_DATA.grad, 'cm') cfg = []; cfg.badchannel = {'A234'}; [raw_DATA] = ft_channelrepair(cfg, raw_DATA) the input is raw data with 248 channels and 201 trials repairing channel A234 using neighbour A121 using neighbour A143 using neighbour A154 using neighbour A173 using neighbour A224 using neighbour A8 using neighbour A91 repairing bad channels for trial 1 repairing bad channels for trial 2 repairing bad channels for trial 3 ... ------------------------------------ But channels like A121 and A143 are far away from the bad channel A234. How can they be used as neighbours (i.e. within 4cm, the default value for cfg.neighbourdist) for this bad channel? Any suggestions? Thanks a lot. Jim _______________________________________________ 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 megjim1 at gmail.com Thu Jun 30 17:39:23 2011 From: megjim1 at gmail.com (Jim Li) Date: Thu, 30 Jun 2011 10:39:23 -0500 Subject: [FieldTrip] channelrepair issue In-Reply-To: References: Message-ID: Hi Jan-Mathijs, >From Fieldtrip data structure I saw that the coordinate of A234 is [ -7.2133 9.1712 5.7117]. And it's [14.4320 -0.0683 0.4437] for A121. All these are in "cm". So the distance between the two channels are 24.1172cm. I checked 4D's orignial file and found the channel coordinates to agree with what I read from Fieldtrip. So I'm wondering how those coils 24.1172cm apart can be considered neighbours (within 4cms). Thanks a lot, Jim On Thu, Jun 30, 2011 at 1:50 AM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Hi Jim, where exactly are they located with respect to the bad channel? > > Best, > > Jan-Mathijs > > > On Jun 30, 2011, at 8:05 AM, Jim Li wrote: > > Dear all, > > We have 4D's WH3600 MEG system (248 channels) and we found the > ----------------- > > cfg = []; > > cfg.dataset = > 'e,rfhp0.1Hz'; > > cfg.trialdef.eventtype = 'TRIGGER'; > > cfg.trialdef.eventvalue = 320; > > cfg.trialdef.prestim = 1; > > cfg.trialdef.poststim = 1 > ; > > cfg = ft_definetrial(cfg); > > cfg.blc = > 'yes'; > > cfg.blcwindow = [-1 0]; > > cfg.channel = {'MEG'}; > > raw_DATA = ft_preprocessing(cfg); > > raw_DATA.grad = ft_convert_units(raw_DATA.grad, 'cm') > > cfg = []; > cfg.badchannel = {'A234'}; > [raw_DATA] = ft_channelrepair(cfg, raw_DATA) > the input is raw data with 248 channels and 201 trials > repairing channel A234 > using neighbour A121 > using neighbour A143 > using neighbour A154 > using neighbour A173 > using neighbour A224 > using neighbour A8 > using neighbour A91 > repairing bad channels for trial 1 > repairing bad channels for trial 2 > repairing bad channels for trial 3 > ... > ------------------------------------ > > But channels like A121 and A143 are far away from the bad channel A234. How > can they be used as neighbours (i.e. within 4cm, the default value for > cfg.neighbourdist) for this bad channel? > > Any suggestions? > > Thanks a lot. > > Jim > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > > _______________________________________________ > 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 odidodi at hotmail.com Wed Jun 1 09:10:30 2011 From: odidodi at hotmail.com (odelia nakar) Date: Wed, 1 Jun 2011 07:10:30 +0000 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>, <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl>, , , <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com>, , <4DDB5A14.3090102@uni-oldenburg.de>, <34CEBDBD-7738-403D-A563-4A6FDBD83C04@mac.com>, , Message-ID: Hi all, Thank you all for the discussion. I'm sorry I response only now, I went on a vacation... I actually didn't want to run the ICA on trials with blinks, rather on all trials, but to remove the component only for trials with a blink. Your critics concern my idea as well, since if I have any kind of correlation between condition and blink I might yield a difference that does not exist between conditions... Considering your suggestion, Mahesh, unfortunately I don't have EOG recording for this experiment. Thanks again for the discussion, Odelia. Date: Fri, 27 May 2011 00:32:01 -0400 From: mahesh.casiraghi at gmail.com To: yuvharpaz at gmail.com; fieldtrip at donders.ru.nl Subject: Re: [FieldTrip] ICA+frqanalysis questions Dear Yuval and discussion group, it seems to me that what you are proposing is getting close to what proposed by the hybrid approach of regica described here: Manousos A. Klados, Christos Papadelis, Christoph Braun, Panagiotis D. Bamidis, REG-ICA: A hybrid methodology combining Blind Source Separation and regression techniques for the rejection of ocular artifacts, Biomedical Signal Processing and Control, In Press, Corrected Proof, Available online 16 March 2011, ISSN 1746-8094, DOI: 10.1016/j.bspc.2011.02.001. They suggest to selectively run regression based AR only on those components which correlate with EOG signals. This makes sense to me and I have been trying to experiment that on some old data, although with no clear conclusions yet. It may be worth a try for Odelia: Anybody out there with some insights for this - or maybe a similar - approach? Cheers, Mahesh Mahesh M. CasiraghiPhD candidate - Cognitive Sciences Roberto Dell'Acqua Lab, University of PadovaPierre Jolicoeur Lab, Univesité de Montréal mahesh.casiraghi at umontreal.ca I have the conviction that when Physiology will be far enough advanced, the poet, the philosopher, and the physiologist will all understand each other. Claude Bernard On Thu, May 26, 2011 at 11:40 PM, Yuval Harpaz wrote: Dear discussion groupDid anybody consider smoothing or filtering the component trace before rejecting it? it seems that the added noise to no-blink trials is in a frequency higher than that typical to blinks. what if we evaluate the component weight, creating a trace for the eyeblink component for every trial, then bandpass filter the blink trace , say 0.1-25Hz, and only then remove the component from the data? yuval On 27 May 2011 06:16, Joseph Dien wrote: Stefan, just to be clear, I don't think any of us were saying not to use ICA to correct blinks. David was just saying that there are potential concerns when one only applies the ICA to the blink trials rather than to all the trials. I myself use EEGlab's infomax implementation in the automatic eyeblink correction tool of my EP Toolkit (http://sourceforge.net/projects/erppcatoolkit/). Now that said, I should add a little more nuance to my response. One of the things I observed (or rather, that Tim Curran pointed out to me) is that when you apply ICA to remove eyeblink artifacts in this manner, it can actually substantially increase the noise level in the data, so for the trials without eyeblinks it can have a considerable cost. So in order to balance the cost/benefit ratio, what I did was to include a trial by trial criterion that the putative eyeblink factors would only be removed if doing so reduced the overall variance of the trial. This approach does still have some potential for causing the concerns that David raises but not as much as only applying the ICA to blink trials since it does end up getting applied to non-blink trials too. This does mean that one should be cautious about any apparent effects in the artifact corrected data that are centered around the eyes (that have a blink topography) but that goes without saying in any case. So anyway, I agree, it's not perfect but seems to be the best available option. Cheers! Joe On May 24, 2011, at 3:11 AM, Stefan Debener wrote: Hi Odelia, I have a slightly different opinion here. It is certainly true that any filter has the tendency to distort data (with distortion I mean that data consists of a mixture of some wanted, true signal and some unwanted signal, and that the removal of the unwanted part of the signal is neither complete nor specific). In our lab we regularly use ICA for artefact removal (and more), and the benefit/gain is clearly are much larger than the distortion. In fact there are a number of examples out showing that currently only ICA (or related tools) can recover the study of (a substantial fraction of the wanted) EEG signal (but again, it is NOT a perfect tool at all), in particular in cases where other means of SNR enhancement don't work well (averaging, spectral analysis). I am happy to provide references if you are interested... For the evaluation of outcome it would be reasonable to not evaluate the ERP alone, as this could be misleading. Better evaluate the sensitivity and specificity of an eye blink attentuation approach on the single trial (and single subject) level, this will give you good insight. And it is worth keeping in mind that the preprocessing of the data (among other issues, like the quality of the recording and so on) largely determines the quality of the output (for some introduction you may look up chapter 3.1 in Ullsperger & Debener, 2010, Simultaneous EEG and FMRI, Oxford University Press). Just by a different preprocessing ICA output could vary between crap and excellent unmixing. Thus a poor ICA eye blink attenuation would make me a bit suspicious... Best, Stefan Am 5/24/11 4:00 AM, schrieb Alexander J. Shackman: And for a related perspective, see McMenamin, B. W., Shackman, A. J., Greischar, L. L. & Davidson, R. J. (2011). Electromyogenic artifacts and electroencephalographic inferences revisited, Neuroimage, 54, 4-9. http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf On Mon, May 23, 2011 at 8:07 PM, Joseph Dien wrote: I agree with David's reasoning. You may find the following article to be of help as well in understanding the issues involved: Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of simulated ERPs: Promax versus Infomax rotations. Human Brain Mapping, 28(8), 742-763. Cheers! Joe On May 23, 2011, at 11:57 AM, David Groppe wrote: Hi Odelia, When you use ICA (or any other spatial filter) to correct for EEG artifacts, you're going to distort your data some by removing true EEG activity in addition to the artifact (for an explanation, see: http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). So to minimize distortion, it would be better not to apply ICA artifact correction to artifact-free data. However, if the frequency of the artifact differs across experimental conditions, it could confound your analysis. For example, I suspect people blink more often to targets in an oddball experiment than standards. Thus if you apply ICA only to blinky trials, you could find a difference between the EEG response to standards and targets that simply reflects the fact ICA removed more EEG activity in the target trials (i.e., it wouldn't reflect a true difference in neural processing). hope this helps, -David On Mon, May 23, 2011 at 1:44 AM, odelia nakar wrote: Hi all, I'm troubled by the fact that when I use ICA for blinks\eyes movements removal, I remove the relevant components also from trials that do not contain blinks\eyes movements. In order to avoid this bias we thought to combine the data before ICA ("data" structure) with the data after ICA ("dataica" structure), only in specific trials, as follows: datall=dataica; datall.trial=data.trial; datall.time=data.time; blinks=[2 4 5 8 bla bla 156]; for ind=1:length(blinks) datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; end To my first question: I just wanted to check that there is no problem with that, or any reason not to use it. Another issue- I use motor learning task, and I'm trying to understand what happens through the process, in terms of power-frequency changes through the process. How would you recommend that I'd use the ft_freqanalysis function? What method to use (or what do I need to consider when choosing the method field)? Thanks a lot, Odelia. _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- David Groppe, Ph.D. Postdoctoral Researcher Kutaslab Dept. of Cognitive Science University of California, San Diego http://www.cogsci.ucsd.edu/~dgroppe/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------------------------------------------------------------------------- Joseph Dien E-mail: jdien07 at mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://homepage.mac.com/jdien07/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Alexander J. Shackman, Ph.D. Wisconsin Psychiatric Institute & Clinics and Department of Psychology University of Wisconsin-Madison 1202 West Johnson Street Madison, Wisconsin 53706 Telephone: +1 (608) 358-5025 Fax: +1 (608) 265-2875 Email: shackman at wisc.edu http://psyphz.psych.wisc.edu/~shackman _______________________________________________ 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 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Y.Harpaz a link to the BIU MEG lab: http://faculty.biu.ac.il/~goldsa/index.html "Many were increasingly of the opinion that they'd all made a big mistake in coming down from the trees in the first place. And some said that even the trees had been a bad move, and that no one should ever have left the oceans". Douglas Adams _______________________________________________ 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 suforraxi at gmail.com Wed Jun 1 11:23:54 2011 From: suforraxi at gmail.com (Matteo Demuru) Date: Wed, 1 Jun 2011 11:23:54 +0200 Subject: [FieldTrip] WPLI question Message-ID: Hi, I have question about the WPLI: I would like to know why it can have either positive or negative value? It seems to me that it could be due from the relation (lagging or leading) between two signals, but I am not sure. Taking the absolute value of the WPLI is it a way to preserve the 'synchronization infomation' discardig which signal is leading or lagging? Thanks Matteo -------------- next part -------------- An HTML attachment was scrubbed... URL: From martinvinck at gmail.com Wed Jun 1 12:07:17 2011 From: martinvinck at gmail.com (Martin Vinck) Date: Wed, 1 Jun 2011 12:07:17 +0200 Subject: [FieldTrip] WPLI question In-Reply-To: References: Message-ID: <345B36F9-D0E3-43F4-8B7B-25333BB5681E@gmail.com> Hi Mateo, As it is computed in ft_connectivity_wpli it preserves the information about the sign, i.e. whether the average imaginary component of the cross-spectrum is positive or negative. That is, it estimates the average imaginary component of the cross-spectrum divided by the average magnitude of this imaginary component. By taking the absolute value over the output one gets a measure of the strength of the interaction,- WPLI as it is defined in the paper, by taking the sign one gets a measure of the direction of the interaction. The debiased WPLI estimator gets negative however as a consequence of the debiasing method - different issue. Best, Martin. From Elena.Orekhova at neuro.gu.se Wed Jun 1 12:23:29 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Wed, 1 Jun 2011 10:23:29 +0000 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECA991@exchccr1.neuro.gu.se> Dear fieldtrippers, This message is mainly for Neuromag users. When I do 'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. If I combine the two types of sensors without weighting, the result is meaningless. Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements. Does anybody know how to deal with this problem? Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.wibral at web.de Wed Jun 1 16:04:46 2011 From: michael.wibral at web.de (Michael Wibral) Date: Wed, 1 Jun 2011 16:04:46 +0200 (CEST) Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis Message-ID: <1960081272.1639684.1306937086986.JavaMail.fmail@mwmweb084> An HTML attachment was scrubbed... URL: From zechuan_he at hotmail.com Wed Jun 1 15:35:07 2011 From: zechuan_he at hotmail.com (Zeddy He) Date: Wed, 1 Jun 2011 11:35:07 -0200 Subject: [FieldTrip] Emotiv headset realtime capture In-Reply-To: References: Message-ID: Hi Valentin, I am not entirely sure exactly what part of the process you're not sure about. I'm new to fieldtrip as well and I have never heard of emotiv until today. I have, however, been playing around with FieldTrip's realtime acquisition part for the last couple of weeks(acq2ft, AcqBuffer), and maybe able to offer some pointers in getting it set up on your system. It seems that to use emotive2ft, you would have to compile it first, call upon it in matlab before starting your emotive software, and then start the emotiv software. I am not exactly sure what can read the bufferdata, though ft_realtime_signalviewer as well as viewer.exe may be good functions/programs to start off with. If you're using acq2ft or Acqbuffer already for realtime acquistion from another CTF device, you could try running one of those first either by standalone or their MATLAB equivilent functions, and then run emotiv2ft in matlab without any passed in parameters(unless you didn't decide to put the buffer on localhost:1972). You also might be able to just let the function create it's own buffer by giving it a new port, and then draw from that port seperately later on. Some troubles I've ran into while using FieldTrip's realtime functions include: shmget() errors on linux systems firewall blocking port number type in-compatibility and perhaps a couple others I can't recall at the moment. If you think I might be capable of assisting you, let me know and I'll see if I can give you additional details. Regards Zeddy > From: valentin.umbach at hu-berlin.de > Date: Tue, 31 May 2011 18:51:17 +0200 > To: fieldtrip at donders.ru.nl > Subject: [FieldTrip] Emotiv headset realtime capture > > Hi, I'm new to FieldTrip and I'm interested in using it to capture > realtime data from the Emotiv headset using this interface: > http://fieldtrip.fcdonders.nl/development/realtime/emotiv > I'm not clear about how to make calls to this interface from within > Matlab. Also, I would like to know if it's possible to access not just > the raw EEG, but also the API output of the detection libraries > (Affectiv Suite...). > Any help is greatly appreciated! > > Best, Valentin > > -- > Dipl.-Psych. Valentin J. Umbach > Institut für Psychologie > Humboldt-Universität zu Berlin > Rudower Chaussee 18 > 12489 Berlin > Tel. +49 30 2093 9438 > E-Mail: valentin.umbach at hu-berlin.de > > _______________________________________________ > 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 michael.wibral at web.de Thu Jun 2 13:18:04 2011 From: michael.wibral at web.de (michael.wibral at web.de) Date: Thu, 2 Jun 2011 13:18:04 +0200 (CEST) Subject: [FieldTrip] Poblem with options for ft_volumesegment Message-ID: <511684614.2148844.1307013484440.JavaMail.fmail@mwmweb077> An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Jun 2 13:26:45 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 2 Jun 2011 13:26:45 +0200 Subject: [FieldTrip] Poblem with options for ft_volumesegment In-Reply-To: <511684614.2148844.1307013484440.JavaMail.fmail@mwmweb077> References: <511684614.2148844.1307013484440.JavaMail.fmail@mwmweb077> Message-ID: Dear Michael, Thanks for reporting this; we'll look into it. Best, JM On Jun 2, 2011, at 1:18 PM, michael.wibral at web.de wrote: > Dear FT'ers, > > Davide Rivolta posted a problem with ft_volumesegment a while ago. > We have meanwhile solved this problem. > > There is (FT from may 31st) a problem with the handling of the > > cfg.smooth > > option. > > It's default is 'no', according to the function HELP. > However in line 434 of ft_volumesegment, this option is put into a > numerical array - this makes sense for a smoothing value. Also if no > specification is given at all, then a NaN is inserted into the > array. However if "no" is set explicitely then ft_getopt tries to > insert the string 'no' into the array which leads to an error. Below > is a script that is running and the error is once again detailed in > the commets. > In my opinion this could be fixed by simply updating te function HELP. > > Michael > > %%Brain segmentation – MRI > > > mri = ft_read_mri('NPD18_V2.mri'); > > cfg = []; > > cfg.spmversion = 'spm8'; > > cfg.output = 'tpm'; > > cfg.template = 'T1.nii'; > > cfg.units = 'mm'; > > cfg.write = 'no'; > > cfg.coordsys = 'ctf'; > > cfg.downsample = 2; > > cfg.smooth = NaN; % works. option 'no' as recommended (!) in > the function HELP throws an > > % error because ft_getopt > on line 434 of ft_volumesegment > > % tries to put a string of > length two into an array that is for numbers > > % leaving out this option > also worked, but some > > % people might try to use > this option > > segmentedmri = ft_volumesegment(cfg, mri); > > save ('segmentedmri'); > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Thu Jun 2 18:22:03 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Thu, 2 Jun 2011 16:22:03 +0000 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <1960081272.1639684.1306937086986.JavaMail.fmail@mwmweb084> References: <1960081272.1639684.1306937086986.JavaMail.fmail@mwmweb084> Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECAB58@exchccr1.neuro.gu.se> Dear Michael, I have tried to multiply the leadfield by -1 as you suggested: for i = 1 : size (grid.leadfield, 2) grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); end This had no effect on the 'lcmv' output. I attached the pictures for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ In this experiment I measured evoked field in response to the unilateral (left) click. The source is expected to be in the right superior temporal cortex. This is the case for ‘GRA only' and ’MAG only’ datasets. The combined sensors give meaningless result. Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Wednesday, June 01, 2011 4:04 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Elena, could you give the following a try: invert (*-1) the leadfileds for one of the two sensor types. Let me know what happens. I would also be interested in taking a look at the results - maybe you could sent images off-list: Michael.Wibral web.de. Michael ________________________________ Von: "Elena Orekhova" Gesendet: Jun 1, 2011 12:23:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "Arial"; }@font-face { font-family: "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: Times; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear fieldtrippers, This message is mainly for Neuromag users. When I do 'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. If I combine the two types of sensors without weighting, the result is meaningless. Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements. Does anybody know how to deal with this problem? Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: lcmv_St1_gra_1p2-1p5.jpg Type: image/jpeg Size: 22987 bytes Desc: lcmv_St1_gra_1p2-1p5.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: lcmv_St1_mag_1p2-1p5.jpg Type: image/jpeg Size: 22978 bytes Desc: lcmv_St1_mag_1p2-1p5.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: lcmv_St1_mag+gra_1p2-1p5.jpg Type: image/jpeg Size: 22576 bytes Desc: lcmv_St1_mag+gra_1p2-1p5.jpg URL: From michael.wibral at web.de Thu Jun 2 19:20:07 2011 From: michael.wibral at web.de (Michael Wibral) Date: Thu, 2 Jun 2011 19:20:07 +0200 (CEST) Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis Message-ID: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Thu Jun 2 20:03:16 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Thu, 2 Jun 2011 18:03:16 +0000 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F03ECAB58@exchccr1.neuro.gu.se> References: <1960081272.1639684.1306937086986.JavaMail.fmail@mwmweb084>, <32CC77C0C8A7AD4B9410934642608E1F03ECAB58@exchccr1.neuro.gu.se> Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECAB81@exchccr1.neuro.gu.se> Dear Michael, I did normalize the data (sourcepst.avg.nai=sourcepst.avg.pow./sourcepre.avg.pow) as it was suggested in the tutorial. I used the same scales in all plots for comparison purposes. If automatic scaling is used the result for MAG+GRA does not look any better (see attachment). >What you could do as a workaround is to average the separate results with a weighting per voxel and that >is corresponding to the squared norms of the leadfields for the respective modalities for a given voxel , this >would guarantee equal amounts of backprojected noise from both modalities (if I'm not mistaken). Thank you for your suggestion. I may use it as a last resort. Hopefully, there is still a way to get more optimal solution using both GRA and MAG in the same analysis... Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Elena Orekhova [Elena.Orekhova at neuro.gu.se] Sent: Thursday, June 02, 2011 6:22 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Michael, I have tried to multiply the leadfield by -1 as you suggested: for i = 1 : size (grid.leadfield, 2) grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); end This had no effect on the 'lcmv' output. I attached the pictures for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ In this experiment I measured evoked field in response to the unilateral (left) click. The source is expected to be in the right superior temporal cortex. This is the case for ‘GRA only' and ’MAG only’ datasets. The combined sensors give meaningless result. Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Wednesday, June 01, 2011 4:04 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Elena, could you give the following a try: invert (*-1) the leadfileds for one of the two sensor types. Let me know what happens. I would also be interested in taking a look at the results - maybe you could sent images off-list: Michael.Wibral web.de. Michael ________________________________ Von: "Elena Orekhova" Gesendet: Jun 1, 2011 12:23:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "Arial"; }@font-face { font-family: "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: Times; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear fieldtrippers, This message is mainly for Neuromag users. When I do 'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. If I combine the two types of sensors without weighting, the result is meaningless. Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements. Does anybody know how to deal with this problem? Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: lcmv_St1_mag+gra_autoscale.jpg Type: image/jpeg Size: 22257 bytes Desc: lcmv_St1_mag+gra_autoscale.jpg URL: From smoratti at psi.ucm.es Fri Jun 3 11:00:18 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Fri, 03 Jun 2011 11:00:18 +0200 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> References: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> Message-ID: <722801BA-5C22-4A69-8F87-18C1C54A7F00@psi.ucm.es> Hi Michael y Elena, I am following your discussion with great interest as I have just started to work with Neuromag data. As FT uses the MNE toolbox to read the data I assume that the SSP vectors are applied to the data during reading the data. However, the SSP vectors are stored in "data.hdr.orig.projs". However, when I go on with averaging in the ERF from timelockanalysis I cannot find this info. So my question is, does FT apply the SSP vectors later on also to the leadfield when calculating it? I assume that not, as the SSP vectors are not passed on further. How can I apply the SSP vectors to the leadfield to get correct results? Best and thanks, STephan El 02/06/2011, a las 19:20, Michael Wibral escribió: > Hi Elena, > > I assume that you were well aware of the difficulties in beamforming evoked activty and baseline normalisation and these things, your results really look that way. I mus say I am quite puzzled by the results - could it be a color scaling problem in the plot? I think this mmay be a problem because most of your plot is a peak power, only a tiny corner seems to be in a low-amplitude range. > > What you could do as a workaround is to average the separate results with a weighting per voxel and that is corresponding to the squared norms of the leadfields for the respective modalities for a given voxel , this would guarantee equal amounts of backprojected noise from both modalities (if I'm not mistaken). > > Michael > PS: I am away for a couple of days, but after that, I'll be happy to resume this discussion. > > > Von: "Elena Orekhova" > Gesendet: Jun 2, 2011 6:22:03 PM > An: "Email discussion list for the FieldTrip project" > Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis > > @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } > Dear Michael, > > > I have tried to multiply the leadfield by -1 as you suggested: > > > for i = 1 : size (grid.leadfield, 2) > > grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); > > end > > > This had no effect on the 'lcmv' output. I attached the pictures for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ > > > In this experiment I measured evoked field in response to the unilateral (left) click. > > The source is expected to be in the right superior temporal cortex. This is the case for ‘GRA only' and ’MAG only’ datasets. The combined sensors give meaningless result. > > > Elena > > > From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] > Sent: Wednesday, June 01, 2011 4:04 PM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis > > > Dear Elena, > > could you give the following a try: invert (*-1) the leadfileds for one of the two sensor types. Let me know what happens. > I would also be interested in taking a look at the results - maybe you could sent images off-list: Michael.Wibral web.de. > > Michael > > > > Von: "Elena Orekhova" > Gesendet: Jun 1, 2011 12:23:29 PM > An: "fieldtrip at donders.ru.nl" > Betreff: [FieldTrip] combining magnetometers and planad gradiometers for analysis > > @font-face { font-family: "Arial"; }@font-face { font-family: "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: Times; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } > Dear fieldtrippers, > > This message is mainly for Neuromag users. > > > When I do 'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. > > If I combine the two types of sensors without weighting, the result is meaningless. > > Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements. Does anybody know how to deal with this problem? > > > > Elena > > > > _______________________________________________ > 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 jan.schoffelen at donders.ru.nl Fri Jun 3 13:11:02 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 3 Jun 2011 13:11:02 +0200 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <722801BA-5C22-4A69-8F87-18C1C54A7F00@psi.ucm.es> References: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> <722801BA-5C22-4A69-8F87-18C1C54A7F00@psi.ucm.es> Message-ID: <77A55ECC-5A84-4839-9093-75FA499D3D31@donders.ru.nl> Hi Stephan et al, Any balancing coefficients (e.g. the digital weights for the bti- system, or ctf's 3d order gradient coefficients) are only applied to the leadfield if they end up in the data.grad.tra matrix. These .tra matrices will be compiled when reading the data header, by functions like XXX2grad (in fileio/private: ctf2grad, bti2grad, fif2grad). You can check whether it is constructed using hdr.orig.projs. If not, it may be worthwile to implement I guess. Best, JM On Jun 3, 2011, at 11:00 AM, Stephan Moratti wrote: > Hi Michael y Elena, > > I am following your discussion with great interest as I have just > started to work with Neuromag data. As FT uses the MNE toolbox to > read the data I assume that the SSP vectors are applied to the data > during reading the data. However, the SSP vectors are stored in > "data.hdr.orig.projs". However, when I go on with averaging in the > ERF from timelockanalysis I cannot find this info. So my question > is, does FT apply the SSP vectors later on also to the leadfield > when calculating it? I assume that not, as the SSP vectors are not > passed on further. How can I apply the SSP vectors to the leadfield > to get correct results? > > Best and thanks, > > STephan > > El 02/06/2011, a las 19:20, Michael Wibral escribió: > >> Hi Elena, >> >> I assume that you were well aware of the difficulties in >> beamforming evoked activty and baseline normalisation and these >> things, your results really look that way. I mus say I am quite >> puzzled by the results - could it be a color scaling problem in the >> plot? I think this mmay be a problem because most of your plot is a >> peak power, only a tiny corner seems to be in a low-amplitude range. >> >> What you could do as a workaround is to average the separate >> results with a weighting per voxel and that is corresponding to >> the squared norms of the leadfields for the respective modalities >> for a given voxel , this would guarantee equal amounts of >> backprojected noise from both modalities (if I'm not mistaken). >> >> Michael >> PS: I am away for a couple of days, but after that, I'll be happy >> to resume this discussion. >> >> >> Von: "Elena Orekhova" >> Gesendet: Jun 2, 2011 6:22:03 PM >> An: "Email discussion list for the FieldTrip project" > > >> Betreff: Re: [FieldTrip] combining magnetometers and planad >> gradiometers for analysis >> >> @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face >> { font-family: "Cambria Math"; }@font-face { font-family: >> "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal, >> li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: >> 12pt; font-family: Cambria; }.MsoChpDefault { font-family: >> Cambria; }div.WordSection1 { page: WordSection1; } >> Dear Michael, >> >> >> I have tried to multiply the leadfield by -1 as you suggested: >> >> >> for i = 1 : size (grid.leadfield, 2) >> >> grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); >> >> end >> >> >> This had no effect on the 'lcmv' output. I attached the pictures >> for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ >> >> >> In this experiment I measured evoked field in response to the >> unilateral (left) click. >> >> The source is expected to be in the right superior temporal >> cortex. This is the case for ‘GRA only' and ’MAG only’ datasets. >> The combined sensors give meaningless result. >> >> >> Elena >> >> >> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl >> ] on behalf of Michael Wibral [michael.wibral at web.de] >> Sent: Wednesday, June 01, 2011 4:04 PM >> To: Email discussion list for the FieldTrip project >> Subject: Re: [FieldTrip] combining magnetometers and planad >> gradiometers for analysis >> >> >> Dear Elena, >> >> could you give the following a try: invert (*-1) the leadfileds for >> one of the two sensor types. Let me know what happens. >> I would also be interested in taking a look at the results - maybe >> you could sent images off-list: Michael.Wibral web.de. >> >> Michael >> >> >> >> Von: "Elena Orekhova" >> Gesendet: Jun 1, 2011 12:23:29 PM >> An: "fieldtrip at donders.ru.nl" >> Betreff: [FieldTrip] combining magnetometers and planad >> gradiometers for analysis >> >> @font-face { font-family: "Arial"; }@font-face { font-family: >> "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D >> "; }@font-face { font-family: "Cambria Math"; }@font-face { font- >> family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal >> { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: >> Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; >> font-family: Times; }.MsoChpDefault { font-family: >> Cambria; }div.WordSection1 { page: WordSection1; } >> Dear fieldtrippers, >> >> This message is mainly for Neuromag users. >> >> >> When I do 'lcmv' beamforming analysis separately on planar >> gradiometers or magnetometers, I get quite meaningful results. >> >> If I combine the two types of sensors without weighting, the result >> is meaningless. >> >> Apparently, the algorithm does not take care of different scales >> and units of the GRA and MAG measurements. Does anybody know how >> to deal with this problem? >> >> >> >> Elena >> >> >> >> _______________________________________________ >> 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 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Fri Jun 3 14:25:46 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Fri, 3 Jun 2011 12:25:46 +0000 Subject: [FieldTrip] cfg.method = 'sam' Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECAC4F@exchccr1.neuro.gu.se> Dear colleagues, Sorry, I posted much on the list recent time. I want to figure out howto run SAM analysis on my data. When I run 'lcmv' beamformer on my averaged dataset it works fine: cfg = []; cfg.grad = hdr.grad; cfg.method = 'lcmv'; cfg.grid = grid; cfg.vol = vol_cm; cfg.reducerank=2; cfg.keepfilter = 'yes' cfg.channel = MAG; %MAG = {'MEG0721', 'MEG0731',... } source = ft_sourceanalysis(cfg, tlckavg); When I do the same with cfg.method = 'lcmv' option, I get the error: ***************************** ??? Undefined function or method 'beamformer_sam' for input arguments of type 'struct'. Error in ==> sourceanalysis at 1158 dip(i) = beamformer_sam(grid, sens, vol, squeeze(avg(i,:,:)), squeeze(Cy(i,:,:)), optarg{:}); Error in ==> ft_sourceanalysis at 11 [varargout{1:nargout}] = funhandle(varargin{:}); Does anybody know how to make the ‘SAM’ option to work? Does anybody used cfg.method = 'lcmv' option in the Fieldtrip??? Regards, Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Fri Jun 3 14:57:47 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Fri, 3 Jun 2011 12:57:47 +0000 Subject: [FieldTrip] cfg.method = 'sam' Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECAC6B@exchccr1.neuro.gu.se> Dear colleagues, Sorry, I posted much on the list recent time. I want to figure out how to run SAM analysis on my data. When I run 'lcmv' beamformer on my averaged dataset it works fine: cfg = []; cfg.grad = hdr.grad; cfg.method = 'lcmv'; cfg.grid = grid; cfg.vol = vol_cm; cfg.reducerank=2; cfg.keepfilter = 'yes' cfg.channel = MAG; %MAG = {'MEG0721', 'MEG0731',... } source = ft_sourceanalysis(cfg, tlckavg); When I do the same with cfg.method = 'sam' option, I get the error: ***************************** ??? Undefined function or method 'beamformer_sam' for input arguments of type 'struct'. Error in ==> sourceanalysis at 1158 dip(i) = beamformer_sam(grid, sens, vol, squeeze(avg(i,:,:)), squeeze(Cy(i,:,:)), optarg{:}); Error in ==> ft_sourceanalysis at 11 [varargout{1:nargout}] = funhandle(varargin{:}); Does anybody know how to make the ‘SAM’ option to work? Does anybody used cfg.method = 'sam' option in the Fieldtrip??? Regards, Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Fri Jun 3 15:08:53 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Fri, 03 Jun 2011 15:08:53 +0200 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <77A55ECC-5A84-4839-9093-75FA499D3D31@donders.ru.nl> References: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> <722801BA-5C22-4A69-8F87-18C1C54A7F00@psi.ucm.es> <77A55ECC-5A84-4839-9093-75FA499D3D31@donders.ru.nl> Message-ID: <32BF5576-A020-41A6-AF11-0879E03067FD@psi.ucm.es> Hi Jan-Mathijs, I had just a look at fif2grad.m and it seems to me that the information of hdr.orig.projs is not used to construct the .tra field. It only codes for magnetometers 1 and for the two gradiometers 1 and -1 (to get the difference). Going through the code I found out that FT uses mne2grad.m rather than fif2grad.m. But mne2grad.m does not use the info in hdr.orig.projs. Thus, it seems the information does not go into grad.tra. (So I guess the topographies and leadfields will not be correct when SSP vectors are used). Best, Stephan El 03/06/2011, a las 13:11, jan-mathijs schoffelen escribió: > Hi Stephan et al, > > Any balancing coefficients (e.g. the digital weights for the bti-system, or ctf's 3d order gradient coefficients) are only applied to the leadfield if they end up in the data.grad.tra matrix. These .tra matrices will be compiled when reading the data header, by functions like XXX2grad (in fileio/private: ctf2grad, bti2grad, fif2grad). > You can check whether it is constructed using hdr.orig.projs. > If not, it may be worthwile to implement I guess. > > Best, > > JM > > > > On Jun 3, 2011, at 11:00 AM, Stephan Moratti wrote: > >> Hi Michael y Elena, >> >> I am following your discussion with great interest as I have just started to work with Neuromag data. As FT uses the MNE toolbox to read the data I assume that the SSP vectors are applied to the data during reading the data. However, the SSP vectors are stored in "data.hdr.orig.projs". However, when I go on with averaging in the ERF from timelockanalysis I cannot find this info. So my question is, does FT apply the SSP vectors later on also to the leadfield when calculating it? I assume that not, as the SSP vectors are not passed on further. How can I apply the SSP vectors to the leadfield to get correct results? >> >> Best and thanks, >> >> STephan >> >> El 02/06/2011, a las 19:20, Michael Wibral escribió: >> >>> Hi Elena, >>> >>> I assume that you were well aware of the difficulties in beamforming evoked activty and baseline normalisation and these things, your results really look that way. I mus say I am quite puzzled by the results - could it be a color scaling problem in the plot? I think this mmay be a problem because most of your plot is a peak power, only a tiny corner seems to be in a low-amplitude range. >>> >>> What you could do as a workaround is to average the separate results with a weighting per voxel and that is corresponding to the squared norms of the leadfields for the respective modalities for a given voxel , this would guarantee equal amounts of backprojected noise from both modalities (if I'm not mistaken). >>> >>> Michael >>> PS: I am away for a couple of days, but after that, I'll be happy to resume this discussion. >>> >>> >>> Von: "Elena Orekhova" >>> Gesendet: Jun 2, 2011 6:22:03 PM >>> An: "Email discussion list for the FieldTrip project" >>> Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis >>> >>> @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } >>> Dear Michael, >>> >>> >>> I have tried to multiply the leadfield by -1 as you suggested: >>> >>> >>> for i = 1 : size (grid.leadfield, 2) >>> >>> grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); >>> >>> end >>> >>> >>> This had no effect on the 'lcmv' output. I attached the pictures for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ >>> >>> >>> In this experiment I measured evoked field in response to the unilateral (left) click. >>> >>> The source is expected to be in the right superior temporal cortex. This is the case for ‘GRA only' and ’MAG only’ datasets. The combined sensors give meaningless result. >>> >>> >>> Elena >>> >>> >>> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] >>> Sent: Wednesday, June 01, 2011 4:04 PM >>> To: Email discussion list for the FieldTrip project >>> Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis >>> >>> >>> Dear Elena, >>> >>> could you give the following a try: invert (*-1) the leadfileds for one of the two sensor types. Let me know what happens. >>> I would also be interested in taking a look at the results - maybe you could sent images off-list: Michael.Wibral web.de. >>> >>> Michael >>> >>> >>> >>> Von: "Elena Orekhova" >>> Gesendet: Jun 1, 2011 12:23:29 PM >>> An: "fieldtrip at donders.ru.nl" >>> Betreff: [FieldTrip] combining magnetometers and planad gradiometers for analysis >>> >>> @font-face { font-family: "Arial"; }@font-face { font-family: "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: Times; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } >>> Dear fieldtrippers, >>> >>> This message is mainly for Neuromag users. >>> >>> >>> When I do 'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. >>> >>> If I combine the two types of sensors without weighting, the result is meaningless. >>> >>> Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements. Does anybody know how to deal with this problem? >>> >>> >>> >>> Elena >>> >>> >>> >>> _______________________________________________ >>> 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 >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > _______________________________________________ > 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 jan.schoffelen at donders.ru.nl Fri Jun 3 15:22:10 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 3 Jun 2011 15:22:10 +0200 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <32BF5576-A020-41A6-AF11-0879E03067FD@psi.ucm.es> References: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> <722801BA-5C22-4A69-8F87-18C1C54A7F00@psi.ucm.es> <77A55ECC-5A84-4839-9093-75FA499D3D31@donders.ru.nl> <32BF5576-A020-41A6-AF11-0879E03067FD@psi.ucm.es> Message-ID: <9A770E4F-6106-4136-BADB-5BBCBE84862D@donders.ru.nl> Dear Stephan, Ah, you're right. I forgot about the mne2grad... Sorry. Regarding the SSP vectors I forgot to mention that of course the sensor data needs to have the SSP vectors incorporated as well, if such info is to be applied to the leadfields too? Either the data on disk is already balanced, or the coefficients need to be applied after reading in the unbalanced data. I don't know enough about the elekta- software/mne-software to know what is happening to the data when the ssp vectors are computed, but once we know enough details it should be straightforward to build it into fieldtrip. Best, JM On Jun 3, 2011, at 3:08 PM, Stephan Moratti wrote: > Hi Jan-Mathijs, > > I had just a look at fif2grad.m and it seems to me that the > information of hdr.orig.projs is not used to construct the .tra > field. It only codes for magnetometers 1 and for the two > gradiometers 1 and -1 (to get the difference). Going through the > code I found out that FT uses mne2grad.m rather than fif2grad.m. But > mne2grad.m does not use the info in hdr.orig.projs. Thus, it seems > the information does not go into grad.tra. (So I guess the > topographies and leadfields will not be correct when SSP vectors are > used). > > Best, > > Stephan > > El 03/06/2011, a las 13:11, jan-mathijs schoffelen escribió: > >> Hi Stephan et al, >> >> Any balancing coefficients (e.g. the digital weights for the bti- >> system, or ctf's 3d order gradient coefficients) are only applied >> to the leadfield if they end up in the data.grad.tra matrix. >> These .tra matrices will be compiled when reading the data header, >> by functions like XXX2grad (in fileio/private: ctf2grad, bti2grad, >> fif2grad). >> You can check whether it is constructed using hdr.orig.projs. >> If not, it may be worthwile to implement I guess. >> >> Best, >> >> JM >> >> >> >> On Jun 3, 2011, at 11:00 AM, Stephan Moratti wrote: >> >>> Hi Michael y Elena, >>> >>> I am following your discussion with great interest as I have just >>> started to work with Neuromag data. As FT uses the MNE toolbox to >>> read the data I assume that the SSP vectors are applied to the >>> data during reading the data. However, the SSP vectors are stored >>> in "data.hdr.orig.projs". However, when I go on with averaging in >>> the ERF from timelockanalysis I cannot find this info. So my >>> question is, does FT apply the SSP vectors later on also to the >>> leadfield when calculating it? I assume that not, as the SSP >>> vectors are not passed on further. How can I apply the SSP vectors >>> to the leadfield to get correct results? >>> >>> Best and thanks, >>> >>> STephan >>> >>> El 02/06/2011, a las 19:20, Michael Wibral escribió: >>> >>>> Hi Elena, >>>> >>>> I assume that you were well aware of the difficulties in >>>> beamforming evoked activty and baseline normalisation and these >>>> things, your results really look that way. I mus say I am quite >>>> puzzled by the results - could it be a color scaling problem in >>>> the plot? I think this mmay be a problem because most of your >>>> plot is a peak power, only a tiny corner seems to be in a low- >>>> amplitude range. >>>> >>>> What you could do as a workaround is to average the separate >>>> results with a weighting per voxel and that is corresponding to >>>> the squared norms of the leadfields for the respective modalities >>>> for a given voxel , this would guarantee equal amounts of >>>> backprojected noise from both modalities (if I'm not mistaken). >>>> >>>> Michael >>>> PS: I am away for a couple of days, but after that, I'll be happy >>>> to resume this discussion. >>>> >>>> >>>> Von: "Elena Orekhova" >>>> Gesendet: Jun 2, 2011 6:22:03 PM >>>> An: "Email discussion list for the FieldTrip project" >>> > >>>> Betreff: Re: [FieldTrip] combining magnetometers and planad >>>> gradiometers for analysis >>>> >>>> @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face >>>> { font-family: "Cambria Math"; }@font-face { font-family: >>>> "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal, >>>> li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font- >>>> size: 12pt; font-family: Cambria; }.MsoChpDefault { font-family: >>>> Cambria; }div.WordSection1 { page: WordSection1; } >>>> Dear Michael, >>>> >>>> >>>> I have tried to multiply the leadfield by -1 as you suggested: >>>> >>>> >>>> for i = 1 : size (grid.leadfield, 2) >>>> >>>> grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i} >>>> (3:3:306, :); >>>> >>>> end >>>> >>>> >>>> This had no effect on the 'lcmv' output. I attached the pictures >>>> for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ >>>> >>>> >>>> In this experiment I measured evoked field in response to the >>>> unilateral (left) click. >>>> >>>> The source is expected to be in the right superior temporal >>>> cortex. This is the case for ‘GRA only' and ’MAG only’ >>>> datasets. The combined sensors give meaningless result. >>>> >>>> >>>> Elena >>>> >>>> >>>> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl >>>> ] on behalf of Michael Wibral [michael.wibral at web.de] >>>> Sent: Wednesday, June 01, 2011 4:04 PM >>>> To: Email discussion list for the FieldTrip project >>>> Subject: Re: [FieldTrip] combining magnetometers and planad >>>> gradiometers for analysis >>>> >>>> >>>> Dear Elena, >>>> >>>> could you give the following a try: invert (*-1) the leadfileds >>>> for one of the two sensor types. Let me know what happens. >>>> I would also be interested in taking a look at the results - >>>> maybe you could sent images off-list: Michael.Wibral web.de. >>>> >>>> Michael >>>> >>>> >>>> >>>> Von: "Elena Orekhova" >>>> Gesendet: Jun 1, 2011 12:23:29 PM >>>> An: "fieldtrip at donders.ru.nl" >>>> Betreff: [FieldTrip] combining magnetometers and planad >>>> gradiometers for analysis >>>> >>>> @font-face { font-family: "Arial"; }@font-face { font-family: >>>> "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D >>>> "; }@font-face { font-family: "Cambria Math"; }@font-face { font- >>>> family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal >>>> { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: >>>> Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: >>>> 10pt; font-family: Times; }.MsoChpDefault { font-family: >>>> Cambria; }div.WordSection1 { page: WordSection1; } >>>> Dear fieldtrippers, >>>> >>>> This message is mainly for Neuromag users. >>>> >>>> >>>> When I do 'lcmv' beamforming analysis separately on planar >>>> gradiometers or magnetometers, I get quite meaningful results. >>>> >>>> If I combine the two types of sensors without weighting, the >>>> result is meaningless. >>>> >>>> Apparently, the algorithm does not take care of different scales >>>> and units of the GRA and MAG measurements. Does anybody know how >>>> to deal with this problem? >>>> >>>> >>>> >>>> Elena >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> Dr. J.M. (Jan-Mathijs) Schoffelen >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> J.Schoffelen at donders.ru.nl >> Telephone: 0031-24-3614793 >> >> _______________________________________________ >> 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 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri Jun 3 15:23:34 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 3 Jun 2011 15:23:34 +0200 Subject: [FieldTrip] cfg.method = 'sam' In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F03ECAC6B@exchccr1.neuro.gu.se> References: <32CC77C0C8A7AD4B9410934642608E1F03ECAC6B@exchccr1.neuro.gu.se> Message-ID: Hi Elena, At some point we had an implementation for sam in FieldTrip. Apparently, this has been taken out of the release version. I don't know whether this was on purpose, or whether there was a good reason to do so. The reason you get an error is that the function is missing. We will look into the missing function issue. For the time being, you could try lcmv, which is very similar to sam. Best, Jan-Mathijs On Jun 3, 2011, at 2:57 PM, Elena Orekhova wrote: > Dear colleagues, > Sorry, I posted much on the list recent time. I want to figure out > how to run SAM analysis on my data. > > When I run 'lcmv' beamformer on my averaged dataset it works fine: > cfg = []; > cfg.grad = hdr.grad; > cfg.method = 'lcmv'; > cfg.grid = grid; > cfg.vol = vol_cm; > cfg.reducerank=2; > cfg.keepfilter = 'yes' > cfg.channel = MAG; %MAG = {'MEG0721', 'MEG0731',... } > source = ft_sourceanalysis(cfg, tlckavg); > > > When I do the same with cfg.method = 'sam' option, > I get the error: > ***************************** > ??? Undefined function or method 'beamformer_sam' for input > arguments of type 'struct'. > > Error in ==> sourceanalysis at 1158 > dip(i) = beamformer_sam(grid, sens, vol, squeeze(avg(i,:,:)), > squeeze(Cy(i,:,:)), > optarg{:}); > > Error in ==> ft_sourceanalysis at 11 > [varargout{1:nargout}] = funhandle(varargin{:}); > > Does anybody know how to make the ‘SAM’ option to work? > Does anybody used cfg.method = 'sam' option in the Fieldtrip??? > > Regards, > Elena > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at inria.fr Fri Jun 3 15:30:25 2011 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Fri, 3 Jun 2011 09:30:25 -0400 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <9A770E4F-6106-4136-BADB-5BBCBE84862D@donders.ru.nl> References: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> <722801BA-5C22-4A69-8F87-18C1C54A7F00@psi.ucm.es> <77A55ECC-5A84-4839-9093-75FA499D3D31@donders.ru.nl> <32BF5576-A020-41A6-AF11-0879E03067FD@psi.ucm.es> <9A770E4F-6106-4136-BADB-5BBCBE84862D@donders.ru.nl> Message-ID: Hi everyone, > I don't know enough about the elekta-software/mne-software to know what is > happening to the data when the ssp vectors are computed, but once we know > enough details it should be straightforward to build it into fieldtrip. SSP vectors are stored in fif files and applied to data only if requested. In a typical MNE workflow, the SSP vectors are no directly applied to the raw file (avoid data duplication on disk) but rather to the noise covariance matrix and consequently in the whitening matrix. When computing an inverse solution, the whitening matrix is used on the data and the lead field, hence taking into account the SSP vectors. Hope this helps. -- Alexandre Gramfort, PhD gramfort at nmr.mgh.harvard.edu Dept. of Radiology MGH Martinos Center / Harvard Medical School http://www-sop.inria.fr/members/Alexandre.Gramfort/ From smoratti at psi.ucm.es Fri Jun 3 16:06:28 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Fri, 03 Jun 2011 16:06:28 +0200 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: References: <1642515741.2746461.1307035207966.JavaMail.fmail@mwmweb067> <722801BA-5C22-4A69-8F87-18C1C54A7F00@psi.ucm.es> <77A55ECC-5A84-4839-9093-75FA499D3D31@donders.ru.nl> <32BF5576-A020-41A6-AF11-0879E03067FD@psi.ucm.es> <9A770E4F-6106-4136-BADB-5BBCBE84862D@donders.ru.nl> Message-ID: Hi everyone, Thanks Alexandre for the info. I went a little bit through the FT code and it seems that it reads the raw data without applying the SSP vectors on the data (raw.proj is empty!!). I saw in mne_ex_read_raw.m that you have to activate the projectors and then get the proj matrix with mne_make_projector_info .m It is a chan by chan matrix. So adding the proj matrix to the raw structure I understand that by using fiff_read_raw_segment .m I get the data filtered by the SSP vectors. So now my stupid? question: If I just multiply the grad.tra matrix by the proj matrix, this would fix everything (plotting topos and leadfield calculation???) best, Stephan El 03/06/2011, a las 15:30, Alexandre Gramfort escribió: > Hi everyone, > >> I don't know enough about the elekta-software/mne-software to know what is >> happening to the data when the ssp vectors are computed, but once we know >> enough details it should be straightforward to build it into fieldtrip. > > SSP vectors are stored in fif files and applied to data only if requested. > > In a typical MNE workflow, the SSP vectors are no directly applied to the raw > file (avoid data duplication on disk) but rather to the noise covariance matrix > and consequently in the whitening matrix. When computing an inverse solution, > the whitening matrix is used on the data and the lead field, hence taking > into account the SSP vectors. > > Hope this helps. > > -- > Alexandre Gramfort, PhD > gramfort at nmr.mgh.harvard.edu > Dept. of Radiology MGH Martinos Center / Harvard Medical School > http://www-sop.inria.fr/members/Alexandre.Gramfort/ > _______________________________________________ > 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 sylvana.schister at utah.edu Fri Jun 3 19:09:21 2011 From: sylvana.schister at utah.edu (Sylvana) Date: Fri, 03 Jun 2011 11:09:21 -0600 Subject: [FieldTrip] Question about layout for Neuromag data Message-ID: <1307120961.4481.1.camel@weston-desktop> Greetings - I have preprocessed and computed TF analysis on a set of neuromag data that I will like to visualize using ft_multiplotTFR. I found out that the function crashes when I try to plot the data. After trying to understand the source of the problem and comparing my analysis to the ones explained in the different tutorials, I found out that the layout produced for these data contains fields 'lay.width' and 'lay.height' that are zero vectors. These vectors are used in ft_multiplotTFR to define the axes of the different plots. Has anyone encountered this problem before? Any clue how to overcome it? I am a just getting familiar with FT and although I have read and followed the tutorials, I wouldn't exclude the possibility that I am doing something wrong. I will appreciate any help you can offer. Have a great day! Sylvana From michael.wibral at web.de Fri Jun 3 23:05:05 2011 From: michael.wibral at web.de (michael.wibral at web.de) Date: Fri, 3 Jun 2011 23:05:05 +0200 (CEST) Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis Message-ID: <533029427.749303.1307135105021.JavaMail.www-data@mwebmailfe05.dlan.cinetic.de> dear neuromag / fieldtrip community, just a small question so I can keep up with the dsicussion: I thought that (t)SSS would nor project in a classical sense, i.e. for activities from inside the head leadfields would not have to be corrected? at least this I have read on the neuromeg list. So in most respcts the data should be treated just like rawdata - with standard coil positions after the motion correction ? maybe someone can shed more light on this? michael -----Ursprüngliche Nachricht----- Von: "Alexandre Gramfort" Gesendet: 03.06.11 15:30:25 An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis >Hi everyone, > > > I don't know enough about the elekta-software/mne-software to know what is > > happening to the data when the ssp vectors are computed, but once we know > > enough details it should be straightforward to build it into fieldtrip. > > SSP vectors are stored in fif files and applied to data only if requested. > > In a typical MNE workflow, the SSP vectors are no directly applied to the raw > file (avoid data duplication on disk) but rather to the noise covariance matrix > and consequently in the whitening matrix. When computing an inverse solution, > the whitening matrix is used on the data and the lead field, hence taking > into account the SSP vectors. > > Hope this helps. > > -- > Alexandre Gramfort, PhD > gramfort at nmr.mgh.harvard.edu > Dept. of Radiology MGH Martinos Center / Harvard Medical School > http://www-sop.inria.fr/members/Alexandre.Gramfort/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: From tony.w.wilson at gmail.com Sat Jun 4 00:09:08 2011 From: tony.w.wilson at gmail.com (Tony W. Wilson) Date: Fri, 3 Jun 2011 17:09:08 -0500 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <533029427.749303.1307135105021.JavaMail.www-data@mwebmailfe05.dlan.cinetic.de> References: <533029427.749303.1307135105021.JavaMail.www-data@mwebmailfe05.dlan.cinetic.de> Message-ID: Dear Michael, everyone, I believe you are correct. Most Neuromag sites have SSP vectors computed for data acquisitions; some groups occasionally recompute these per subject. These acquisition SSP vectors are stored in the fif file, but not applied w/o user intervention. In addition, I believe the tag relating to these vectors is removed from the fif file if you apply (t)SSS (through Maxfilter). However, I am not totally certain because I have never tried to apply these SSP vectors after applying SSS. Regardless, during analysis I treat the motion corrected t(SSS) output files just like raw data files. ... It is also worth noting here that one can compute new sets of SSP vectors in the MNE software (not directly related to the data acquisition vectors) and save these with the fif file for later use. I am not sure if these SSP vectors can be used outside of the MNE software. Tony On Fri, Jun 3, 2011 at 4:05 PM, wrote: > dear neuromag / fieldtrip community, > > just a small question so I can keep up with the dsicussion: > I thought that (t)SSS would nor project in a classical sense, i.e. for > activities from inside the head leadfields would not have to be corrected? > at least this I have read on the neuromeg list. So in most respcts the data > should be treated just like rawdata - with standard coil positions after the > motion correction ? > > maybe someone can shed more light on this? > > michael > > -----Ursprüngliche Nachricht----- > Von: "Alexandre Gramfort" > Gesendet: 03.06.11 15:30:25 > An: "Email discussion list for the FieldTrip project" < > fieldtrip at donders.ru.nl> > Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers > for analysis > > >Hi everyone, > > > > > I don't know enough about the elekta-software/mne-software to know what > is > > > happening to the data when the ssp vectors are computed, but once we > know > > > enough details it should be straightforward to build it into fieldtrip. > > > > SSP vectors are stored in fif files and applied to data only if > requested. > > > > In a typical MNE workflow, the SSP vectors are no directly applied to the > raw > > file (avoid data duplication on disk) but rather to the noise covariance > matrix > > and consequently in the whitening matrix. When computing an inverse > solution, > > the whitening matrix is used on the data and the lead field, hence taking > > into account the SSP vectors. > > > > Hope this helps. > > > > -- > > Alexandre Gramfort, PhD > > gramfort at nmr.mgh.harvard.edu > > Dept. of Radiology MGH Martinos Center / Harvard Medical School > > http://www-sop.inria.fr/members/Alexandre.Gramfort/ > > _______________________________________________ > > 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 smoratti at psi.ucm.es Sat Jun 4 11:54:55 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Sat, 04 Jun 2011 11:54:55 +0200 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: References: <533029427.749303.1307135105021.JavaMail.www-data@mwebmailfe05.dlan.cinetic.de> Message-ID: <60211D3C-5BDA-49AE-8F17-B83594F7DB09@psi.ucm.es> Dear everyone, It would be cool to have the possibility to choose if one wants to apply the SSP vectors or not. Some sites use them, others use SSS or tSSS, depends how noisy your environment is. I think it is good that the data is read in raw format and that the SSP vectors are not applied as default, but it would be great to have the possibility to do so. What do you think? Stephan El 04/06/2011, a las 0:09, Tony W. Wilson escribió: > Dear Michael, everyone, > I believe you are correct. Most Neuromag sites have SSP vectors > computed for data acquisitions; some groups occasionally recompute > these per subject. These acquisition SSP vectors are stored in the > fif file, but not applied w/o user intervention. In addition, I > believe the tag relating to these vectors is removed from the fif > file if you apply (t)SSS (through Maxfilter). However, I am not > totally certain because I have never tried to apply these SSP > vectors after applying SSS. Regardless, during analysis I treat the > motion corrected t(SSS) output files just like raw data files. ... > It is also worth noting here that one can compute new sets of SSP > vectors in the MNE software (not directly related to the data > acquisition vectors) and save these with the fif file for later > use. I am not sure if these SSP vectors can be used outside of the > MNE software. > > Tony > > On Fri, Jun 3, 2011 at 4:05 PM, wrote: > dear neuromag / fieldtrip community, > > just a small question so I can keep up with the dsicussion: > I thought that (t)SSS would nor project in a classical sense, i.e. > for activities from inside the head leadfields would not have to be > corrected? at least this I have read on the neuromeg list. So in > most respcts the data should be treated just like rawdata - with > standard coil positions after the motion correction ? > > maybe someone can shed more light on this? > > michael > > -----Ursprüngliche Nachricht----- > Von: "Alexandre Gramfort" > Gesendet: 03.06.11 15:30:25 > An: "Email discussion list for the FieldTrip project" > > Betreff: Re: [FieldTrip] combining magnetometers and planad > gradiometers for analysis > > >Hi everyone, > > > > > I don't know enough about the elekta-software/mne-software to > know what is > > > happening to the data when the ssp vectors are computed, but > once we know > > > enough details it should be straightforward to build it into > fieldtrip. > > > > SSP vectors are stored in fif files and applied to data only if > requested. > > > > In a typical MNE workflow, the SSP vectors are no directly applied > to the raw > > file (avoid data duplication on disk) but rather to the noise > covariance matrix > > and consequently in the whitening matrix. When computing an > inverse solution, > > the whitening matrix is used on the data and the lead field, hence > taking > > into account the SSP vectors. > > > > Hope this helps. > > > > -- > > Alexandre Gramfort, PhD > > gramfort at nmr.mgh.harvard.edu > > Dept. of Radiology MGH Martinos Center / Harvard Medical School > > http://www-sop.inria.fr/members/Alexandre.Gramfort/ > > _______________________________________________ > > 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 ________________________________________________________ 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 Mon Jun 6 12:37:53 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Mon, 06 Jun 2011 12:37:53 +0200 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: References: <533029427.749303.1307135105021.JavaMail.www-data@mwebmailfe05.dlan.cinetic.de> Message-ID: <6B0B1BCA-8D99-4123-93CA-830E7E4D07B8@psi.ucm.es> Dear all, Looking at the MNE toolbox code, I think the following could be done to get the SSP projection if wanted: %% do SSP projection on data %%%% added by stephan moratti to do SSP for k = 1:length(data.hdr.orig.projs) data.hdr.orig.projs(k).active = true; end fprintf(1,'%d projection items activated\n',length(data.hdr.orig.projs)); [proj,nproj] = mne_make_projector_info(data.hdr.orig); data.hdr.orig.raw.proj = proj; % now apply to data for i = 1:length(data.trial) data.trial{i} = proj*data.trial{i}; end However, I am not sure how to put them into the grad.tra field. Best, Stephan El 04/06/2011, a las 00:09, Tony W. Wilson escribió: > Dear Michael, everyone, > I believe you are correct. Most Neuromag sites have SSP vectors computed for data acquisitions; some groups occasionally recompute these per subject. These acquisition SSP vectors are stored in the fif file, but not applied w/o user intervention. In addition, I believe the tag relating to these vectors is removed from the fif file if you apply (t)SSS (through Maxfilter). However, I am not totally certain because I have never tried to apply these SSP vectors after applying SSS. Regardless, during analysis I treat the motion corrected t(SSS) output files just like raw data files. ... It is also worth noting here that one can compute new sets of SSP vectors in the MNE software (not directly related to the data acquisition vectors) and save these with the fif file for later use. I am not sure if these SSP vectors can be used outside of the MNE software. > > Tony > > On Fri, Jun 3, 2011 at 4:05 PM, wrote: > dear neuromag / fieldtrip community, > > just a small question so I can keep up with the dsicussion: > I thought that (t)SSS would nor project in a classical sense, i.e. for activities from inside the head leadfields would not have to be corrected? at least this I have read on the neuromeg list. So in most respcts the data should be treated just like rawdata - with standard coil positions after the motion correction ? > > maybe someone can shed more light on this? > > michael > > -----Ursprüngliche Nachricht----- > Von: "Alexandre Gramfort" > Gesendet: 03.06.11 15:30:25 > An: "Email discussion list for the FieldTrip project" > Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis > > >Hi everyone, > > > > > I don't know enough about the elekta-software/mne-software to know what is > > > happening to the data when the ssp vectors are computed, but once we know > > > enough details it should be straightforward to build it into fieldtrip. > > > > SSP vectors are stored in fif files and applied to data only if requested. > > > > In a typical MNE workflow, the SSP vectors are no directly applied to the raw > > file (avoid data duplication on disk) but rather to the noise covariance matrix > > and consequently in the whitening matrix. When computing an inverse solution, > > the whitening matrix is used on the data and the lead field, hence taking > > into account the SSP vectors. > > > > Hope this helps. > > > > -- > > Alexandre Gramfort, PhD > > gramfort at nmr.mgh.harvard.edu > > Dept. of Radiology MGH Martinos Center / Harvard Medical School > > http://www-sop.inria.fr/members/Alexandre.Gramfort/ > > _______________________________________________ > > 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 ________________________________________________________ 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 valentin.umbach at hu-berlin.de Mon Jun 6 14:18:51 2011 From: valentin.umbach at hu-berlin.de (Valentin J. Umbach) Date: Mon, 6 Jun 2011 14:18:51 +0200 Subject: [FieldTrip] Emotiv headset realtime capture Message-ID: Hi Zeddy, thanks alot for your reply. FieldTrip comes with a precompiled version of emotiv2ft.exe. However, I can't get this to connect with my hardware. I've been trying to change some code in emotiv2ft.cc, but I couldn't compile it using mingw (as suggested here: http://fieldtrip.fcdonders.nl/development/realtime/emotiv). If you haven't worked with the Emotiv headset, this might be too specific. I wonder who wrote the interface to FieldTrip - someone must have connected the two before... Best, Valentin - Zitierten Text ausblenden - > > Message: 4 > Date: Wed, 1 Jun 2011 11:35:07 -0200 > From: Zeddy He > To: > Subject: Re: [FieldTrip] Emotiv headset realtime capture > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > > Hi Valentin, > > I am not entirely sure exactly what part of the process you're not sure about. I'm new to fieldtrip as well and I have never heard of emotiv until today. I have, however, been playing around with FieldTrip's realtime acquisition part for the last couple of weeks(acq2ft, AcqBuffer), and maybe able to offer some pointers in getting it set up on your system. > It seems that to use emotive2ft, you would have to compile it first, call upon it in matlab before starting your emotive software, and then start the emotiv software. I am not exactly sure what can read the bufferdata, though ft_realtime_signalviewer as well as viewer.exe may be good functions/programs to start off with. > If you're using acq2ft or Acqbuffer already for realtime acquistion from another CTF device, you could try running one of those first either by standalone or their MATLAB equivilent functions, and then run emotiv2ft in matlab without any passed in parameters(unless you didn't decide to put the buffer on localhost:1972). You also might be able to just let the function create it's own buffer by giving it a new port, and then draw from that port seperately later on. > Some troubles I've ran into while using FieldTrip's realtime functions include: > shmget() errors on linux systems > firewall blocking port > number type in-compatibility > and perhaps a couple others I can't recall at the moment. > > If you think I might be capable of assisting you, let me know and I'll see if I can give you additional details. > > Regards > > Zeddy > > >> From: valentin.umbach at hu-berlin.de >> Date: Tue, 31 May 2011 18:51:17 +0200 >> To: fieldtrip at donders.ru.nl >> Subject: [FieldTrip] Emotiv headset realtime capture >> >> Hi, I'm new to FieldTrip and I'm interested in using it to capture >> realtime data from the Emotiv headset using this interface: >> http://fieldtrip.fcdonders.nl/development/realtime/emotiv >> I'm not clear about how to make calls to this interface from within >> Matlab. Also, I would like to know if it's possible to access not just >> the raw EEG, but also the API output of the detection libraries >> (Affectiv Suite...). >> Any help is greatly appreciated! >> >> Best, Valentin >> >> -- >> Dipl.-Psych. Valentin J. Umbach >> Institut f?r Psychologie >> Humboldt-Universit?t zu Berlin >> Rudower Chaussee 18 >> 12489 Berlin >> Tel. +49 30 2093 9438 >> E-Mail: valentin.umbach at hu-berlin.de >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From n.a.kloosterman at uva.nl Mon Jun 6 15:28:41 2011 From: n.a.kloosterman at uva.nl (Kloosterman, Niels) Date: Mon, 6 Jun 2011 13:28:41 +0000 Subject: [FieldTrip] Problem passing arguments to peerslave command line executable Message-ID: Dear Fieldtrippers, Although I have succesfully used the command-line ./peerslave.glnxa64 to launch slaves for parallel analysis of my batch jobs, I am somehow not able to pass arguments to the command, for example ./peerslave.glnxa64 --number 8, to launch 8 slaves at once. Could anybody tell me what’s going on? When I execute without arguments this line pops up: peerslave[9705]: peerinit: niels at gb-r35n18.irc.sara.nl, id = 4020038417 All seems fine: the master is indeed able to send jobs to the slave. No other information is printed to the shell when it gets a job or whatever (is this normal?). Now when I try to run the --help I get this: niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./peerslave.glnxa64 --help peerslave[9753]: peerinit: niels at gb-r35n18.irc.sara.nl, id = 2887682376 parser: cannot open file --help peerslave[9753]: cannot read the configuration file And when I try to do --number 8: niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./peerslave.glnxa64 --number 8 peerslave[9759]: peerinit: niels at gb-r35n18.irc.sara.nl, id = 3997336815 ./peerslave.glnxa64: unrecognized option '--number' peerslave[9759]: invalid command line options I have recompiled the peerslave.glnxa64 by editing the Makefile and using make, but the problem stays. I am using MATLAB 2011a on a 64 bit linux node with 8 cores on a grid computer, which I access using ssh –X. Any ideas would be appreciated! Best, Niels Kloosterman -- Niels A. Kloosterman MSc.| PhD student | University of Amsterdam | Cognitive Neuroscience Group | Dept. of Psychology | Roetersstraat 15, A614 | 1018 WB Amsterdam | Tel: +31 20 525 6847 -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Mon Jun 6 20:32:07 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 6 Jun 2011 20:32:07 +0200 Subject: [FieldTrip] Emotiv headset realtime capture In-Reply-To: References: Message-ID: Dear Valentin The interface was implemented by Stefan Klanke here at the Donders for the BrainGain project, but he is not working with us any more. He has been testing it and it worked for him. I don't have an emotiv headset myself, but think that Ali Bahramisharif (CC), one of our colleagues, is in possession of the headset that Stefan used for testing. I checked the fieldtrip/realtime/acquisition/emotiv/emotiv2ft.cc source code, and from what I see it it requires additional software from emotiv that is not included with the fieldtrip release. See http://emotiv.com/developer/SDK/UserManual.pdf and specifically chapter 5. If that emotiv software developers kit is missing from your computer, you'll be getting errors that the compiler cannot find the edk.h, EmoStateDLL.h and/or edkErrorCode.h header files. It might also be that you need import libraries on your compile path. Please have a look in fieldtrip/realtime/acquisition/emotiv/Makefile for some further instructions. Hope this helps. If not, Ali (CC) might be able to provide some additional information. best, Robert On 6 Jun 2011, at 14:18, Valentin J. Umbach wrote: > Hi Zeddy, > > thanks alot for your reply. > FieldTrip comes with a precompiled version of emotiv2ft.exe. However, > I can't get this to connect with my hardware. I've been trying to > change some code in emotiv2ft.cc, but I couldn't compile it using > mingw (as suggested here: > http://fieldtrip.fcdonders.nl/development/realtime/emotiv). > If you haven't worked with the Emotiv headset, this might be too > specific. I wonder who wrote the interface to FieldTrip - someone must > have connected the two before... > > Best, Valentin > - Zitierten Text ausblenden - > >> >> Message: 4 >> Date: Wed, 1 Jun 2011 11:35:07 -0200 >> From: Zeddy He >> To: >> Subject: Re: [FieldTrip] Emotiv headset realtime capture >> Message-ID: >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Hi Valentin, >> >> I am not entirely sure exactly what part of the process you're not sure about. I'm new to fieldtrip as well and I have never heard of emotiv until today. I have, however, been playing around with FieldTrip's realtime acquisition part for the last couple of weeks(acq2ft, AcqBuffer), and maybe able to offer some pointers in getting it set up on your system. >> It seems that to use emotive2ft, you would have to compile it first, call upon it in matlab before starting your emotive software, and then start the emotiv software. I am not exactly sure what can read the bufferdata, though ft_realtime_signalviewer as well as viewer.exe may be good functions/programs to start off with. >> If you're using acq2ft or Acqbuffer already for realtime acquistion from another CTF device, you could try running one of those first either by standalone or their MATLAB equivilent functions, and then run emotiv2ft in matlab without any passed in parameters(unless you didn't decide to put the buffer on localhost:1972). You also might be able to just let the function create it's own buffer by giving it a new port, and then draw from that port seperately later on. >> Some troubles I've ran into while using FieldTrip's realtime functions include: >> shmget() errors on linux systems >> firewall blocking port >> number type in-compatibility >> and perhaps a couple others I can't recall at the moment. >> >> If you think I might be capable of assisting you, let me know and I'll see if I can give you additional details. >> >> Regards >> >> Zeddy >> >> >>> From: valentin.umbach at hu-berlin.de >>> Date: Tue, 31 May 2011 18:51:17 +0200 >>> To: fieldtrip at donders.ru.nl >>> Subject: [FieldTrip] Emotiv headset realtime capture >>> >>> Hi, I'm new to FieldTrip and I'm interested in using it to capture >>> realtime data from the Emotiv headset using this interface: >>> http://fieldtrip.fcdonders.nl/development/realtime/emotiv >>> I'm not clear about how to make calls to this interface from within >>> Matlab. Also, I would like to know if it's possible to access not just >>> the raw EEG, but also the API output of the detection libraries >>> (Affectiv Suite...). >>> Any help is greatly appreciated! >>> >>> Best, Valentin >>> >>> -- >>> Dipl.-Psych. Valentin J. Umbach >>> Institut f?r Psychologie >>> Humboldt-Universit?t zu Berlin >>> Rudower Chaussee 18 >>> 12489 Berlin >>> Tel. +49 30 2093 9438 >>> E-Mail: valentin.umbach at hu-berlin.de >>> >>> _______________________________________________ >>> 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 r.oostenveld at donders.ru.nl Mon Jun 6 20:39:18 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 6 Jun 2011 20:39:18 +0200 Subject: [FieldTrip] cfg.method = 'sam' In-Reply-To: References: <32CC77C0C8A7AD4B9410934642608E1F03ECAC6B@exchccr1.neuro.gu.se> Message-ID: Dear Elena The SAM implementation was contributed some time ago by Gareth Barnes, but apaprently went missing in the release version. I found the missing files in an older versionand just added them to the latest release version(*). Note that I did not test them for some time and also did not test them right now. It might be that you'll get follow up problems. If so, better report them on bugzilla.fcdonders.nl and not on the email list. best regards, Robert PS (*) please download the FT version of this evening, which will include the beamformer_sam function which you need for cfg.method='sam' in ft_sourceanalysis. On 3 Jun 2011, at 15:23, jan-mathijs schoffelen wrote: > Hi Elena, > > At some point we had an implementation for sam in FieldTrip. Apparently, this has been taken out of the release version. I don't know whether this was on purpose, or whether there was a good reason to do so. > The reason you get an error is that the function is missing. We will look into the missing function issue. > For the time being, you could try lcmv, which is very similar to sam. > > Best, > > Jan-Mathijs > > > On Jun 3, 2011, at 2:57 PM, Elena Orekhova wrote: > >> Dear colleagues, >> Sorry, I posted much on the list recent time. I want to figure out how to run SAM analysis on my data. >> >> When I run 'lcmv' beamformer on my averaged dataset it works fine: >> cfg = []; >> cfg.grad = hdr.grad; >> cfg.method = 'lcmv'; >> cfg.grid = grid; >> cfg.vol = vol_cm; >> cfg.reducerank=2; >> cfg.keepfilter = 'yes' >> cfg.channel = MAG; %MAG = {'MEG0721', 'MEG0731',... } >> source = ft_sourceanalysis(cfg, tlckavg); >> >> >> When I do the same with cfg.method = 'sam' option, >> I get the error: >> ***************************** >> ??? Undefined function or method 'beamformer_sam' for input arguments of type 'struct'. >> >> Error in ==> sourceanalysis at 1158 >> dip(i) = beamformer_sam(grid, sens, vol, squeeze(avg(i,:,:)), squeeze(Cy(i,:,:)), >> optarg{:}); >> >> Error in ==> ft_sourceanalysis at 11 >> [varargout{1:nargout}] = funhandle(varargin{:}); >> >> Does anybody know how to make the ‘SAM’ option to work? >> Does anybody used cfg.method = 'sam' option in the Fieldtrip??? >> >> Regards, >> Elena >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > _______________________________________________ > 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 r.oostenveld at donders.ru.nl Mon Jun 6 21:18:53 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 6 Jun 2011 21:18:53 +0200 Subject: [FieldTrip] questions about realtime buffer In-Reply-To: References: Message-ID: Dear Amelie > I’m implementing a realtime buffer in C++ pretty much like in “demo_combined” : my application creates a buffer server and an acquisition client. > I encountered a first problem when trying to close the buffer server cleanly, but with some small changes in tcpsocket.c and tcpserver.c, I think I solved the problem. > If these modifications can be useful for other users and do not create other problems, I will share them. If you have changes that don't break the ANSI-C compilation then I am certainly happy to include them in our version. Please go to http://bugzilla.fcdonders.nl and submit a bug/request in which you attach the updated files. > I encounter now a new problem : what if there are several acquisition clients ? > I tried to create several couples “buffer-server + acquisition client” in different threads in my application, but it does not work at all, because of global variables (I suppose). > It seems that one buffer server can not manage several acquisition clients, but I’m not sure of this point. > Did anyone encounter this problem (or solve it) ? > Or do anyone have an idea ? You are right about the global variables. The buffer is implemented using multithreading and to ensure that incoming data (Write) does not interfere with outgoing (read) data a mutex (http://en.wikipedia.org/wiki/Mutual_exclusion) is set. That mutex is shared throughout the code so that all pieces of code are aware of when they are allowed to change the buffer content. Having multiple buffers would require multiple mutexes and multiple (separately identifyable) memory segments for the actual data. That would require a lot of changes to the code. You can run multiple buffers on the same computer, but you would have to start them separately and they would have to have different TCP ports. The application you are writing could write different aspects to the different TCP ports. You can use fieldtrip/realtime/general/buffer.exe, which in fact is a compiled version of fieldtrip/realtime/buffer/test/demo_buffer. Note that you would use it as buffer.exe localhost 2340 buffer.exe localhost 2341 buffer.exe localhost 2342 buffer.exe localhost 2343 to start 4 buffers on ports 2340-2343. The "localhost" argument is not used, but still appears to be required according to the demo_buffer.c source code. Of course it is cumbersome to have to start the 4 seperate processes on top of your own application. On unix-like computers you should be able to write a single application that at the beginning forks into a parent and child, where the parent continues as your application and where the child (which is then a separate process) can start the buffer. You can fork multiple times, to have multiple buffers (one per child). best Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: From batrod at gmail.com Tue Jun 7 00:51:20 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Mon, 6 Jun 2011 17:51:20 -0500 Subject: [FieldTrip] Weird trialfun_general error Message-ID: Dear fieldtrippers, i just noticed and found the origin of a weird error obtained with the trialfun_general function, i thought it could be useful to send it here. I use the ft_definetrial function on a file obtained using the merge function in EEGlab. Apparently, this function is adding some triggers with the value 'boundary' in the new file, indicating the old frontier between the dataset that have been merged. The funny part is that the trialfun_general() function in fieltrip is using the intersect() matlab function to match event values. Moreover, im using 27 different event values to indicate point of interest (112,114,116,122,etc...) All of my event values dont create any problems except the value 114 because intersect('boundary',114) = 114 whereas it gives an empty result with any other of my values... Therefore, for that particular event value, there was a dimension mismatch between trl and val in trialfun_general. I just removed events with 'boundary' values and it worked. Best regards, Rodolphe Nenert, Ph.D. -------------- next part -------------- An HTML attachment was scrubbed... URL: From johemart at gmail.com Tue Jun 7 01:36:51 2011 From: johemart at gmail.com (=?ISO-8859-1?Q?Johann_Heinz_Mart=EDnez_Huartos?=) Date: Tue, 7 Jun 2011 01:36:51 +0200 Subject: [FieldTrip] Reference to non-existent field 'statistic' !????? Message-ID: Hello dear fieldtrip guys. Im new using this toolbox and i dont understand why is happened this error that i think it must be easy to solve but I have tryed and nothing happend. The thing is that im following (step by step) the tutorial for multivariableanalysis from fieldtrip wiki using the data that web link offer us. But when I run the command: stat = ft_timelockstatistics(cfg,tleft,tright); there are appear those errors: ??? Reference to non-existent field 'statistic'. Error in ==> prepare_design at 67 if any(strcmp(cfg.statistic,{'indepsamplesT','indepsamplesregrT','indepsamplesZcoh','indepsamplesF'})) Error in ==> statistics_wrapper at 249 [cfg] = prepare_design(cfg); Error in ==> ft_timelockstatistics at 123 [stat, cfg] = statistics_wrapper(cfg, varargin{:}); Error in ==> JohannTestFieldtrip at 45 stat = ft_timelockstatistics(cfg,tleft,tright); and i Dunno what can i do... Im using Matlab (R2011a) and the (fieldtrip-20110603). I have been looking for the documentation and i coundt find out how to fix it. Is it probably the matlab version very new? Which would be the last matlab version available using for? Thanks -- Atentamente: Johann Martínez. -------------- next part -------------- An HTML attachment was scrubbed... URL: From n.a.kloosterman at uva.nl Tue Jun 7 10:33:39 2011 From: n.a.kloosterman at uva.nl (Kloosterman, Niels) Date: Tue, 7 Jun 2011 08:33:39 +0000 Subject: [FieldTrip] Problem passing arguments to peerslave command line executable Message-ID: Dear Fieldtrippers, Although I have succesfully used the command-line ./peerslave.glnxa64 to launch slaves for parallel analysis of my batch jobs, I am somehow not able to pass arguments to the command, for example ./peerslave.glnxa64 --number 8, to launch 8 slaves at once. Could anybody tell me what’s going on? When I execute without arguments this line pops up: niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./peerslave.glnxa64 peerslave[9705]: peerinit: niels at gb-r35n18.irc.sara.nl, id = 4020038417 All seems fine: the master is indeed able to send jobs to the slave. No other information is printed to the shell when it gets a job or whatever (is this normal?). Now when I try to run the --help I get this: niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./peerslave.glnxa64 --help peerslave[9753]: peerinit: niels at gb-r35n18.irc.sara.nl, id = 2887682376 parser: cannot open file --help peerslave[9753]: cannot read the configuration file And when I try to do --number 8: niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./peerslave.glnxa64 --number 8 peerslave[9759]: peerinit: niels at gb-r35n18.irc.sara.nl, id = 3997336815 ./peerslave.glnxa64: unrecognized option '--number' peerslave[9759]: invalid command line options I have recompiled the peerslave.glnxa64 by editing the Makefile and using make, but the problem persists. I am using MATLAB 2011a on a 64 bit linux node with 8 cores, which I access interactively using ssh –X. Any ideas would be appreciated! Best, Niels Kloosterman -- Niels A. Kloosterman MSc.| PhD student | University of Amsterdam | Cognitive Neuroscience Group | Dept. of Psychology | Roetersstraat 15, A614 | 1018 WB Amsterdam | Tel: +31 20 525 6847 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Tue Jun 7 12:53:24 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Tue, 7 Jun 2011 10:53:24 +0000 Subject: [FieldTrip] courses Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECAF47@exchccr1.neuro.gu.se> Dear FieldTrip gurus, Are you planning any FieldTrip courses for the users in the nearest future? Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From valentin.umbach at hu-berlin.de Tue Jun 7 13:47:18 2011 From: valentin.umbach at hu-berlin.de (Valentin J. Umbach) Date: Tue, 7 Jun 2011 13:47:18 +0200 Subject: [FieldTrip] fieldtrip Digest, Vol 7, Issue 13 In-Reply-To: References: Message-ID: Dear Robert, thank you for your helpful information. The Problem seems to be that I only have the "Developer" version of the headset (and the accompanying SDK), whereas the one used in the interface is the "Researcher" version (or above). The DLL (and header files) supplied in my SDK lacks some of the functions used in emotiv2ft. So I either have to upgrade my SDK or rewrite the interface to only use my functionality (at this point I'm not interested in the "raw" EEG, but rather the output of Emotiv's own "EmoEngine" - this should work with my version). Best, Valentin > Message: 1 > Date: Mon, 6 Jun 2011 20:32:07 +0200 > From: Robert Oostenveld > To: Email discussion list for the FieldTrip project >         > Cc: Ali Bahramisharif > Subject: Re: [FieldTrip] Emotiv headset realtime capture > Message-ID: > Content-Type: text/plain; charset=us-ascii > > Dear Valentin > > The interface was implemented by Stefan Klanke here at the Donders for the BrainGain project, but he is not  working with us any more. He has been testing it and it worked for him. I don't have an emotiv headset myself, but think that Ali Bahramisharif (CC), one of our colleagues, is in possession of the headset that Stefan used for testing. > > I checked the fieldtrip/realtime/acquisition/emotiv/emotiv2ft.cc source code, and from what I see it it requires additional software from emotiv that is not included with the fieldtrip release. See http://emotiv.com/developer/SDK/UserManual.pdf and specifically chapter 5. If that emotiv software developers kit is missing from your computer, you'll be getting errors that the compiler cannot find the edk.h, EmoStateDLL.h and/or edkErrorCode.h header files. It might also be that you need import libraries on your compile path. Please have a look in fieldtrip/realtime/acquisition/emotiv/Makefile for some further instructions. > > Hope this helps. If not, Ali (CC) might be able to provide some additional information. > > best, > Robert From bornalikundu at gmail.com Tue Jun 7 22:01:46 2011 From: bornalikundu at gmail.com (Bornali Kundu) Date: Tue, 7 Jun 2011 15:01:46 -0500 Subject: [FieldTrip] Test interactions for multi-level factors Message-ID: Greetings, We are interested in testing the main effects and interactions between 2 factors that have more than 2 levels (a 2x4 within subjects design) using the cluster-based permutation test for either time domain or time-frequency domain data. Has anyone done this using Fieldtrip scripts? There is only one such contrast for a 2x2 design thus the interaction effects can be tested using a t test on design cell differences. However, for a factor with more levels, is there a way to perhaps specify contrasts to test the full effect of the interaction? Would setting cfg.contrastcoefs to something work? Otherwise, is there a way to specify this in cfg.design? Thanks so much for your time, Bornali Kundu -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at donders.ru.nl Wed Jun 8 14:54:48 2011 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Wed, 8 Jun 2011 14:54:48 +0200 Subject: [FieldTrip] Reference to non-existent field 'statistic' !????? In-Reply-To: References: Message-ID: Dear Johann, The function prepare_design should not be called by statistics_wrapper in this specific case, since the cfg.design is specified in this tutorial example. cfg.design = [ones(size(tleft.trial,1),1); 2*ones(size(tright.trial,1),1)]; Be sure to specifically add the multivariate directory and subdirectories to your path for this example, otherwise it will crash complaining of not finding other functions (for example ft_mv_standardizer.m) Best, Johanna On 7 June 2011 01:36, Johann Heinz Martínez Huartos wrote: > Hello dear fieldtrip guys. > > Im new using this toolbox and i dont understand why is happened this error > that i think it must be easy to solve but I have tryed and nothing happend. > The thing is that im following (step by step) the tutorial for > multivariableanalysis from fieldtrip wiki using the data that web link offer > us. But when I run the command: > > stat = ft_timelockstatistics(cfg,tleft,tright); > > there are appear those errors: > > ??? Reference to non-existent field 'statistic'. > > Error in ==> prepare_design at 67 > if > any(strcmp(cfg.statistic,{'indepsamplesT','indepsamplesregrT','indepsamplesZcoh','indepsamplesF'})) > > Error in ==> statistics_wrapper at 249 > [cfg] = prepare_design(cfg); > > Error in ==> ft_timelockstatistics at 123 > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > Error in ==> JohannTestFieldtrip at 45 > stat = ft_timelockstatistics(cfg,tleft,tright); > > and i Dunno what can i do... > > Im using Matlab (R2011a) and the (fieldtrip-20110603). I have been looking > for the documentation and i coundt find out how to fix it. > > Is it probably the matlab version very new? > Which would be the last matlab version available using for? > > Thanks > > > -- > Atentamente: > Johann Martínez. > > _______________________________________________ > 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 johemart at gmail.com Wed Jun 8 22:14:18 2011 From: johemart at gmail.com (=?ISO-8859-1?Q?Johann_Heinz_Mart=EDnez_Huartos?=) Date: Wed, 8 Jun 2011 22:14:18 +0200 Subject: [FieldTrip] Reference to non-existent field 'statistic' !????? In-Reply-To: References: Message-ID: Hello dear. Thnks a lot for your comments. I was very useful, eventually i was added all the fieldtrip directory including its subdirectories in order to avoid future problems and at the end it was succesfully instaled in my Matlab R2011b version. Best. Johann. On 8 June 2011 14:54, Johanna Zumer wrote: > Dear Johann, > > The function prepare_design should not be called by statistics_wrapper in > this specific case, since the cfg.design is specified in this tutorial > example. > > cfg.design = [ones(size(tleft.trial,1),1); 2*ones(size(tright.trial,1),1)]; > > > Be sure to specifically add the multivariate directory and subdirectories > to your path for this example, otherwise it will crash complaining of not > finding other functions (for example ft_mv_standardizer.m) > > Best, > Johanna > > > On 7 June 2011 01:36, Johann Heinz Martínez Huartos wrote: > >> Hello dear fieldtrip guys. >> >> Im new using this toolbox and i dont understand why is happened this error >> that i think it must be easy to solve but I have tryed and nothing happend. >> The thing is that im following (step by step) the tutorial for >> multivariableanalysis from fieldtrip wiki using the data that web link offer >> us. But when I run the command: >> >> stat = ft_timelockstatistics(cfg,tleft,tright); >> >> there are appear those errors: >> >> ??? Reference to non-existent field 'statistic'. >> >> Error in ==> prepare_design at 67 >> if >> any(strcmp(cfg.statistic,{'indepsamplesT','indepsamplesregrT','indepsamplesZcoh','indepsamplesF'})) >> >> Error in ==> statistics_wrapper at 249 >> [cfg] = prepare_design(cfg); >> >> Error in ==> ft_timelockstatistics at 123 >> [stat, cfg] = statistics_wrapper(cfg, varargin{:}); >> >> Error in ==> JohannTestFieldtrip at 45 >> stat = ft_timelockstatistics(cfg,tleft,tright); >> >> and i Dunno what can i do... >> >> Im using Matlab (R2011a) and the (fieldtrip-20110603). I have been looking >> for the documentation and i coundt find out how to fix it. >> >> Is it probably the matlab version very new? >> Which would be the last matlab version available using for? >> >> Thanks >> >> >> -- >> Atentamente: >> Johann Martínez. >> >> _______________________________________________ >> 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 > -- Atentamente: Johann Martínez. M.Sc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From amelie.serpollet at cea.fr Thu Jun 9 10:52:42 2011 From: amelie.serpollet at cea.fr (=?iso-8859-1?Q?SERPOLLET_Am=E9lie_228173?=) Date: Thu, 9 Jun 2011 10:52:42 +0200 Subject: [FieldTrip] questions about realtime buffer In-Reply-To: References: Message-ID: Dear Robert, Thank you for your answer. I was trying to run several buffers in the same process, but running them in different processes as you describe it seems to be very easier. The modifications I did to close the buffer cleanly make possible to run a new buffer after closing one, in the same process. Maybe it is not necessary if buffers are created in different processes, but they are few modifications and I find it is still convenient, so I submit it. Best regards Amélie ________________________________ De : Robert Oostenveld [mailto:r.oostenveld at donders.ru.nl] Envoyé : lundi 6 juin 2011 21:19 À : Email discussion list for the FieldTrip project Cc : SERPOLLET Amélie 228173 Objet : Re: [FieldTrip] questions about realtime buffer Dear Amelie I'm implementing a realtime buffer in C++ pretty much like in "demo_combined" : my application creates a buffer server and an acquisition client. I encountered a first problem when trying to close the buffer server cleanly, but with some small changes in tcpsocket.c and tcpserver.c, I think I solved the problem. If these modifications can be useful for other users and do not create other problems, I will share them. If you have changes that don't break the ANSI-C compilation then I am certainly happy to include them in our version. Please go to http://bugzilla.fcdonders.nl and submit a bug/request in which you attach the updated files. I encounter now a new problem : what if there are several acquisition clients ? I tried to create several couples "buffer-server + acquisition client" in different threads in my application, but it does not work at all, because of global variables (I suppose). It seems that one buffer server can not manage several acquisition clients, but I'm not sure of this point. Did anyone encounter this problem (or solve it) ? Or do anyone have an idea ? You are right about the global variables. The buffer is implemented using multithreading and to ensure that incoming data (Write) does not interfere with outgoing (read) data a mutex (http://en.wikipedia.org/wiki/Mutual_exclusion) is set. That mutex is shared throughout the code so that all pieces of code are aware of when they are allowed to change the buffer content. Having multiple buffers would require multiple mutexes and multiple (separately identifyable) memory segments for the actual data. That would require a lot of changes to the code. You can run multiple buffers on the same computer, but you would have to start them separately and they would have to have different TCP ports. The application you are writing could write different aspects to the different TCP ports. You can use fieldtrip/realtime/general/buffer.exe, which in fact is a compiled version of fieldtrip/realtime/buffer/test/demo_buffer. Note that you would use it as buffer.exe localhost 2340 buffer.exe localhost 2341 buffer.exe localhost 2342 buffer.exe localhost 2343 to start 4 buffers on ports 2340-2343. The "localhost" argument is not used, but still appears to be required according to the demo_buffer.c source code. Of course it is cumbersome to have to start the 4 seperate processes on top of your own application. On unix-like computers you should be able to write a single application that at the beginning forks into a parent and child, where the parent continues as your application and where the child (which is then a separate process) can start the buffer. You can fork multiple times, to have multiple buffers (one per child). best Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Jun 9 15:19:14 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 9 Jun 2011 15:19:14 +0200 Subject: [FieldTrip] courses In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F03ECAF47@exchccr1.neuro.gu.se> References: <32CC77C0C8A7AD4B9410934642608E1F03ECAF47@exchccr1.neuro.gu.se> Message-ID: <5B0A148A-D4F0-454F-B60B-E47ECCA47E75@donders.ru.nl> Dear Elena For 2011 there are no courses planned any more in Nijmege, which are open to external participants (there will be a course for local studens in the Donders Graduate School in the autumn). The next course in Nijmegen will be the MEG Toolkit course, which most likely will be somewhere in the spring of 2012. For 2011 we are currently considering a course in Paris at the end of this year. I believe that Stefan and Saskia are considering to do another course in New York later this year, although I don't know any details for the New York plans. At the upcoming HBM meeting in Quebec there will be an educational course in which FieldTrip and the other open source academic toolboxes will play a (relatively small) role. Although I don't think it is efficient to travel to Quebec just for this part, it might be interesting for you to attend if you are attending the HBM conference anyway. See http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3437 and for the program one of the last pages of http://www.humanbrainmapping.org/files/2011MeetingFiles/Descriptions/HBM%202011%20Educational%20Program.pdf Please note that we are open to invitations for presenting the FieldTrip course at external sites. This year we have already been in Tuebingen, St Louis, and New York, and if there is an interesting venue, an enthousiastic local organizer and funding can be arranged to cover the expenses, most likely some experienced users/developers from Nijmegen can be found or appointed to present a 2,5 day course at the external site. best regards, Robert On 7 Jun 2011, at 12:53, Elena Orekhova wrote: > Dear FieldTrip gurus, > > Are you planning any FieldTrip courses for the users in the nearest > future? > > Elena > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From r.oostenveld at donders.ru.nl Thu Jun 9 17:02:38 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 9 Jun 2011 17:02:38 +0200 Subject: [FieldTrip] Problem passing arguments to peerslave command line executable In-Reply-To: References: Message-ID: <33AD75FB-959A-4F3B-AD5B-1ABBD9F2C1DE@donders.ru.nl> Hi Niels On 7 Jun 2011, at 10:33, Kloosterman, Niels wrote: > Although I have succesfully used the command-line ./ > peerslave.glnxa64 to launch slaves for parallel analysis of my batch > jobs, I am somehow not able to pass arguments to the command, for > example ./peerslave.glnxa64 --number 8, to launch 8 slaves at once. > Could anybody tell me what’s going on? I'll give it a try. > When I execute without arguments this line pops up: > > niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./ > peerslave.glnxa64 > peerslave[9705]: peerinit: niels at gb-r35n18.irc.sara.nl, id = > 4020038417 > > All seems fine: the master is indeed able to send jobs to the slave. > No other information is printed to the shell when it gets a job or > whatever (is this normal?). Yes, that is normal. Since we are running the peerslaves at the Donders on our ~50 node cluster on the background, the default (compiled) behaviour is to use the syslog facility. If I were to start them from a cronjob, I would either get very lengthy mails (which cron sends if the process finishes), or not get any information (when I redirect the output to /dev/null). To keep track of all processes on all nodes, we use a syslog server. The peerslave messages are all sent to a single syslog server where I can track them all in /var/log/ peerslave.log Note however that if you recompile, you can change this. Have a look at this section in peer.h #if SYSLOG == 0 #define PANIC(format, ...) {exit(-1);} #define DEBUG(level, format, ...) { } #elif SYSLOG == 1 #define PANIC(format, ...) {syslog(LOG_ERR, format, ## __VA_ARGS__); exit(-1);} #define DEBUG(level, format, ...) {syslog(level, format, ## __VA_ARGS__);} #elif SYSLOG == 2 #define PANIC(format, ...) {fprintf(stderr, format"\n", ## __VA_ARGS__); exit(-1);} #define DEBUG(level, format, ...) {fprintf(stderr, format"\n", ## __VA_ARGS__);} #elif SYSLOG == 3 #define PANIC(format, ...) {mexPrintf(format"\n", ## __VA_ARGS__); exit(-1);} #define DEBUG(level, format, ...) {if (level<=syslog_level) mexPrintf(format"\n", ## __VA_ARGS__);} #endif At compile time you can specify whether the output goes to syslog (1), stderr (2) or whether mexPrintf shoudl be used (for the mex file, 3). Probably you'll want to add -DSYSLOG=2 to the compile flags. Furthermore note that the syslog level is used to control how much info is given. That is controlled with the --verbose=number option on the peerslave command line. > Now when I try to run the --help I get this: > > niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./ > peerslave.glnxa64 --help > peerslave[9753]: peerinit: niels at gb-r35n18.irc.sara.nl, id = > 2887682376 > parser: cannot open file --help > peerslave[9753]: cannot read the configuration file Hmm, this is not good. It appears that it misinterprets the cmd line option. > And when I try to do --number 8: > > niels at gb-r35n18:~/matlab/fieldtrip-20110526/peer/bin$ ./ > peerslave.glnxa64 --number 8 > peerslave[9759]: peerinit: niels at gb-r35n18.irc.sara.nl, id = > 3997336815 > ./peerslave.glnxa64: unrecognized option '--number' > peerslave[9759]: invalid command line options Again here the cmd line option is misinterpreted. This one I can reproduce roboos at mentat258> ../bin/peerslave.glnxa64 --number 8 peerslave[14690]: peerinit: roboos at mentat258.dccn.nl, id = 2375758516 ../bin/peerslave.glnxa64: unrecognized option `--number' peerslave[14690]: invalid command line options I'll file a bug for it. For the meantime, I suggest you look into the configuration files. That is also how we are using them at the Donders, you can find an example below. best Robert ------------------------ cut here ------------------------ # has 12GB of RAM, one CPU and 4 cores # Intel(R) Xeon(R) CPU W3530 @ 2.80GHz [peer] matlab=/opt/cluster/matlab2010b -nodisplay -singleCompThread timavail=86399 smartcpu=1 smartmem=1 udsserver=1 [peer] matlab=/opt/cluster/matlab2010b -nodisplay -singleCompThread timavail=3599 smartcpu=1 smartmem=1 udsserver=1 [peer] matlab=/opt/cluster/matlab2010b -nodisplay -singleCompThread timavail=3599 smartcpu=1 smartmem=1 udsserver=1 [peer] matlab=/opt/cluster/matlab2010b -nodisplay -singleCompThread timavail=599 smartcpu=1 smartmem=1 udsserver=1 ------------------------ cut here ------------------------ From michael.wibral at web.de Thu Jun 9 17:05:49 2011 From: michael.wibral at web.de (Michael Wibral) Date: Thu, 9 Jun 2011 17:05:49 +0200 (CEST) Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis Message-ID: <327769233.351093.1307631949517.JavaMail.fmail@mwmweb082> An HTML attachment was scrubbed... URL: From michael.wibral at web.de Thu Jun 9 17:06:47 2011 From: michael.wibral at web.de (Michael Wibral) Date: Thu, 9 Jun 2011 17:06:47 +0200 (CEST) Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis Message-ID: <619181926.351452.1307632007849.JavaMail.fmail@mwmweb082> An HTML attachment was scrubbed... URL: From johan.bergmann at yahoo.com Thu Jun 9 20:35:54 2011 From: johan.bergmann at yahoo.com (Johan Bergmann) Date: Thu, 9 Jun 2011 11:35:54 -0700 (PDT) Subject: [FieldTrip] Converting time stamps into NCS. Message-ID: <213089.20008.qm@web45503.mail.sp1.yahoo.com> Hello, I have a .mat file containing a single column of voltage values which i wish to convert to the ncs file format. I cannot seem to achieve this, please can someone show me a usage example. Cheers, Johan. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Thu Jun 9 22:48:34 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Thu, 9 Jun 2011 20:48:34 +0000 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <619181926.351452.1307632007849.JavaMail.fmail@mwmweb082> References: <619181926.351452.1307632007849.JavaMail.fmail@mwmweb082> Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECB515@exchccr1.neuro.gu.se> Dear Michael, I still have not resolved this problem and do not know whether is specific for my data(or program bag) or the other Neuromag users also had it. Do you use Neuromag? Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Thursday, June 09, 2011 5:06 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Hi Elena, disregard my last email, I overlooked the att. Michael ________________________________ Von: "Elena Orekhova" Gesendet: Jun 2, 2011 8:03:16 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Verdana"; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear Michael, I did normalize the data (sourcepst.avg.nai=sourcepst.avg.pow./sourcepre.avg.pow) as it was suggested in the tutorial. I used the same scales in all plots for comparison purposes. If automatic scaling is used the result for MAG+GRA does not look any better (see attachment). >What you could do as a workaround is to average the separate results with a weighting per voxel and that >is corresponding to the squared norms of the leadfields for the respective modalities for a given voxel , this >would guarantee equal amounts of backprojected noise from both modalities (if I'm not mistaken). Thank you for your suggestion. I may use it as a last resort. Hopefully, there is still a way to get more optimal solution using both GRA and MAG in the same analysis... Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Elena Orekhova [Elena.Orekhova at neuro.gu.se] Sent: Thursday, June 02, 2011 6:22 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis BODY {direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;} Dear Michael, I have tried to multiply the leadfield by -1 as you suggested: for i = 1 : size (grid.leadfield, 2) grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); end This had no effect on the 'lcmv' output. I attached the pictures for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ In this experiment I measured evoked field in response to the unilateral (left) click. The source is expected to be in the right superior temporal cortex. This is the case for ‘GRA only' and ’MAG only’ datasets. The combined sensors give meaningless result. Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Wednesday, June 01, 2011 4:04 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Elena, could you give the following a try: invert (*-1) the leadfileds for one of the two sensor types. Let me know what happens. I would also be interested in taking a look at the results - maybe you could sent images off-list: Michael.Wibral web.de. Michael ________________________________ Von: "Elena Orekhova" Gesendet: Jun 1, 2011 12:23:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "Arial"; }@font-face { font-family: "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: Times; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear fieldtrippers, This message is mainly for Neuromag users. When I do 'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. If I combine the two types of sensors without weighting, the result is meaningless. Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements. Does anybody know how to deal with this problem? Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri Jun 10 09:45:30 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 10 Jun 2011 09:45:30 +0200 Subject: [FieldTrip] Converting time stamps into NCS. In-Reply-To: <213089.20008.qm@web45503.mail.sp1.yahoo.com> References: <213089.20008.qm@web45503.mail.sp1.yahoo.com> Message-ID: <550011EB-7B66-40F1-87BB-77974ED41D1B@donders.ru.nl> Dear Johan You can use ft_write_data(FILENAME, DAT, 'header', HDR, 'dataformat', 'neuralynx_ncs') where you have to provide the filename, the data (as 1*Nsamples matrix) and the header (i.e. everything in upper case in the example). For the header you have to provide a matlab structure such as the one that is returned by ft_read_header returns when you read an original neuralynx ncs file. I suggest that you look into the ft_write_data function at line 529 for further details. best Robert On 9 Jun 2011, at 20:35, Johan Bergmann wrote: > Hello, > > I have a .mat file containing a single column of voltage values > which i wish to convert to the ncs file format. I cannot seem to > achieve this, please can someone show me a usage example. > > Cheers, > > Johan. > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From johan.bergmann at yahoo.com Fri Jun 10 12:39:37 2011 From: johan.bergmann at yahoo.com (Johan Bergmann) Date: Fri, 10 Jun 2011 03:39:37 -0700 (PDT) Subject: [FieldTrip] Converting time stamps into NCS. In-Reply-To: <550011EB-7B66-40F1-87BB-77974ED41D1B@donders.ru.nl> References: <213089.20008.qm@web45503.mail.sp1.yahoo.com> <550011EB-7B66-40F1-87BB-77974ED41D1B@donders.ru.nl> Message-ID: <629642.35556.qm@web45515.mail.sp1.yahoo.com> Dear Robert, Thanks for your response. I have taken a look at the code in ft_write_data. My original file was not from a .ncs file format it was from a .mcd file format, scaled in micro volts and a continuous recording. So, i have a "900x1 double" voltage values as a variable called "data" in Matlab. I call: ft_write_data(new_file.ncs, data, '?', ? , 'matlab', '?') ft_write_data(FILENAME, DAT, 'header', HDR, 'dataformat', 'neuralynx_ncs') sorry for the simplistic question. Thanks, Johan. ________________________________ From: Robert Oostenveld To: Email discussion list for the FieldTrip project Sent: Fri, June 10, 2011 8:45:30 AM Subject: Re: [FieldTrip] Converting time stamps into NCS. Dear Johan You can use ft_write_data(FILENAME, DAT, 'header', HDR, 'dataformat', 'neuralynx_ncs') where you have to provide the filename, the data (as 1*Nsamples matrix) and the header (i.e. everything in upper case in the example). For the header you have to provide a matlab structure such as the one that is returned by ft_read_header returns when you read an original neuralynx ncs file. I suggest that you look into the ft_write_data function at line 529 for further details. best Robert On 9 Jun 2011, at 20:35, Johan Bergmann wrote: > Hello, > > I have a .mat file containing a single column of voltage values which i wish to >convert to the ncs file format. I cannot seem to achieve this, please can >someone show me a usage example. > > Cheers, > > Johan. > _______________________________________________ > 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 tobias.staudigl at uni-konstanz.de Fri Jun 10 12:42:51 2011 From: tobias.staudigl at uni-konstanz.de (Tobias Staudigl) Date: Fri, 10 Jun 2011 12:42:51 +0200 Subject: [FieldTrip] granger causality Message-ID: <4DF1F52B.3000406@uni-konstanz.de> Dear all, I am trying to make sense out of a granger-causality analysis i did using ft-functions. I have two condition in which i already identified a sig. difference in plv. now i would like to know the directionality of the coupling in one of the conditions. To this end, I use granger causality as implemented in fieldtrip (see below for details). At the moment, i have 3 questions. (As i am not very familiar with using fieldtrip, i may have missed something obvious). Q 1: If I understood correctly, the grangerspectrum (granger.grangerspctrm) gives me values for the granger-causality in a matrix [nChannel, nChannel, Freqs]. Does [1,2,:] give me the granger-causality of Channel1 predicting Channel2, or the other way round? Q2: The plotting function gives me an error: ft_connectivityplot(cfg, granger) ??? Error using ==> seloverdim at 36 cannot select over multiple dimensions at the same time Error in ==> ft_selectdata at 528 if selectchan, data = seloverdim(data, 'chan', selchan, fb); end Error in ==> ft_connectivityplot at 79 data = ft_selectdata(data, 'channel', cfg.channel); Q3: How do i statistically validate the measures i get fromthe granger-analysis? Is there some recommended statistical test? Is it correct to do bootstrapping / permutation testing? What I could do on my data is shuffle the trials across conditions, compute granger causality on the shuffeld data, and compair this distribution with the value i get from the data. Maybe, somebody is experienced in using granger and could help me out! Any advice appreciated! Thanks a lot! tobi I used the following ft_functions according to the online tutorial: %% MVAR cfg = []; cfg.order = 2; cfg.toolbox = 'bsmart'; mdata = ft_mvaranalysis(cfg, data); %% transfer function cfg = []; cfg.method = 'mvar'; mfreq = ft_freqanalysis(cfg, mdata); %% granger cfg = []; cfg.method = 'granger'; granger = ft_connectivityanalysis(cfg, mfreq); %% cfg = []; cfg.zparam = 'grangerspctrm'; %cfg.channel = 'all'; ft_connectivityplot(cfg, granger); -- Tobias Staudigl Fachbereich Psychologie - ZPR Postfach ZPR 78457 Konstanz ZPR, Haus 12 Tel.: +49 (0)7531 / 88 - 5703 From jan.schoffelen at donders.ru.nl Fri Jun 10 13:00:12 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 10 Jun 2011 13:00:12 +0200 Subject: [FieldTrip] granger causality In-Reply-To: <4DF1F52B.3000406@uni-konstanz.de> References: <4DF1F52B.3000406@uni-konstanz.de> Message-ID: <01F5D123-C4D5-42B2-9D93-CC3B4E86BD66@donders.ru.nl> Hi Tobias, > > Q 1: > If I understood correctly, the grangerspectrum > (granger.grangerspctrm) gives me values for the granger-causality in > a matrix [nChannel, nChannel, Freqs]. > Does [1,2,:] give me the granger-causality of Channel1 predicting > Channel2, or the other way round? > The FieldTrip convention is indeed (1,2,:) relates to 1->2 > Q2: > The plotting function gives me an error: > > ft_connectivityplot(cfg, granger) > > ??? Error using ==> seloverdim at 36 > cannot select over multiple dimensions at the same time > > Error in ==> ft_selectdata at 528 > if selectchan, data = seloverdim(data, 'chan', selchan, fb); end > > Error in ==> ft_connectivityplot at 79 > data = ft_selectdata(data, 'channel', cfg.channel); Please update your fieldtrip version. There is a fix (dated 22-04) that should take care of this > Q3: > How do i statistically validate the measures i get fromthe granger- > analysis? > Is there some recommended statistical test? > Is it correct to do bootstrapping / permutation testing? > What I could do on my data is shuffle the trials across conditions, > compute granger causality on the shuffeld data, and compair this > distribution with the value i get from the data. This is a very relevant issue. From what you describe it seems as if you want to compare across conditions. The shuffling across conditions is what we do as well, although it remains open to debate how meaningful it is to compare granger causality indices across conditions. And, also, if you are able to reject your null-hypothesis, whether your decision to reject it is actually due to the actual granger causality being different, or by some other confounding quantity. Best wishes, Jan-Mathijs > Maybe, somebody is experienced in using granger and could help me out! > Any advice appreciated! > > Thanks a lot! > tobi > > > I used the following ft_functions according to the online tutorial: > > %% MVAR > cfg = []; > cfg.order = 2; > cfg.toolbox = 'bsmart'; > mdata = ft_mvaranalysis(cfg, data); > > %% transfer function > cfg = []; > cfg.method = 'mvar'; > mfreq = ft_freqanalysis(cfg, mdata); > > %% granger > cfg = []; > cfg.method = 'granger'; > granger = ft_connectivityanalysis(cfg, mfreq); > > %% > cfg = []; > cfg.zparam = 'grangerspctrm'; > %cfg.channel = 'all'; > ft_connectivityplot(cfg, granger); > > -- > Tobias Staudigl > Fachbereich Psychologie - ZPR > Postfach ZPR > 78457 Konstanz > ZPR, Haus 12 > Tel.: +49 (0)7531 / 88 - 5703 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From jan.schoffelen at donders.ru.nl Fri Jun 10 13:01:58 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 10 Jun 2011 13:01:58 +0200 Subject: [FieldTrip] Weird trialfun_general error In-Reply-To: References: Message-ID: <59055861-365E-4FD7-A85C-C57C2FF430C4@donders.ru.nl> Hi Rodolphe, This is a funny bug. It goes wrong in trialfun_general when the intersect() tries to compare a string (event(i).vale being 'boundary') with a list of numbers (your event values). This leads in your case to unwanted behavior, and I can imagine that this will cause problems elsewhere too. We'll look into it and fix it. Thanks for the notification. Best, Jan-Mathijs On Jun 7, 2011, at 12:51 AM, Rodolphe Nenert wrote: > Dear fieldtrippers, > > i just noticed and found the origin of a weird error obtained with > the trialfun_general function, i thought it could be useful to send > it here. > I use the ft_definetrial function on a file obtained using the merge > function in EEGlab. Apparently, this function is adding some > triggers with the value 'boundary' in the new file, indicating the > old frontier between the dataset that have been merged. > The funny part is that the trialfun_general() function in fieltrip > is using the intersect() matlab function to match event values. > Moreover, im using 27 different event values to indicate point of > interest (112,114,116,122,etc...) > All of my event values dont create any problems except the value > 114 because intersect('boundary',114) = 114 whereas it gives an > empty result with any other of my values... > Therefore, for that particular event value, there was a dimension > mismatch between trl and val in trialfun_general. > > I just removed events with 'boundary' values and it worked. > > Best regards, > > Rodolphe Nenert, Ph.D. > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From g.dimitriadis at donders.ru.nl Fri Jun 10 16:52:54 2011 From: g.dimitriadis at donders.ru.nl (George Dimitriadis) Date: Fri, 10 Jun 2011 16:52:54 +0200 Subject: [FieldTrip] (no subject) In-Reply-To: <550011EB-7B66-40F1-87BB-77974ED41D1B@donders.ru.nl> References: <213089.20008.qm@web45503.mail.sp1.yahoo.com> <550011EB-7B66-40F1-87BB-77974ED41D1B@donders.ru.nl> Message-ID: <00ed01cc277e$170492c0$450db840$@dimitriadis@donders.ru.nl> Hello guys, In ft_plot_topo.m at line 69 you say if isempty(tag), tag=''; Could you please turn the comma into a ; because it breaks my code. Thanks From TAVABIK at email.chop.edu Fri Jun 10 18:59:03 2011 From: TAVABIK at email.chop.edu (Tavabi, Kambiz) Date: Fri, 10 Jun 2011 12:59:03 -0400 Subject: [FieldTrip] working with neuromag data In-Reply-To: <887659131.308634.1301386835573.JavaMail.root@sculptor.zimbra.ru.nl> References: <717208384.308488.1301386421578.JavaMail.root@sculptor.zimbra.ru.nl>, <887659131.308634.1301386835573.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: As per advise from Arjen, I was able to use following steps 1) ft_preprocessing on your stimulus averaged epoch data. This should give you a data structure with 6 trials (which are actually the averages per condition). 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat this so you end up with 6 timelocked structures representing the 6 different conditions. to create individual condition averaged ft data structures which I can visualize using ft_topoplotER(cfg,data) data: avg: [338x651 double] var: [338x651 double] fsample: 1000 time: [1x651 double] dof: [338x651 double] label: {338x1 cell} dimord: 'chan_time' grad: [1x1 struct] cfg: [1x1 struct] however when i use; cfg = []; cfg.showlabels = 'yes'; cfg.fontsize = 6; cfg.ylim = [-10e-13 10e-13] ft_multiplotER(cfg, data); Fieldtrip chruns through creating the selection avg along dimension 1 selection dof along dimension 1 selection var along dimension 1 creating layout from data.grad creating layout for neuromag306 system but the resutling figure is an empty figure containing only layout with ch lables without any data what so ever. Any ideas why this might be? -Kambiz. ------------------------------------------------------------- Kambiz Tavabi PhD Biomedical Imaging Laboratory The Children's Hospital of Philadelphia 34th Street and Civic Center Boulevard Philadelphia, Pa. 19104 Tel: 267.426.0302 email: tavabik at email.chop.edu ------------------------------------------------------------- ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. [a.stolk at fcdonders.ru.nl] Sent: Tuesday, March 29, 2011 4:20 AM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] working with neuromag data Dear Kambiz, I think I see your point. Your data presumably is already preprocessed and timelocked (averaged over trials) with neuromag software. I then take it that you have 6 different conditions which you would like to plot separately and possibly test at the group level. Since the data is already averaged, I'd recommend to do the following to get your data back on track. 1) ft_preprocessing on your stimulus averaged epoch data. This should give you a data structure with 6 trials (which are actually the averages per condition). 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat this so you end up with 6 timelocked structures representing the 6 different conditions. 3) plot or grandaverage (see tutorials how to proceed as your data now should be 'ft-friendly'). Goodluck, Arjen ----- "Kambiz Tavabi" schreef: > Van: "Kambiz Tavabi" > Aan: "Email discussion list for the FieldTrip project" > Verzonden: Dinsdag 29 maart 2011 01:10:14 > Onderwerp: Re: [FieldTrip] working with neuromag data > > Dear Arjen - Thanks for your response. Just to clarify the low level > functions ft_read_header & ft_read_data are mentioned in the ft > getting started tutorial. I believe they're recommended to make sure > the data is ft friendly. In my case the data is ft friendly. My data > is also pre-processed and already 'time-locked'--meaning that I have > stimulus averaged epoch data in fif format for all my subjects. My > question is how to proceed from there? I've been through the pages you > refer to but have not been able to piece together my data in such a > way to proceed with grand-averaging and carrying out stats. > -Kambiz. > ------------------------------------------------------------- > Kambiz Tavabi PhD > Biomedical Imaging Laboratory > The Children's Hospital of Philadelphia > 34th Street and Civic Center Boulevard > Philadelphia, Pa. 19104 > Tel: 267.426.0302 > email: tavabik at email.chop.edu > ------------------------------------------------------------- > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > [a.stolk at fcdonders.ru.nl] > Sent: Monday, March 28, 2011 4:05 PM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] working with neuromag data > > Dear Kambiz, > > While you are able to use the 'low level' ft_read_header and > ft_read_data functions, you should be able to preprocess and analyze > your neuromag data using the 'high level' functions such as > ft_preprocessing (which calls the low level functions mentioned > above). > > How to proceed depends on what you want to do with your data. If you > have triggers stored in your dataset that are synchronuous with the > recorded brain activity, it'd be recommended to start with the > following tutorial on how to select your trials: > > http://fieldtrip.fcdonders.nl/tutorial/preprocessing > > Since your experience with FT is still limited as you say, I believe > the following text may provide a good overview of what the data, once > read in to FT (i.e. matlab) environment, may look like: > > http://fieldtrip.fcdonders.nl/walkthrough > > Typically, your next steps involve single-subject timelocked analysis, > then grand-average and perform statistics at the group level. For an > overview of the steps and protocols, see: > > http://fieldtrip.fcdonders.nl/tutorial/analysis_protocols > > Hope this has helped for a start, > > Arjen > > > ----- "Kambiz Tavabi" schreef: > > > Van: "Kambiz Tavabi" > > Aan: "Email discussion list for the FieldTrip project" > > > Verzonden: Maandag 28 maart 2011 20:59:36 > > Onderwerp: [FieldTrip] working with neuromag data > > > > Greetings - I have preprocessed/averaged neuromag data for a group > of > > subjects that I'd like to visualize, compute grandaverage and carry > > out sensor level statistics on. The only help I managed to find on > the > > Fieldtrip site/list Re: neurmag data concerns getting started e.g., > > with ft_read_header and ft_read_data. In my case these programs > work > > fine meaning that I can proceed with further analysis. > > On a side, in my limited experience with FT, a major problem I run > > into frequently is that there is no clear suggestion(s) on how to > > proceed with data that is not raw. I understand it is impossible to > > cover all analysis scenarios, but it is often the case that working > > with CTF, or in particular Elekta system, the data is likely to be > in > > a post-preprocessed phase. Everytime I've tried to work with ft, It > > seems to me that if I don't start with square one in fieldtrip, it > is > > difficult to figure out how to use downstream programs to work on > the > > data. > > That said, in my case I have the output from ft_read_header: > > > > label: {338x1 cell} > > nChans: 338 > > Fs: 1000 > > grad: [1x1 struct] > > unit: {1x338 cell} > > nSamples: 651 > > nSamplesPre: 100 > > nTrials: 6 > > orig: [1x1 struct] > > > > and output from ft_read_data > > > > [338x651x6] that being channels by samples by number of stimulus > > averaged epochs. To proceed, ideally I'd like to compute a > > grandaverage for each condition, visualize them in a multiplot, and > > carry out sensor level stats. To be able to do this I understand I > > need the output from ft_timelockanalysis, how do I arrange my data > as > > such? I am assuming it is already in that state. Thanks for your > > time. > > > > -Kambiz. > > ------------------------------------------------------------- > > Kambiz Tavabi PhD > > Biomedical Imaging Laboratory > > The Children's Hospital of Philadelphia > > 34th Street and Civic Center Boulevard > > Philadelphia, Pa. 19104 > > Tel: 267.426.0302 > > email: tavabik at email.chop.edu > > ------------------------------------------------------------- > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- A non-text attachment was scrubbed... Name: multiplot.jpg Type: image/jpeg Size: 47066 bytes Desc: multiplot.jpg URL: From TAVABIK at email.chop.edu Fri Jun 10 20:21:30 2011 From: TAVABIK at email.chop.edu (Tavabi, Kambiz) Date: Fri, 10 Jun 2011 14:21:30 -0400 Subject: [FieldTrip] working with neuromag data In-Reply-To: References: <717208384.308488.1301386421578.JavaMail.root@sculptor.zimbra.ru.nl>, <887659131.308634.1301386835573.JavaMail.root@sculptor.zimbra.ru.nl>, Message-ID: As per advise from Arjen, I was able to use following steps 1) ft_preprocessing on your stimulus averaged epoch data. This should give you a data structure with 6 trials (which are actually the averages per condition). 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat this so you end up with 6 timelocked structures representing the 6 different conditions. to create individual condition averaged ft data structures which I can visualize using ft_topoplotER(cfg,data) data: avg: [338x651 double] var: [338x651 double] fsample: 1000 time: [1x651 double] dof: [338x651 double] label: {338x1 cell} dimord: 'chan_time' grad: [1x1 struct] cfg: [1x1 struct] however when i use; cfg = []; cfg.showlabels = 'yes'; cfg.fontsize = 6; cfg.ylim = [-10e-13 10e-13] ft_multiplotER(cfg, data); Fieldtrip chruns through creating the selection avg along dimension 1 selection dof along dimension 1 selection var along dimension 1 creating layout from data.grad creating layout for neuromag306 system but the resutling figure is an empty figure containing only layout with ch lables without any data what so ever. Any ideas why this might be? Following up my question on plotting: Why would the granaverge structure lose the channel layout information instead of carrying it over from the Timelock structure? ft_topoplotER(cfg,grandavgc1) ??? Error using ==> ft_prepare_layout at 532 no layout detected, please specify cfg.layout Error in ==> ft_topoplotER at 408 lay = ft_prepare_layout(cfg, data); -Kambiz. ------------------------------------------------------------- Kambiz Tavabi PhD Biomedical Imaging Laboratory The Children's Hospital of Philadelphia 34th Street and Civic Center Boulevard Philadelphia, Pa. 19104 Tel: 267.426.0302 email: tavabik at email.chop.edu ------------------------------------------------------------- ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. [a.stolk at fcdonders.ru.nl] Sent: Tuesday, March 29, 2011 4:20 AM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] working with neuromag data Dear Kambiz, I think I see your point. Your data presumably is already preprocessed and timelocked (averaged over trials) with neuromag software. I then take it that you have 6 different conditions which you would like to plot separately and possibly test at the group level. Since the data is already averaged, I'd recommend to do the following to get your data back on track. 1) ft_preprocessing on your stimulus averaged epoch data. This should give you a data structure with 6 trials (which are actually the averages per condition). 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat this so you end up with 6 timelocked structures representing the 6 different conditions. 3) plot or grandaverage (see tutorials how to proceed as your data now should be 'ft-friendly'). Goodluck, Arjen ----- "Kambiz Tavabi" schreef: > Van: "Kambiz Tavabi" > Aan: "Email discussion list for the FieldTrip project" > Verzonden: Dinsdag 29 maart 2011 01:10:14 > Onderwerp: Re: [FieldTrip] working with neuromag data > > Dear Arjen - Thanks for your response. Just to clarify the low level > functions ft_read_header & ft_read_data are mentioned in the ft > getting started tutorial. I believe they're recommended to make sure > the data is ft friendly. In my case the data is ft friendly. My data > is also pre-processed and already 'time-locked'--meaning that I have > stimulus averaged epoch data in fif format for all my subjects. My > question is how to proceed from there? I've been through the pages you > refer to but have not been able to piece together my data in such a > way to proceed with grand-averaging and carrying out stats. > -Kambiz. > ------------------------------------------------------------- > Kambiz Tavabi PhD > Biomedical Imaging Laboratory > The Children's Hospital of Philadelphia > 34th Street and Civic Center Boulevard > Philadelphia, Pa. 19104 > Tel: 267.426.0302 > email: tavabik at email.chop.edu > ------------------------------------------------------------- > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > [a.stolk at fcdonders.ru.nl] > Sent: Monday, March 28, 2011 4:05 PM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] working with neuromag data > > Dear Kambiz, > > While you are able to use the 'low level' ft_read_header and > ft_read_data functions, you should be able to preprocess and analyze > your neuromag data using the 'high level' functions such as > ft_preprocessing (which calls the low level functions mentioned > above). > > How to proceed depends on what you want to do with your data. If you > have triggers stored in your dataset that are synchronuous with the > recorded brain activity, it'd be recommended to start with the > following tutorial on how to select your trials: > > http://fieldtrip.fcdonders.nl/tutorial/preprocessing > > Since your experience with FT is still limited as you say, I believe > the following text may provide a good overview of what the data, once > read in to FT (i.e. matlab) environment, may look like: > > http://fieldtrip.fcdonders.nl/walkthrough > > Typically, your next steps involve single-subject timelocked analysis, > then grand-average and perform statistics at the group level. For an > overview of the steps and protocols, see: > > http://fieldtrip.fcdonders.nl/tutorial/analysis_protocols > > Hope this has helped for a start, > > Arjen > > > ----- "Kambiz Tavabi" schreef: > > > Van: "Kambiz Tavabi" > > Aan: "Email discussion list for the FieldTrip project" > > > Verzonden: Maandag 28 maart 2011 20:59:36 > > Onderwerp: [FieldTrip] working with neuromag data > > > > Greetings - I have preprocessed/averaged neuromag data for a group > of > > subjects that I'd like to visualize, compute grandaverage and carry > > out sensor level statistics on. The only help I managed to find on > the > > Fieldtrip site/list Re: neurmag data concerns getting started e.g., > > with ft_read_header and ft_read_data. In my case these programs > work > > fine meaning that I can proceed with further analysis. > > On a side, in my limited experience with FT, a major problem I run > > into frequently is that there is no clear suggestion(s) on how to > > proceed with data that is not raw. I understand it is impossible to > > cover all analysis scenarios, but it is often the case that working > > with CTF, or in particular Elekta system, the data is likely to be > in > > a post-preprocessed phase. Everytime I've tried to work with ft, It > > seems to me that if I don't start with square one in fieldtrip, it > is > > difficult to figure out how to use downstream programs to work on > the > > data. > > That said, in my case I have the output from ft_read_header: > > > > label: {338x1 cell} > > nChans: 338 > > Fs: 1000 > > grad: [1x1 struct] > > unit: {1x338 cell} > > nSamples: 651 > > nSamplesPre: 100 > > nTrials: 6 > > orig: [1x1 struct] > > > > and output from ft_read_data > > > > [338x651x6] that being channels by samples by number of stimulus > > averaged epochs. To proceed, ideally I'd like to compute a > > grandaverage for each condition, visualize them in a multiplot, and > > carry out sensor level stats. To be able to do this I understand I > > need the output from ft_timelockanalysis, how do I arrange my data > as > > such? I am assuming it is already in that state. Thanks for your > > time. > > > > -Kambiz. > > ------------------------------------------------------------- > > Kambiz Tavabi PhD > > Biomedical Imaging Laboratory > > The Children's Hospital of Philadelphia > > 34th Street and Civic Center Boulevard > > Philadelphia, Pa. 19104 > > Tel: 267.426.0302 > > email: tavabik at email.chop.edu > > ------------------------------------------------------------- > > _______________________________________________ > > 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 a.stolk at fcdonders.ru.nl Sat Jun 11 09:26:58 2011 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Sat, 11 Jun 2011 09:26:58 +0200 (CEST) Subject: [FieldTrip] working with neuromag data In-Reply-To: Message-ID: <621524636.372728.1307777218636.JavaMail.root@sculptor.zimbra.ru.nl> Dear Kambiz, Does your data.avg contain NaNs or real numbers? In the latter case; do they fall in the plotting range as specified by your cfg.ylim? Yours, Arjen ----- "Kambiz Tavabi" schreef: > Van: "Kambiz Tavabi" > Aan: "Email discussion list for the FieldTrip project" > Verzonden: Vrijdag 10 juni 2011 18:59:03 > Onderwerp: Re: [FieldTrip] working with neuromag data > > As per advise from Arjen, I was able to use following steps > 1) ft_preprocessing on your stimulus averaged epoch data. This should > give you a data structure with 6 trials (which are actually the > averages per condition). > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat > this so you end up with 6 timelocked structures representing the 6 > different conditions. > to create individual condition averaged ft data structures which I can > visualize using ft_topoplotER(cfg,data) > data: > avg: [338x651 double] > var: [338x651 double] > fsample: 1000 > time: [1x651 double] > dof: [338x651 double] > label: {338x1 cell} > dimord: 'chan_time' > grad: [1x1 struct] > cfg: [1x1 struct] > however when i use; > cfg = []; > cfg.showlabels = 'yes'; > cfg.fontsize = 6; > cfg.ylim = [-10e-13 10e-13] > ft_multiplotER(cfg, data); > Fieldtrip chruns through creating the > selection avg along dimension 1 > selection dof along dimension 1 > selection var along dimension 1 > creating layout from data.grad > creating layout for neuromag306 system > > but the resutling figure is an empty figure containing only layout > with ch lables without any data what so ever. Any ideas why this might > be? > > > > -Kambiz. > ------------------------------------------------------------- > Kambiz Tavabi PhD > Biomedical Imaging Laboratory > The Children's Hospital of Philadelphia > 34th Street and Civic Center Boulevard > Philadelphia, Pa. 19104 > Tel: 267.426.0302 > email: tavabik at email.chop.edu > ------------------------------------------------------------- > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > [a.stolk at fcdonders.ru.nl] > Sent: Tuesday, March 29, 2011 4:20 AM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] working with neuromag data > > Dear Kambiz, > > I think I see your point. Your data presumably is already preprocessed > and timelocked (averaged over trials) with neuromag software. I then > take it that you have 6 different conditions which you would like to > plot separately and possibly test at the group level. > > Since the data is already averaged, I'd recommend to do the following > to get your data back on track. > > 1) ft_preprocessing on your stimulus averaged epoch data. This should > give you a data structure with 6 trials (which are actually the > averages per condition). > > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat > this so you end up with 6 timelocked structures representing the 6 > different conditions. > > 3) plot or grandaverage (see tutorials how to proceed as your data now > should be 'ft-friendly'). > > Goodluck, > Arjen > > > > > > > ----- "Kambiz Tavabi" schreef: > > > Van: "Kambiz Tavabi" > > Aan: "Email discussion list for the FieldTrip project" > > > Verzonden: Dinsdag 29 maart 2011 01:10:14 > > Onderwerp: Re: [FieldTrip] working with neuromag data > > > > Dear Arjen - Thanks for your response. Just to clarify the low > level > > functions ft_read_header & ft_read_data are mentioned in the ft > > getting started tutorial. I believe they're recommended to make > sure > > the data is ft friendly. In my case the data is ft friendly. My > data > > is also pre-processed and already 'time-locked'--meaning that I > have > > stimulus averaged epoch data in fif format for all my subjects. My > > question is how to proceed from there? I've been through the pages > you > > refer to but have not been able to piece together my data in such a > > way to proceed with grand-averaging and carrying out stats. > > -Kambiz. > > ------------------------------------------------------------- > > Kambiz Tavabi PhD > > Biomedical Imaging Laboratory > > The Children's Hospital of Philadelphia > > 34th Street and Civic Center Boulevard > > Philadelphia, Pa. 19104 > > Tel: 267.426.0302 > > email: tavabik at email.chop.edu > > ------------------------------------------------------------- > > ________________________________________ > > From: fieldtrip-bounces at donders.ru.nl > > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > > [a.stolk at fcdonders.ru.nl] > > Sent: Monday, March 28, 2011 4:05 PM > > To: Email discussion list for the FieldTrip project > > Subject: Re: [FieldTrip] working with neuromag data > > > > Dear Kambiz, > > > > While you are able to use the 'low level' ft_read_header and > > ft_read_data functions, you should be able to preprocess and > analyze > > your neuromag data using the 'high level' functions such as > > ft_preprocessing (which calls the low level functions mentioned > > above). > > > > How to proceed depends on what you want to do with your data. If > you > > have triggers stored in your dataset that are synchronuous with the > > recorded brain activity, it'd be recommended to start with the > > following tutorial on how to select your trials: > > > > http://fieldtrip.fcdonders.nl/tutorial/preprocessing > > > > Since your experience with FT is still limited as you say, I > believe > > the following text may provide a good overview of what the data, > once > > read in to FT (i.e. matlab) environment, may look like: > > > > http://fieldtrip.fcdonders.nl/walkthrough > > > > Typically, your next steps involve single-subject timelocked > analysis, > > then grand-average and perform statistics at the group level. For > an > > overview of the steps and protocols, see: > > > > http://fieldtrip.fcdonders.nl/tutorial/analysis_protocols > > > > Hope this has helped for a start, > > > > Arjen > > > > > > ----- "Kambiz Tavabi" schreef: > > > > > Van: "Kambiz Tavabi" > > > Aan: "Email discussion list for the FieldTrip project" > > > > > Verzonden: Maandag 28 maart 2011 20:59:36 > > > Onderwerp: [FieldTrip] working with neuromag data > > > > > > Greetings - I have preprocessed/averaged neuromag data for a > group > > of > > > subjects that I'd like to visualize, compute grandaverage and > carry > > > out sensor level statistics on. The only help I managed to find > on > > the > > > Fieldtrip site/list Re: neurmag data concerns getting started > e.g., > > > with ft_read_header and ft_read_data. In my case these programs > > work > > > fine meaning that I can proceed with further analysis. > > > On a side, in my limited experience with FT, a major problem I > run > > > into frequently is that there is no clear suggestion(s) on how to > > > proceed with data that is not raw. I understand it is impossible > to > > > cover all analysis scenarios, but it is often the case that > working > > > with CTF, or in particular Elekta system, the data is likely to > be > > in > > > a post-preprocessed phase. Everytime I've tried to work with ft, > It > > > seems to me that if I don't start with square one in fieldtrip, > it > > is > > > difficult to figure out how to use downstream programs to work on > > the > > > data. > > > That said, in my case I have the output from ft_read_header: > > > > > > label: {338x1 cell} > > > nChans: 338 > > > Fs: 1000 > > > grad: [1x1 struct] > > > unit: {1x338 cell} > > > nSamples: 651 > > > nSamplesPre: 100 > > > nTrials: 6 > > > orig: [1x1 struct] > > > > > > and output from ft_read_data > > > > > > [338x651x6] that being channels by samples by number of stimulus > > > averaged epochs. To proceed, ideally I'd like to compute a > > > grandaverage for each condition, visualize them in a multiplot, > and > > > carry out sensor level stats. To be able to do this I understand > I > > > need the output from ft_timelockanalysis, how do I arrange my > data > > as > > > such? I am assuming it is already in that state. Thanks for your > > > time. > > > > > > -Kambiz. > > > ------------------------------------------------------------- > > > Kambiz Tavabi PhD > > > Biomedical Imaging Laboratory > > > The Children's Hospital of Philadelphia > > > 34th Street and Civic Center Boulevard > > > Philadelphia, Pa. 19104 > > > Tel: 267.426.0302 > > > email: tavabik at email.chop.edu > > > ------------------------------------------------------------- > > > _______________________________________________ > > > 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 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Sun Jun 12 10:40:48 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Sun, 12 Jun 2011 10:40:48 +0200 Subject: [FieldTrip] (no subject) In-Reply-To: <00ed01cc277e$170492c0$450db840$@dimitriadis@donders.ru.nl> References: <213089.20008.qm@web45503.mail.sp1.yahoo.com> <550011EB-7B66-40F1-87BB-77974ED41D1B@donders.ru.nl> <00ed01cc277e$170492c0$450db840$@dimitriadis@donders.ru.nl> Message-ID: <4DF47B90.1020400@donders.ru.nl> Hi George, first of all, I just changed the code after I read your mail - but I doubt that this fixes your problem. Anyway, what version of Matlab are you using that causes a comma to break your code? In a lot of fieldtrip functions, we are using if(z), x=y; end; Did this not work for some Matlab versions? If this was the case, you could not use ft_multiplotER, for example, because ft_plot_vector does have a lot of these if-clauses. Are you sure it is this comma and not something else that breaks your code? Please excuse my skepticism :) Best, Jörn On 6/10/2011 4:52 PM, George Dimitriadis wrote: > Hello guys, > > In ft_plot_topo.m at line 69 you say if isempty(tag), tag=''; > Could you please turn the comma into a ; because it breaks my code. > > Thanks > > _______________________________________________ > 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 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 Kapitelweg 29 NL-6525 EN Nijmegen The Netherlands From cmuehl at gmail.com Sun Jun 12 17:56:49 2011 From: cmuehl at gmail.com (Christian Muehl) Date: Sun, 12 Jun 2011 17:56:49 +0200 Subject: [FieldTrip] Final Call for Papers: Affective BCI Workshop, Memphis, USA Message-ID: ** Final Call for Papers ** 2nd Workshop on Affective Brain-Computer Interfaces (aBCI) Workshop at ACII 2011 (October 9-12), Memphis, USA, October 9, 2011 Apologies for multiple postings http://hmi.ewi.utwente.nl/abci2011 http://www.acii2011.org The second workshop on affective brain-computer interfaces will explore the advantages and limitations of using neuro-physiological signals as a modality for the automatic recognition of affective and cognitive states, and the possibilities of using this information about the user state in innovative and adaptive applications. The goal is to bring researchers from the communities of brain computer interfacing, affective computing, neuro-ergonomics, affective and cognitive neuroscience together to present state-of-the-art progress and visions on the various overlaps between those disciplines. Recent research in brain-computer interfaces (BCI) shows that brain activity can be used as an active/voluntary, or passive/involuntary control modality in man-machine interaction. While active BCI paradigms have received a lot of attention in recent years, research on passive approaches to BCI still desperately needs concerted activity. However, it has been shown more than once that brain activations can carry information about the affective and cognitive state of a subject, and that the interaction between humans and machines can be aided by the recognition of those user states. To achieve robust passive BCIs, efforts from applied and basic sciences have to be combined. On the one hand, applied fields such as affective computing aim at the development of applications that adapt to changes in the user states and thereby enrich the interaction, leading to a more natural and effective usability. On the other hand, basic research in neuroscience advances our understanding of the neural processes associated with emotions. Furthermore, similar advancements are being made for more cognitive mental states, for example, attention, fatigue, and work load, which strongly interact with affective states. Topics of interest include, but are not limited to: * emotion elicitation and data collection for affective BCI * detection of affective and cognitive states with BCI and other modalities * adaptive interfaces and affective BCI Invited Talk: 'Brain Dynamics of Affective Engagement' by Scott Makeig, SCCN, University of California at San Diego, USA The workshop will be held in conjunction with the 4th International conference on Affective Computing and Intelligent Interaction (ACII2011) at the FedEx Institute of Technology at the University of Memphis, TN. Submission Instructions * The papers should feature original empirical work, theoretical work, or a well defendable but arguable position of the authors (i.e., not submitted, in submission, or submitted to another conference or journal while in review). * Papers will be published in the proceedings of ACII 2011 by Springer. Papers should not exceed 10 pages and should be formatted according to the Springer LNCS formatting guidelines http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0. * Papers must be submitted as PDF through the EasyChair conference system, which can be accessed through the workshop web site and the ACII conference website. * For further information, contact abci at cs.utwente.nl Important Dates: 15th of June: Workshop papers due 1st of July: Notification of Acceptance 18th of July: Camera-ready papers due 9th of October: Workshop Programme Chairs: * Anton Nijholt, Universiteit Twente, The Netherlands * Brendan Allison, TU Graz, Austria * Stephen Dunne, Starlab Barcelona, Spain * Dirk Heylen, University of Twente, The Netherlands Local Organizer: * Christian Mühl, University of Twente, The Netherlands Programme Committee: * Egon L. van den Broek, University of Twente, The Netherlands * Touradj Ebrahimi, EPFL, Lausanne, Switzerland * Peter Desain, Radboud University Nijmegen, The Netherlands * Jan B.F. van Erp, TNO Human Factors, Soesterberg, The Netherlands * Stephen Fairclough, John Moores University, Liverpool, UK * Gary Garcia Molina, Philips Research, Eindhoven, The Netherlands * Audrey Girouard, Queen's University, Kingston, Canada * Jonghwa Kim, University of Augsburg, Germany * Brent Lance, Army Research Laboratory/TNB, Aberdeen Proving Ground, USA * Robert Leeb, University of Lausanne, Switzerland * Scott Makeig, University of California at San Diego, USA * Femke Nijboer, University of Twente, The Netherlands * Ioannis Patras, Queen Mary University, London, UK * Thierry Pun, University of Geneva, Switzerland * Tanja Schultz, Karlsruhe Institute of Technology (KIT), Germany * Olga Sourina, NanYang Technological University, Singapore * Thomas J. Sullivan, NeuroSky, San Jose, USA * Thorsten Zander, Graz University of Technology, Austria From michael.wibral at web.de Mon Jun 13 14:20:33 2011 From: michael.wibral at web.de (Michael Wibral) Date: Mon, 13 Jun 2011 14:20:33 +0200 (CEST) Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis Message-ID: <826564097.1273685.1307967633954.JavaMail.fmail@mwmweb071> Dear Elena, we do not use neuromag data. So I cannot say anything wrt to neuromag data. On theoretical grounds, the problem is that both sensor types have highly varying SNR from brain location to brain location. While SNR gets worse with depth for both sensor types, this happens more rapidly with the gradiometers. For example for a deep source that means: Gradiometers have little true signal but standard noise, since their leadfields are small, the inverse of their leadfield is big and noise contributions to your voxels are high, for magnetometers its sligtly different. So if one naively uses both types in one inversion noise will often be dominated by gradiometers and signal by magnetometers. For shallow sources its reverse , the noise will be dominated by the high noise of the magnetometers and the signal comes from the gradiometers, so again things will be matched unfortunately. i guess this creates the relatively homogenic power distribution you observe (unless there's a bug in the code or the analysis setup - see below). For some background you might want to have a look at: Commonalities and differences among vectorized beamformers in electromagnetic source imaging. Huang MX et al, Brain Topogr. Do handle this two things are necessary: 1. Compute the beamformer filters for data that have baseline and task combined. searate filter computation will almost certainly create problems. 2. To localize activity use the statistics function not some simple difference measure or relative power picture. For the reasons above, this might still not work. In this case the best workaround would be a weighted average with different, leadfield dependend weights for each voxel and modality. A simpler possibility might be simple averaging (this might work for your case, since source look very similar for the two modalities). Michael ------------------------------------------------------------ Von: "Elena Orekhova" Gesendet: 09.06.2011 22:48:34 An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Michael, I still have not resolved this problem and do not know whether  is specific for my data(or program bag) or the other Neuromag users also had it. Do you use Neuromag? Elena ------------------------------------------------------------ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Thursday, June 09, 2011 5:06 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis     Hi Elena, disregard my last email, I overlooked the att. Michael ------------------------------------------------------------ Von: "Elena Orekhova" Gesendet: Jun 2, 2011 8:03:16 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Verdana"; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear Michael,   I did normalize the data (sourcepst.avg.nai=sourcepst.avg.pow./sourcepre.avg.pow) as it was suggested in the tutorial.   I used the same scales in all plots for comparison purposes. If  automatic scaling is used the result for MAG+GRA does not look any better (see attachment).   >What you could do as a workaround is to average the separate results with a weighting per voxel and  that >is corresponding to the squared norms of the leadfields for the respective modalities for a given voxel , this >would guarantee equal amounts of backprojected noise from both modalities (if I'm not mistaken).   Thank you for your suggestion.  I may use it as a last resort.  Hopefully, there is still a way to get more optimal solution using both GRA and MAG in the same analysis...     Elena ------------------------------------------------------------ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Elena Orekhova [Elena.Orekhova at neuro.gu.se] Sent: Thursday, June 02, 2011 6:22 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis     BODY {direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;} Dear Michael,   I have tried to multiply the leadfield by -1 as you suggested:   for i = 1 : size (grid.leadfield, 2)     grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); end   This had no effect on the 'lcmv' output. I attached the pictures for ‘GRA only, ’MAG only’ and ‘GRA + MAG’   In this experiment I measured evoked field in response to  the unilateral (left) click. The source is expected to be in the right superior temporal cortex.  This is the case  for  ‘GRA only' and ’MAG only’ datasets. The combined sensors give meaningless result.   Elena   ------------------------------------------------------------ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Wednesday, June 01, 2011 4:04 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis     Dear Elena, could you give the following a try: invert (*-1) the leadfileds for one of the two sensor types. Let me know what happens. I would also be interested in taking a look at the results - maybe you could sent images off-list: Michael.Wibral web.de. Michael ------------------------------------------------------------ Von: "Elena Orekhova" Gesendet: Jun 1, 2011 12:23:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "Arial"; }@font-face { font-family: "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: Times; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear  fieldtrippers, This message is mainly for Neuromag users.   When I do  'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. If I combine the two types of sensors without weighting, the result is meaningless. Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements.  Does anybody know how to deal with this problem?     Elena     From tobias.staudigl at uni-konstanz.de Mon Jun 13 15:02:55 2011 From: tobias.staudigl at uni-konstanz.de (Tobias Staudigl) Date: Mon, 13 Jun 2011 15:02:55 +0200 Subject: [FieldTrip] granger causality In-Reply-To: <01F5D123-C4D5-42B2-9D93-CC3B4E86BD66@donders.ru.nl> References: <4DF1F52B.3000406@uni-konstanz.de> <01F5D123-C4D5-42B2-9D93-CC3B4E86BD66@donders.ru.nl> Message-ID: <4DF60A7F.9060505@uni-konstanz.de> Thanks a lot for your answer, Jan-Mathijs , what "other confounding quantity" were you thinking of concerning the shuffling across conditions? There is another question i have: Is there a way to estimate the order of the mvar-model in fieldtrip, or would one do it as implemented in the bsmart toolbox? The bsmart toolbox uses the Akaike Information Criterion to find the right order parameter. However, this criterion sometimes seems to have trouble finding a reasonable model-order. Does anybody know a toolbox that uses other criterions, e.g., Bayesian Information Criterion? And, what is a "reasonable range of the model-order"? Is there any convention or standard? E.g., I m thinking of something like: "This order is too small/big to be meaningful in this particular frequency band / for this particular connectivity measure." Any advice, ideas or literature suggestions welcome! Thank you very much, tobi Am 10.06.2011 13:00, schrieb jan-mathijs schoffelen: > Hi Tobias, > >> >> Q 1: >> If I understood correctly, the grangerspectrum >> (granger.grangerspctrm) gives me values for the granger-causality in >> a matrix [nChannel, nChannel, Freqs]. >> Does [1,2,:] give me the granger-causality of Channel1 predicting >> Channel2, or the other way round? >> > > The FieldTrip convention is indeed (1,2,:) relates to 1->2 > >> Q2: >> The plotting function gives me an error: >> >> ft_connectivityplot(cfg, granger) >> >> ??? Error using ==> seloverdim at 36 >> cannot select over multiple dimensions at the same time >> >> Error in ==> ft_selectdata at 528 >> if selectchan, data = seloverdim(data, 'chan', selchan, fb); end >> >> Error in ==> ft_connectivityplot at 79 >> data = ft_selectdata(data, 'channel', cfg.channel); > > Please update your fieldtrip version. There is a fix (dated 22-04) > that should take care of this > >> Q3: >> How do i statistically validate the measures i get fromthe >> granger-analysis? >> Is there some recommended statistical test? >> Is it correct to do bootstrapping / permutation testing? >> What I could do on my data is shuffle the trials across conditions, >> compute granger causality on the shuffeld data, and compair this >> distribution with the value i get from the data. > > This is a very relevant issue. From what you describe it seems as if > you want to compare across conditions. The shuffling across conditions > is what we do as well, although it remains open to debate how > meaningful it is to compare granger causality indices across > conditions. And, also, if you are able to reject your null-hypothesis, > whether your decision to reject it is actually due to the actual > granger causality being different, or by some other confounding quantity. > > Best wishes, > > Jan-Mathijs > > >> Maybe, somebody is experienced in using granger and could help me out! >> Any advice appreciated! >> >> Thanks a lot! >> tobi >> >> >> I used the following ft_functions according to the online tutorial: >> >> %% MVAR >> cfg = []; >> cfg.order = 2; >> cfg.toolbox = 'bsmart'; >> mdata = ft_mvaranalysis(cfg, data); >> >> %% transfer function >> cfg = []; >> cfg.method = 'mvar'; >> mfreq = ft_freqanalysis(cfg, mdata); >> >> %% granger >> cfg = []; >> cfg.method = 'granger'; >> granger = ft_connectivityanalysis(cfg, mfreq); >> >> %% >> cfg = []; >> cfg.zparam = 'grangerspctrm'; >> %cfg.channel = 'all'; >> ft_connectivityplot(cfg, granger); >> >> -- >> Tobias Staudigl >> Fachbereich Psychologie - ZPR >> Postfach ZPR >> 78457 Konstanz >> ZPR, Haus 12 >> Tel.: +49 (0)7531 / 88 - 5703 >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Tobias Staudigl Fachbereich Psychologie - ZPR Postfach ZPR 78457 Konstanz ZPR, Haus 12 Tel.: +49 (0)7531 / 88 - 5703 From Elena.Orekhova at neuro.gu.se Mon Jun 13 16:31:35 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Mon, 13 Jun 2011 14:31:35 +0000 Subject: [FieldTrip] combining magnetometers and planad gradiometers for analysis In-Reply-To: <826564097.1273685.1307967633954.JavaMail.fmail@mwmweb071> References: <826564097.1273685.1307967633954.JavaMail.fmail@mwmweb071> Message-ID: <32CC77C0C8A7AD4B9410934642608E1F1333583E@exchccr1.neuro.gu.se> Dear Michael, Thank you for your explanations. As I understand, there is no routine way of handling combined gradiometers and magnetometers in Fieldtrip. I feel that the easiest way will be to average, as you have suggested, or to take a subset of the sensors (GRA or MAG). Elena ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Monday, June 13, 2011 2:20 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Elena, we do not use neuromag data. So I cannot say anything wrt to neuromag data. On theoretical grounds, the problem is that both sensor types have highly varying SNR from brain location to brain location. While SNR gets worse with depth for both sensor types, this happens more rapidly with the gradiometers. For example for a deep source that means: Gradiometers have little true signal but standard noise, since their leadfields are small, the inverse of their leadfield is big and noise contributions to your voxels are high, for magnetometers its sligtly different. So if one naively uses both types in one inversion noise will often be dominated by gradiometers and signal by magnetometers. For shallow sources its reverse , the noise will be dominated by the high noise of the magnetometers and the signal comes from the gradiometers, so again things will be matched unfortunately. i guess this creates the relatively homogenic power distribution you observe (unless there's a bug in the code or the analysis setup - see below). For some background you might want to have a look at: Commonalities and differences among vectorized beamformers in electromagnetic source imaging. Huang MX et al, Brain Topogr. Do handle this two things are necessary: 1. Compute the beamformer filters for data that have baseline and task combined. searate filter computation will almost certainly create problems. 2. To localize activity use the statistics function not some simple difference measure or relative power picture. For the reasons above, this might still not work. In this case the best workaround would be a weighted average with different, leadfield dependend weights for each voxel and modality. A simpler possibility might be simple averaging (this might work for your case, since source look very similar for the two modalities). Michael ------------------------------------------------------------ Von: "Elena Orekhova" Gesendet: 09.06.2011 22:48:34 An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Michael, I still have not resolved this problem and do not know whether is specific for my data(or program bag) or the other Neuromag users also had it. Do you use Neuromag? Elena ------------------------------------------------------------ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Thursday, June 09, 2011 5:06 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Hi Elena, disregard my last email, I overlooked the att. Michael ------------------------------------------------------------ Von: "Elena Orekhova" Gesendet: Jun 2, 2011 8:03:16 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Verdana"; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear Michael, I did normalize the data (sourcepst.avg.nai=sourcepst.avg.pow./sourcepre.avg.pow) as it was suggested in the tutorial. I used the same scales in all plots for comparison purposes. If automatic scaling is used the result for MAG+GRA does not look any better (see attachment). >What you could do as a workaround is to average the separate results with a weighting per voxel and that >is corresponding to the squared norms of the leadfields for the respective modalities for a given voxel , this >would guarantee equal amounts of backprojected noise from both modalities (if I'm not mistaken). Thank you for your suggestion. I may use it as a last resort. Hopefully, there is still a way to get more optimal solution using both GRA and MAG in the same analysis... Elena ------------------------------------------------------------ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Elena Orekhova [Elena.Orekhova at neuro.gu.se] Sent: Thursday, June 02, 2011 6:22 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis BODY {direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;} Dear Michael, I have tried to multiply the leadfield by -1 as you suggested: for i = 1 : size (grid.leadfield, 2) grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}(3:3:306, :); end This had no effect on the 'lcmv' output. I attached the pictures for ‘GRA only, ’MAG only’ and ‘GRA + MAG’ In this experiment I measured evoked field in response to the unilateral (left) click. The source is expected to be in the right superior temporal cortex. This is the case for ‘GRA only' and ’MAG only’ datasets. The combined sensors give meaningless result. Elena ------------------------------------------------------------ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Wednesday, June 01, 2011 4:04 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis Dear Elena, could you give the following a try: invert (*-1) the leadfileds for one of the two sensor types. Let me know what happens. I would also be interested in taking a look at the results - maybe you could sent images off-list: Michael.Wibral web.de. Michael ------------------------------------------------------------ Von: "Elena Orekhova" Gesendet: Jun 1, 2011 12:23:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] combining magnetometers and planad gradiometers for analysis @font-face { font-family: "Arial"; }@font-face { font-family: "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: Times; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear fieldtrippers, This message is mainly for Neuromag users. When I do 'lcmv' beamforming analysis separately on planar gradiometers or magnetometers, I get quite meaningful results. If I combine the two types of sensors without weighting, the result is meaningless. Apparently, the algorithm does not take care of different scales and units of the GRA and MAG measurements. Does anybody know how to deal with this problem? Elena _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From TAVABIK at email.chop.edu Mon Jun 13 20:50:39 2011 From: TAVABIK at email.chop.edu (Tavabi, Kambiz) Date: Mon, 13 Jun 2011 14:50:39 -0400 Subject: [FieldTrip] working with neuromag data In-Reply-To: <621524636.372728.1307777218636.JavaMail.root@sculptor.zimbra.ru.nl> References: <621524636.372728.1307777218636.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Dear Arjen, The data.avt I am using to plot with ft_multiplotER is infact real numbers, quite small numbers on the order of x.xxxe-15, but I still get no visualization using cfg.ylim(min(data.avg), max(data.avg) or extremely small numbers eg., cfg.ylim [-3e-50 3e-50]. Conversely, ft_topoplotER seems to work just fine with the exception of a couple of warnings: 1- some points fall outside the outline, please consider using another layout >ft_plot_topo line 112 and ft_topoplotER line 719 2- Duplicate x-y data points detected: using average of the z values >ft_plot_topo line 144 and ft_topoplotER line 719. What does this warning mean? Regards, Kambiz -----Original Message----- From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. Sent: Saturday, June 11, 2011 3:27 AM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] working with neuromag data Dear Kambiz, Does your data.avg contain NaNs or real numbers? In the latter case; do they fall in the plotting range as specified by your cfg.ylim? Yours, Arjen ----- "Kambiz Tavabi" schreef: > Van: "Kambiz Tavabi" > Aan: "Email discussion list for the FieldTrip project" > Verzonden: Vrijdag 10 juni 2011 18:59:03 > Onderwerp: Re: [FieldTrip] working with neuromag data > > As per advise from Arjen, I was able to use following steps > 1) ft_preprocessing on your stimulus averaged epoch data. This should > give you a data structure with 6 trials (which are actually the > averages per condition). > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat > this so you end up with 6 timelocked structures representing the 6 > different conditions. > to create individual condition averaged ft data structures which I can > visualize using ft_topoplotER(cfg,data) > data: > avg: [338x651 double] > var: [338x651 double] > fsample: 1000 > time: [1x651 double] > dof: [338x651 double] > label: {338x1 cell} > dimord: 'chan_time' > grad: [1x1 struct] > cfg: [1x1 struct] > however when i use; > cfg = []; > cfg.showlabels = 'yes'; > cfg.fontsize = 6; > cfg.ylim = [-10e-13 10e-13] > ft_multiplotER(cfg, data); > Fieldtrip chruns through creating the > selection avg along dimension 1 > selection dof along dimension 1 > selection var along dimension 1 > creating layout from data.grad > creating layout for neuromag306 system > > but the resutling figure is an empty figure containing only layout > with ch lables without any data what so ever. Any ideas why this might > be? > > > > -Kambiz. > ------------------------------------------------------------- > Kambiz Tavabi PhD > Biomedical Imaging Laboratory > The Children's Hospital of Philadelphia > 34th Street and Civic Center Boulevard > Philadelphia, Pa. 19104 > Tel: 267.426.0302 > email: tavabik at email.chop.edu > ------------------------------------------------------------- > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > [a.stolk at fcdonders.ru.nl] > Sent: Tuesday, March 29, 2011 4:20 AM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] working with neuromag data > > Dear Kambiz, > > I think I see your point. Your data presumably is already preprocessed > and timelocked (averaged over trials) with neuromag software. I then > take it that you have 6 different conditions which you would like to > plot separately and possibly test at the group level. > > Since the data is already averaged, I'd recommend to do the following > to get your data back on track. > > 1) ft_preprocessing on your stimulus averaged epoch data. This should > give you a data structure with 6 trials (which are actually the > averages per condition). > > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat > this so you end up with 6 timelocked structures representing the 6 > different conditions. > > 3) plot or grandaverage (see tutorials how to proceed as your data now > should be 'ft-friendly'). > > Goodluck, > Arjen > > > > > > > ----- "Kambiz Tavabi" schreef: > > > Van: "Kambiz Tavabi" > > Aan: "Email discussion list for the FieldTrip project" > > > Verzonden: Dinsdag 29 maart 2011 01:10:14 > > Onderwerp: Re: [FieldTrip] working with neuromag data > > > > Dear Arjen - Thanks for your response. Just to clarify the low > level > > functions ft_read_header & ft_read_data are mentioned in the ft > > getting started tutorial. I believe they're recommended to make > sure > > the data is ft friendly. In my case the data is ft friendly. My > data > > is also pre-processed and already 'time-locked'--meaning that I > have > > stimulus averaged epoch data in fif format for all my subjects. My > > question is how to proceed from there? I've been through the pages > you > > refer to but have not been able to piece together my data in such a > > way to proceed with grand-averaging and carrying out stats. > > -Kambiz. > > ------------------------------------------------------------- > > Kambiz Tavabi PhD > > Biomedical Imaging Laboratory > > The Children's Hospital of Philadelphia > > 34th Street and Civic Center Boulevard > > Philadelphia, Pa. 19104 > > Tel: 267.426.0302 > > email: tavabik at email.chop.edu > > ------------------------------------------------------------- > > ________________________________________ > > From: fieldtrip-bounces at donders.ru.nl > > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > > [a.stolk at fcdonders.ru.nl] > > Sent: Monday, March 28, 2011 4:05 PM > > To: Email discussion list for the FieldTrip project > > Subject: Re: [FieldTrip] working with neuromag data > > > > Dear Kambiz, > > > > While you are able to use the 'low level' ft_read_header and > > ft_read_data functions, you should be able to preprocess and > analyze > > your neuromag data using the 'high level' functions such as > > ft_preprocessing (which calls the low level functions mentioned > > above). > > > > How to proceed depends on what you want to do with your data. If > you > > have triggers stored in your dataset that are synchronuous with the > > recorded brain activity, it'd be recommended to start with the > > following tutorial on how to select your trials: > > > > http://fieldtrip.fcdonders.nl/tutorial/preprocessing > > > > Since your experience with FT is still limited as you say, I > believe > > the following text may provide a good overview of what the data, > once > > read in to FT (i.e. matlab) environment, may look like: > > > > http://fieldtrip.fcdonders.nl/walkthrough > > > > Typically, your next steps involve single-subject timelocked > analysis, > > then grand-average and perform statistics at the group level. For > an > > overview of the steps and protocols, see: > > > > http://fieldtrip.fcdonders.nl/tutorial/analysis_protocols > > > > Hope this has helped for a start, > > > > Arjen > > > > > > ----- "Kambiz Tavabi" schreef: > > > > > Van: "Kambiz Tavabi" > > > Aan: "Email discussion list for the FieldTrip project" > > > > > Verzonden: Maandag 28 maart 2011 20:59:36 > > > Onderwerp: [FieldTrip] working with neuromag data > > > > > > Greetings - I have preprocessed/averaged neuromag data for a > group > > of > > > subjects that I'd like to visualize, compute grandaverage and > carry > > > out sensor level statistics on. The only help I managed to find > on > > the > > > Fieldtrip site/list Re: neurmag data concerns getting started > e.g., > > > with ft_read_header and ft_read_data. In my case these programs > > work > > > fine meaning that I can proceed with further analysis. > > > On a side, in my limited experience with FT, a major problem I > run > > > into frequently is that there is no clear suggestion(s) on how to > > > proceed with data that is not raw. I understand it is impossible > to > > > cover all analysis scenarios, but it is often the case that > working > > > with CTF, or in particular Elekta system, the data is likely to > be > > in > > > a post-preprocessed phase. Everytime I've tried to work with ft, > It > > > seems to me that if I don't start with square one in fieldtrip, > it > > is > > > difficult to figure out how to use downstream programs to work on > > the > > > data. > > > That said, in my case I have the output from ft_read_header: > > > > > > label: {338x1 cell} > > > nChans: 338 > > > Fs: 1000 > > > grad: [1x1 struct] > > > unit: {1x338 cell} > > > nSamples: 651 > > > nSamplesPre: 100 > > > nTrials: 6 > > > orig: [1x1 struct] > > > > > > and output from ft_read_data > > > > > > [338x651x6] that being channels by samples by number of stimulus > > > averaged epochs. To proceed, ideally I'd like to compute a > > > grandaverage for each condition, visualize them in a multiplot, > and > > > carry out sensor level stats. To be able to do this I understand > I > > > need the output from ft_timelockanalysis, how do I arrange my > data > > as > > > such? I am assuming it is already in that state. Thanks for your > > > time. > > > > > > -Kambiz. > > > ------------------------------------------------------------- > > > Kambiz Tavabi PhD > > > Biomedical Imaging Laboratory > > > The Children's Hospital of Philadelphia > > > 34th Street and Civic Center Boulevard > > > Philadelphia, Pa. 19104 > > > Tel: 267.426.0302 > > > email: tavabik at email.chop.edu > > > ------------------------------------------------------------- > > > _______________________________________________ > > > 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 > > _______________________________________________ > 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 marcel.heers at googlemail.com Mon Jun 13 23:48:04 2011 From: marcel.heers at googlemail.com (Marcel Heers) Date: Mon, 13 Jun 2011 23:48:04 +0200 Subject: [FieldTrip] courses In-Reply-To: <5B0A148A-D4F0-454F-B60B-E47ECCA47E75@donders.ru.nl> References: <32CC77C0C8A7AD4B9410934642608E1F03ECAF47@exchccr1.neuro.gu.se> <5B0A148A-D4F0-454F-B60B-E47ECCA47E75@donders.ru.nl> Message-ID: Dear Robert, might there be a chance for external person to participate in the fieldtrip course in Paris at the end of the year? Best regards, Marcel 2011/6/9 Robert Oostenveld : > Dear Elena > > For 2011 there are no courses planned any more in Nijmege, which are open to > external participants (there will be a course for local studens in the > Donders Graduate School in the autumn). The next course in Nijmegen will be > the MEG Toolkit course, which most likely will be somewhere in the spring of > 2012. > > For 2011 we are currently considering a course in Paris at the end of this > year. I believe that Stefan and Saskia are considering to do another course > in New York later this year, although I don't know any details for the New > York plans. > > At the upcoming HBM meeting in Quebec there will be an educational course in > which FieldTrip and the other open source academic toolboxes will play a > (relatively small) role. Although I don't think it is efficient to travel to > Quebec just for this part, it might be interesting for you to attend if you > are attending the HBM conference anyway. See > http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3437 > and for the program one of the last pages of > http://www.humanbrainmapping.org/files/2011MeetingFiles/Descriptions/HBM%202011%20Educational%20Program.pdf > > Please note that we are open to invitations for presenting the FieldTrip > course at external sites. This year we have already been in Tuebingen, St > Louis, and New York, and if there is an interesting venue, an enthousiastic > local organizer and funding can be arranged to cover the expenses, most > likely some experienced users/developers from Nijmegen can be found or > appointed to present a 2,5 day course at the external site. > > best regards, > Robert > > > > On 7 Jun 2011, at 12:53, Elena Orekhova wrote: > >> Dear FieldTrip gurus, >> >> Are you planning  any FieldTrip courses for the users in the nearest >> future? >> >> Elena >> >> _______________________________________________ >> 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 > -- Dr. Marcel Heers, M.D. Fischenbergstr. 10 D-58455 Witten phone: +49-2302-2034057 From jan.schoffelen at donders.ru.nl Wed Jun 15 15:51:01 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 15 Jun 2011 15:51:01 +0200 Subject: [FieldTrip] functionality change of ft_prepare_sourcemodel Message-ID: <0A5873EA-0666-4EDD-9AAB-13CA8EDA12FC@donders.ru.nl> Dear all, We implemented a slight change in the default behaviour of ft_prepare_sourcemodel. This is a fieldtrip function (often not called directly by you), which creates a specified source model for inverse reconstruction. Typically, this is a 3D regular grid, or a 2D mesh of the cortical sheet. The function is typically called with additional input arguments, specifying geometric objects, such as a volume conductor model of the head, or a description of the sensor-array. To make a long story short, before you had the option to specify cfg.sourceunits and cfg.mriunits. Cfg.sourceunits refers to the metrical unit of the dipole positions, and this defaulted (if you didn't explicitly specify it) to 'cm'. As of yet, it will default to the metrical units in the input data, i.e. the units of the sensor-array (if provided), or the units of the volume conductor of the head. For example, for neuromag and 4d- neuroimaging users the default will now be a grid with 'm' as a unit. Cfg.mriunits is as of now deprecated, and was used to specify the units of the (optional) input anatomical or segmented mri. Nowadays, these structures explicitly contain a unit, so that can be easily recovered from the data. We will build in explicit checks on the units in which different geometric objects are defined (many of those are already in place, e.g. ensuring same units for volume conductor model of the head and sensor positions) in the near future. For now, if you want to have explicitly the same behavior as before, you need to specify cfg.sourceunits to be 'cm'. Best wishes, Jan-Mathijs Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From cmuehl at gmail.com Thu Jun 16 18:22:02 2011 From: cmuehl at gmail.com (Christian Muehl) Date: Thu, 16 Jun 2011 18:22:02 +0200 Subject: [FieldTrip] Extended Deadline: Affective BCI Workshop, Memphis, USA Message-ID: ** Final Call for Papers - Extended Deadline ** 2nd Workshop on Affective Brain-Computer Interfaces (aBCI) Workshop at ACII 2011 (October 9-12), Memphis, USA, October 9, 2011 Apologies for multiple postings http://hmi.ewi.utwente.nl/abci2011 http://www.acii2011.org The second workshop on affective brain-computer interfaces will explore the advantages and limitations of using neuro-physiological signals as a modality for the automatic recognition of affective and cognitive states, and the possibilities of using this information about the user state in innovative and adaptive applications. The goal is to bring researchers from the communities of brain computer interfacing, affective computing, neuro-ergonomics, affective and cognitive neuroscience together to present state-of-the-art progress and visions on the various overlaps between those disciplines. Recent research in brain-computer interfaces (BCI) shows that brain activity can be used as an active/voluntary, or passive/involuntary control modality in man-machine interaction. While active BCI paradigms have received a lot of attention in recent years, research on passive approaches to BCI still desperately needs concerted activity. However, it has been shown more than once that brain activations can carry information about the affective and cognitive state of a subject, and that the interaction between humans and machines can be aided by the recognition of those user states. To achieve robust passive BCIs, efforts from applied and basic sciences have to be combined. On the one hand, applied fields such as affective computing aim at the development of applications that adapt to changes in the user states and thereby enrich the interaction, leading to a more natural and effective usability. On the other hand, basic research in neuroscience advances our understanding of the neural processes associated with emotions. Furthermore, similar advancements are being made for more cognitive mental states, for example, attention, fatigue, and work load, which strongly interact with affective states. Topics of interest include, but are not limited to: * emotion elicitation and data collection for affective BCI * detection of affective and cognitive states with BCI and other modalities * adaptive interfaces and affective BCI Invited Talk: 'Brain Dynamics of Affective Engagement' by Scott Makeig, SCCN, University of California at San Diego, USA The workshop will be held in conjunction with the 4th International conference on Affective Computing and Intelligent Interaction (ACII2011) at the FedEx Institute of Technology at the University of Memphis, TN. Submission Instructions * The papers should feature original empirical work, theoretical work, or a well defendable but arguable position of the authors (i.e., not submitted, in submission, or submitted to another conference or journal while in review). * Papers will be published in the proceedings of ACII 2011 by Springer. Papers should not exceed 10 pages and should be formatted according to the Springer LNCS formatting guidelines http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0. * Papers must be submitted as PDF through the EasyChair conference system, which can be accessed through the workshop web site and the ACII conference website. * For further information, contact abci at cs.utwente.nl Important Dates: 22nd of June: Workshop papers due 7th of July: Notification of Acceptance 24th of July: Camera-ready papers due 9th of October: Workshop Programme Chairs: * Anton Nijholt, Universiteit Twente, The Netherlands * Brendan Allison, TU Graz, Austria * Stephen Dunne, Starlab Barcelona, Spain * Dirk Heylen, University of Twente, The Netherlands Local Organizer: * Christian Mühl, University of Twente, The Netherlands Programme Committee: * Egon L. van den Broek, University of Twente, The Netherlands * Touradj Ebrahimi, EPFL, Lausanne, Switzerland * Peter Desain, Radboud University Nijmegen, The Netherlands * Jan B.F. van Erp, TNO Human Factors, Soesterberg, The Netherlands * Stephen Fairclough, John Moores University, Liverpool, UK * Gary Garcia Molina, Philips Research, Eindhoven, The Netherlands * Audrey Girouard, Queen's University, Kingston, Canada * Jonghwa Kim, University of Augsburg, Germany * Brent Lance, Army Research Laboratory/TNB, Aberdeen Proving Ground, USA * Robert Leeb, University of Lausanne, Switzerland * Scott Makeig, University of California at San Diego, USA * Femke Nijboer, University of Twente, The Netherlands * Ioannis Patras, Queen Mary University, London, UK * Thierry Pun, University of Geneva, Switzerland * Tanja Schultz, Karlsruhe Institute of Technology (KIT), Germany * Olga Sourina, NanYang Technological University, Singapore * Thomas J. Sullivan, NeuroSky, San Jose, USA * Thorsten Zander, Graz University of Technology, Austria From TAVABIK at email.chop.edu Thu Jun 16 18:31:54 2011 From: TAVABIK at email.chop.edu (Tavabi, Kambiz) Date: Thu, 16 Jun 2011 12:31:54 -0400 Subject: [FieldTrip] working with neuromag data In-Reply-To: <621524636.372728.1307777218636.JavaMail.root@sculptor.zimbra.ru.nl> References: , <621524636.372728.1307777218636.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Dear Arjen, The data.avg I am using to plot with ft_multiplotER is infact real numbers, quite small numbers on the order of x.xxxe-15, but I still get no visualization using cfg.ylim(min(data.avg), max(data.avg) or extremely small numbers eg., cfg.ylim [-3e-50 3e-50]. Conversely, ft_topoplotER seems to work just fine with the exception of a couple of warnings: 1- some points fall outside the outline, please consider using another layout >ft_plot_topo line 112 and ft_topoplotER line 719 2- Duplicate x-y data points detected: using average of the z values >ft_plot_topo line 144 and ft_topoplotER line 719. What does this warning mean? >From what I understand the ft_multiplotER step is necessary to carry out sensor level analysis of the data? As I mentioned previously, the grand average data structure does not contain the proper layout information that is in the timelock structure. Is this purposefully done, or am I doing something wrong here? Regards, -Kambiz. ------------------------------------------------------------- Kambiz Tavabi PhD Biomedical Imaging Laboratory The Children's Hospital of Philadelphia 34th Street and Civic Center Boulevard Philadelphia, Pa. 19104 Tel: 267.426.0302 email: tavabik at email.chop.edu ------------------------------------------------------------- ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. [a.stolk at fcdonders.ru.nl] Sent: Saturday, June 11, 2011 3:26 AM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] working with neuromag data Dear Kambiz, Does your data.avg contain NaNs or real numbers? In the latter case; do they fall in the plotting range as specified by your cfg.ylim? Yours, Arjen ----- "Kambiz Tavabi" schreef: > Van: "Kambiz Tavabi" > Aan: "Email discussion list for the FieldTrip project" > Verzonden: Vrijdag 10 juni 2011 18:59:03 > Onderwerp: Re: [FieldTrip] working with neuromag data > > As per advise from Arjen, I was able to use following steps > 1) ft_preprocessing on your stimulus averaged epoch data. This should > give you a data structure with 6 trials (which are actually the > averages per condition). > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat > this so you end up with 6 timelocked structures representing the 6 > different conditions. > to create individual condition averaged ft data structures which I can > visualize using ft_topoplotER(cfg,data) > data: > avg: [338x651 double] > var: [338x651 double] > fsample: 1000 > time: [1x651 double] > dof: [338x651 double] > label: {338x1 cell} > dimord: 'chan_time' > grad: [1x1 struct] > cfg: [1x1 struct] > however when i use; > cfg = []; > cfg.showlabels = 'yes'; > cfg.fontsize = 6; > cfg.ylim = [-10e-13 10e-13] > ft_multiplotER(cfg, data); > Fieldtrip chruns through creating the > selection avg along dimension 1 > selection dof along dimension 1 > selection var along dimension 1 > creating layout from data.grad > creating layout for neuromag306 system > > but the resutling figure is an empty figure containing only layout > with ch lables without any data what so ever. Any ideas why this might > be? > > > > -Kambiz. > ------------------------------------------------------------- > Kambiz Tavabi PhD > Biomedical Imaging Laboratory > The Children's Hospital of Philadelphia > 34th Street and Civic Center Boulevard > Philadelphia, Pa. 19104 > Tel: 267.426.0302 > email: tavabik at email.chop.edu > ------------------------------------------------------------- > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > [a.stolk at fcdonders.ru.nl] > Sent: Tuesday, March 29, 2011 4:20 AM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] working with neuromag data > > Dear Kambiz, > > I think I see your point. Your data presumably is already preprocessed > and timelocked (averaged over trials) with neuromag software. I then > take it that you have 6 different conditions which you would like to > plot separately and possibly test at the group level. > > Since the data is already averaged, I'd recommend to do the following > to get your data back on track. > > 1) ft_preprocessing on your stimulus averaged epoch data. This should > give you a data structure with 6 trials (which are actually the > averages per condition). > > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And repeat > this so you end up with 6 timelocked structures representing the 6 > different conditions. > > 3) plot or grandaverage (see tutorials how to proceed as your data now > should be 'ft-friendly'). > > Goodluck, > Arjen > > > > > > > ----- "Kambiz Tavabi" schreef: > > > Van: "Kambiz Tavabi" > > Aan: "Email discussion list for the FieldTrip project" > > > Verzonden: Dinsdag 29 maart 2011 01:10:14 > > Onderwerp: Re: [FieldTrip] working with neuromag data > > > > Dear Arjen - Thanks for your response. Just to clarify the low > level > > functions ft_read_header & ft_read_data are mentioned in the ft > > getting started tutorial. I believe they're recommended to make > sure > > the data is ft friendly. In my case the data is ft friendly. My > data > > is also pre-processed and already 'time-locked'--meaning that I > have > > stimulus averaged epoch data in fif format for all my subjects. My > > question is how to proceed from there? I've been through the pages > you > > refer to but have not been able to piece together my data in such a > > way to proceed with grand-averaging and carrying out stats. > > -Kambiz. > > ------------------------------------------------------------- > > Kambiz Tavabi PhD > > Biomedical Imaging Laboratory > > The Children's Hospital of Philadelphia > > 34th Street and Civic Center Boulevard > > Philadelphia, Pa. 19104 > > Tel: 267.426.0302 > > email: tavabik at email.chop.edu > > ------------------------------------------------------------- > > ________________________________________ > > From: fieldtrip-bounces at donders.ru.nl > > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > > [a.stolk at fcdonders.ru.nl] > > Sent: Monday, March 28, 2011 4:05 PM > > To: Email discussion list for the FieldTrip project > > Subject: Re: [FieldTrip] working with neuromag data > > > > Dear Kambiz, > > > > While you are able to use the 'low level' ft_read_header and > > ft_read_data functions, you should be able to preprocess and > analyze > > your neuromag data using the 'high level' functions such as > > ft_preprocessing (which calls the low level functions mentioned > > above). > > > > How to proceed depends on what you want to do with your data. If > you > > have triggers stored in your dataset that are synchronuous with the > > recorded brain activity, it'd be recommended to start with the > > following tutorial on how to select your trials: > > > > http://fieldtrip.fcdonders.nl/tutorial/preprocessing > > > > Since your experience with FT is still limited as you say, I > believe > > the following text may provide a good overview of what the data, > once > > read in to FT (i.e. matlab) environment, may look like: > > > > http://fieldtrip.fcdonders.nl/walkthrough > > > > Typically, your next steps involve single-subject timelocked > analysis, > > then grand-average and perform statistics at the group level. For > an > > overview of the steps and protocols, see: > > > > http://fieldtrip.fcdonders.nl/tutorial/analysis_protocols > > > > Hope this has helped for a start, > > > > Arjen > > > > > > ----- "Kambiz Tavabi" schreef: > > > > > Van: "Kambiz Tavabi" > > > Aan: "Email discussion list for the FieldTrip project" > > > > > Verzonden: Maandag 28 maart 2011 20:59:36 > > > Onderwerp: [FieldTrip] working with neuromag data > > > > > > Greetings - I have preprocessed/averaged neuromag data for a > group > > of > > > subjects that I'd like to visualize, compute grandaverage and > carry > > > out sensor level statistics on. The only help I managed to find > on > > the > > > Fieldtrip site/list Re: neurmag data concerns getting started > e.g., > > > with ft_read_header and ft_read_data. In my case these programs > > work > > > fine meaning that I can proceed with further analysis. > > > On a side, in my limited experience with FT, a major problem I > run > > > into frequently is that there is no clear suggestion(s) on how to > > > proceed with data that is not raw. I understand it is impossible > to > > > cover all analysis scenarios, but it is often the case that > working > > > with CTF, or in particular Elekta system, the data is likely to > be > > in > > > a post-preprocessed phase. Everytime I've tried to work with ft, > It > > > seems to me that if I don't start with square one in fieldtrip, > it > > is > > > difficult to figure out how to use downstream programs to work on > > the > > > data. > > > That said, in my case I have the output from ft_read_header: > > > > > > label: {338x1 cell} > > > nChans: 338 > > > Fs: 1000 > > > grad: [1x1 struct] > > > unit: {1x338 cell} > > > nSamples: 651 > > > nSamplesPre: 100 > > > nTrials: 6 > > > orig: [1x1 struct] > > > > > > and output from ft_read_data > > > > > > [338x651x6] that being channels by samples by number of stimulus > > > averaged epochs. To proceed, ideally I'd like to compute a > > > grandaverage for each condition, visualize them in a multiplot, > and > > > carry out sensor level stats. To be able to do this I understand > I > > > need the output from ft_timelockanalysis, how do I arrange my > data > > as > > > such? I am assuming it is already in that state. Thanks for your > > > time. > > > > > > -Kambiz. > > > ------------------------------------------------------------- > > > Kambiz Tavabi PhD > > > Biomedical Imaging Laboratory > > > The Children's Hospital of Philadelphia > > > 34th Street and Civic Center Boulevard > > > Philadelphia, Pa. 19104 > > > Tel: 267.426.0302 > > > email: tavabik at email.chop.edu > > > ------------------------------------------------------------- > > > _______________________________________________ > > > 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 > > _______________________________________________ > 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 fieldtrip at greenant.net Thu Jun 16 18:42:58 2011 From: fieldtrip at greenant.net (frank@greenant.net) Date: Fri, 17 Jun 2011 02:42:58 +1000 Subject: [FieldTrip] Using ICA to filter data In-Reply-To: References: Message-ID: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> I am trying to use fieldtrip to filter EOG data obtained in an MRI. I want to be able to spot the saccades in the samples and ideally measure their onset at the end of each trial. As you may guess, it's quite noisy and it's broad spectrum noise, despite pre-filtering. Ideally, I would like to isolate the component that corresponds to the MRI interference and then filter this out. I have managed to import the data and can run ft_componentanalysis but it fails with: runica() - data size (1,30720) too small My data is single channel, 40 epochs, each of 6 seconds (time locked to stim onset but not saccade onset) Is there a different method I should be using? I have posted some sample data and the current script (which reads in the data and runs preprocessing) to the following urls: http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat http://greenant.net/temp/EOG_analysis.m From batrod at gmail.com Thu Jun 16 18:48:07 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Thu, 16 Jun 2011 11:48:07 -0500 Subject: [FieldTrip] Using ICA to filter data In-Reply-To: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> Message-ID: To summarize, the ICA will decompose your signal into as many components as Electrodes. Therefore, trying to decompose only one source is useless. Did you use a full net of electrodes into your MRI machine or only EOG electrodes? Hope this helps, Rodolphe N. On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net wrote: > I am trying to use fieldtrip to filter EOG data obtained in an MRI. > I want to be able to spot the saccades in the samples and ideally measure > their onset at the > end of each trial. > > As you may guess, it's quite noisy and it's broad spectrum noise, despite > pre-filtering. > > Ideally, I would like to isolate the component that corresponds to the MRI > interference > and then filter this out. > > I have managed to import the data and can run ft_componentanalysis > but it fails with: > > runica() - data size (1,30720) too small > > My data is single channel, 40 epochs, each of 6 seconds (time locked to > stim onset but not saccade onset) > Is there a different method I should be using? > > I have posted some sample data and the current script (which reads in the > data and runs preprocessing) to the following urls: > > http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat > http://greenant.net/temp/EOG_analysis.m > _______________________________________________ > 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 fieldtrip at greenant.net Thu Jun 16 20:16:45 2011 From: fieldtrip at greenant.net (frank@greenant.net) Date: Fri, 17 Jun 2011 04:16:45 +1000 Subject: [FieldTrip] Using ICA to filter data In-Reply-To: References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> Message-ID: It's a bit of a unique experiment, we're trying to use an ECG machine to acquire EOG, so it's only a single output channel. i guess what I need is a temporal ICA rather than a spatial one... On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: > To summarize, the ICA will decompose your signal into as many components as Electrodes. > Therefore, trying to decompose only one source is useless. > Did you use a full net of electrodes into your MRI machine or only EOG electrodes? > > Hope this helps, > > Rodolphe N. > > On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net wrote: > I am trying to use fieldtrip to filter EOG data obtained in an MRI. > I want to be able to spot the saccades in the samples and ideally measure their onset at the > end of each trial. > > As you may guess, it's quite noisy and it's broad spectrum noise, despite pre-filtering. > > Ideally, I would like to isolate the component that corresponds to the MRI interference > and then filter this out. > > I have managed to import the data and can run ft_componentanalysis > but it fails with: > > runica() - data size (1,30720) too small > > My data is single channel, 40 epochs, each of 6 seconds (time locked to stim onset but not saccade onset) > Is there a different method I should be using? > > I have posted some sample data and the current script (which reads in the > data and runs preprocessing) to the following urls: > > http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat > http://greenant.net/temp/EOG_analysis.m > _______________________________________________ > 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 a.stolk at fcdonders.ru.nl Thu Jun 16 20:33:38 2011 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Thu, 16 Jun 2011 20:33:38 +0200 (CEST) Subject: [FieldTrip] working with neuromag data In-Reply-To: <1394883530.423835.1308249012378.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <1699057884.423853.1308249218140.JavaMail.root@sculptor.zimbra.ru.nl> Dear Kambiz, To answer your first question, I do not know what this error when calling ft_topoplotER means. Secondly, ft_multiplotTFR is a visualization step of the data and not an analysis step. It is not necessary to call this function before proceeding, but giving that it works far from what you'd expect, it tells us something's wrong. :) At your third question; what do you mean with layout information? Information on the gradiometer and magnetometer definitions? Keep in mind that when creating a grand-average, you cannot effectively average these. Ok, for a plan de campagne; are you using the most recent version of FT? If so, could you send me your data in a .mat file? Please send it to my e-mail address and not the FT list. Yours, Arjen Are you using the most recent version of FT? ----- "Kambiz Tavabi" schreef: > Van: "Kambiz Tavabi" > Aan: "Email discussion list for the FieldTrip project" > Verzonden: Donderdag 16 juni 2011 18:31:54 > Onderwerp: Re: [FieldTrip] working with neuromag data > > Dear Arjen, > The data.avg I am using to plot with ft_multiplotER is infact real > numbers, quite small numbers on the order of x.xxxe-15, but I still > get no visualization using cfg.ylim(min(data.avg), max(data.avg) or > extremely small numbers eg., cfg.ylim [-3e-50 3e-50]. Conversely, > ft_topoplotER seems to work just fine with the exception of a couple > of warnings: > 1- some points fall outside the outline, please consider using another > layout >ft_plot_topo line 112 and ft_topoplotER line 719 > 2- Duplicate x-y data points detected: using average of the z values > >ft_plot_topo line 144 and ft_topoplotER line 719. What does this > warning mean? > > >From what I understand the ft_multiplotER step is necessary to carry > out sensor level analysis of the data? > > As I mentioned previously, the grand average data structure does not > contain the proper layout information that is in the timelock > structure. Is this purposefully done, or am I doing something wrong > here? > > Regards, > > -Kambiz. > ------------------------------------------------------------- > Kambiz Tavabi PhD > Biomedical Imaging Laboratory > The Children's Hospital of Philadelphia > 34th Street and Civic Center Boulevard > Philadelphia, Pa. 19104 > Tel: 267.426.0302 > email: tavabik at email.chop.edu > ------------------------------------------------------------- > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > [a.stolk at fcdonders.ru.nl] > Sent: Saturday, June 11, 2011 3:26 AM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] working with neuromag data > > Dear Kambiz, > > Does your data.avg contain NaNs or real numbers? In the latter case; > do they fall in the plotting range as specified by your cfg.ylim? > > Yours, > Arjen > > ----- "Kambiz Tavabi" schreef: > > > Van: "Kambiz Tavabi" > > Aan: "Email discussion list for the FieldTrip project" > > > Verzonden: Vrijdag 10 juni 2011 18:59:03 > > Onderwerp: Re: [FieldTrip] working with neuromag data > > > > As per advise from Arjen, I was able to use following steps > > 1) ft_preprocessing on your stimulus averaged epoch data. This > should > > give you a data structure with 6 trials (which are actually the > > averages per condition). > > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And > repeat > > this so you end up with 6 timelocked structures representing the 6 > > different conditions. > > to create individual condition averaged ft data structures which I > can > > visualize using ft_topoplotER(cfg,data) > > data: > > avg: [338x651 double] > > var: [338x651 double] > > fsample: 1000 > > time: [1x651 double] > > dof: [338x651 double] > > label: {338x1 cell} > > dimord: 'chan_time' > > grad: [1x1 struct] > > cfg: [1x1 struct] > > however when i use; > > cfg = []; > > cfg.showlabels = 'yes'; > > cfg.fontsize = 6; > > cfg.ylim = [-10e-13 10e-13] > > ft_multiplotER(cfg, data); > > Fieldtrip chruns through creating the > > selection avg along dimension 1 > > selection dof along dimension 1 > > selection var along dimension 1 > > creating layout from data.grad > > creating layout for neuromag306 system > > > > but the resutling figure is an empty figure containing only layout > > with ch lables without any data what so ever. Any ideas why this > might > > be? > > > > > > > > -Kambiz. > > ------------------------------------------------------------- > > Kambiz Tavabi PhD > > Biomedical Imaging Laboratory > > The Children's Hospital of Philadelphia > > 34th Street and Civic Center Boulevard > > Philadelphia, Pa. 19104 > > Tel: 267.426.0302 > > email: tavabik at email.chop.edu > > ------------------------------------------------------------- > > ________________________________________ > > From: fieldtrip-bounces at donders.ru.nl > > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > > [a.stolk at fcdonders.ru.nl] > > Sent: Tuesday, March 29, 2011 4:20 AM > > To: Email discussion list for the FieldTrip project > > Subject: Re: [FieldTrip] working with neuromag data > > > > Dear Kambiz, > > > > I think I see your point. Your data presumably is already > preprocessed > > and timelocked (averaged over trials) with neuromag software. I > then > > take it that you have 6 different conditions which you would like > to > > plot separately and possibly test at the group level. > > > > Since the data is already averaged, I'd recommend to do the > following > > to get your data back on track. > > > > 1) ft_preprocessing on your stimulus averaged epoch data. This > should > > give you a data structure with 6 trials (which are actually the > > averages per condition). > > > > 2) ft_timelockanalysis with cfg.trials = 1 (2,3..until 6). And > repeat > > this so you end up with 6 timelocked structures representing the 6 > > different conditions. > > > > 3) plot or grandaverage (see tutorials how to proceed as your data > now > > should be 'ft-friendly'). > > > > Goodluck, > > Arjen > > > > > > > > > > > > > > ----- "Kambiz Tavabi" schreef: > > > > > Van: "Kambiz Tavabi" > > > Aan: "Email discussion list for the FieldTrip project" > > > > > Verzonden: Dinsdag 29 maart 2011 01:10:14 > > > Onderwerp: Re: [FieldTrip] working with neuromag data > > > > > > Dear Arjen - Thanks for your response. Just to clarify the low > > level > > > functions ft_read_header & ft_read_data are mentioned in the ft > > > getting started tutorial. I believe they're recommended to make > > sure > > > the data is ft friendly. In my case the data is ft friendly. My > > data > > > is also pre-processed and already 'time-locked'--meaning that I > > have > > > stimulus averaged epoch data in fif format for all my subjects. > My > > > question is how to proceed from there? I've been through the > pages > > you > > > refer to but have not been able to piece together my data in such > a > > > way to proceed with grand-averaging and carrying out stats. > > > -Kambiz. > > > ------------------------------------------------------------- > > > Kambiz Tavabi PhD > > > Biomedical Imaging Laboratory > > > The Children's Hospital of Philadelphia > > > 34th Street and Civic Center Boulevard > > > Philadelphia, Pa. 19104 > > > Tel: 267.426.0302 > > > email: tavabik at email.chop.edu > > > ------------------------------------------------------------- > > > ________________________________________ > > > From: fieldtrip-bounces at donders.ru.nl > > > [fieldtrip-bounces at donders.ru.nl] On Behalf Of Stolk, A. > > > [a.stolk at fcdonders.ru.nl] > > > Sent: Monday, March 28, 2011 4:05 PM > > > To: Email discussion list for the FieldTrip project > > > Subject: Re: [FieldTrip] working with neuromag data > > > > > > Dear Kambiz, > > > > > > While you are able to use the 'low level' ft_read_header and > > > ft_read_data functions, you should be able to preprocess and > > analyze > > > your neuromag data using the 'high level' functions such as > > > ft_preprocessing (which calls the low level functions mentioned > > > above). > > > > > > How to proceed depends on what you want to do with your data. If > > you > > > have triggers stored in your dataset that are synchronuous with > the > > > recorded brain activity, it'd be recommended to start with the > > > following tutorial on how to select your trials: > > > > > > http://fieldtrip.fcdonders.nl/tutorial/preprocessing > > > > > > Since your experience with FT is still limited as you say, I > > believe > > > the following text may provide a good overview of what the data, > > once > > > read in to FT (i.e. matlab) environment, may look like: > > > > > > http://fieldtrip.fcdonders.nl/walkthrough > > > > > > Typically, your next steps involve single-subject timelocked > > analysis, > > > then grand-average and perform statistics at the group level. For > > an > > > overview of the steps and protocols, see: > > > > > > http://fieldtrip.fcdonders.nl/tutorial/analysis_protocols > > > > > > Hope this has helped for a start, > > > > > > Arjen > > > > > > > > > ----- "Kambiz Tavabi" schreef: > > > > > > > Van: "Kambiz Tavabi" > > > > Aan: "Email discussion list for the FieldTrip project" > > > > > > > Verzonden: Maandag 28 maart 2011 20:59:36 > > > > Onderwerp: [FieldTrip] working with neuromag data > > > > > > > > Greetings - I have preprocessed/averaged neuromag data for a > > group > > > of > > > > subjects that I'd like to visualize, compute grandaverage and > > carry > > > > out sensor level statistics on. The only help I managed to find > > on > > > the > > > > Fieldtrip site/list Re: neurmag data concerns getting started > > e.g., > > > > with ft_read_header and ft_read_data. In my case these programs > > > work > > > > fine meaning that I can proceed with further analysis. > > > > On a side, in my limited experience with FT, a major problem I > > run > > > > into frequently is that there is no clear suggestion(s) on how > to > > > > proceed with data that is not raw. I understand it is > impossible > > to > > > > cover all analysis scenarios, but it is often the case that > > working > > > > with CTF, or in particular Elekta system, the data is likely to > > be > > > in > > > > a post-preprocessed phase. Everytime I've tried to work with > ft, > > It > > > > seems to me that if I don't start with square one in fieldtrip, > > it > > > is > > > > difficult to figure out how to use downstream programs to work > on > > > the > > > > data. > > > > That said, in my case I have the output from ft_read_header: > > > > > > > > label: {338x1 cell} > > > > nChans: 338 > > > > Fs: 1000 > > > > grad: [1x1 struct] > > > > unit: {1x338 cell} > > > > nSamples: 651 > > > > nSamplesPre: 100 > > > > nTrials: 6 > > > > orig: [1x1 struct] > > > > > > > > and output from ft_read_data > > > > > > > > [338x651x6] that being channels by samples by number of > stimulus > > > > averaged epochs. To proceed, ideally I'd like to compute a > > > > grandaverage for each condition, visualize them in a multiplot, > > and > > > > carry out sensor level stats. To be able to do this I > understand > > I > > > > need the output from ft_timelockanalysis, how do I arrange my > > data > > > as > > > > such? I am assuming it is already in that state. Thanks for > your > > > > time. > > > > > > > > -Kambiz. > > > > ------------------------------------------------------------- > > > > Kambiz Tavabi PhD > > > > Biomedical Imaging Laboratory > > > > The Children's Hospital of Philadelphia > > > > 34th Street and Civic Center Boulevard > > > > Philadelphia, Pa. 19104 > > > > Tel: 267.426.0302 > > > > email: tavabik at email.chop.edu > > > > ------------------------------------------------------------- > > > > _______________________________________________ > > > > 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 > > > > _______________________________________________ > > 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 bibi.raquel at gmail.com Thu Jun 16 21:38:31 2011 From: bibi.raquel at gmail.com (Raquel Bibi) Date: Thu, 16 Jun 2011 15:38:31 -0400 Subject: [FieldTrip] Reading data from ASA 4 Message-ID: Dear Fieldtrippers, I am trying to read in ASA 4 files that were saved as an EEGProbe .cnt file. I am using Windows 7 64bit and Matlab 2010. Although I've downloaded the newest files from ANT, I an unable to read the proper MEX files. Is there something special I must do in order for Matlab to invoke the MEX file. I believe the files from ANT have already been compiled. Since I am unfamiliar with MEX files and our new EEG system, any information would be greatly appreciated. Currently, get errors due to the fact that the MEX file are not being used. Thanks, Raquel -------------- next part -------------- An HTML attachment was scrubbed... URL: From batrod at gmail.com Fri Jun 17 00:37:45 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Thu, 16 Jun 2011 17:37:45 -0500 Subject: [FieldTrip] Using ICA to filter data In-Reply-To: References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> Message-ID: Im still afraid that the power of this analysis will be very low. Maybe you can try an ICA on your fMRI data and try to correlate each component with your EOG timecourse. Rodolphe N. On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net wrote: > It's a bit of a unique experiment, we're trying to use an ECG machine > to acquire EOG, so it's only a single output channel. > > i guess what I need is a temporal ICA rather than a spatial one... > > On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: > > To summarize, the ICA will decompose your signal into as many components as > Electrodes. > Therefore, trying to decompose only one source is useless. > Did you use a full net of electrodes into your MRI machine or only EOG > electrodes? > > Hope this helps, > > Rodolphe N. > > On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net < > fieldtrip at greenant.net> wrote: > >> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >> I want to be able to spot the saccades in the samples and ideally measure >> their onset at the >> end of each trial. >> >> As you may guess, it's quite noisy and it's broad spectrum noise, despite >> pre-filtering. >> >> Ideally, I would like to isolate the component that corresponds to the MRI >> interference >> and then filter this out. >> >> I have managed to import the data and can run ft_componentanalysis >> but it fails with: >> >> runica() - data size (1,30720) too small >> >> My data is single channel, 40 epochs, each of 6 seconds (time locked to >> stim onset but not saccade onset) >> Is there a different method I should be using? >> >> I have posted some sample data and the current script (which reads in the >> data and runs preprocessing) to the following urls: >> >> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >> http://greenant.net/temp/EOG_analysis.m >> _______________________________________________ >> 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 smoratti at psi.ucm.es Fri Jun 17 09:01:45 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Fri, 17 Jun 2011 09:01:45 +0200 Subject: [FieldTrip] Problems with Neuromag Data after SSS In-Reply-To: References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> Message-ID: <76A4F15A-0795-44E8-8658-AA73CAA45CD9@psi.ucm.es> Hello everybody, I had no problems reading Neuromag data, but when I want to read data treated with SSS I get the following error: ??? Error using ==> fiff_read_tag at 232 Cannot handle other than dense or sparse matrices yet Error in ==> fiff_open at 80 tag = fiff_read_tag(fid,dirpos); Error in ==> fiff_read_meas_info at 82 [ fid, tree ] = fiff_open(source); Error in ==> ft_read_header at 1049 orig = fiff_read_meas_info(filename); Error in ==> mytrialfun_Neuromag_face at 3 hdr = ft_read_header(cfg.dataset); Error in ==> ft_definetrial at 139 trl = feval(cfg.trialfun, cfg); Any idea, what I could do? Best, Stephan El 17/06/2011, a las 0:37, Rodolphe Nenert escribió: > Im still afraid that the power of this analysis will be very low. > Maybe you can try an ICA on your fMRI data and try to correlate each > component with your EOG timecourse. > > Rodolphe N. > > On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net > wrote: > It's a bit of a unique experiment, we're trying to use an ECG machine > to acquire EOG, so it's only a single output channel. > > i guess what I need is a temporal ICA rather than a spatial one... > > On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: > >> To summarize, the ICA will decompose your signal into as many >> components as Electrodes. >> Therefore, trying to decompose only one source is useless. >> Did you use a full net of electrodes into your MRI machine or only >> EOG electrodes? >> >> Hope this helps, >> >> Rodolphe N. >> >> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net > > wrote: >> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >> I want to be able to spot the saccades in the samples and ideally >> measure their onset at the >> end of each trial. >> >> As you may guess, it's quite noisy and it's broad spectrum noise, >> despite pre-filtering. >> >> Ideally, I would like to isolate the component that corresponds to >> the MRI interference >> and then filter this out. >> >> I have managed to import the data and can run ft_componentanalysis >> but it fails with: >> >> runica() - data size (1,30720) too small >> >> My data is single channel, 40 epochs, each of 6 seconds (time >> locked to stim onset but not saccade onset) >> Is there a different method I should be using? >> >> I have posted some sample data and the current script (which reads >> in the >> data and runs preprocessing) to the following urls: >> >> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >> http://greenant.net/temp/EOG_analysis.m >> _______________________________________________ >> 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 ________________________________________________________ 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 lhunt at fmrib.ox.ac.uk Fri Jun 17 09:28:27 2011 From: lhunt at fmrib.ox.ac.uk (Laurence Hunt) Date: Fri, 17 Jun 2011 08:28:27 +0100 Subject: [FieldTrip] Problems with Neuromag Data after SSS In-Reply-To: <76A4F15A-0795-44E8-8658-AA73CAA45CD9@psi.ucm.es> References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> <76A4F15A-0795-44E8-8658-AA73CAA45CD9@psi.ucm.es> Message-ID: <32F04EF7-8D0F-4C73-9C3D-11AB66BF8E81@fmrib.ox.ac.uk> Hi Stephan, Did you do anything else to the data besides applying SSS? I use SSS on all my data and haven't encountered this problem before. Does it apply to all your datasets or just one specific file? Laurence =========================================== Laurence Hunt, DPhil Student Centre for Functional MRI of the Brain (FMRIB), University of Oxford lhunt at fmrib.ox.ac.uk Phone: (+44)1865-(2)22738 =========================================== On 17 Jun 2011, at 08:01, Stephan Moratti wrote: > Hello everybody, > > I had no problems reading Neuromag data, but when I want to read data treated with SSS I get the following error: > > ??? Error using ==> fiff_read_tag at 232 > Cannot handle other than dense or sparse matrices yet > > Error in ==> fiff_open at 80 > tag = fiff_read_tag(fid,dirpos); > > Error in ==> fiff_read_meas_info at 82 > [ fid, tree ] = fiff_open(source); > > Error in ==> ft_read_header at 1049 > orig = fiff_read_meas_info(filename); > > Error in ==> mytrialfun_Neuromag_face at 3 > hdr = ft_read_header(cfg.dataset); > > Error in ==> ft_definetrial at 139 > trl = feval(cfg.trialfun, cfg); > > Any idea, what I could do? > > Best, > > Stephan > > > El 17/06/2011, a las 0:37, Rodolphe Nenert escribió: > >> Im still afraid that the power of this analysis will be very low. >> Maybe you can try an ICA on your fMRI data and try to correlate each component with your EOG timecourse. >> >> Rodolphe N. >> >> On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net wrote: >> It's a bit of a unique experiment, we're trying to use an ECG machine >> to acquire EOG, so it's only a single output channel. >> >> i guess what I need is a temporal ICA rather than a spatial one... >> >> On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: >> >>> To summarize, the ICA will decompose your signal into as many components as Electrodes. >>> Therefore, trying to decompose only one source is useless. >>> Did you use a full net of electrodes into your MRI machine or only EOG electrodes? >>> >>> Hope this helps, >>> >>> Rodolphe N. >>> >>> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net wrote: >>> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >>> I want to be able to spot the saccades in the samples and ideally measure their onset at the >>> end of each trial. >>> >>> As you may guess, it's quite noisy and it's broad spectrum noise, despite pre-filtering. >>> >>> Ideally, I would like to isolate the component that corresponds to the MRI interference >>> and then filter this out. >>> >>> I have managed to import the data and can run ft_componentanalysis >>> but it fails with: >>> >>> runica() - data size (1,30720) too small >>> >>> My data is single channel, 40 epochs, each of 6 seconds (time locked to stim onset but not saccade onset) >>> Is there a different method I should be using? >>> >>> I have posted some sample data and the current script (which reads in the >>> data and runs preprocessing) to the following urls: >>> >>> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >>> http://greenant.net/temp/EOG_analysis.m >>> _______________________________________________ >>> 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 > > > ________________________________________________________ > 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 > > > _______________________________________________ > 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 sherrykhan78 at gmail.com Sat Jun 18 00:28:14 2011 From: sherrykhan78 at gmail.com (Sheraz Khan) Date: Fri, 17 Jun 2011 18:28:14 -0400 Subject: [FieldTrip] Suitable value of cfg.wcm_weight Message-ID: Hello everyone. I am new to fieldtrip, and using "cluster based statistics", I am using "cfg.clusterstatistics=wcm" as my option. Can any experience field-tripper suggest suitable value of* "cfg.wcm_weight"*, Thanks Sheraz On Fri, Jun 17, 2011 at 3:01 AM, Stephan Moratti wrote: > Hello everybody, > > I had no problems reading Neuromag data, but when I want to read data > treated with SSS I get the following error: > > ??? Error using ==> fiff_read_tag at 232 > Cannot handle other than dense or sparse matrices yet > > Error in ==> fiff_open at 80 > tag = fiff_read_tag(fid,dirpos); > > Error in ==> fiff_read_meas_info at 82 > [ fid, tree ] = fiff_open(source); > > Error in ==> ft_read_header at 1049 > orig = fiff_read_meas_info(filename); > > Error in ==> mytrialfun_Neuromag_face at 3 > hdr = ft_read_header(cfg.dataset); > > Error in ==> ft_definetrial at 139 > trl = feval(cfg.trialfun, cfg); > > Any idea, what I could do? > > Best, > > Stephan > > > El 17/06/2011, a las 0:37, Rodolphe Nenert escribió: > > Im still afraid that the power of this analysis will be very low. > Maybe you can try an ICA on your fMRI data and try to correlate each > component with your EOG timecourse. > > Rodolphe N. > > On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net < > fieldtrip at greenant.net> wrote: > >> It's a bit of a unique experiment, we're trying to use an ECG machine >> to acquire EOG, so it's only a single output channel. >> >> i guess what I need is a temporal ICA rather than a spatial one... >> >> On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: >> >> To summarize, the ICA will decompose your signal into as many components >> as Electrodes. >> Therefore, trying to decompose only one source is useless. >> Did you use a full net of electrodes into your MRI machine or only EOG >> electrodes? >> >> Hope this helps, >> >> Rodolphe N. >> >> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net < >> fieldtrip at greenant.net> wrote: >> >>> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >>> I want to be able to spot the saccades in the samples and ideally measure >>> their onset at the >>> end of each trial. >>> >>> As you may guess, it's quite noisy and it's broad spectrum noise, despite >>> pre-filtering. >>> >>> Ideally, I would like to isolate the component that corresponds to the >>> MRI interference >>> and then filter this out. >>> >>> I have managed to import the data and can run ft_componentanalysis >>> but it fails with: >>> >>> runica() - data size (1,30720) too small >>> >>> My data is single channel, 40 epochs, each of 6 seconds (time locked to >>> stim onset but not saccade onset) >>> Is there a different method I should be using? >>> >>> I have posted some sample data and the current script (which reads in the >>> data and runs preprocessing) to the following urls: >>> >>> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >>> http://greenant.net/temp/EOG_analysis.m >>> _______________________________________________ >>> 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 > > > > ________________________________________________________ > 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 > > > > _______________________________________________ > 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 fieldtrip at greenant.net Sat Jun 18 08:56:57 2011 From: fieldtrip at greenant.net (frank@greenant.net) Date: Sat, 18 Jun 2011 16:56:57 +1000 Subject: [FieldTrip] Using ICA to filter data In-Reply-To: References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> Message-ID: <17D1903D-8B16-4CA7-8581-7D6221A57E59@greenant.net> My apologies, I think I may have been a bit unclear about the aims of collecting the data. We're aiming to measure saccadic onset from the signal on a per-trial basis. I was hoping to isolate the MRI noise "component" and subtract this from the EOG signal component to give a cleaner EOG signal. Can the ICA module be applied in the temporal domain in this fashion? There are 40 single session trials of 6 seconds each, I would have thought that'd be enough data to give it a try. Also open to any suggestions as to other adaptive filter techniques.... Thanks On 17/06/2011, at 8:37 AM, Rodolphe Nenert wrote: > Im still afraid that the power of this analysis will be very low. > Maybe you can try an ICA on your fMRI data and try to correlate each component with your EOG timecourse. > > Rodolphe N. > > On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net wrote: > It's a bit of a unique experiment, we're trying to use an ECG machine > to acquire EOG, so it's only a single output channel. > > i guess what I need is a temporal ICA rather than a spatial one... > > On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: > >> To summarize, the ICA will decompose your signal into as many components as Electrodes. >> Therefore, trying to decompose only one source is useless. >> Did you use a full net of electrodes into your MRI machine or only EOG electrodes? >> >> Hope this helps, >> >> Rodolphe N. >> >> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net wrote: >> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >> I want to be able to spot the saccades in the samples and ideally measure their onset at the >> end of each trial. >> >> As you may guess, it's quite noisy and it's broad spectrum noise, despite pre-filtering. >> >> Ideally, I would like to isolate the component that corresponds to the MRI interference >> and then filter this out. >> >> I have managed to import the data and can run ft_componentanalysis >> but it fails with: >> >> runica() - data size (1,30720) too small >> >> My data is single channel, 40 epochs, each of 6 seconds (time locked to stim onset but not saccade onset) >> Is there a different method I should be using? >> >> I have posted some sample data and the current script (which reads in the >> data and runs preprocessing) to the following urls: >> >> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >> http://greenant.net/temp/EOG_analysis.m >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From manuel.mercier at einstein.yu.edu Sat Jun 18 11:09:55 2011 From: manuel.mercier at einstein.yu.edu (Manuel Mercier) Date: Sat, 18 Jun 2011 05:09:55 -0400 Subject: [FieldTrip] wavelet analysis Message-ID: <6ac7ddd3f73a325534c24be6edd039d2.squirrel@netmail.aecom.yu.edu> Dear Field-trippers I recently ran some time frequency analysis using the wavelet method. I was surprise to see that whereas I asked for a step of 1Hz, it was not the case every alternate step (for foi=2:1:10 ; I got [2 3.2 4 5.2 6 7.2 8 9.2 10]), and it was also the case when I changed the toi (2.5, 1.5 with constant trials length of 2.5 sec and sampling freq 1000Hz). I found a kind of explanation following the faq (http://fieldtrip.fcdonders.nl/faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_wavelet_formerly_wltconvol_in_ft_freqanalyis). Still it is not clear to me why this refers to Fourier transform. >From my (none specialist) point of view it is possible to produce a wavelet of any size (Hz;Dt). It is clear that there is some limitations based on the duration of the epochs and the number of time points. But in the present case it shouldn't be a problem, is it? Would be please if someone can help me with this issue. Thanks in advance Manuel From yossiarzouan at ucla.edu Sat Jun 18 17:37:27 2011 From: yossiarzouan at ucla.edu (Yossi Arzouan) Date: Sat, 18 Jun 2011 18:37:27 +0300 Subject: [FieldTrip] influences between the regions In-Reply-To: <1324085935.896862.1306654007541.JavaMail.fmail@mwmweb084> References: <1324085935.896862.1306654007541.JavaMail.fmail@mwmweb084> Message-ID: Dear Aka if that is still relevant maybe our lately published paper on connectivity using Complexity System approach can be a starting point : http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0019345 Big Words, Halved Brains and Small Worlds: Complex Brain Networks of Figurative Language Comprehension Best Wishes Yossi On Sun, May 29, 2011 at 10:26 AM, Michael Wibral wrote: > Dear Aka, > > there is a connectivity Toolbox in fieldtrip, isn't there? > At least I know there was something under development so maybe someone on > the list can help out. > > If that doesn't help or if you are specifically interested in information > transfer you might also try the transfer entropy toolbox 'TRENTOOL' ( > www.trentool.de). > > Michael > > > ------------------------------ > *Von:* "Aka Demon" > *Gesendet:* May 27, 2011 10:43:11 AM > *An:* fieldtrip at donders.ru.nl > *Betreff:* [FieldTrip] influences between the regions > > > Dear experts > > After analyzing memory experiment EEG/MEG and source localization data, i > figured out that there is little I can say about the interactions between > the activated regions as I don’t have any information about the connection > between the activated areas. > > So I was wondering if there are some useful works/tools that I can use to > explorer the influences between the regions (such as information transfer > from one region to the other). > > Thanks a lot > > Aka > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- ____________________________________________________________ Yossi Arzouan, PhD Postdoctoral Fellow at UCLA (Zaidel Lab.) and Haifa Univ (Breznitz and Karni Labs) Cell : 972-54-4446645; Skype : yossi_arzouan www : http://www.complexity-research.org/user/yossiarzouan http://faculty.biu.ac.il/~goldsa/index.html http://www.zaidellab.org/ http://ejsafra.haifa.ac.il/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Sun Jun 19 17:20:41 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Sun, 19 Jun 2011 17:20:41 +0200 Subject: [FieldTrip] Problems with Neuromag Data after SSS In-Reply-To: <32F04EF7-8D0F-4C73-9C3D-11AB66BF8E81@fmrib.ox.ac.uk> References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> <76A4F15A-0795-44E8-8658-AA73CAA45CD9@psi.ucm.es> <32F04EF7-8D0F-4C73-9C3D-11AB66BF8E81@fmrib.ox.ac.uk> Message-ID: Hi Lauren, Thanks for your reply. Yes I had it with 6 data sets where SSS was applied. I had them copied from the HP workstation to our server and from there to my Mac. Could it be a little and big endian thing provoked by moving the files from different platforms? Stephan El 17/06/2011, a las 9:28, Laurence Hunt escribió: > Hi Stephan, > > Did you do anything else to the data besides applying SSS? I use SSS > on all my data and haven't encountered this problem before. Does it > apply to all your datasets or just one specific file? > > Laurence > > =========================================== > Laurence Hunt, DPhil Student > Centre for Functional MRI of the Brain (FMRIB), > University of Oxford > lhunt at fmrib.ox.ac.uk > Phone: (+44)1865-(2)22738 > =========================================== > > On 17 Jun 2011, at 08:01, Stephan Moratti wrote: > >> Hello everybody, >> >> I had no problems reading Neuromag data, but when I want to read >> data treated with SSS I get the following error: >> >> ??? Error using ==> fiff_read_tag at 232 >> Cannot handle other than dense or sparse matrices yet >> >> Error in ==> fiff_open at 80 >> tag = fiff_read_tag(fid,dirpos); >> >> Error in ==> fiff_read_meas_info at 82 >> [ fid, tree ] = fiff_open(source); >> >> Error in ==> ft_read_header at 1049 >> orig = fiff_read_meas_info(filename); >> >> Error in ==> mytrialfun_Neuromag_face at 3 >> hdr = ft_read_header(cfg.dataset); >> >> Error in ==> ft_definetrial at 139 >> trl = feval(cfg.trialfun, cfg); >> >> Any idea, what I could do? >> >> Best, >> >> Stephan >> >> >> El 17/06/2011, a las 0:37, Rodolphe Nenert escribió: >> >>> Im still afraid that the power of this analysis will be very low. >>> Maybe you can try an ICA on your fMRI data and try to correlate >>> each component with your EOG timecourse. >>> >>> Rodolphe N. >>> >>> On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net >> > wrote: >>> It's a bit of a unique experiment, we're trying to use an ECG >>> machine >>> to acquire EOG, so it's only a single output channel. >>> >>> i guess what I need is a temporal ICA rather than a spatial one... >>> >>> On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: >>> >>>> To summarize, the ICA will decompose your signal into as many >>>> components as Electrodes. >>>> Therefore, trying to decompose only one source is useless. >>>> Did you use a full net of electrodes into your MRI machine or >>>> only EOG electrodes? >>>> >>>> Hope this helps, >>>> >>>> Rodolphe N. >>>> >>>> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net >>> > wrote: >>>> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >>>> I want to be able to spot the saccades in the samples and ideally >>>> measure their onset at the >>>> end of each trial. >>>> >>>> As you may guess, it's quite noisy and it's broad spectrum noise, >>>> despite pre-filtering. >>>> >>>> Ideally, I would like to isolate the component that corresponds >>>> to the MRI interference >>>> and then filter this out. >>>> >>>> I have managed to import the data and can run ft_componentanalysis >>>> but it fails with: >>>> >>>> runica() - data size (1,30720) too small >>>> >>>> My data is single channel, 40 epochs, each of 6 seconds (time >>>> locked to stim onset but not saccade onset) >>>> Is there a different method I should be using? >>>> >>>> I have posted some sample data and the current script (which >>>> reads in the >>>> data and runs preprocessing) to the following urls: >>>> >>>> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >>>> http://greenant.net/temp/EOG_analysis.m >>>> _______________________________________________ >>>> 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 >> >> >> ________________________________________________________ >> 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 >> >> >> _______________________________________________ >> 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 ________________________________________________________ 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 v.litvak at ion.ucl.ac.uk Sun Jun 19 21:08:45 2011 From: v.litvak at ion.ucl.ac.uk (Vladimir Litvak) Date: Sun, 19 Jun 2011 20:08:45 +0100 Subject: [FieldTrip] Problems with Neuromag Data after SSS In-Reply-To: References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> <76A4F15A-0795-44E8-8658-AA73CAA45CD9@psi.ucm.es> <32F04EF7-8D0F-4C73-9C3D-11AB66BF8E81@fmrib.ox.ac.uk> Message-ID: Dear Stephan, It might be that or that you transferred the files as ascii in FTP rather than binary. I've seen this error before and showed the file to Matti Hamalainen. He said the file was corrupted. Best, Vladimir On Sun, Jun 19, 2011 at 4:20 PM, Stephan Moratti wrote: > Hi Lauren, > Thanks for your reply. Yes I had it with 6 data sets where SSS was applied. > I had them copied from the HP workstation to our server and from there to my > Mac. Could it be a little and big endian thing provoked by moving the files > from different platforms? > Stephan > El 17/06/2011, a las 9:28, Laurence Hunt escribió: > > Hi Stephan, > Did you do anything else to the data besides applying SSS? I use SSS on all > my data and haven't encountered this problem before. Does it apply to all > your datasets or just one specific file? > Laurence > =========================================== > Laurence Hunt, DPhil Student >  Centre for Functional MRI of the Brain (FMRIB), > University of Oxford > lhunt at fmrib.ox.ac.uk > Phone: (+44)1865-(2)22738 > =========================================== > On 17 Jun 2011, at 08:01, Stephan Moratti wrote: > > Hello everybody, > I had no problems reading Neuromag data, but when I want to read data > treated with SSS I get the following error: > ??? Error using ==> fiff_read_tag at 232 > Cannot handle other than dense or sparse matrices yet > Error in ==> fiff_open at 80 >     tag = fiff_read_tag(fid,dirpos); > Error in ==> fiff_read_meas_info at 82 >     [ fid, tree ] = fiff_open(source); > Error in ==> ft_read_header at 1049 >     orig = fiff_read_meas_info(filename); > Error in ==> mytrialfun_Neuromag_face at 3 > hdr = ft_read_header(cfg.dataset); > Error in ==> ft_definetrial at 139 >     trl   = feval(cfg.trialfun, cfg); > Any idea, what I could do? > Best, > Stephan > > El 17/06/2011, a las 0:37, Rodolphe Nenert escribió: > > Im still afraid that the power of this analysis will be very low. > Maybe you can try an ICA on your fMRI data and try to correlate each > component with your EOG timecourse. > Rodolphe N. > > On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net > wrote: >> >> It's a bit of a unique experiment, we're trying to use an ECG machine >> to acquire EOG, so it's only a single output channel. >> i guess what I need is a temporal ICA rather than a spatial one... >> On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: >> >> To summarize, the ICA will decompose your signal into as many components >> as Electrodes. >> Therefore, trying to decompose only one source is useless. >> Did you use a full net of electrodes into your MRI machine or only EOG >> electrodes? >> Hope this helps, >> Rodolphe N. >> >> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net >> wrote: >>> >>> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >>> I want to be able to spot the saccades in the samples and ideally measure >>> their onset at the >>> end of each trial. >>> >>> As you may guess, it's quite noisy and it's broad spectrum noise, despite >>> pre-filtering. >>> >>> Ideally, I would like to isolate the component that corresponds to the >>> MRI interference >>> and then filter this out. >>> >>> I have managed to import the data and can run ft_componentanalysis >>> but it fails with: >>> >>> runica() - data size (1,30720) too small >>> >>> My data is single channel, 40 epochs, each of 6 seconds (time locked to >>> stim onset but not saccade onset) >>> Is there a different method I should be using? >>> >>> I have posted some sample data and the current script (which reads in the >>> data and runs preprocessing) to the following urls: >>> >>> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >>> http://greenant.net/temp/EOG_analysis.m >>> _______________________________________________ >>> 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 > > ________________________________________________________ > 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 > > > _______________________________________________ > 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 > > ________________________________________________________ > 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 > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From lhunt at fmrib.ox.ac.uk Mon Jun 20 00:04:46 2011 From: lhunt at fmrib.ox.ac.uk (Laurence Hunt) Date: Sun, 19 Jun 2011 23:04:46 +0100 Subject: [FieldTrip] Problems with Neuromag Data after SSS In-Reply-To: References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> <76A4F15A-0795-44E8-8658-AA73CAA45CD9@psi.ucm.es> <32F04EF7-8D0F-4C73-9C3D-11AB66BF8E81@fmrib.ox.ac.uk> Message-ID: <9C063DE1-06F4-461D-9EE4-094F439CDDE8@fmrib.ox.ac.uk> p.s. If this is the problem, try copying using scp from the mac command line, using Terminal - this has always worked for me ok. The files are big endian but this shouldn't be affected by copying to a mac. Laurence On 19 Jun 2011, at 20:08, Vladimir Litvak wrote: > Dear Stephan, > > It might be that or that you transferred the files as ascii in FTP > rather than binary. I've seen this error before and showed the file to > Matti Hamalainen. He said the file was corrupted. > > Best, > > Vladimir > > On Sun, Jun 19, 2011 at 4:20 PM, Stephan Moratti wrote: >> Hi Lauren, >> Thanks for your reply. Yes I had it with 6 data sets where SSS was applied. >> I had them copied from the HP workstation to our server and from there to my >> Mac. Could it be a little and big endian thing provoked by moving the files >> from different platforms? >> Stephan >> El 17/06/2011, a las 9:28, Laurence Hunt escribió: >> >> Hi Stephan, >> Did you do anything else to the data besides applying SSS? I use SSS on all >> my data and haven't encountered this problem before. Does it apply to all >> your datasets or just one specific file? >> Laurence >> =========================================== >> Laurence Hunt, DPhil Student >> Centre for Functional MRI of the Brain (FMRIB), >> University of Oxford >> lhunt at fmrib.ox.ac.uk >> Phone: (+44)1865-(2)22738 >> =========================================== >> On 17 Jun 2011, at 08:01, Stephan Moratti wrote: >> >> Hello everybody, >> I had no problems reading Neuromag data, but when I want to read data >> treated with SSS I get the following error: >> ??? Error using ==> fiff_read_tag at 232 >> Cannot handle other than dense or sparse matrices yet >> Error in ==> fiff_open at 80 >> tag = fiff_read_tag(fid,dirpos); >> Error in ==> fiff_read_meas_info at 82 >> [ fid, tree ] = fiff_open(source); >> Error in ==> ft_read_header at 1049 >> orig = fiff_read_meas_info(filename); >> Error in ==> mytrialfun_Neuromag_face at 3 >> hdr = ft_read_header(cfg.dataset); >> Error in ==> ft_definetrial at 139 >> trl = feval(cfg.trialfun, cfg); >> Any idea, what I could do? >> Best, >> Stephan >> >> El 17/06/2011, a las 0:37, Rodolphe Nenert escribió: >> >> Im still afraid that the power of this analysis will be very low. >> Maybe you can try an ICA on your fMRI data and try to correlate each >> component with your EOG timecourse. >> Rodolphe N. >> >> On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net >> wrote: >>> >>> It's a bit of a unique experiment, we're trying to use an ECG machine >>> to acquire EOG, so it's only a single output channel. >>> i guess what I need is a temporal ICA rather than a spatial one... >>> On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: >>> >>> To summarize, the ICA will decompose your signal into as many components >>> as Electrodes. >>> Therefore, trying to decompose only one source is useless. >>> Did you use a full net of electrodes into your MRI machine or only EOG >>> electrodes? >>> Hope this helps, >>> Rodolphe N. >>> >>> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net >>> wrote: >>>> >>>> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >>>> I want to be able to spot the saccades in the samples and ideally measure >>>> their onset at the >>>> end of each trial. >>>> >>>> As you may guess, it's quite noisy and it's broad spectrum noise, despite >>>> pre-filtering. >>>> >>>> Ideally, I would like to isolate the component that corresponds to the >>>> MRI interference >>>> and then filter this out. >>>> >>>> I have managed to import the data and can run ft_componentanalysis >>>> but it fails with: >>>> >>>> runica() - data size (1,30720) too small >>>> >>>> My data is single channel, 40 epochs, each of 6 seconds (time locked to >>>> stim onset but not saccade onset) >>>> Is there a different method I should be using? >>>> >>>> I have posted some sample data and the current script (which reads in the >>>> data and runs preprocessing) to the following urls: >>>> >>>> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >>>> http://greenant.net/temp/EOG_analysis.m >>>> _______________________________________________ >>>> 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 >> >> ________________________________________________________ >> 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 >> >> >> _______________________________________________ >> 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 >> >> ________________________________________________________ >> 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 >> >> >> >> _______________________________________________ >> 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 smoratti at psi.ucm.es Mon Jun 20 08:26:46 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Mon, 20 Jun 2011 08:26:46 +0200 Subject: [FieldTrip] Problems with Neuromag Data after SSS In-Reply-To: References: <9DD7CDDE-0F25-4457-9FD8-0272659CD8F4@greenant.net> <76A4F15A-0795-44E8-8658-AA73CAA45CD9@psi.ucm.es> <32F04EF7-8D0F-4C73-9C3D-11AB66BF8E81@fmrib.ox.ac.uk> Message-ID: Dear Vladimir, Thanks for this hint. I will check this! Best, Stephan El 19/06/2011, a las 21:08, Vladimir Litvak escribió: > Dear Stephan, > > It might be that or that you transferred the files as ascii in FTP > rather than binary. I've seen this error before and showed the file to > Matti Hamalainen. He said the file was corrupted. > > Best, > > Vladimir > > On Sun, Jun 19, 2011 at 4:20 PM, Stephan Moratti > wrote: >> Hi Lauren, >> Thanks for your reply. Yes I had it with 6 data sets where SSS was >> applied. >> I had them copied from the HP workstation to our server and from >> there to my >> Mac. Could it be a little and big endian thing provoked by moving >> the files >> from different platforms? >> Stephan >> El 17/06/2011, a las 9:28, Laurence Hunt escribió: >> >> Hi Stephan, >> Did you do anything else to the data besides applying SSS? I use >> SSS on all >> my data and haven't encountered this problem before. Does it apply >> to all >> your datasets or just one specific file? >> Laurence >> =========================================== >> Laurence Hunt, DPhil Student >> Centre for Functional MRI of the Brain (FMRIB), >> University of Oxford >> lhunt at fmrib.ox.ac.uk >> Phone: (+44)1865-(2)22738 >> =========================================== >> On 17 Jun 2011, at 08:01, Stephan Moratti wrote: >> >> Hello everybody, >> I had no problems reading Neuromag data, but when I want to read data >> treated with SSS I get the following error: >> ??? Error using ==> fiff_read_tag at 232 >> Cannot handle other than dense or sparse matrices yet >> Error in ==> fiff_open at 80 >> tag = fiff_read_tag(fid,dirpos); >> Error in ==> fiff_read_meas_info at 82 >> [ fid, tree ] = fiff_open(source); >> Error in ==> ft_read_header at 1049 >> orig = fiff_read_meas_info(filename); >> Error in ==> mytrialfun_Neuromag_face at 3 >> hdr = ft_read_header(cfg.dataset); >> Error in ==> ft_definetrial at 139 >> trl = feval(cfg.trialfun, cfg); >> Any idea, what I could do? >> Best, >> Stephan >> >> El 17/06/2011, a las 0:37, Rodolphe Nenert escribió: >> >> Im still afraid that the power of this analysis will be very low. >> Maybe you can try an ICA on your fMRI data and try to correlate each >> component with your EOG timecourse. >> Rodolphe N. >> >> On Thu, Jun 16, 2011 at 1:16 PM, frank at greenant.net > > >> wrote: >>> >>> It's a bit of a unique experiment, we're trying to use an ECG >>> machine >>> to acquire EOG, so it's only a single output channel. >>> i guess what I need is a temporal ICA rather than a spatial one... >>> On 17/06/2011, at 2:48 AM, Rodolphe Nenert wrote: >>> >>> To summarize, the ICA will decompose your signal into as many >>> components >>> as Electrodes. >>> Therefore, trying to decompose only one source is useless. >>> Did you use a full net of electrodes into your MRI machine or only >>> EOG >>> electrodes? >>> Hope this helps, >>> Rodolphe N. >>> >>> On Thu, Jun 16, 2011 at 11:42 AM, frank at greenant.net >>> wrote: >>>> >>>> I am trying to use fieldtrip to filter EOG data obtained in an MRI. >>>> I want to be able to spot the saccades in the samples and ideally >>>> measure >>>> their onset at the >>>> end of each trial. >>>> >>>> As you may guess, it's quite noisy and it's broad spectrum noise, >>>> despite >>>> pre-filtering. >>>> >>>> Ideally, I would like to isolate the component that corresponds >>>> to the >>>> MRI interference >>>> and then filter this out. >>>> >>>> I have managed to import the data and can run ft_componentanalysis >>>> but it fails with: >>>> >>>> runica() - data size (1,30720) too small >>>> >>>> My data is single channel, 40 epochs, each of 6 seconds (time >>>> locked to >>>> stim onset but not saccade onset) >>>> Is there a different method I should be using? >>>> >>>> I have posted some sample data and the current script (which >>>> reads in the >>>> data and runs preprocessing) to the following urls: >>>> >>>> http://greenant.net/temp/1_2_MRI_2011-04-29%2016:19:33.mat >>>> http://greenant.net/temp/EOG_analysis.m >>>> _______________________________________________ >>>> 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 >> >> ________________________________________________________ >> 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 >> >> >> _______________________________________________ >> 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 >> >> ________________________________________________________ >> 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 >> >> >> >> _______________________________________________ >> 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 ________________________________________________________ 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 a.wollbrink at uni-muenster.de Mon Jun 20 14:45:54 2011 From: a.wollbrink at uni-muenster.de (Andreas Wollbrink) Date: Mon, 20 Jun 2011 14:45:54 +0200 Subject: [FieldTrip] concatenating data to a single trial data set Message-ID: <4DFF4102.3020101@uni-muenster.de> Dear all, in order not to run into a RAM memory overload when performing an ICA on MEG data I subdivided the raw data into several equally long segments (chops) using ft_preprocessing with varying cfg.trl settings. After applying ft_componentanalysis to each of these chops I removed some (bad) components and backprojected the data to seperate data matrices using the following code: cfg = []; cfg.component = badCompVec; % to be removed component(s) dataCorr = ft_rejectcomponent(cfg, compData); Finally I like to concatenate these data to a continuous (single trial) data matrix in order to compare it with the original raw data set and perform the further timelock analysis on it. I tried using ft_appenddata for this issue. Doing so one gets a multi trial data matrix which I could not convert to single trial continuous data matrix using e.g. ft_redefinetrial. I would appreciate any help in how to solve this problem. Thanks in advance. Andreas Wollbrink -- ====================================================================== Andreas Wollbrink, Biomedical Engineer Institute for Biomagnetism and Biosignalanalysis Muenster University Hospital Malmedyweg 15 phone: +49-(0)251-83-52546 D-48149 Muenster mobil: +49-(0)160-98527553 Germany fax: +49-(0)251-83-56874 e-Mail: a.wollbrink at uni-muenster.de ====================================================================== From eelke.spaak at donders.ru.nl Mon Jun 20 15:35:14 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 20 Jun 2011 15:35:14 +0200 Subject: [FieldTrip] concatenating data to a single trial data set In-Reply-To: <4DFF4102.3020101@uni-muenster.de> References: <4DFF4102.3020101@uni-muenster.de> Message-ID: Dear Andreas, The way I concatenate data is just 'manually', so without the intervention of FieldTrip. To do this, you will have to concatenate the arrays in both the data.trial and the data.time cell array. In pseudocode: initialize matrix data_concat of size channels X total time points initialize matrix time_concat of size 1 X total time points loop over data.trial and data.time (have the same size) data_concat(:,appropriate time indices) = data.trial{k}(:,:); time_concat(1,appropriate time indices) = data.time{k}(:); end loop data.trial = data_concat; data.time = time_concat; That should do the trick. I would have provided actual code, were it not that I am doing something slightly different from what you are asking. I hope this helps! Best, Eelke 2011/6/20 Andreas Wollbrink : > Dear all, > > in order not to run into a RAM memory overload when performing an ICA on MEG > data I subdivided the raw data into several equally long segments (chops) > using ft_preprocessing with varying cfg.trl settings. > After applying ft_componentanalysis to each of these chops I removed some > (bad) components and backprojected the data to seperate data matrices using > the following code: > > cfg = []; > cfg.component = badCompVec; % to be removed component(s) > dataCorr = ft_rejectcomponent(cfg, compData); > > > Finally I like to concatenate these data to a continuous (single trial) data > matrix in order to compare it with the original raw data set and perform the > further timelock analysis on it. > > I tried using ft_appenddata for this issue. Doing so one gets a multi trial > data matrix which I could not convert to single trial continuous data matrix > using e.g. ft_redefinetrial. > > I would appreciate any help in how to solve this problem. > > Thanks in advance. > > Andreas Wollbrink > -- > > > ====================================================================== > >  Andreas Wollbrink, Biomedical Engineer > >  Institute for Biomagnetism and Biosignalanalysis >  Muenster University Hospital > >  Malmedyweg 15         phone:   +49-(0)251-83-52546 >  D-48149 Muenster      mobil:   +49-(0)160-98527553 >  Germany               fax:     +49-(0)251-83-56874 >                        e-Mail: a.wollbrink at uni-muenster.de > > ====================================================================== > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From nathanweisz at mac.com Mon Jun 20 17:15:50 2011 From: nathanweisz at mac.com (Nathan Weisz) Date: Mon, 20 Jun 2011 17:15:50 +0200 Subject: [FieldTrip] concatenating data to a single trial data set In-Reply-To: References: <4DFF4102.3020101@uni-muenster.de> Message-ID: hi andreas, perhaps i misunderstood something. but your RAM worries concern the ICA computation? then after running your ICA & getting the components, why don't you just read the raw data again with the option as continuous data (cfg.continuous i think). then apply the components to the single-trial raw data and finally reject the bad components. less efficient than elkes solution, rather the lazy one :-) cheers, n On 20.06.2011, at 15:35, Eelke Spaak wrote: > Dear Andreas, > > The way I concatenate data is just 'manually', so without the > intervention of FieldTrip. To do this, you will have to concatenate > the arrays in both the data.trial and the data.time cell array. > > In pseudocode: > > initialize matrix data_concat of size channels X total time points > initialize matrix time_concat of size 1 X total time points > > loop over data.trial and data.time (have the same size) > data_concat(:,appropriate time indices) = data.trial{k}(:,:); > time_concat(1,appropriate time indices) = data.time{k}(:); > end loop > > data.trial = data_concat; > data.time = time_concat; > > That should do the trick. I would have provided actual code, were it > not that I am doing something slightly different from what you are > asking. > > I hope this helps! > > Best, > Eelke > > 2011/6/20 Andreas Wollbrink : >> Dear all, >> >> in order not to run into a RAM memory overload when performing an ICA on MEG >> data I subdivided the raw data into several equally long segments (chops) >> using ft_preprocessing with varying cfg.trl settings. >> After applying ft_componentanalysis to each of these chops I removed some >> (bad) components and backprojected the data to seperate data matrices using >> the following code: >> >> cfg = []; >> cfg.component = badCompVec; % to be removed component(s) >> dataCorr = ft_rejectcomponent(cfg, compData); >> >> >> Finally I like to concatenate these data to a continuous (single trial) data >> matrix in order to compare it with the original raw data set and perform the >> further timelock analysis on it. >> >> I tried using ft_appenddata for this issue. Doing so one gets a multi trial >> data matrix which I could not convert to single trial continuous data matrix >> using e.g. ft_redefinetrial. >> >> I would appreciate any help in how to solve this problem. >> >> Thanks in advance. >> >> Andreas Wollbrink >> -- >> >> >> ====================================================================== >> >> Andreas Wollbrink, Biomedical Engineer >> >> Institute for Biomagnetism and Biosignalanalysis >> Muenster University Hospital >> >> Malmedyweg 15 phone: +49-(0)251-83-52546 >> D-48149 Muenster mobil: +49-(0)160-98527553 >> Germany fax: +49-(0)251-83-56874 >> e-Mail: a.wollbrink at uni-muenster.de >> >> ====================================================================== >> _______________________________________________ >> 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 jan.schoffelen at donders.ru.nl Tue Jun 21 09:08:34 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 21 Jun 2011 09:08:34 +0200 Subject: [FieldTrip] wavelet analysis In-Reply-To: <6ac7ddd3f73a325534c24be6edd039d2.squirrel@netmail.aecom.yu.edu> References: <6ac7ddd3f73a325534c24be6edd039d2.squirrel@netmail.aecom.yu.edu> Message-ID: <9B183DFC-CD62-489D-9F0B-C2292AFFAF1A@donders.ru.nl> Dear Manuel, Thanks for your message. I gave the faq a good read, and I agree that the answer can be made a bit more clear. I updated the faqs you mentioned and hope that this explains the issue better. Let me know if it is still not clear. Best wishes, Jan-Mathijs On Jun 18, 2011, at 11:09 AM, Manuel Mercier wrote: > Dear Field-trippers > I recently ran some time frequency analysis using the wavelet method. > I was surprise to see that whereas I asked for a step of 1Hz, it was > not > the case every alternate step (for foi=2:1:10 ; I got [2 3.2 4 5.2 6 > 7.2 8 > 9.2 10]), and it was also the case when I changed the toi (2.5, 1.5 > with > constant trials length of 2.5 sec and sampling freq 1000Hz). > I found a kind of explanation following the faq > (http://fieldtrip.fcdonders.nl/faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_wavelet_formerly_wltconvol_in_ft_freqanalyis > ). > Still it is not clear to me why this refers to Fourier transform. >> From my (none specialist) point of view it is possible to produce a > wavelet of any size (Hz;Dt). > It is clear that there is some limitations based on the duration of > the > epochs and the number of time points. But in the present case it > shouldn't > be a problem, is it? > Would be please if someone can help me with this issue. > Thanks in advance > > Manuel > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From a.wollbrink at uni-muenster.de Tue Jun 21 10:05:19 2011 From: a.wollbrink at uni-muenster.de (Andreas Wollbrink) Date: Tue, 21 Jun 2011 10:05:19 +0200 Subject: [FieldTrip] concatenating data to a single trial data set In-Reply-To: References: <4DFF4102.3020101@uni-muenster.de> Message-ID: <4E0050BF.80008@uni-muenster.de> Dear Eelke, dear Nathan, thanks for your help on a way to concatenate the data. In the end I successfully used a mixture of both approaches you suggested. Best, Andreas On 06/20/11 15:35, Eelke Spaak wrote: > Dear Andreas, > > The way I concatenate data is just 'manually', so without the > intervention of FieldTrip. To do this, you will have to concatenate > the arrays in both the data.trial and the data.time cell array. > > In pseudocode: > > initialize matrix data_concat of size channels X total time points > initialize matrix time_concat of size 1 X total time points > > loop over data.trial and data.time (have the same size) > data_concat(:,appropriate time indices) = data.trial{k}(:,:); > time_concat(1,appropriate time indices) = data.time{k}(:); > end loop > > data.trial = data_concat; > data.time = time_concat; > > That should do the trick. I would have provided actual code, were it > not that I am doing something slightly different from what you are > asking. > > I hope this helps! > > Best, > Eelke > > 2011/6/20 Andreas Wollbrink: >> Dear all, >> >> in order not to run into a RAM memory overload when performing an ICA on MEG >> data I subdivided the raw data into several equally long segments (chops) >> using ft_preprocessing with varying cfg.trl settings. >> After applying ft_componentanalysis to each of these chops I removed some >> (bad) components and backprojected the data to seperate data matrices using >> the following code: >> >> cfg = []; >> cfg.component = badCompVec; % to be removed component(s) >> dataCorr = ft_rejectcomponent(cfg, compData); >> >> >> Finally I like to concatenate these data to a continuous (single trial) data >> matrix in order to compare it with the original raw data set and perform the >> further timelock analysis on it. >> >> I tried using ft_appenddata for this issue. Doing so one gets a multi trial >> data matrix which I could not convert to single trial continuous data matrix >> using e.g. ft_redefinetrial. >> >> I would appreciate any help in how to solve this problem. >> >> Thanks in advance. >> >> Andreas Wollbrink >> -- >> >> >> ====================================================================== >> >> Andreas Wollbrink, Biomedical Engineer >> >> Institute for Biomagnetism and Biosignalanalysis >> Muenster University Hospital >> >> Malmedyweg 15 phone: +49-(0)251-83-52546 >> D-48149 Muenster mobil: +49-(0)160-98527553 >> Germany fax: +49-(0)251-83-56874 >> e-Mail: a.wollbrink at uni-muenster.de >> >> ====================================================================== >> _______________________________________________ >> 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 -- ====================================================================== Andreas Wollbrink, Biomedical Engineer Institute for Biomagnetism and Biosignalanalysis Muenster University Hospital Malmedyweg 15 phone: +49-(0)251-83-52546 D-48149 Muenster mobil: +49-(0)160-98527553 Germany fax: +49-(0)251-83-56874 e-Mail: a.wollbrink at uni-muenster.de ====================================================================== From drivolta81 at gmail.com Tue Jun 21 15:24:31 2011 From: drivolta81 at gmail.com (Davide Rivolta) Date: Tue, 21 Jun 2011 15:24:31 +0200 Subject: [FieldTrip] downsampling MEG data Message-ID: Dear fieldtrippers, I have recorded some MEG data with a sampling rate of 6000 Hz. I would need to downsample it to 600 Hz. What is the best way to do it? It something I have to do in the preprocessing I guess. Any advice would be really appreciated, Thanks, Davide -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Tue Jun 21 15:29:59 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 21 Jun 2011 15:29:59 +0200 Subject: [FieldTrip] downsampling MEG data In-Reply-To: References: Message-ID: Dear Davide, Have a look at the ft_resampledata function: http://fieldtrip.fcdonders.nl/reference/ft_resampledata Best, Eelke 2011/6/21 Davide Rivolta : > Dear fieldtrippers, > > I have recorded some MEG data with a sampling rate of 6000 Hz. > I would need to downsample it to 600 Hz. > > What is the best way to do it? > > It something I have to do in the preprocessing I guess. > > Any advice would be really appreciated, > > Thanks, > > Davide > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From batrod at gmail.com Tue Jun 21 15:37:54 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Tue, 21 Jun 2011 08:37:54 -0500 Subject: [FieldTrip] downsampling MEG data In-Reply-To: References: Message-ID: Dear Davide, the function ft_resampledata should do that perfectly ! :) On Tue, Jun 21, 2011 at 8:24 AM, Davide Rivolta wrote: > Dear fieldtrippers, > > I have recorded some MEG data with a sampling rate of 6000 Hz. > I would need to downsample it to 600 Hz. > > What is the best way to do it? > > It something I have to do in the preprocessing I guess. > > Any advice would be really appreciated, > > Thanks, > > Davide > > _______________________________________________ > 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 Jun 21 16:08:21 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 21 Jun 2011 16:08:21 +0200 Subject: [FieldTrip] Publications using FieldTrip: add your own! Message-ID: Dear Fieldtrippers, We have revamped the list of publications using FieldTrip on our wiki website. I wrote a plugin for Dokuwiki, enabling the wiki to parse BibTeX code (see http://www.bibtex.org/ if you don't know what this is). This allows all of you to easily add your publications using FieldTrip to our wiki, improving the visibility of both FieldTrip and your papers. The list is quite extensive already, but we explicitly invite all of you to browse through it and add anything we might have missed. Editing the page is done by going to Page tools (top left, above the site menu) --> Edit this page. If you are not familiar with BibTeX syntax, it is probably easiest to just look at what is already there and use that as an example. Note that the list will be automatically sorted by year and by first author, so you can just insert new entries wherever you like. Visit http://fieldtrip.fcdonders.nl/publications to see the new page. Best, Eelke From johanna.zumer at donders.ru.nl Tue Jun 21 16:56:20 2011 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Tue, 21 Jun 2011 16:56:20 +0200 Subject: [FieldTrip] code change in ft_compute_leadfield.m Message-ID: Dear FieldTrip users, I've made a small change to ft_compute_leadfield (available in tonight's release) regarding how the 'reducerank' option is handled, if multiple dipole locations are entered all at once into ft_compute_leadfield.m. This will *not* affect the vast majority of users, since usually ft_compute_leadfield is called by higher FT functions and not directly by users. For example, it will not affect you if you create a leadfield either by calling ft_prepare_leadfield or by letting ft_sourceanalysis compute the leadfield for you (regardless of your 'reducedrank' option), since these higher level FT functions call ft_compute_leadfield in a for-loop over dipole location (and _not_ multiple dipole locations at once). For completeness, here's a list of (rare) cases when it will affect your results: 1) If you call ft_compute_leadfield directly with Nx3 dipoles (N>1) and reducerank='yes' (or =2) 2) If you use a refdip in beamformer_DICS or beamformer_PCC, or a supdip in beamformer_PCC, of *more than 1 dipole location* at a time (Nx3 refdip or subdip, where N>1), AND you specified reducerank='yes' (or =2) in any of these cases. 3) Default behaviour of calling ft_dipolefitting will not change. However if you call dipole_fit directly with more than one dipole AND reducerank='yes' (or =2). Please let me know if this isn't clear. Best, Johanna -------------- next part -------------- An HTML attachment was scrubbed... URL: From BelluscB at ninds.nih.gov Tue Jun 21 23:24:16 2011 From: BelluscB at ninds.nih.gov (Belluscio, Beth (NIH/NINDS) [E]) Date: Tue, 21 Jun 2011 17:24:16 -0400 Subject: [FieldTrip] define events for ft_definetrial Message-ID: <794DFDD3C128EF44AC49ADC58FD0090C04F09E165B@NIHMLBX10.nih.gov> HI all- I use CFT data sets in which I use a trigger channel to define various stimuli (usually called stim1, stim2, stim3). Each stim repeats several times (120) during the data file. The time points corresponding to each stim are catalogued in the MarkerFile.mrk file. I would like to use these markers to define trials around each stim. I used to do this with the following set of commands: cfg = []; cfg.dataset = 'TS1.ds'; cfg.trialdef.eventtype = 'stim1'; cfg.trialdef.prestim = 0.1; cfg.trialdef.posstim = 3.0; cfg = ft_definetrial(cfg) Now when I do this I get the following error messages: readCTFds: Data set error: size of meg4 files(s) 0 bytes (from dir command) 1126080000 (from res4 file) ??? Attempt to reference field of non-structure array. Error in ==> trialfun_general at 111 For i=find(strcmp(cfg.trialdef.eventtype, {event.types})) Error in==> ft_definetrial at 126 [trl, event] = feval(cfg.trialfun, cfg) Is this a problem with the way I am defining the events? How can I use these markers within the data file to specify events in fieldtrip? Thanks, Beth Belluscio MD-PhD Clinical Fellow Human Motor Control Section NINDS, NIH 301-402-3495 -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at fcdonders.ru.nl Wed Jun 22 08:12:48 2011 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Wed, 22 Jun 2011 08:12:48 +0200 (CEST) Subject: [FieldTrip] define events for ft_definetrial In-Reply-To: <794DFDD3C128EF44AC49ADC58FD0090C04F09E165B@NIHMLBX10.nih.gov> Message-ID: <49300862.469268.1308723168601.JavaMail.root@sculptor.zimbra.ru.nl> Hi Beth, Just wondering. Did you copy those lines from your script? If so, please try cfg.trialdef.poststim = 3.0; (notice the t). Yours, Arjen ----- "Beth Belluscio (NIH/NINDS) [E]" schreef: > Van: "Beth Belluscio (NIH/NINDS) [E]" > Aan: "fieldtrip at donders.ru.nl" > Verzonden: Dinsdag 21 juni 2011 23:24:16 > Onderwerp: [FieldTrip] define events for ft_definetrial > > > HI all-   I use CFT data sets in which I use a trigger channel to define various stimuli (usually called stim1, stim2, stim3).  Each stim repeats several times (120) during the data file.  The time points corresponding to each stim are catalogued in the MarkerFile.mrk file.  I would like to use these markers to define trials around each stim.  I used to do this with the following set of commands:                 cfg = [];                 cfg.dataset = ‘TS1.ds’;                 cfg.trialdef.eventtype = ‘stim1’;                 cfg.trialdef.prestim = 0.1;                 cfg.trialdef.posstim = 3.0;                 cfg = ft_definetrial(cfg) Now when I do this I get the following error messages:                 readCTFds: Data set error:  size of meg4 files(s)                                 0 bytes (from dir command)                                 1126080000 (from res4 file)                 ??? Attempt to reference field of non-structure array.                 Error in è trialfun_general at 111                 For i=find(strcmp(cfg.trialdef.eventtype, {event.types}))                                 Error in è ft_definetrial at 126                 [trl, event] = feval(cfg.trialfun, cfg) Is this a problem with the way I am defining the events?  How can I use these markers within the data file to specify events in fieldtrip? Thanks, Beth Belluscio MD-PhD Clinical Fellow Human Motor Control Section NINDS, NIH 301-402-3495 > _______________________________________________ > 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 Jun 22 08:59:04 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 22 Jun 2011 08:59:04 +0200 Subject: [FieldTrip] define events for ft_definetrial In-Reply-To: <794DFDD3C128EF44AC49ADC58FD0090C04F09E165B@NIHMLBX10.nih.gov> References: <794DFDD3C128EF44AC49ADC58FD0090C04F09E165B@NIHMLBX10.nih.gov> Message-ID: <4D29A1F9-957B-41E4-8CBC-582BF0AD25D6@donders.ru.nl> Dear Beth, It could be that your dataset is corrupt. > readCTFds: Data set error: size of meg4 files(s) > 0 bytes (from dir command) > 1126080000 (from res4 file) This is namely a low level reading error. It then percolates to the next step, where > > ??? Attempt to reference field of non-structure array. which is most likely caused by FieldTrip not having been successful in creating an event structure. > > Error in è trialfun_general at 111 > For i=find(strcmp(cfg.trialdef.eventtype, > {event.types})) > > Error inè ft_definetrial at 126 > [trl, event] = feval(cfg.trialfun, cfg) > > Is this a problem with the way I am defining the events? How can I > use these markers within the data file to specify events in fieldtrip? Does this pertain to this particular dataset? Best Jan-Mathijs PS: please update to a more recent version of FieldTrip: the content of the line number in which the errer occurs does not coincide with my version > > Thanks, > > Beth Belluscio MD-PhD > Clinical Fellow > Human Motor Control Section > NINDS, NIH > 301-402-3495 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From lulswinnik at gmail.com Thu Jun 23 12:30:35 2011 From: lulswinnik at gmail.com (Ekaterina Vinnik) Date: Thu, 23 Jun 2011 11:30:35 +0100 Subject: [FieldTrip] Champalimaud Neuroscience Symposium announcement; early registration deadline 30 of June Message-ID: The Champalimaud Neuroscience Symposium will bring together researchers from around the world who are interested in solving the puzzle of the brain. The Programme includes 30 distinguished speakers (including Gyorgy Buzsaki, Antonio Damasio, Jim DiCarlo, Ranulfo Romo, Erin Schuman and Haim Sompolinsky) and poster sessions. The Symposium will take place at the Champalimaud Centre for the Unknown on the waterfront in central Lisbon, Portugal. We are looking forward to a lively and stimulating scientific meeting, and we hope that you will join us. more information at http://symposium.neuro.fchampalimaud.org/ http://www.facebook.com/event.php?eid=191246457589517 The early registration deadline is 30 of June (150/300 euro fee), though abstracts are not due till 31 of August. Travel grants available! Join us in Lisbon, All the best, Ekaterina -- Ekaterina Vinnik, MD, PhD Behavioural neuroscience lab, Champalimaud Neuroscience, Lisbon, Portugal +351918951392 lulswinnik at gmail.com From ekanal at cmu.edu Fri Jun 24 16:21:47 2011 From: ekanal at cmu.edu (Kanal Eliezer) Date: Fri, 24 Jun 2011 10:21:47 -0400 Subject: [FieldTrip] plot ave + variance Message-ID: Hello fieldtrip - Is there a simple way to plot a timelock average along with confidence intervals? I simply want to see how much the data varied across trials. The structure returned by the ft_timelock function contains a `var` element, but the data it contains is many order of magnitude smaller than that in the `ave` element. Thanks - Elli -------------------- Eliezer Kanal, Ph.D. Postdoctoral Fellow Center for the Neural Basis of Cognition Carnegie Mellon University 4400 Fifth Ave, Suite 110A Pittsburgh PA 15213 P: 412-268-4115 F: 412-268-5060 From akiko at nyu.edu Fri Jun 24 17:42:20 2011 From: akiko at nyu.edu (Akiko Ikkai) Date: Fri, 24 Jun 2011 11:42:20 -0400 Subject: [FieldTrip] ft_sourceanalysis & ft_sourceinterpolate Message-ID: Hi, I'm working on beamformer with MEG data, and having trouble making ft_sourceanalysis and/or ft_sourceinterpolate work. It appears that anatomical MRI and source data do not align, although anatomical MRI ("mri_aligned") and the result of ft_prepare_singleshell ("vol_cm") are both aligned with MEG helmet. Is there any way I could verify that the output of ft_sourceanalysis is not distorted (i.e. same space as input)? I'm using fieldtrip-20110525 version. Thanks in advance! Akiko Below is my code: 1. compute the common filter cfg = []; cfg.grad = data_common.grad; % data_common = baseline + left + right cfg.grid.xgrid = -15:0.5:15; cfg.grid.ygrid = -15:0.5:15; cfg.grid.zgrid = -15:0.5:15; cfg.inwardshift = -2; cfg.vol = vol_cm; % this is from segmented "mri_aligned" cfg.channel = {'all'}; cfg.reducerank = 2; cfg.frequency = 10; cfg.method = 'dics'; cfg.projectnoise = 'yes'; cfg.keepfilter = 'yes'; cfg.feedback = 'no'; cfg.realfilter = 'yes'; cfg.lambda = '0.005%'; source_common = ft_sourceanalysis(cfg, freq_common) 2. compute the spatial filter for one of the conditions (using grid & filter from the step 1) cfg = []; cfg.grad = data_common.grad; cfg.grid.pos = source_common.pos; % using grid & filter from the common filter cfg.grid.filter = source_common.avg.filter; cfg.vol = vol_cm; cfg.channel = {'all'}; cfg.reducerank = 2; cfg.frequency = 10; cfg.method = 'dics'; cfg.projectnoise = 'yes'; cfg.keepfilter = 'no'; cfg.feedback = 'no'; cfg.realfilter = 'yes'; cfg.lambda = '0.005%'; source_left = ft_sourceanalysis(cfg, freq_stiml); source_left.unit = 'cm'; source_left.dim = source_common.dim; 3. calculate difference source_left_bl = source_left; source_left_bl.avg.pow = source_left_bl.avg.pow ./ source_common.avg.pow; 4. interpolate source to anatomical MRI space cfg = []; cfg.method = 'linear'; source_left_bl_int = ft_sourceinterpolate(cfg, source_left_bl,mri_aligned); -------------- next part -------------- An HTML attachment was scrubbed... URL: From ekanal at cmu.edu Fri Jun 24 21:17:42 2011 From: ekanal at cmu.edu (Kanal Eliezer) Date: Fri, 24 Jun 2011 15:17:42 -0400 Subject: [FieldTrip] plot ave + variance In-Reply-To: <31844_1308925377_p5OEMuo1011583_B732C6AD-E522-4B28-8D7A-0660CF0520A8@cmu.edu> References: <31844_1308925377_p5OEMuo1011583_B732C6AD-E522-4B28-8D7A-0660CF0520A8@cmu.edu> Message-ID: I apologize; I wasn't thinking. stdev = var^2. Elli On Jun 24, 2011, at 10:21 AM, Kanal Eliezer wrote: > Hello fieldtrip - > > Is there a simple way to plot a timelock average along with confidence intervals? I simply want to see how much the data varied across trials. The structure returned by the ft_timelock function contains a `var` element, but the data it contains is many order of magnitude smaller than that in the `ave` element. Thanks - > > Elli > > > -------------------- > Eliezer Kanal, Ph.D. > Postdoctoral Fellow > Center for the Neural Basis of Cognition > Carnegie Mellon University > 4400 Fifth Ave, Suite 110A > Pittsburgh PA 15213 > P: 412-268-4115 > F: 412-268-5060 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From paul_c at gmx.de Mon Jun 27 10:11:51 2011 From: paul_c at gmx.de (Paul Czienskowski) Date: Mon, 27 Jun 2011 10:11:51 +0200 Subject: [FieldTrip] Brainvision renamer tool In-Reply-To: References: <31844_1308925377_p5OEMuo1011583_B732C6AD-E522-4B28-8D7A-0660CF0520A8@cmu.edu> Message-ID: <4E083B47.4070008@gmx.de> Dear all, I wrote a small brainvision renamer tool based on RegEx patters which I needed to make the filenames of my EEG-Recordings more consistent. If anyone is interested in, check out http://code.google.com/p/eeg-renamer/ Cheers, Paul -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 From Hanneke.vanDijk at med.uni-duesseldorf.de Mon Jun 27 10:38:03 2011 From: Hanneke.vanDijk at med.uni-duesseldorf.de (Hanneke.vanDijk at med.uni-duesseldorf.de) Date: Mon, 27 Jun 2011 10:38:03 +0200 Subject: [FieldTrip] ft_databrowser Message-ID: <72E993C35FB11743B79FF9286E5B6D8B029F8B2A@Mail2-UKD.VMED.UKD> Dear FT-ers, I have discovered ft_databrowser a few weeks ago (maybe abit late ;-))! Thanks so much for implementing this, I like it. I am setting up a small presentation about artifact rejection using FT and decided to use the tutorial data (Subject01.ds) to generate some examples. When I use the raw dataset and cfg.continuous = 'yes', it runs fine but after preprocessing (as in the online tutorial; and cfg.continuous = 'no') I run into this problem: cfg = ft_databrowser(cfg,dataFIC); the input is raw data with 152 channels and 87 trials redrawing with viewmode butterfly fetching data... done fetching artifacts... done preprocessing data... done plotting data... ??? Reference to non-existent field 'hlim'. Error in ==> ft_databrowser>redraw_cb at 1003 eventtim = (eventtim - opt.hlim(1)) / (opt.hlim(2) - opt.hlim(1)); % convert to value relative to box, i.e. from 0 to 1 Error in ==> ft_databrowser at 434 redraw_cb(h); 'opt' indeed does not contain 'hlim' and also no 'hpos' which is asked for a line later. I think it originates in the input given into the function guidata. I hope you can help me! Groetjes Hanneke __________________________________________ Dr. Hanneke van Dijk http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNe urowiss/Team/HannekevanDijk/page.html Institute for Clinical Neuroscience, Heinrich Heine Universitaet Duesseldorf, Germany Hanneke.vanDijk at med.uni-duesseldorf.de Tel. +49 (0) 211 81 13074 __________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Tue Jun 28 09:19:13 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 28 Jun 2011 09:19:13 +0200 Subject: [FieldTrip] ft_databrowser In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8B029F8B2A@Mail2-UKD.VMED.UKD> References: <72E993C35FB11743B79FF9286E5B6D8B029F8B2A@Mail2-UKD.VMED.UKD> Message-ID: <4E098071.6010502@donders.ru.nl> Dear Hanneke, Thanks for reporting this. We are currently working on improving the databrowser in terms of code readability, which also includes removing some bugs. We will also deal with this one, if not already done (I will check) Best, Jörn On 6/27/2011 10:38 AM, Hanneke.vanDijk at med.uni-duesseldorf.de wrote: > > Dear FT-ers, > > I have discovered ft_databrowser a few weeks ago (maybe abit late > ;-))! Thanks so much for implementing this, I like it. > > I am setting up a small presentation about artifact rejection using FT > and decided to use the tutorial data (Subject01.ds) to generate some > examples. When I use the raw dataset and cfg.continuous = 'yes', it > runs fine but after preprocessing (as in the online tutorial; and > cfg.continuous = 'no') I run into this problem: > > cfg = ft_databrowser(cfg,dataFIC); > > the input is raw data with 152 channels and 87 trials > > redrawing with viewmode butterfly > > fetching data... done > > fetching artifacts... done > > preprocessing data... done > > plotting data... ??? Reference to non-existent field 'hlim'. > > Error in ==> ft_databrowser>redraw_cb at 1003 > > eventtim = (eventtim - opt.hlim(1)) / (opt.hlim(2) - > opt.hlim(1)); % convert to value relative to > > box, i.e. from 0 to 1 > > Error in ==> ft_databrowser at 434 > > redraw_cb(h); > > 'opt' indeed does not contain 'hlim' and also no 'hpos' which is asked > for a line later. I think it originates in the input given into the > function guidata. > > I hope you can help me! > > Groetjes Hanneke > > __________________________________________ > > Dr. Hanneke van Dijk > > http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html > > Institute for Clinical Neuroscience, > > Heinrich Heine Universitaet Duesseldorf, Germany > > Hanneke.vanDijk at med.uni-duesseldorf.de > > > Tel. +49 (0) 211 81 13074 > > __________________________________________ > > > _______________________________________________ > 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 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 suforraxi at gmail.com Tue Jun 28 14:46:28 2011 From: suforraxi at gmail.com (Matteo Demuru) Date: Tue, 28 Jun 2011 14:46:28 +0200 Subject: [FieldTrip] WPLI statistic, permutation like test?? Message-ID: Hi, I have a couple of questions about using the WPLI index to assess the phase on my MEG data. The experiment consists of recordings during a mental calculation task: I have 30 sec in which each subject performed continuously an arithmetic operation. It seems to me that WPLI index required more than one trial in order to be computed. Am I right? (Is this necessary in order to reduce volume conduction problems?) I could divide my 30 sec in 5 sec-trials to create my trials, but I was wandering if this could be a misuse of the WPLI, i.e. WPLI is not appropriate for my experiment. I am also interested in assessing the significance of WPLI index, I would like to gauge the significance per se of my WPLI values. The idea is to calculate the WPLI distribution under the null hypothesis (not phase coupling) for each pair of channels in this way: Example to assess the significance of WPLI value for ch1 vs ch2 1) Calculate the WPLI for ch1 and ch2, this would be the observed WPLI (WPLI_observed) 2) Randomly permute the ch2 time series 3) Calculate the WPLI for ch1 and ch2 (WPLI_i) 4) Repeat step 2 and 3 (for instance 100 times) in order to create the WPLI_i distribution 5) Calculate the proportion ( # (WPLI_i > WPLI_observed) / # (WPLI_i ) ) of WPLI_i which are greater than the WPLI_observed, if this proportion is < 0.05 I could say that the WPLI_observed represents a significant degree of phase, otherwise not. Does it make sense or is it not the right approach? Let suppose this is a correct approach, I have two other questions: First, usually when I compute the WPLI value between two channels I obtain a number of WPLI values according to the cross-spectrum times (one WPLI for each sliding window), in the steps above I am assuming to compute the average WPLI_observed and the average WPLI_i for each step. Does this raise any problems? Second, is it a problem using the same random permutations employed to obtain ch1-ch2 (WPLI_i distribution) to calculate also the ch1-ch3 (WPLI_i distribution). This is just an implementatiion question. I would like to know if I could shuffle the time series of other channels in one step (i.e. for ch1 something like data.trial{other_than_ch1,perm}), and finally extract just the column relative to ch1 from WPLI matrix. thanks Matteo -------------- next part -------------- An HTML attachment was scrubbed... URL: From dimitri.bayle at inserm.fr Tue Jun 28 15:14:43 2011 From: dimitri.bayle at inserm.fr (Dimitri BAYLE) Date: Tue, 28 Jun 2011 15:14:43 +0200 Subject: [FieldTrip] DICS conditions comparison Message-ID: <4E09D3C3.6050906@inserm.fr> Dear Fieldtrip-users, I have a general question about source analysis comparison. I want to compare visual alpha deactivation between 2 conditions (A and B), both containing a baseline (pre) interval and a poststimulus interval, and both showing a strong occipital visual deactivation when comparing the relative contrast ((preA-postA)/preA). To compare A and B, should i calculated a common filter for the baseline and another one for the poststimulus interval, or used the same filter (calculated on which interval)? After applying the filter to all individuals trials (pre and post stimulus), is it better to 1) average alls trials, then calculated the relative contrast for A and for B ((pre-post)/pre)), and substract A and B relative contrast to reveal the difference or 2) calculated the relative contrast for each individuals trials, then average all relatives contrast per conditions (A and B), and substract A and B? Thanks for your help Dimitri From michael.wibral at web.de Tue Jun 28 20:34:28 2011 From: michael.wibral at web.de (Michael Wibral) Date: Tue, 28 Jun 2011 20:34:28 +0200 (CEST) Subject: [FieldTrip] WPLI statistic, permutation like test?? Message-ID: <7105645.2302309.1309286068611.JavaMail.fmail@mwmweb088> An HTML attachment was scrubbed... URL: From suforraxi at gmail.com Wed Jun 29 10:01:15 2011 From: suforraxi at gmail.com (Matteo Demuru) Date: Wed, 29 Jun 2011 10:01:15 +0200 Subject: [FieldTrip] WPLI statistic, permutation like test?? In-Reply-To: <7105645.2302309.1309286068611.JavaMail.fmail@mwmweb088> References: <7105645.2302309.1309286068611.JavaMail.fmail@mwmweb088> Message-ID: Hi Micheal, It seems to me that if you shuffle the trials and then compute the WPLI, the result is the same as if you do not shuffle. For example I have tried compute the WPLI on my trials and then switch trial{1} with trial{2} and the obtained WPLI is the same. Matteo On Tue, Jun 28, 2011 at 8:34 PM, Michael Wibral wrote: > Hi Matteo, > > I am not an expert on the WPLI measures, but to me it seems that in doing > > > "2) Randomly permute the ch2 time series" > > you're destroying a lot of ch2's properties (ie.g. it's spectrum will get a > lot of high ferquencies this way) and this will typically lead to false > positives. This is why permutation tests for connectivity measures typically > shuffle trials (i.e. permute data in a very controlled way, keeping the > intrinsic structure of the data). > > Michael > > > ------------------------------ > *Von:* "Matteo Demuru" > *Gesendet:* Jun 28, 2011 2:46:28 PM > *An:* fieldtrip at donders.ru.nl > *Betreff:* [FieldTrip] WPLI statistic, permutation like test?? > > > Hi, > > I have a couple of questions about using the WPLI index to assess the phase > on my MEG data. > > The experiment consists of recordings during a mental calculation task: I > have 30 sec in which each subject performed continuously an arithmetic > operation. > > It seems to me that WPLI index required more than one trial in order to be > computed. Am I right? (Is this necessary in order to reduce volume > conduction problems?) > I could divide my 30 sec in 5 sec-trials to create my trials, but I was > wandering if this could be a misuse of the WPLI, i.e. WPLI is not > appropriate for my experiment. > > I am also interested in assessing the significance of WPLI index, I would > like to gauge the significance per se of my WPLI values. > The idea is to calculate the WPLI distribution under the null hypothesis > (not phase coupling) for each pair of channels in this way: > > Example to assess the significance of WPLI value for ch1 vs ch2 > > 1) Calculate the WPLI for ch1 and ch2, this would be the observed WPLI > (WPLI_observed) > > 2) Randomly permute the ch2 time series > > 3) Calculate the WPLI for ch1 and ch2 (WPLI_i) > > 4) Repeat step 2 and 3 (for instance 100 times) in order to create the WPLI_i > distribution > > 5) Calculate the proportion ( # (WPLI_i > WPLI_observed) / # (WPLI_i ) ) > of WPLI_i which are greater than the WPLI_observed, if this proportion > is < 0.05 I could say that the WPLI_observed represents a significant > degree of phase, otherwise not. > > Does it make sense or is it not the right approach? > > Let suppose this is a correct approach, I have two other questions: > > First, usually when I compute the WPLI value between two channels I obtain > a number of WPLI values according to the cross-spectrum times (one WPLI for > each sliding window), in the steps above I am assuming to compute the > average WPLI_observed and the average WPLI_i for each step. Does this > raise any problems? > > Second, is it a problem using the same random permutations employed to > obtain ch1-ch2 (WPLI_i distribution) to calculate also the ch1-ch3 (WPLI_i distribution). > This is just an implementatiion question. I would like to know if I could > shuffle the time series of other channels in one step (i.e. for ch1 > something like data.trial{other_than_ch1,perm}), and finally extract just > the column relative to ch1 from WPLI matrix. > > thanks > > Matteo > > > > > > > > > > _______________________________________________ > 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 michael.wibral at web.de Wed Jun 29 17:35:29 2011 From: michael.wibral at web.de (Michael Wibral) Date: Wed, 29 Jun 2011 17:35:29 +0200 (CEST) Subject: [FieldTrip] WPLI statistic, permutation like test?? Message-ID: <786760757.45247.1309361729100.JavaMail.fmail@mwmweb077> An HTML attachment was scrubbed... URL: From paul_c at gmx.de Wed Jun 29 20:54:06 2011 From: paul_c at gmx.de (Paul Czienskowski) Date: Wed, 29 Jun 2011 20:54:06 +0200 Subject: [FieldTrip] ft_databrowser problems and questions Message-ID: <4E0B74CE.3050306@gmx.de> Dear all, I'm trying to plot ICA components with the ft_databrowser function. First of all the topoplots seem to look not like I'm used to. The topoplots I've seen this far filled out the whole circle and not only the rectangle it fills here (see attachment). Second one is, that sometimes, the functions starts to plot unselected components overlaying the selected components. Additionally there is a Question I have. I marked artifacts in the original data (with the ft_databrowser function) and hoped, they would be shown in the ft_databrowser too, when I'm plotting the components. Is there any (easy) way to accomplish this? Cheers, Paul -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 -------------- next part -------------- A non-text attachment was scrubbed... Name: 1to8.png Type: image/png Size: 38959 bytes Desc: not available URL: From megjim1 at gmail.com Thu Jun 30 08:05:08 2011 From: megjim1 at gmail.com (Jim Li) Date: Thu, 30 Jun 2011 01:05:08 -0500 Subject: [FieldTrip] channelrepair issue Message-ID: Dear all, We have 4D's WH3600 MEG system (248 channels) and we found the ----------------- cfg = []; cfg.dataset = 'e,rfhp0.1Hz'; cfg.trialdef.eventtype = 'TRIGGER'; cfg.trialdef.eventvalue = 320; cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 1; cfg = ft_definetrial(cfg); cfg.blc = 'yes'; cfg.blcwindow = [-1 0]; cfg.channel = {'MEG'}; raw_DATA = ft_preprocessing(cfg); raw_DATA.grad = ft_convert_units(raw_DATA.grad, 'cm') cfg = []; cfg.badchannel = {'A234'}; [raw_DATA] = ft_channelrepair(cfg, raw_DATA) the input is raw data with 248 channels and 201 trials repairing channel A234 using neighbour A121 using neighbour A143 using neighbour A154 using neighbour A173 using neighbour A224 using neighbour A8 using neighbour A91 repairing bad channels for trial 1 repairing bad channels for trial 2 repairing bad channels for trial 3 ... ------------------------------------ But channels like A121 and A143 are far away from the bad channel A234. How can they be used as neighbours (i.e. within 4cm, the default value for cfg.neighbourdist) for this bad channel? Any suggestions? Thanks a lot. Jim -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Jun 30 08:50:25 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 30 Jun 2011 08:50:25 +0200 Subject: [FieldTrip] channelrepair issue In-Reply-To: References: Message-ID: Hi Jim, where exactly are they located with respect to the bad channel? Best, Jan-Mathijs On Jun 30, 2011, at 8:05 AM, Jim Li wrote: > Dear all, > > We have 4D's WH3600 MEG system (248 channels) and we found the > ----------------- > cfg = []; > > cfg.dataset = > > 'e,rfhp0.1Hz'; > cfg.trialdef.eventtype = 'TRIGGER'; > > cfg.trialdef.eventvalue = 320; > > cfg.trialdef.prestim = 1; > > cfg.trialdef.poststim = 1 > > ; > cfg = ft_definetrial(cfg); > > cfg.blc = > > 'yes'; > cfg.blcwindow = [-1 0]; > > cfg.channel = {'MEG'}; > > raw_DATA = ft_preprocessing(cfg); > > raw_DATA.grad = ft_convert_units(raw_DATA.grad, 'cm') > > > cfg = []; > cfg.badchannel = {'A234'}; > [raw_DATA] = ft_channelrepair(cfg, raw_DATA) > the input is raw data with 248 channels and 201 trials > repairing channel A234 > using neighbour A121 > using neighbour A143 > using neighbour A154 > using neighbour A173 > using neighbour A224 > using neighbour A8 > using neighbour A91 > repairing bad channels for trial 1 > repairing bad channels for trial 2 > repairing bad channels for trial 3 > ... > ------------------------------------ > > But channels like A121 and A143 are far away from the bad channel > A234. How can they be used as neighbours (i.e. within 4cm, the > default value for cfg.neighbourdist) for this bad channel? > > Any suggestions? > > Thanks a lot. > > Jim > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Thu Jun 30 09:45:57 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 30 Jun 2011 09:45:57 +0200 Subject: [FieldTrip] ft_databrowser problems and questions In-Reply-To: <4E0B74CE.3050306@gmx.de> References: <4E0B74CE.3050306@gmx.de> Message-ID: <4E0C29B5.8060201@donders.ru.nl> Dear Paul, the topoplot bug you get should have been resolved in some newer FieldTrip version, I can remember this one and resolved it a while ago. The overlaying plotting is simply caused because you click too fast. The function plots the individual topos- and time courses. Any callback from one of the buttons does not interrupt this plotting, meaning that it will clear the axes, continue plotting the topos- and time courses if this was not already finished and then start plotting the new topos- and time courses. This will be resolved in a newer version (see below). About the third question: In the current implementation, this is not possible. However, we just started restructuring the code for the databrowser, and in my opinion it should be ready to be made public. In the new implementation, you can annotate and see annotated artifacts in component viewmode. I will keep you up to date on this. Best, Jörn ThisOn 6/29/2011 8:54 PM, Paul Czienskowski wrote: > Dear all, > > I'm trying to plot ICA components with the ft_databrowser function. > First of all the topoplots seem to look not like I'm used to. The > topoplots I've seen this far filled out the whole circle and not only > the rectangle it fills here (see attachment). Second one is, that > sometimes, the functions starts to plot unselected components > overlaying the selected components. > Additionally there is a Question I have. I marked artifacts in the > original data (with the ft_databrowser function) and hoped, they would > be shown in the ft_databrowser too, when I'm plotting the components. > Is there any (easy) way to accomplish this? > > Cheers, > Paul > > > > > _______________________________________________ > 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 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 odidodi at hotmail.com Thu Jun 30 11:04:55 2011 From: odidodi at hotmail.com (odelia nakar) Date: Thu, 30 Jun 2011 09:04:55 +0000 Subject: [FieldTrip] channelrepair issue In-Reply-To: References: Message-ID: Hi Jim, Try : cfg.neighbourdist = 0.03; I found it good for my data. (When you run the function the channels that repaired your data is displayed in the command window). Good luck! Odelia. Date: Thu, 30 Jun 2011 01:05:08 -0500 From: megjim1 at gmail.com To: fieldtrip at donders.ru.nl Subject: [FieldTrip] channelrepair issue Dear all, We have 4D's WH3600 MEG system (248 channels) and we found the ----------------- cfg = []; cfg.dataset = 'e,rfhp0.1Hz'; cfg.trialdef.eventtype = 'TRIGGER'; cfg.trialdef.eventvalue = 320; cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 1; cfg = ft_definetrial(cfg); cfg.blc = 'yes'; cfg.blcwindow = [-1 0]; cfg.channel = {'MEG'}; raw_DATA = ft_preprocessing(cfg); raw_DATA.grad = ft_convert_units(raw_DATA.grad, 'cm') cfg = []; cfg.badchannel = {'A234'}; [raw_DATA] = ft_channelrepair(cfg, raw_DATA) the input is raw data with 248 channels and 201 trials repairing channel A234 using neighbour A121 using neighbour A143 using neighbour A154 using neighbour A173 using neighbour A224 using neighbour A8 using neighbour A91 repairing bad channels for trial 1 repairing bad channels for trial 2 repairing bad channels for trial 3 ... ------------------------------------ But channels like A121 and A143 are far away from the bad channel A234. How can they be used as neighbours (i.e. within 4cm, the default value for cfg.neighbourdist) for this bad channel? Any suggestions? Thanks a lot. Jim _______________________________________________ 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 megjim1 at gmail.com Thu Jun 30 17:39:23 2011 From: megjim1 at gmail.com (Jim Li) Date: Thu, 30 Jun 2011 10:39:23 -0500 Subject: [FieldTrip] channelrepair issue In-Reply-To: References: Message-ID: Hi Jan-Mathijs, >From Fieldtrip data structure I saw that the coordinate of A234 is [ -7.2133 9.1712 5.7117]. And it's [14.4320 -0.0683 0.4437] for A121. All these are in "cm". So the distance between the two channels are 24.1172cm. I checked 4D's orignial file and found the channel coordinates to agree with what I read from Fieldtrip. So I'm wondering how those coils 24.1172cm apart can be considered neighbours (within 4cms). Thanks a lot, Jim On Thu, Jun 30, 2011 at 1:50 AM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Hi Jim, where exactly are they located with respect to the bad channel? > > Best, > > Jan-Mathijs > > > On Jun 30, 2011, at 8:05 AM, Jim Li wrote: > > Dear all, > > We have 4D's WH3600 MEG system (248 channels) and we found the > ----------------- > > cfg = []; > > cfg.dataset = > 'e,rfhp0.1Hz'; > > cfg.trialdef.eventtype = 'TRIGGER'; > > cfg.trialdef.eventvalue = 320; > > cfg.trialdef.prestim = 1; > > cfg.trialdef.poststim = 1 > ; > > cfg = ft_definetrial(cfg); > > cfg.blc = > 'yes'; > > cfg.blcwindow = [-1 0]; > > cfg.channel = {'MEG'}; > > raw_DATA = ft_preprocessing(cfg); > > raw_DATA.grad = ft_convert_units(raw_DATA.grad, 'cm') > > cfg = []; > cfg.badchannel = {'A234'}; > [raw_DATA] = ft_channelrepair(cfg, raw_DATA) > the input is raw data with 248 channels and 201 trials > repairing channel A234 > using neighbour A121 > using neighbour A143 > using neighbour A154 > using neighbour A173 > using neighbour A224 > using neighbour A8 > using neighbour A91 > repairing bad channels for trial 1 > repairing bad channels for trial 2 > repairing bad channels for trial 3 > ... > ------------------------------------ > > But channels like A121 and A143 are far away from the bad channel A234. How > can they be used as neighbours (i.e. within 4cm, the default value for > cfg.neighbourdist) for this bad channel? > > Any suggestions? > > Thanks a lot. > > Jim > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: