From Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE Tue Feb 2 11:16:40 2010 From: Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE (Hanneke Van Dijk) Date: Tue, 2 Feb 2010 11:16:40 +0100 Subject: BUG in ft_topoplotER (cfg.xlim) version 20100127 Message-ID: Dear all, I wanted to report a bug in ft_topoplotER (Fieldtrip version 20100127), regarding the use of cfg.xlim. It doesn't seem to use cfg.xlim when you choose one, but just to use the 'maxmin'. When I average the data over xlim myself I get a completely different topoplot then when I use cfg.xlim for the same range. I wouldn't have known if I didn't need to average over xlim for other reasons. It seems to happen between lines 445 and 452. The data are selected for cfg.ylim and cfg.component but not for cfg.xlim. This changes the outlook on my data completely, and I think this could be important for all users of this version. Therefore I send it to the entire mailing list. I have changed it now to: 444 % make dat structure with one value for each channel 445 dat = getsubfield(data, cfg.zparam); 446 if ~isempty(cfg.yparam), 447 dat = dat(:, ymin:ymax, xmin:xmax); 448 dat = nanmean(nanmean(dat, 2), 3); 449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part Hanneke added 450 dat = dat(:, xmin:xmax); 451 dat = nanmean(dat, 2); 452 end 453 454 dat = dat(:); This helps for me and it is very important for me as well, my data looks meaningfull now! Best and good luck! Hanneke -------------------------------------------------- Institut für Klinische Neurowissenschaften und Medizinische Psychologie Gebäude-Nr.: 23.02 Ebene: 03 Zimmer-Nr.: 47 Tel.: 0211-81-13074 Mail : hanneke.vandijk at med.uni-duesseldorf.de http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at FCDONDERS.RU.NL Tue Feb 2 12:03:09 2010 From: a.stolk at FCDONDERS.RU.NL (a.stolk@fcdonders.ru.nl) Date: Tue, 2 Feb 2010 12:03:09 +0100 Subject: BUG in ft_topoplotER (cfg.xlim) version 20100127 In-Reply-To: <12550216.2564201265108507127.JavaMail.root@watertor.uci.ru.nl> Message-ID: Hi Hanneke, Thank you for your report. Could you specify some more details to help locating the problem? Are you trying to plot event-related fields or components (I'm asking this because of our earlier mail exchanges)? For the latter, I could recommend the ft_topoplotIC function. This one has maxmin values for the z-axis by default, but is more intuitive. An example: cfg = []; cfg.layout = 'NM122_ver.lay'; cfg.component = 1; ft_topoplotIC(cfg,comp); Best, Arjen ----- Original Message ----- From: "Hanneke Van Dijk" To: FIELDTRIP at NIC.SURFNET.NL Sent: Tuesday, February 2, 2010 11:16:40 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 Dear all, I wanted to report a bug in ft_topoplotER (Fieldtrip version 20100127), regarding the use of cfg.xlim. It doesn't seem to use cfg.xlim when you choose one, but just to use the 'maxmin'. When I average the data over xlim myself I get a completely different topoplot then when I use cfg.xlim for the same range. I wouldn't have known if I didn't need to average over xlim for other reasons. It seems to happen between lines 445 and 452. The data are selected for cfg.ylim and cfg.component but not for cfg.xlim. This changes the outlook on my data completely, and I think this could be important for all users of this version. Therefore I send it to the entire mailing list. I have changed it now to: 444 % make dat structure with one value for each channel 445 dat = getsubfield(data, cfg.zparam); 446 if ~isempty(cfg.yparam), 447 dat = dat(:, ymin:ymax, xmin:xmax); 448 dat = nanmean(nanmean(dat, 2), 3); 449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part Hanneke added 450 dat = dat(:, xmin:xmax); 451 dat = nanmean(dat, 2); 452 end 453 454 dat = dat(:); This helps for me and it is very important for me as well, my data looks meaningfull now! Best and good luck! Hanneke -------------------------------------------------- Institut für Klinische Neurowissenschaften und Medizinische Psychologie Gebäude-Nr.: 23.02 Ebene: 03 Zimmer-Nr.: 47 Tel.: 0211-81-13074 Mail : hanneke.vandijk at med.uni-duesseldorf.de http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE Tue Feb 2 12:40:14 2010 From: Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE (Hanneke Van Dijk) Date: Tue, 2 Feb 2010 12:40:14 +0100 Subject: AW: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 Message-ID: Hi Arjen, This time I am plotting cortico-muscular coherence obtained from ft_freqanalysis_mtmfft with fourier output and then using ft_connectivityanalysis. I wanted to plot the coherence on helmet-level only for 8-12 Hz. I attached the figures; When I do the average over the .cohspctrm field myself (or add the line I reported before) I get the left plot (figure 2) and if I say cfg.xlim I get the right plot (figure 1). Groetjes Hanneke -------------------------------------------------- Institut für Klinische Neurowissenschaften und Medizinische Psychologie Gebäude-Nr.: 23.02 Ebene: 03 Zimmer-Nr.: 47 Tel.: 0211-81-13074 Mail : hanneke.vandijk at med.uni-duesseldorf.de http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html -----Ursprüngliche Nachricht----- Von: FieldTrip discussion list im Auftrag von a.stolk at fcdonders.ru.nl Gesendet: Di 02.02.2010 12:03 An: FIELDTRIP at NIC.SURFNET.NL Betreff: Re: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 Hi Hanneke, Thank you for your report. Could you specify some more details to help locating the problem? Are you trying to plot event-related fields or components (I'm asking this because of our earlier mail exchanges)? For the latter, I could recommend the ft_topoplotIC function. This one has maxmin values for the z-axis by default, but is more intuitive. An example: cfg = []; cfg.layout = 'NM122_ver.lay'; cfg.component = 1; ft_topoplotIC(cfg,comp); Best, Arjen ----- Original Message ----- From: "Hanneke Van Dijk" To: FIELDTRIP at NIC.SURFNET.NL Sent: Tuesday, February 2, 2010 11:16:40 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 Dear all, I wanted to report a bug in ft_topoplotER (Fieldtrip version 20100127), regarding the use of cfg.xlim. It doesn't seem to use cfg.xlim when you choose one, but just to use the 'maxmin'. When I average the data over xlim myself I get a completely different topoplot then when I use cfg.xlim for the same range. I wouldn't have known if I didn't need to average over xlim for other reasons. It seems to happen between lines 445 and 452. The data are selected for cfg.ylim and cfg.component but not for cfg.xlim. This changes the outlook on my data completely, and I think this could be important for all users of this version. Therefore I send it to the entire mailing list. I have changed it now to: 444 % make dat structure with one value for each channel 445 dat = getsubfield(data, cfg.zparam); 446 if ~isempty(cfg.yparam), 447 dat = dat(:, ymin:ymax, xmin:xmax); 448 dat = nanmean(nanmean(dat, 2), 3); 449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part Hanneke added 450 dat = dat(:, xmin:xmax); 451 dat = nanmean(dat, 2); 452 end 453 454 dat = dat(:); This helps for me and it is very important for me as well, my data looks meaningfull now! Best and good luck! Hanneke -------------------------------------------------- Institut für Klinische Neurowissenschaften und Medizinische Psychologie Gebäude-Nr.: 23.02 Ebene: 03 Zimmer-Nr.: 47 Tel.: 0211-81-13074 Mail : hanneke.vandijk at med.uni-duesseldorf.de http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. figure; cfgp=[]; cfgp.cohrefchannel = {'MEG063+064'}; cfgp.xparam = 'freq'; cfgp.zparam = 'cohspctrm'; cfgp.layout = 'NM122combined_test.lay'; cfgp.showlabels = 'yes'; cfgp.xlim = [8 12]; %cfgp.zlim = [0 1]; ft_topoplotER(cfgp,fd_ccc_off);colorbar ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE Tue Feb 2 12:41:32 2010 From: Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE (Hanneke Van Dijk) Date: Tue, 2 Feb 2010 12:41:32 +0100 Subject: BUG in ft_topoplotER (cfg.xlim) version 20100127 Message-ID: Sorry, somehow the attachment didn't go allright, I'll try it again. -------------------------------------------------- Institut für Klinische Neurowissenschaften und Medizinische Psychologie Gebäude-Nr.: 23.02 Ebene: 03 Zimmer-Nr.: 47 Tel.: 0211-81-13074 Mail : hanneke.vandijk at med.uni-duesseldorf.de http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html -----Ursprüngliche Nachricht----- Von: FieldTrip discussion list im Auftrag von Hanneke Van Dijk Gesendet: Di 02.02.2010 12:40 An: FIELDTRIP at NIC.SURFNET.NL Betreff: [FIELDTRIP] AW: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 Hi Arjen, This time I am plotting cortico-muscular coherence obtained from ft_freqanalysis_mtmfft with fourier output and then using ft_connectivityanalysis. I wanted to plot the coherence on helmet-level only for 8-12 Hz. I attached the figures; When I do the average over the .cohspctrm field myself (or add the line I reported before) I get the left plot (figure 2) and if I say cfg.xlim I get the right plot (figure 1). Groetjes Hanneke -------------------------------------------------- Institut für Klinische Neurowissenschaften und Medizinische Psychologie Gebäude-Nr.: 23.02 Ebene: 03 Zimmer-Nr.: 47 Tel.: 0211-81-13074 Mail : hanneke.vandijk at med.uni-duesseldorf.de http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html -----Ursprüngliche Nachricht----- Von: FieldTrip discussion list im Auftrag von a.stolk at fcdonders.ru.nl Gesendet: Di 02.02.2010 12:03 An: FIELDTRIP at NIC.SURFNET.NL Betreff: Re: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 Hi Hanneke, Thank you for your report. Could you specify some more details to help locating the problem? Are you trying to plot event-related fields or components (I'm asking this because of our earlier mail exchanges)? For the latter, I could recommend the ft_topoplotIC function. This one has maxmin values for the z-axis by default, but is more intuitive. An example: cfg = []; cfg.layout = 'NM122_ver.lay'; cfg.component = 1; ft_topoplotIC(cfg,comp); Best, Arjen ----- Original Message ----- From: "Hanneke Van Dijk" To: FIELDTRIP at NIC.SURFNET.NL Sent: Tuesday, February 2, 2010 11:16:40 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 Dear all, I wanted to report a bug in ft_topoplotER (Fieldtrip version 20100127), regarding the use of cfg.xlim. It doesn't seem to use cfg.xlim when you choose one, but just to use the 'maxmin'. When I average the data over xlim myself I get a completely different topoplot then when I use cfg.xlim for the same range. I wouldn't have known if I didn't need to average over xlim for other reasons. It seems to happen between lines 445 and 452. The data are selected for cfg.ylim and cfg.component but not for cfg.xlim. This changes the outlook on my data completely, and I think this could be important for all users of this version. Therefore I send it to the entire mailing list. I have changed it now to: 444 % make dat structure with one value for each channel 445 dat = getsubfield(data, cfg.zparam); 446 if ~isempty(cfg.yparam), 447 dat = dat(:, ymin:ymax, xmin:xmax); 448 dat = nanmean(nanmean(dat, 2), 3); 449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part Hanneke added 450 dat = dat(:, xmin:xmax); 451 dat = nanmean(dat, 2); 452 end 453 454 dat = dat(:); This helps for me and it is very important for me as well, my data looks meaningfull now! Best and good luck! Hanneke -------------------------------------------------- Institut für Klinische Neurowissenschaften und Medizinische Psychologie Gebäude-Nr.: 23.02 Ebene: 03 Zimmer-Nr.: 47 Tel.: 0211-81-13074 Mail : hanneke.vandijk at med.uni-duesseldorf.de http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. figure; cfgp=[]; cfgp.cohrefchannel = {'MEG063+064'}; cfgp.xparam = 'freq'; cfgp.zparam = 'cohspctrm'; cfgp.layout = 'NM122combined_test.lay'; cfgp.showlabels = 'yes'; cfgp.xlim = [8 12]; %cfgp.zlim = [0 1]; ft_topoplotER(cfgp,fd_ccc_off);colorbar ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE Tue Feb 2 12:43:05 2010 From: Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE (Hanneke van Dijk) Date: Tue, 2 Feb 2010 12:43:05 +0100 Subject: AW: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8B0F358C@Mail2-UKD.VMED.UKD> Message-ID: Maybe like this then sorry for the large amount of mails... On Tue, Feb 2, 2010 at 12:40 PM, Hanneke Van Dijk < Hanneke.vanDijk at med.uni-duesseldorf.de> wrote: > Hi Arjen, > > This time I am plotting cortico-muscular coherence obtained from > ft_freqanalysis_mtmfft with fourier output and then using > ft_connectivityanalysis. I wanted to plot the coherence on helmet-level only > for 8-12 Hz. I attached the figures; When I do the average over the > .cohspctrm field myself (or add the line I reported before) I get the left > plot (figure 2) and if I say cfg.xlim I get the right plot (figure 1). > > Groetjes Hanneke > > > > -------------------------------------------------- > Institut für Klinische Neurowissenschaften und Medizinische Psychologie > Gebäude-Nr.: 23.02 > Ebene: 03 Zimmer-Nr.: 47 > Tel.: 0211-81-13074 > Mail : hanneke.vandijk at med.uni-duesseldorf.de > > http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html > > > > -----Ursprüngliche Nachricht----- > Von: FieldTrip discussion list im Auftrag von a.stolk at fcdonders.ru.nl > Gesendet: Di 02.02.2010 12:03 > An: FIELDTRIP at NIC.SURFNET.NL > Betreff: Re: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 > > Hi Hanneke, > > Thank you for your report. Could you specify some more details to help > locating the problem? > > Are you trying to plot event-related fields or components (I'm asking this > because of our earlier mail exchanges)? For the latter, I could recommend > the ft_topoplotIC function. This one has maxmin values for the z-axis by > default, but is more intuitive. > > An example: > > cfg = []; > cfg.layout = 'NM122_ver.lay'; > cfg.component = 1; > ft_topoplotIC(cfg,comp); > > > Best, > Arjen > > > > > > > > > > > ----- Original Message ----- > From: "Hanneke Van Dijk" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Tuesday, February 2, 2010 11:16:40 AM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 > > Dear all, > > I wanted to report a bug in ft_topoplotER (Fieldtrip version 20100127), > regarding the use of cfg.xlim. It doesn't seem to use cfg.xlim when you > choose one, but just to use the 'maxmin'. When I average the data over xlim > myself I get a completely different topoplot then when I use cfg.xlim for > the same range. I wouldn't have known if I didn't need to average over xlim > for other reasons. > > It seems to happen between lines 445 and 452. The data are selected for > cfg.ylim and cfg.component but not for cfg.xlim. This changes the outlook on > my data completely, and I think this could be important for all users of > this version. Therefore I send it to the entire mailing list. > > I have changed it now to: > 444 % make dat structure with one value for each channel > 445 dat = getsubfield(data, cfg.zparam); > 446 if ~isempty(cfg.yparam), > 447 dat = dat(:, ymin:ymax, xmin:xmax); > 448 dat = nanmean(nanmean(dat, 2), 3); > 449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part Hanneke > added > 450 dat = dat(:, xmin:xmax); > 451 dat = nanmean(dat, 2); > 452 end > 453 > 454 dat = dat(:); > > This helps for me and it is very important for me as well, my data looks > meaningfull now! > > Best and good luck! > > Hanneke > > > > > -------------------------------------------------- > Institut für Klinische Neurowissenschaften und Medizinische Psychologie > Gebäude-Nr.: 23.02 > Ebene: 03 Zimmer-Nr.: 47 > Tel.: 0211-81-13074 > Mail : hanneke.vandijk at med.uni-duesseldorf.de > > http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > figure; > cfgp=[]; > cfgp.cohrefchannel = {'MEG063+064'}; > cfgp.xparam = 'freq'; > cfgp.zparam = 'cohspctrm'; > cfgp.layout = 'NM122combined_test.lay'; > cfgp.showlabels = 'yes'; > cfgp.xlim = [8 12]; > %cfgp.zlim = [0 1]; > ft_topoplotER(cfgp,fd_ccc_off);colorbar > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: cfgxlimplots.jpeg Type: image/jpeg Size: 114815 bytes Desc: not available URL: From jean-michel.badier at UNIVMED.FR Tue Feb 2 14:43:46 2010 From: jean-michel.badier at UNIVMED.FR (Jean-Michel Badier) Date: Tue, 2 Feb 2010 14:43:46 +0100 Subject: reading mri from ASA format Message-ID: Dear all, As a quite new user of fieldtrip I found that it is possible to read mri stored with ASA mri format. Two points : 1.It seems that the routine read_asa_mri will only read mri stored in uint8 data format for each voxel. Unfortunately ASA also stores the data on unit16 format. I have changed the code of the routine and it seems that the mri can be correctly read. I did not go further (model generation for localization for instance) and I do not know yet the eventual consequence of the change in the code. Note that there are two keywords in the ASA mri header “BytesPerPixel” (1 or 2 in my examples) and PixelDataType (unsigned in y examples) that should help to correctly read the files. 2.As a ASA user I already have the segmentation done by this commercial software. Is there any way to retrieve directly the segmentation that have been already made? The segmentation file is read by the read_asa_mri but it is not use in the read_mri program that call it. Thanks a lot Jean-Michel ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Tue Feb 2 16:28:23 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Tue, 2 Feb 2010 16:28:23 +0100 Subject: AW: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 In-Reply-To: Message-ID: Dear Hanneke, Just to follow up: it seems there was a discrepancy between the part of code you copied (and adjusted) into one of your previous e-mails, and the code of the latest ft_topoplotER. > 444 % make dat structure with one value for each channel > 445 dat = getsubfield(data, cfg.zparam); > 446 if ~isempty(cfg.yparam), > 447 dat = dat(:, ymin:ymax, xmin:xmax); > 448 dat = nanmean(nanmean(dat, 2), 3); > 449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part > Hanneke added > 450 dat = dat(:, xmin:xmax); > 451 dat = nanmean(dat, 2); > 452 end > 453 > 454 dat = dat(:); There seems to be an 'else' missing after line 449. I guess your problem will be solved when you upgrade to the latest fieldtrip version. Sorry for the inconvenience, Jan-Mathijs On Feb 2, 2010, at 12:43 PM, Hanneke van Dijk wrote: > Maybe like this then sorry for the large amount of mails... > > On Tue, Feb 2, 2010 at 12:40 PM, Hanneke Van Dijk > wrote: > Hi Arjen, > > This time I am plotting cortico-muscular coherence obtained from > ft_freqanalysis_mtmfft with fourier output and then using > ft_connectivityanalysis. I wanted to plot the coherence on helmet- > level only for 8-12 Hz. I attached the figures; When I do the > average over the .cohspctrm field myself (or add the line I reported > before) I get the left plot (figure 2) and if I say cfg.xlim I get > the right plot (figure 1). > > Groetjes Hanneke > > > > -------------------------------------------------- > Institut für Klinische Neurowissenschaften und Medizinische > Psychologie > Gebäude-Nr.: 23.02 > Ebene: 03 Zimmer-Nr.: 47 > Tel.: 0211-81-13074 > Mail : hanneke.vandijk at med.uni-duesseldorf.de > http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html > > > > -----Ursprüngliche Nachricht----- > Von: FieldTrip discussion list im Auftrag von a.stolk at fcdonders.ru.nl > Gesendet: Di 02.02.2010 12:03 > An: FIELDTRIP at NIC.SURFNET.NL > Betreff: Re: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version > 20100127 > > Hi Hanneke, > > Thank you for your report. Could you specify some more details to > help locating the problem? > > Are you trying to plot event-related fields or components (I'm > asking this because of our earlier mail exchanges)? For the latter, > I could recommend the ft_topoplotIC function. This one has maxmin > values for the z-axis by default, but is more intuitive. > > An example: > > cfg = []; > cfg.layout = 'NM122_ver.lay'; > cfg.component = 1; > ft_topoplotIC(cfg,comp); > > > Best, > Arjen > > > > > > > > > > > ----- Original Message ----- > From: "Hanneke Van Dijk" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Tuesday, February 2, 2010 11:16:40 AM GMT +01:00 Amsterdam / > Berlin / Bern / Rome / Stockholm / Vienna > Subject: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 > > Dear all, > > I wanted to report a bug in ft_topoplotER (Fieldtrip version > 20100127), regarding the use of cfg.xlim. It doesn't seem to use > cfg.xlim when you choose one, but just to use the 'maxmin'. When I > average the data over xlim myself I get a completely different > topoplot then when I use cfg.xlim for the same range. I wouldn't > have known if I didn't need to average over xlim for other reasons. > > It seems to happen between lines 445 and 452. The data are selected > for cfg.ylim and cfg.component but not for cfg.xlim. This changes > the outlook on my data completely, and I think this could be > important for all users of this version. Therefore I send it to the > entire mailing list. > > I have changed it now to: > 444 % make dat structure with one value for each channel > 445 dat = getsubfield(data, cfg.zparam); > 446 if ~isempty(cfg.yparam), > 447 dat = dat(:, ymin:ymax, xmin:xmax); > 448 dat = nanmean(nanmean(dat, 2), 3); > 449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part > Hanneke added > 450 dat = dat(:, xmin:xmax); > 451 dat = nanmean(dat, 2); > 452 end > 453 > 454 dat = dat(:); > > This helps for me and it is very important for me as well, my data > looks meaningfull now! > > Best and good luck! > > Hanneke > > > > > -------------------------------------------------- > Institut für Klinische Neurowissenschaften und Medizinische > Psychologie > Gebäude-Nr.: 23.02 > Ebene: 03 Zimmer-Nr.: 47 > Tel.: 0211-81-13074 > Mail : hanneke.vandijk at med.uni-duesseldorf.de > http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > > figure; > cfgp=[]; > cfgp.cohrefchannel = {'MEG063+064'}; > cfgp.xparam = 'freq'; > cfgp.zparam = 'cohspctrm'; > cfgp.layout = 'NM122combined_test.lay'; > cfgp.showlabels = 'yes'; > cfgp.xlim = [8 12]; > %cfgp.zlim = [0 1]; > ft_topoplotER(cfgp,fd_ccc_off);colorbar > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sangita.dandekar at GMAIL.COM Tue Feb 2 18:22:30 2010 From: sangita.dandekar at GMAIL.COM (Sangita Dandekar) Date: Tue, 2 Feb 2010 12:22:30 -0500 Subject: beamformer on yokogawa data, megplanar.m Message-ID: Hi, Am hoping to apply beamforming based source localization to MEG data from a Yokogawa system. Think I've managed to coregister MRI and sensor coordinate systems, so that part of the problem is pretty much under control. What I'm wondering about is what the assumptions are of the prepare_leadfield and other source localization scripts about the input gradiometer data. Haven't looked at it too closely yet, but does it assume that the input sensor data is planar gradient data? If so am assuming that inputting the raw data from the Yokogawa system (axial gradiometers) is incorrect? Or does fieldtrip distinguish between different types of gradiometers using the input .grad structure? I tried to convert the axial gradiometer data from the yokogawa system to planar gradient data by using the megplanar function as shown below, and receive the following error: (Even if it isn't necessary for source localization, it would be nice to be able to view the data as planar gradient data) >> cfg=[]; >> cfg.planarmethod='sincos'; >> megplanar(cfg, righttrials); the input is raw data with 156 channels and 46 trials ??? Error using ==> checkdata at 478 This function requires ctf151, ctf275, bti148 or bti248 data as input, but you are giving meg data. Error in ==> megplanar at 228 data = checkdata(data, 'datatype', {'raw' 'freq'}, 'feedback', 'yes', 'ismeg', 'yes', 'senstype', {'ctf151', 'ctf275', 'bti148', 'bti248'}); >> Some background information: used the ft yokogawa2grad.m function (stored in private FT directory) to create the gradient structure. Here is what data structure for one set of trials looks like: >> righttrials righttrials = trial: {1x46 cell} label: {1x156 cell} time: {1x46 cell} fsample: 500 grad: [1x1 struct] offset: [46x46 double] cfg: [1x1 struct] >> righttrials.grad ans = pnt: [314x3 double] ori: [314x3 double] tra: [157x314 double] label: {157x1 cell} unit: 'cm' >> Thanks in advance for any help! Sangi ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.litvak at ION.UCL.AC.UK Tue Feb 2 19:07:41 2010 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Tue, 2 Feb 2010 18:07:41 +0000 Subject: beamformer on yokogawa data, megplanar.m In-Reply-To: Message-ID: Dear Sangi, There is no need to convert your data to planar gradient. The assumption is that the relation between coils and channels is described by the grad.tra matrix. You can look at it and make sure it is correct for your system (write back if not). The megplanar function as apparent from the error message has explicit support for some particular MEG systems and Yokogawa is not one of those. I'm not sure how easy it would be to support it generically as there might be several variants of Yokogawa systems which can be quite hard to distinguish. But for your particular system you can try to implement it yourself. Best, Vladimir On Tue, Feb 2, 2010 at 5:22 PM, Sangita Dandekar wrote: > Hi, > Am hoping to apply beamforming based source localization to MEG data from a > Yokogawa system.   Think I've managed to coregister MRI and sensor > coordinate systems, so that part of the problem is pretty much under > control. > What I'm wondering about is what the assumptions are of the > prepare_leadfield and other source localization scripts about the input > gradiometer data.  Haven't looked at it too closely yet, but does it assume > that the input sensor data is planar gradient data?  If so am assuming that > inputting the raw data from the Yokogawa system (axial gradiometers) is > incorrect?   Or does fieldtrip distinguish between different types of > gradiometers using the input .grad structure? > I tried to convert the axial gradiometer data from the yokogawa system to > planar gradient data by using the megplanar function as shown below, and > receive the following error: > (Even if it isn't necessary for source localization, it would be nice to be > able to view the data as planar gradient data) >>> cfg=[]; >>> cfg.planarmethod='sincos'; >>> megplanar(cfg, righttrials); > the input is raw data with 156 channels and 46 trials > ??? Error using ==> checkdata at 478 > This function requires ctf151, ctf275, bti148 or bti248 data as input, but > you are giving meg data. > Error in ==> megplanar at 228 > data  = checkdata(data, 'datatype', {'raw' 'freq'}, 'feedback', 'yes', > 'ismeg', 'yes', 'senstype', {'ctf151', 'ctf275', > 'bti148', 'bti248'}); >>> > Some background information:  used the ft yokogawa2grad.m function (stored > in private FT directory) to create the gradient structure.  Here is what > data structure for > one set of trials looks like: >>> righttrials > righttrials = >       trial: {1x46 cell} >       label: {1x156 cell} >        time: {1x46 cell} >     fsample: 500 >        grad: [1x1 struct] >      offset: [46x46 double] >         cfg: [1x1 struct] >>> righttrials.grad > ans = >       pnt: [314x3 double] >       ori: [314x3 double] >       tra: [157x314 double] >     label: {157x1 cell} >      unit: 'cm' >>> > > > Thanks in advance for any help! > Sangi > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From chintan_student at YAHOO.CO.IN Thu Feb 4 17:22:02 2010 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Thu, 4 Feb 2010 21:52:02 +0530 Subject: regarding besa format and freq analysis Message-ID: Hi everyone,   I am relatively new to fieldtrip.  Can you tell me, once u import .tfc file using besa2fieldtrip. how to process it further and get the analysis data??   Best Regards,   Chintan Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! http://downloads.yahoo.com/in/internetexplorer/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Juergen.Fell at UKB.UNI-BONN.DE Fri Feb 5 04:03:48 2010 From: Juergen.Fell at UKB.UNI-BONN.DE (Juergen Fell) Date: Fri, 5 Feb 2010 04:03:48 +0100 Subject: J.F. is out of the office. Message-ID: Ich werde ab 05.02.2010 nicht im Büro sein. Ich kehre zurück am 16.02.2010. Bitte wenden Sie sich in dringenden Personal- und Finanzangelegenheiten an meine Vertreterin, Frau Ruth Bender (19366). Starting 5.02.2010 I am out of the office and will be back 16.2.2010. I will answer your message after my return. Mit freundlichem Gruss/ kind regards, Juergen Fell. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From aostendorf at BESA.DE Fri Feb 5 11:07:47 2010 From: aostendorf at BESA.DE (Andrea Ostendorf) Date: Fri, 5 Feb 2010 11:07:47 +0100 Subject: regarding besa format and freq analysis In-Reply-To: <974836.26521.qm@web95402.mail.in2.yahoo.com> Message-ID: Dear Chintan, Depending on what you would like to do with your data - possibly plotting and statistical evaluation -, you may find the example script on the Fieldtrip homepage very useful: http://fieldtrip.fcdonders.nl/example/apply_clusterrandanalysis_on_tfrs_of_p ower_that_were_computed_with_besa . besa2fieldtrip converts the tfc files to a structure similar to the output of ft_freqanalysis so freqanalysis itself is not needed. The script shows you how to perform a grand average and how to carry out a statistical test. (It compares the output of the function clusterrandanalysis with the new function freqstatistics - you only need the latter.) As explained in http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq, which may also be of interest to you, Fieldtrip offers several methods for addressing the multiple-comparisons problem. In the script, the method cfg.correctm = 'cluster' is selected. For this, you will currently need some functions from the Image Processing Toolbox although I understand that in the long run, Fieldtrip will include some free functions for the benefit of those who do not have this toolbox. Also, for some options the Statistics toolbox may be required. I suppose that you are working with a BESA version prior to the BESA Research 5.3 that has just been released? The new version 5.3 features a comfortable direct MATLAB interface so you can transfer directly from BESA Research to a MATLAB structure - e.g. automatically by batch commands - and bypass export to and reading from tfc files. To facilitate Fieldtrip use for BESA users, besa2fieldtrip will soon be modified to process the new BESA MATLAB structures as well. On the BESA website (www.besa.de , link ‘Download / MATLAB Scripts’) you can find some easy-to-use sample MATLAB scripts, and shortly, sample scripts using Fieldtrip for TFC and image statistics will be added there as well. Hope this helps you All the best Andrea Dr. Andrea Ostendorf Research & Development MEGIS Software GmbH Freihamer Str. 18 82166 Gräfelfing/Germany HRB München 109956 CEOs: Dr. Michael Scherg, Theodor Scherg _____ From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of shah chintan Sent: Donnerstag, 4. Februar 2010 17:22 To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] regarding besa format and freq analysis Hi everyone, I am relatively new to fieldtrip. Can you tell me, once u import .tfc file using besa2fieldtrip. how to process it further and get the analysis data?? Best Regards, Chintan _____ The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From masaki.maruyama at CEA.FR Fri Feb 5 18:58:34 2010 From: masaki.maruyama at CEA.FR (MARUYAMA Masaki INSERM) Date: Fri, 5 Feb 2010 18:58:34 +0100 Subject: Image_Toolbox requirement in segmentation analysis Message-ID: Hello, Is it possible to remove the absolute requirement of Image_Toolbox in the segmentation analysis? The segmentation had been possible without the toolbox until the version of 2009July06, but it is absolutely necessary in the recent fieldtrip versions. I attached below the error message that I receive in my environment of no Image_Toolbox. I would appreciate your kind help in advance. With best regards, Masaki Maruyama -- Inserm U.992 - Neuroimagerie Cognitive CEA/SAC/DSV/I2BM/NeuroSpin Bât 145, Point Courrier 156 F-91191 GIF/YVETTE, FRANCE Diagnostic Information: Feature: Image_Toolbox FLEXnet Licensing error: -4,132. Error in ==> prepare_mesh_segmentation at 53 seg = imfill((mri.seg==cfg.tissue(i)), 'holes'); Error in ==> ft_prepare_mesh at 70 bnd = prepare_mesh_segmentation(cfg, mri); Error in ==> prepare_mesh at 17 [varargout{1:nargout}] = funhandle(varargin{:}); Error in ==> ft_prepare_singleshell at 58 vol.bnd = prepare_mesh(cfg, mri); Error in ==> prepare_singleshell at 17 [varargout{1:nargout}] = funhandle(varargin{:}); Error in ==> Neurospin_MRI_Preprocessing_V2 at 133 hdm = prepare_singleshell(cfg, segmentedmri); ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bps231 at NYU.EDU Sun Feb 7 19:35:30 2010 From: bps231 at NYU.EDU (Bernhard Staresina) Date: Sun, 7 Feb 2010 19:35:30 +0100 Subject: strange TFR effects Message-ID: Dear Fieldtrip experts, I've come across a strange effect during the calculation of TFRs using multitaper convolution. When I put in the raw data (no preprocessing at all), I get TFRs that look very weird. However, if I use a bandpass filter (preproc_bandpassfilter from 1 to 150 Hz with default settings) just prior to calculating the TFRs, the results look perfectly normal. I'm attaching figures of both versions so you can see the difference. The settings for the TFR calculation are identical for both cases: cfg = []; cfg.channel = 'all'; cfg.output = 'pow'; cfg.pad = 'maxperlen'; cfg.keeptrials = 'yes'; cfg.toi = -0.75:.01:2.0; cfg.method = 'mtmconvol'; cfg.foi = 2:1:120; cfg.t_ftimwin = ones(length(cfg.foi),1); cfg.t_ftimwin(cfg.foi < 30) = .500; cfg.t_ftimwin(cfg.foi >= 30) = .200; cfg.tapsmofrq = linspace(2,20,length(cfg.foi)); cfg.keeptapers = 'no'; The plots represent relative power changes, calculated by subtracting and dividing through the power from -.450 to -.250 ms before stimulus onset. Do you have any clue what's the reason for this difference? Thanks for your help, Bernhard ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: A_unfiltered.jpg Type: image/jpeg Size: 35829 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: B_bp_filtered.jpg Type: image/jpeg Size: 28425 bytes Desc: not available URL: From g.piantoni at NIN.KNAW.NL Mon Feb 8 15:38:15 2010 From: g.piantoni at NIN.KNAW.NL (Giovanni Piantoni) Date: Mon, 8 Feb 2010 15:38:15 +0100 Subject: probability zero Message-ID: Dear FieldTrip users, I am using statistics_montecarlo, which works really well, and I have a theoretical question. After using clustering correction for multiple comparisons, some clusters have a probability of 0. I don't know how to interpret this zero, as the lowest p-value you can get with a nonparametric method is 1/number_of_randomizations (see Nichols & Holmes, 2002). Shouldn't the observed cluster statistic be included in the reference probability distribution? Or has '>=' (greater than or equal to) maybe become a '>' (greater than)? Thanks, Giovanni ------ Giovanni Piantoni, Ph.D. student Dept. Sleep & Cognition Netherlands Institute for Neuroscience Meibergdreef 47 1105 BA Amsterdam (NL) +31 (0)20 5665492 g.piantoni at nin.knaw.nl www.nin.knaw.nl/research_groups/van_someren_group/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From cmuehl at GMAIL.COM Wed Feb 10 09:19:09 2010 From: cmuehl at GMAIL.COM (Christian Muehl) Date: Wed, 10 Feb 2010 09:19:09 +0100 Subject: Special Issue on Affective and Adaptive BCI Interfaces Message-ID: ============================================================== CALL FOR PAPERS ----------------------------------------------------------------------------------------------------- Special Issue on Affective Brain-Computer Interfaces of the International Journal of Autonomous and Adaptive Communication Systems http://www.inderscience.com/browse/index.php?journalCODE=ijaacs Editors: Anton Nijholt et al. ----------------------------------------------------------------------------------------------------- Special Issue ------------------ This Special Issue of the International Journal of Autonomous and Adaptive Communication Systems (IJAACS) is a follow-up of the aBCI satellite workshop of the International Conference on Affective Computing and Intelligent Interaction (ACII), held in Amsterdam in September 2009. This Special Issue, is meant to explore the advantages and limitations of using neurophysiological signals as a modality for the automatic recognition of affective and cognitive states, as well as the possibilities to use this information about the user state in innovative and adaptive applications. Background ---------------- Recent research efforts in brain-computer interfaces (BCI) show that brain activity can be used as an active/voluntary, or passive/involuntary control modality in man-machine interaction. While active BCI paradigms received a lot of attention in recent years, research on passive approaches to BCI is still lacking 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. We encourage submissions exploring one or more of the following topics: * emotion elicitation and data collection for affective BCI * detection of affective and cognitive states with BCI and other modalities * adaptive interfaces and affective BCI, affective BCI applications * embedding affective BCI in active and passive BCI approaches (Revised) Time Schedule ----------------- * February 15 : Deadline for Abstracts * February 18 : Invitation for Full Paper Submission * March 20: Full Paper Deadline Paper submissions ---------------------- Potential authors should first submit a title and a one-page abstract. Please submit them in PDF format to anijholt at cs.utwente.nl. Final papers should be at most 20 pages long and in the format of the IJAACS Journal (see http://www.inderscience.com/mapper.php?id=31). ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From psowman at MACCS.MQ.EDU.AU Fri Feb 12 04:44:35 2010 From: psowman at MACCS.MQ.EDU.AU (Paul Sowman) Date: Fri, 12 Feb 2010 04:44:35 +0100 Subject: Coherence MEG Message-ID: Hi, I'm trying to perform coherence analysis on a data set with 2 channels (source waveforms). I have followed the tute example. All is fine with the frequency analysis however when I attempt the coherence using: cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'all' 'all'}; fd = ft_connectivityanalysis(cfg, freq); I get: averaging crsspctrm over rpt removing dimension rpt from crsspctrm ??? Undefined function or variable "siz". Error in ==> ft_connectivityanalysis>coupling_corr at 485 n = siz(1); Error in ==> ft_connectivityanalysis at 188 [datout, varout, nrpt] = coupling_corr(tmpcfg, data.(inparam), hasrpt, hasjack);I get: Any ideas on where I am going wrong? Regards, Paul ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Fri Feb 12 09:11:47 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Fri, 12 Feb 2010 09:11:47 +0100 Subject: Coherence MEG In-Reply-To: Message-ID: Dear Paul, This was an issue in a past version of fieldtrip. Please download and use the latest version from the ftp-server. Best, Jan-Mathijs On Feb 12, 2010, at 4:44 AM, Paul Sowman wrote: > Hi, I'm trying to perform coherence analysis on a data set with 2 > channels > (source waveforms). I have followed the tute example. All is fine > with the > frequency analysis however when I attempt the coherence using: > > cfg = []; > cfg.method = 'coh'; > cfg.channelcmb = {'all' 'all'}; > fd = ft_connectivityanalysis(cfg, freq); > > I get: > > averaging crsspctrm over rpt > removing dimension rpt from crsspctrm > > ??? Undefined function or variable "siz". > > Error in ==> ft_connectivityanalysis>coupling_corr at 485 > n = siz(1); > > Error in ==> ft_connectivityanalysis at 188 > [datout, varout, nrpt] = coupling_corr(tmpcfg, data.(inparam), > hasrpt, > hasjack);I get: > > Any ideas on where I am going wrong? > > Regards, Paul > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/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: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From e.maris at DONDERS.RU.NL Fri Feb 12 09:35:59 2010 From: e.maris at DONDERS.RU.NL (Eric Maris) Date: Fri, 12 Feb 2010 09:35:59 +0100 Subject: probability zero In-Reply-To: <83ebc8b0934aea8da5243d487e331999.squirrel@ssl.nin.knaw.nl> Message-ID: Hi Giovanni, It is good to know that you would not have this question if the support of the permutation distribution was continuous instead of discrete, because in that case >= and > would produce the same p-value. In most situations, the number of replications is so large that the difference between >= and > is very small. I am aware that this answer is not acceptable for someone who appreciates the discrete nature of the support of the permutation distribution. To those neuroscientists, I can only say that whether you use >= or > is a matter of choice. This choice is of the same type as choosing for 0.05 or 0.01 as your significance level. Best, Eric -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Giovanni Piantoni Sent: maandag 8 februari 2010 15:38 To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] probability zero Dear FieldTrip users, I am using statistics_montecarlo, which works really well, and I have a theoretical question. After using clustering correction for multiple comparisons, some clusters have a probability of 0. I don't know how to interpret this zero, as the lowest p-value you can get with a nonparametric method is 1/number_of_randomizations (see Nichols & Holmes, 2002). Shouldn't the observed cluster statistic be included in the reference probability distribution? Or has '>=' (greater than or equal to) maybe become a '>' (greater than)? Thanks, Giovanni ------ Giovanni Piantoni, Ph.D. student Dept. Sleep & Cognition Netherlands Institute for Neuroscience Meibergdreef 47 1105 BA Amsterdam (NL) +31 (0)20 5665492 g.piantoni at nin.knaw.nl www.nin.knaw.nl/research_groups/van_someren_group/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From gbirot at GMAIL.COM Fri Feb 12 14:54:29 2010 From: gbirot at GMAIL.COM (Gwenael Birot) Date: Fri, 12 Feb 2010 14:54:29 +0100 Subject: function prepare_bemmodel: resulting BEM system matrix is NaN Message-ID: Hello, I am a new user of fieldtrip. I am trying to generate BEM system matrix using the function 'prepare_bemmodel' and the 'bemcp' method. The system matrix 'vol.mat' I obtained using the following code is a 'NaN' matrix. %% -------------- Begin -------------- % ---- load brain mesh % load_bnd is a function to load brainvisa mesh [vol.bnd(1).pnt vol.bnd(1).tri] = load_bnd('../data/mesh/colin_ no_artef.eeg-3.bnd'); vol.bnd(1).tri = vol.bnd(1).tri + 1; vol.bnd(1).pnt = vol.bnd(1).pnt; % ---- load skull mesh [vol.bnd(2).pnt vol.bnd(2).tri] = load_bnd('../data/mesh/colin_no_artef.eeg-2.bnd'); vol.bnd(2).tri = vol.bnd(2).tri + 1; vol.bnd(2).pnt = vol.bnd(2).pnt/1000; % ---- load skin mesh [vol.bnd(3).pnt vol.bnd(3).tri] = load_bnd('../data/mesh/colin_no_artef.eeg-1.bnd'); vol.bnd(3).tri = vol.bnd(3).tri + 1; vol.bnd(3).pnt = vol.bnd(3).pnt; % ---- check meshes figure; triplot(vol.bnd(1).pnt, vol.bnd(1).tri, [], 'faces_skin'); rotate3d figure; triplot(vol.bnd(2).pnt, vol.bnd(2).tri, [], 'faces_skin'); rotate3d figure; triplot(vol.bnd(3).pnt, vol.bnd(3).tri, [], 'faces_skin'); rotate3d % this gives good results, so meshes are correctly loaded % ---- prepare BEM model vol.cond = [0.3300 0.0825 0.3300]; % conductivities vol.skin = 3; % index of skin surface cfg = []; cfg.method = 'bemcp'; vol = prepare_bemmodel(cfg, vol); %% ------------------- End ------------------------ When executing this code I've got the following result in the matlab prompt using the mesh specified in the input volume conductor determining source compartment (1) determining skin compartment (3) not using the isolated source approach Nvert = 1222 Ntri = 2440 weight = 0.095493 , defl = 0.000000 Nverta = 1222 Ntrib = 2440 Nverta = 1222 Ntrib = 2440 Nvert = 1222 Ntri = 2440 weight = -0.095493 , defl = 0.000000 Nverta = 1222 Ntrib = 2440 Warning: Matrix is singular, close to singular or badly scaled. Results may be inaccurate. RCOND = NaN. > In prepare_bemmodel at 187 In test_fieldtrip at 166 Nverta = 1222 Ntrib = 2440 Warning: Matrix is singular, close to singular or badly scaled. Results may be inaccurate. RCOND = NaN. > In prepare_bemmodel at 194 In test_fieldtrip at 166 Nverta = 1222 Ntrib = 2440 Nverta = 1222 Ntrib = 2440 Nvert = 1222 Ntri = 2440 weight = 0.159155 , defl = 0.000818 Warning: Matrix is singular, close to singular or badly scaled. Results may be inaccurate. RCOND = NaN. > In prepare_bemmodel at 220 In test_fieldtrip at 166 and as I mentionned the resulting BEM system matrix vol.mat is a 'NaN' matrix. I guess the problem occurs in this part of the prepare_bemmodel function (beginning at line 152): % -------------------------------------------- % Deal first with surface 1 and 2 (inner and outer skull % NOTE: % C11st/C22st/C33st are simply the matrix C11/C22/C33 minus the identity % matrix, i.e. C11st = C11-eye(N) weight = (vol.cond(1)-vol.cond(2))/((vol.cond(1)+vol.cond(2))*2*pi); C11st = bem_Cii_lin(vol.bnd(1).tri,vol.bnd(1).pnt, weight,defl(1),vol.bnd(1).pnt4); weight = (vol.cond(1)-vol.cond(2))/((vol.cond(2)+vol.cond(3))*2*pi); C21 = bem_Cij_lin(vol.bnd(2).pnt,vol.bnd(1).pnt,vol.bnd(1).tri, weight,defl(1)); tmp1 = C21/C11st; weight = (vol.cond(2)-vol.cond(3))/((vol.cond(1)+vol.cond(2))*2*pi); C12 = bem_Cij_lin(vol.bnd(1).pnt,vol.bnd(2).pnt,vol.bnd(2).tri, weight,defl(2)); weight = (vol.cond(2)-vol.cond(3))/((vol.cond(2)+vol.cond(3))*2*pi); C22st = bem_Cii_lin(vol.bnd(2).tri,vol.bnd(2).pnt, weight,defl(2),vol.bnd(2).pnt4); tmp2 = C12/C22st; % ------------------------------------------------ where the matrix C11st contains three elements equal to NaN. Since C11st is then inverted, the result is a 'NaN' matrix. I'll would very much appreciate your help Thanks Gwenael ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From zaifengg at GMAIL.COM Sun Feb 14 11:16:31 2010 From: zaifengg at GMAIL.COM (gao zai) Date: Sun, 14 Feb 2010 18:16:31 +0800 Subject: Questions on freqanalysis Message-ID: Dear all, I am now trying to do the frequencyanalysis in Fieldtrip. Since the data is analyzed in EEGlab before, thus I first convert the data from EEGlab to Fieldtrip using eeglab2fieldtrip: *data = eeglab2fieldtrip(EEG, 'preprocessing' )*. The data was epoched from -200 ms to 1400ms time-locked to the onset of the stimuli. Then I run the following scripts: cfg = []; cfg.output = 'pow'; cfg.method = 'mtmconvol'; cfg.taper = 'hanning'; cfg.foi = 5:1:30; cfg.t_ftimwin = 7./cfg.foi; % 7 cycles per time window cfg.toi = -0.15:0.05:1.35; % to reduce boundary effects TFRhann = freqanalysis(cfg, data); However, part of the result in TFRhann.*powspctrm* is *NaN*. And I didn't see any problem in the parameters I use. I wonder whether someone can give me some suggestions to fix it? Many thanks. Best, Feng ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at FCDONDERS.RU.NL Sun Feb 14 12:16:24 2010 From: a.stolk at FCDONDERS.RU.NL (a.stolk@fcdonders.ru.nl) Date: Sun, 14 Feb 2010 12:16:24 +0100 Subject: Questions on freqanalysis In-Reply-To: <23712806.130831266146100104.JavaMail.root@watertor.uci.ru.nl> Message-ID: Hi Feng, ft_freqanalysis; method mtmconvol can be considered as a frequency estimation shifting over time (in your case: -0.15 til 1.35 seconds). More specifically, every 0.05 seconds it makes an estimation of the powerspectrum. In order to so, one needs a certain timewindow to base the estimation on. The larger the timewindow, the better the estimation as one then averages over more cycles. You can either specify your timewindow with a steady length or let it be a function of the frequency. You chose the latter, which is fine. But when we consider timepoint "-0.15", frequency "5", and window "7 cycles"; the timewindow is 7 * 1/5 (5 hertz) = 1400 ms. At timepoint -0.15, this ranges from 700 ms before (-0.85 s) until 700 ms after. However, your data begins at -0.2 s and an estimation, therefore, can not be performed for this timepoint (-0.15 s) resulting in a NaN. You'll need to adjust one or more of the parameter settings (according to what is written above), or export more data from eeglab (with offsets), or live with the NaN's (they're displayed in white in ft_singleplotTFR). Also check out the TFR section in fieldtrip's tutorial section. Best, Arjen ----- Original Message ----- From: "gao zai" To: FIELDTRIP at NIC.SURFNET.NL Sent: Sunday, February 14, 2010 11:16:31 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: [FIELDTRIP] Questions on freqanalysis Dear all, I am now trying to do the frequencyanalysis in Fieldtrip. Since the data is analyzed in EEGlab before, thus I first convert the data from EEGlab to Fieldtrip using eeglab2fieldtrip: *data = eeglab2fieldtrip(EEG, 'preprocessing' )*. The data was epoched from -200 ms to 1400ms time-locked to the onset of the stimuli. Then I run the following scripts: cfg = []; cfg.output = 'pow'; cfg.method = 'mtmconvol'; cfg.taper = 'hanning'; cfg.foi = 5:1:30; cfg.t_ftimwin = 7./cfg.foi; % 7 cycles per time window cfg.toi = -0.15:0.05:1.35; % to reduce boundary effects TFRhann = freqanalysis(cfg, data); However, part of the result in TFRhann.*powspctrm* is *NaN*. And I didn't see any problem in the parameters I use. I wonder whether someone can give me some suggestions to fix it? Many thanks. Best, Feng ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From zaifengg at GMAIL.COM Sun Feb 14 12:26:54 2010 From: zaifengg at GMAIL.COM (gao zai) Date: Sun, 14 Feb 2010 19:26:54 +0800 Subject: Questions on freqanalysis In-Reply-To: <21332973.130871266146184356.JavaMail.root@watertor.uci.ru.nl> Message-ID: Dear Arjen, Thanks for your great answer. Have a nice day. Best, Feng On Sun, Feb 14, 2010 at 7:16 PM, a.stolk at fcdonders.ru.nl < a.stolk at fcdonders.ru.nl> wrote: > Hi Feng, > > ft_freqanalysis; method mtmconvol can be considered as a frequency > estimation shifting over time (in your case: -0.15 til 1.35 seconds). More > specifically, every 0.05 seconds it makes an estimation of the > powerspectrum. In order to so, one needs a certain timewindow to base the > estimation on. The larger the timewindow, the better the estimation as one > then averages over more cycles. > > You can either specify your timewindow with a steady length or let it be a > function of the frequency. You chose the latter, which is fine. But when we > consider timepoint "-0.15", frequency "5", and window "7 cycles"; the > timewindow is 7 * 1/5 (5 hertz) = 1400 ms. At timepoint -0.15, this ranges > from 700 ms before (-0.85 s) until 700 ms after. However, your data begins > at -0.2 s and an estimation, therefore, can not be performed for this > timepoint (-0.15 s) resulting in a NaN. > > You'll need to adjust one or more of the parameter settings (according to > what is written above), or export more data from eeglab (with offsets), or > live with the NaN's (they're displayed in white in ft_singleplotTFR). Also > check out the TFR section in fieldtrip's tutorial section. > > Best, > > Arjen > > ----- Original Message ----- > From: "gao zai" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Sunday, February 14, 2010 11:16:31 AM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: [FIELDTRIP] Questions on freqanalysis > > Dear all, > > I am now trying to do the frequencyanalysis in Fieldtrip. Since the data is > analyzed in EEGlab before, thus I first convert the data from EEGlab to > Fieldtrip using eeglab2fieldtrip: *data = eeglab2fieldtrip(EEG, > 'preprocessing' )*. The data was epoched from -200 ms to 1400ms time-locked > to the onset of the stimuli. > > Then I run the following scripts: > > cfg = []; > cfg.output = 'pow'; > cfg.method = 'mtmconvol'; > cfg.taper = 'hanning'; > cfg.foi = 5:1:30; > cfg.t_ftimwin = 7./cfg.foi; % 7 cycles per time window > cfg.toi = -0.15:0.05:1.35; % to reduce boundary effects > TFRhann = freqanalysis(cfg, data); > > However, part of the result in TFRhann.*powspctrm* is *NaN*. And I didn't > see any problem in the parameters I use. I wonder whether someone can give > me some suggestions to fix it? Many thanks. > > Best, > Feng > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sreenivasan.r.nadar at GMAIL.COM Mon Feb 15 01:11:12 2010 From: sreenivasan.r.nadar at GMAIL.COM (Sreenivasan Rajamoni Nadar) Date: Sun, 14 Feb 2010 19:11:12 -0500 Subject: coordinates outside brain volume Message-ID: Dear Users, I am using the FieldTrip to extract single trial source signals using the CTF coordinates. Although I have been successful but for some coordinates the Fieldtrip is giving error as coordinates are outside the brain volume. The same coordinates are very much inside brain volume and the CTF software does not report error to extract the virtual source signals. An expert suggested to "inflate" the sphere model so that coordinates are within brain volume to do the source estimation. Anybody has a better idea to deal the problem in FieldTrip? Thank you Vasan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From psowman at MACCS.MQ.EDU.AU Mon Feb 15 02:03:35 2010 From: psowman at MACCS.MQ.EDU.AU (Paul Sowman) Date: Mon, 15 Feb 2010 02:03:35 +0100 Subject: Coherence MEG Message-ID: Dear Jan-Mathijs, thanks for your reply. You suggest that my problem was confined to the previous version however I have the latest version installed. I am using the fieldtrip-20100210.zip version and have just tried with the fieldtrip-20100214.zip version but still the same message. I don't have any other versions on my path. Any ideas? Thanks in advance. Paul ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Mon Feb 15 09:29:21 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Mon, 15 Feb 2010 09:29:21 +0100 Subject: Coherence MEG In-Reply-To: Message-ID: Dear Paul, Once again I tried to reproduce your error. I downloaded fieldtrip-20100214.zip and ran the tutorial. No error in my case. Are you sure that you removed the old fieldtrip from your path? You can check which version of ft_connectivityanalysis was used (to produce your error) by typing which ft_connectivityanalysis from the command line. Best, Jan-Mathijs On Feb 15, 2010, at 2:03 AM, Paul Sowman wrote: > Dear Jan-Mathijs, thanks for your reply. You suggest that my problem > was > confined to the previous version however I have the latest version > installed. I am using the fieldtrip-20100210.zip version and have > just tried > with the fieldtrip-20100214.zip version but still the same message. > I don't > have any other versions on my path. Any ideas? Thanks in advance. Paul > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/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: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Mon Feb 15 10:16:46 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Mon, 15 Feb 2010 10:16:46 +0100 Subject: Toolkit of Cognitive Neuroscience: advanced data analysis and source modelling of EEG and MEG data Message-ID: Dear all, I would like to point you to our yearly toolkit for EEG and MEG data analysis at the Donders Institute. This year's toolkit will take place from April 12 to April 15. Registration is now open. Have a look at: http://www.ru.nl/neuroimaging/toolkit/ for a preliminary programme and to register. 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: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From rajamonis at MAIL.NIH.GOV Mon Feb 15 13:58:41 2010 From: rajamonis at MAIL.NIH.GOV (Rajamoni Nadar, Sreenivasan (NIH/NIMH) [E]) Date: Mon, 15 Feb 2010 07:58:41 -0500 Subject: coordinates outside brain volume Message-ID: Dear Users, I am using the FieldTrip to extract single trial source signals using the CTF coordinates. Although I have been successful but for some coordinates the Fieldtrip is giving error as coordinates are outside the brain volume. The same coordinates are very much inside brain volume and the CTF software does not report error to extract the virtual source signals. An expert suggested to "inflate" the sphere model so that coordinates are within brain volume to do the source estimation. Anybody has a better idea to deal the problem in FieldTrip? Thank you Vasan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Mon Feb 15 14:25:56 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Mon, 15 Feb 2010 14:25:56 +0100 Subject: coordinates outside brain volume In-Reply-To: Message-ID: Dear Vasan, If you don't fully specify a 'grid' (i.e. the locations of your virtual channels and an assignment whether they are inside the brain volume or not) fieldtrip tries to automatically detect whether the locations (either specified by you, or specified by some semi-clever algorithm) fall inside the volume conductor model. For a single sphere which is fitted to the headsurface (or to the inside of the skull) this could lead to many points being excluded. I think generally there are two ways to deal with it: 1 either explicitly specify your virtual channel locations to be 'inside'. In other words: provide fieldtrip's ft_sourceanalysis with a cfg structure containing a grid, in which you state grid.inside = 1:size(grid.pos,1) and grid.outside = []; 2 alternatively, as already mentioned to you, inflate the single sphere, because for a single sphere volume conductor it's the origin that counts. Alternatively, if you have the anatomical scan of your subject, use a volume conductor model which is more 'realistic', taking the geometry of the inside of the skull into account. Cheers, Jan-Mathijs On Feb 15, 2010, at 1:58 PM, Rajamoni Nadar, Sreenivasan (NIH/NIMH) [E] wrote: > Dear Users, > > I am using the FieldTrip to extract single trial source signals > using the CTF coordinates. Although I have been successful but for > some coordinates the Fieldtrip is giving error as coordinates are > outside the brain volume. The same coordinates are very much inside > brain volume and the CTF software does not report error to extract > the virtual source signals. An expert suggested to "inflate" the > sphere model so that coordinates are within brain volume to do the > source estimation. Anybody has a better idea to deal the problem in > FieldTrip? > > Thank you > > Vasan > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/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: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From ole.jensen at DONDERS.RU.NL Mon Feb 15 17:27:49 2010 From: ole.jensen at DONDERS.RU.NL (Ole Jensen) Date: Mon, 15 Feb 2010 17:27:49 +0100 Subject: megcommunity.org: editors wanted Message-ID: Dear all, We are in the processing of constructing a website for the MEG community (megcommunity.org). Clearly there is a strong need for a forum for providing technical information, conferences/courses, teaching material etc. So far this site has been developed by researchers at the Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen (Ole Jensen and Esther Meeuwissen) and Department of Psychology, Glasgow University (Joachim Gross). We are searching for editors to maintain part of the website. If you are interested or would like to suggest candidates (e.g. assign a student/postdoc) please contact us at megcommunity at gmail.com This e-mail address is being protected from spambots. You need JavaScript enabled to view it To be filled: Editor: research groups and software. Maintain list over research groups and software packages. Would require an initial proactive effort, but long-term maintenance is simple. Note that specifics on groups and software are not intended for the megcommunity.org site but we will link to groups/developers sites. Editor: Education and teacing material We hope to collect representative information to facilitate the teaching of MEG research. Thus a strong proactive effort is required in organizing and collecting teaching material (including ppt slides, links and [references to] articles). We hope to collected material from university courses, toolkits and workshops. The aim is to have comprehensive but sufficient information - i.e. content should be edited. Editor: Peripherals Build and organize a comprehensive list of peripherals used for MEG. This includes visual projectors, auditory devices, somatosensory stimulators, button boxes, presentation software, .... Key characteristics could be listed. This would require a proactive and technically knowledgeable editor. Other ideas are of course most welcome! All the best, Ole Jensen -- Ole Jensen Principal Investigator Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Office : +31 24 36 10884 MEG lab : +31 24 36 10988 Fax : +31 24 36 10989 e-mail : ole.jensen at donders.ru.nl URL : http://ojensen.ruhosting.nl/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bibi.raquel at GMAIL.COM Mon Feb 15 20:44:30 2010 From: bibi.raquel at GMAIL.COM (Raquel Bibi) Date: Mon, 15 Feb 2010 14:44:30 -0500 Subject: Coherence MEG In-Reply-To: Message-ID: Dear Jan-Mathijs, I thouth I'd let you know that I have the same problem. Best, Raquel On Mon, Feb 15, 2010 at 3:29 AM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Dear Paul, > > Once again I tried to reproduce your error. I downloaded > fieldtrip-20100214.zip and ran the tutorial. No error in my case. Are you > sure that you removed the old fieldtrip from your path? You can check which > version of ft_connectivityanalysis was used (to produce your error) by > typing which ft_connectivityanalysis from the command line. > > Best, > > Jan-Mathijs > > > > On Feb 15, 2010, at 2:03 AM, Paul Sowman wrote: > > Dear Jan-Mathijs, thanks for your reply. You suggest that my problem was >> confined to the previous version however I have the latest version >> installed. I am using the fieldtrip-20100210.zip version and have just >> tried >> with the fieldtrip-20100214.zip version but still the same message. I >> don't >> have any other versions on my path. Any ideas? Thanks in advance. Paul >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG >> and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/neuroimaging/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: 0031-24-3668063 > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at DONDERS.RU.NL Tue Feb 16 09:05:10 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Tue, 16 Feb 2010 09:05:10 +0100 Subject: Coherence MEG In-Reply-To: <742c550b1002151144h4d6d091dr1513b336ee48837c@mail.gmail.com> Message-ID: Dear Paul, dear Raquel, I apologize. I misread Paul's e-mail in the first instance, when I thought he was working on the coherence tutorial on the fieldtrip website. I now know what's causing the crash. I noted the error and will think of a solution. For the time being I think you could work around this by calling ft_freqanalysis with cfg.output = 'fourier' (rather than 'powandcsd') and calling ft_connectivityanalysis using the output to the call to ft_freqanalysis. Best wishes, Jan-Mathijs On Feb 15, 2010, at 8:44 PM, Raquel Bibi wrote: > Dear Jan-Mathijs, > I thouth I'd let you know that I have the same problem. > > Best, > > Raquel > > On Mon, Feb 15, 2010 at 3:29 AM, jan-mathijs schoffelen > wrote: > Dear Paul, > > Once again I tried to reproduce your error. I downloaded > fieldtrip-20100214.zip and ran the tutorial. No error in my case. > Are you sure that you removed the old fieldtrip from your path? You > can check which version of ft_connectivityanalysis was used (to > produce your error) by typing which ft_connectivityanalysis from the > command line. > > Best, > > Jan-Mathijs > > > > On Feb 15, 2010, at 2:03 AM, Paul Sowman wrote: > > Dear Jan-Mathijs, thanks for your reply. You suggest that my problem > was > confined to the previous version however I have the latest version > installed. I am using the fieldtrip-20100210.zip version and have > just tried > with the fieldtrip-20100214.zip version but still the same message. > I don't > have any other versions on my path. Any ideas? Thanks in advance. Paul > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/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: 0031-24-3668063 > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/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: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.litvak at ION.UCL.AC.UK Wed Feb 17 11:48:13 2010 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Wed, 17 Feb 2010 10:48:13 +0000 Subject: function prepare_bemmodel: resulting BEM system matrix is NaN In-Reply-To: <4B7BBFD1.30302@ulg.ac.be> Message-ID: FYI ---------- Forwarded message ---------- From: Christophe Phillips Date: Wed, Feb 17, 2010 at 10:07 AM Subject: Re: Fwd: [FIELDTRIP] function prepare_bemmodel: resulting BEM system matrix is NaN To: Vladimir Litvak , gbirot at gmail.com Dear Gwenael, Vladimir, feel free to forward my response to the FieldTrip mailing list though a few emails may be needed to sort out this error... If there are NaN in the 1st BEM matrix generated, C11st, then these will indeed propagate throughout the rest of calculation... This C11st matrix is created by a compiled C-routine to speed up things. The details of the numerical implementation are available here: http://www.fil.ion.ucl.ac.uk/~chrisp/Thesis/these_ch3_numBEM.zip Since the code seems to be working for most people but not on your data, I suspect there is a problem in your mesh. Are you using a mesh you generated yourself ? Or the (deformed) template mesh from SPM ? I assume it's the former. Sometimes, when meshes are generated, there remain "errors" in the mesh, like one triangle becoming infinitely small because 3 vertices collapsed to one single point. I suspect this is the case here. Could you check which vertices lead to a NaN in C11st? Something like [ii,jj] = find(isNaN(C11st)) should give you the index of those vertices. Then check their actual location in 3D (in vol.bnd(1).pnt) and the triangles that use this/those vertices (in vol.bnd(1).tri). If you find something dodgy, then you should correct the mesh... like removing the collapsed vertex/triangle. Best, Chris PS: You should also check that the other matrices Cij don't contain any NaN. ---------- Forwarded message ---------- From: Gwenael Birot Date: Fri, Feb 12, 2010 at 1:54 PM Subject: [FIELDTRIP] function prepare_bemmodel: resulting BEM system matrix is NaN To: FIELDTRIP at nic.surfnet.nl Hello, I am a new user of fieldtrip. I am trying to generate BEM system matrix using the function 'prepare_bemmodel' and the 'bemcp' method. The system matrix 'vol.mat' I obtained using the following code is a 'NaN' matrix. %% -------------- Begin -------------- % ---- load brain mesh % load_bnd is a function to load brainvisa mesh [vol.bnd(1).pnt vol.bnd(1).tri] = load_bnd('../data/mesh/colin_ no_artef.eeg-3.bnd'); vol.bnd(1).tri = vol.bnd(1).tri + 1; vol.bnd(1).pnt = vol.bnd(1).pnt; % ---- load skull mesh [vol.bnd(2).pnt vol.bnd(2).tri] = load_bnd('../data/mesh/colin_no_artef.eeg-2.bnd'); vol.bnd(2).tri = vol.bnd(2).tri + 1; vol.bnd(2).pnt = vol.bnd(2).pnt/1000; % ---- load skin mesh [vol.bnd(3).pnt vol.bnd(3).tri] = load_bnd('../data/mesh/colin_no_artef.eeg-1.bnd'); vol.bnd(3).tri = vol.bnd(3).tri + 1; vol.bnd(3).pnt = vol.bnd(3).pnt; % ---- check meshes figure; triplot(vol.bnd(1).pnt, vol.bnd(1).tri, [], 'faces_skin'); rotate3d figure; triplot(vol.bnd(2).pnt, vol.bnd(2).tri, [], 'faces_skin'); rotate3d figure; triplot(vol.bnd(3).pnt, vol.bnd(3).tri, [], 'faces_skin'); rotate3d % this gives good results, so meshes are correctly loaded % ---- prepare BEM model vol.cond   = [0.3300 0.0825 0.3300]; % conductivities vol.skin   = 3; % index of skin surface cfg = []; cfg.method = 'bemcp'; vol = prepare_bemmodel(cfg, vol); %% ------------------- End ------------------------ When executing this code I've got the following result in the matlab prompt using the mesh specified in the input volume conductor determining source compartment (1) determining skin compartment (3) not using the isolated source approach Nvert = 1222 Ntri = 2440 weight = 0.095493 , defl =  0.000000 Nverta = 1222 Ntrib = 2440 Nverta = 1222 Ntrib = 2440 Nvert = 1222 Ntri = 2440 weight = -0.095493 , defl =  0.000000 Nverta = 1222 Ntrib = 2440 Warning: Matrix is singular, close to singular or badly scaled.          Results may be inaccurate. RCOND = NaN. In prepare_bemmodel at 187   In test_fieldtrip at 166 Nverta = 1222 Ntrib = 2440 Warning: Matrix is singular, close to singular or badly scaled.          Results may be inaccurate. RCOND = NaN. In prepare_bemmodel at 194   In test_fieldtrip at 166 Nverta = 1222 Ntrib = 2440 Nverta = 1222 Ntrib = 2440 Nvert = 1222 Ntri = 2440 weight = 0.159155 , defl =  0.000818 Warning: Matrix is singular, close to singular or badly scaled.          Results may be inaccurate. RCOND = NaN. In prepare_bemmodel at 220   In test_fieldtrip at 166 and as I mentionned the resulting BEM system matrix vol.mat is a 'NaN' matrix. I guess the problem occurs in this part of the prepare_bemmodel function (beginning at line 152):   % --------------------------------------------   % Deal first with surface 1 and 2 (inner and outer skull   % NOTE:   % C11st/C22st/C33st are simply the matrix C11/C22/C33 minus the identity   % matrix, i.e. C11st = C11-eye(N)   weight = (vol.cond(1)-vol.cond(2))/((vol.cond(1)+vol.cond(2))*2*pi);   C11st  = bem_Cii_lin(vol.bnd(1).tri,vol.bnd(1).pnt, weight,defl(1),vol.bnd(1).pnt4);   weight = (vol.cond(1)-vol.cond(2))/((vol.cond(2)+vol.cond(3))*2*pi);   C21    = bem_Cij_lin(vol.bnd(2).pnt,vol.bnd(1).pnt,vol.bnd(1).tri, weight,defl(1));   tmp1   = C21/C11st;   weight = (vol.cond(2)-vol.cond(3))/((vol.cond(1)+vol.cond(2))*2*pi);   C12    = bem_Cij_lin(vol.bnd(1).pnt,vol.bnd(2).pnt,vol.bnd(2).tri, weight,defl(2));   weight = (vol.cond(2)-vol.cond(3))/((vol.cond(2)+vol.cond(3))*2*pi);   C22st  = bem_Cii_lin(vol.bnd(2).tri,vol.bnd(2).pnt, weight,defl(2),vol.bnd(2).pnt4);   tmp2   = C12/C22st;   % ------------------------------------------------ where the matrix C11st contains three elements equal to NaN. Since C11st is then inverted, the result is a 'NaN' matrix. I'll would very much appreciate your help Thanks Gwenael ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From A.Stancak at LIVERPOOL.AC.UK Sat Feb 20 11:38:27 2010 From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej) Date: Sat, 20 Feb 2010 10:38:27 +0000 Subject: EGI 129 electrode layout file Message-ID: Dear FieldTrip community, I was not able to find the *.lay file for the 129-channel EGI net in the FieldTrip/SPM8/EEGlab directories. We plan to plot the 2D topographic maps and I assume plotting will not work without appropriate *.lay file. Would anyone have it? Best wishes Andrej Stancak School of Psychology University of Liverpool ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From arno at CERCO.UPS-TLSE.FR Sat Feb 20 11:52:10 2010 From: arno at CERCO.UPS-TLSE.FR (Arnaud Delorme) Date: Sat, 20 Feb 2010 11:52:10 +0100 Subject: EGI 129 electrode layout file In-Reply-To: <0813B54A9D2C494CACBD693C6A2D4D4C1468F6D038@STAFFMBX2.livad.liv.ac.uk> Message-ID: Dear Andrej, the ".sfp" files are enough. They are in EEGLAB "sample_locs" folder and are automatically imported with any binary or Matlab EGI file (since only 2 weeks ago so in case you are using EEGLAB, download the latest version). You may then save the EEGLAB dataset (.set EEGLAB format) and import it within Fieldtrip or SPM8 using the FILEIO module (the defalt import module for Fieldtrip and SPM8). You may also find the channel location files on the EGI FTP sites. Best, Arno On Feb 20, 2010, at 11:38 AM, Stancak, Andrej wrote: > Dear FieldTrip community, > > I was not able to find the *.lay file for the 129-channel EGI net > in the FieldTrip/SPM8/EEGlab directories. We plan to plot the 2D > topographic maps and I assume plotting will not work without > appropriate *.lay file. > Would anyone have it? > > Best wishes > Andrej Stancak > > School of Psychology > University of Liverpool > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From aostendorf at BESA.DE Mon Feb 22 08:55:05 2010 From: aostendorf at BESA.DE (Andrea Ostendorf) Date: Mon, 22 Feb 2010 08:55:05 +0100 Subject: Invalid MEX file /Question re: ft_clusterplot In-Reply-To: <31A51C77-8960-435E-88F0-79E8851D3D37@cerco.ups-tlse.fr> Message-ID: Dear Fieldtrip community, When trying to use read_mri, I encountered the error "??? Invalid MEX-file 'D:\FieldTrip\fieldtrip-20100219\external\spm2\spm_slice_vol.dll': The specified procedure could not be found. Proceeding along the lines suggested in the FAQ - changing to the SPM2 subdirectory and trying to compile the mex file again (using the MATLAB compiler) - I get a long list of error messages, starting with a complaint about a missing header file. I attach the complete error messages below. As the error messages show, I use MATLAB R2007A and a new Fieldtrip version. I have to admit to not having looked up this topic in the discussion list because of the message that there is a problem with the security certificate. Does anyone have an idea? Any help would be very much appreciated. Regarding ft_clusterplot: I have got the impression that during the check for the existence of clusters, ft_clusterplot assumes the existence of both positive and negative clusters, provided that there are any at all (l.113-115). If there are just positive or negative clusters - as may happen in the case of one-sided tests - this can lead to an error such as ??? Reference to non-existent field 'negclusters'. Error in ==> ft_clusterplot at 119 for iNeg = 1:length(stat.negclusters) All the best Andrea ------------- >> cd D:\FieldTrip\fieldtrip-20100219\external\spm2 >> mex spm_slice_vol.c lcc preprocessor error: spm_slice_vol.c:5 Could not find include file "spm_mapping.h" Error spm_slice_vol.c: 6 missing parameter type Error spm_slice_vol.c: 6 syntax error; found `*' expecting `)' Error spm_slice_vol.c: 6 skipping `*' `plhs' `[' `]' `,' Error spm_slice_vol.c: 6 syntax error; found `int' expecting `{' Error spm_slice_vol.c: 6 missing identifier Error spm_slice_vol.c: 6 syntax error; found `const' expecting `;' Error spm_slice_vol.c: 6 redeclaration of `mxArray' previously declared at spm_slice_vol.c 6 Error spm_slice_vol.c: 6 syntax error; found `*' expecting `;' Error spm_slice_vol.c: 6 undeclared identifier `prhs' Error spm_slice_vol.c: 6 illegal expression Error spm_slice_vol.c: 6 syntax error; found `)' expecting `]' Error spm_slice_vol.c: 6 skipping `)' Error spm_slice_vol.c: 7 type error: pointer expected Error spm_slice_vol.c: 7 type error: pointer expected Warning spm_slice_vol.c: 7 Statement has no effect Error spm_slice_vol.c: 7 syntax error; found `{' expecting `;' Error spm_slice_vol.c: 8 undeclared identifier `MAPTYPE' Error spm_slice_vol.c: 8 undeclared identifier `map' Error spm_slice_vol.c: 8 type error: pointer expected Error spm_slice_vol.c: 9 illegal statement termination Error spm_slice_vol.c: 9 too many errors C:\PROGRA~1\MATLAB\R2007A\BIN\MEX.PL: Error: Compile of 'spm_slice_vol.c' failed. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From teristam at GMAIL.COM Mon Feb 22 10:00:09 2010 From: teristam at GMAIL.COM (teris tam) Date: Mon, 22 Feb 2010 17:00:09 +0800 Subject: fieldtripbuffer error code Message-ID: Dear Fieldtrip experts, I am trying to read event data from fieldtripbuffer in matlab using read_event(), but I receive the following error: ??? ERROR: the buffer returned an error (517) Matlab reported that the error occurred at the line: evt = buffer('get_evt', [], host, port); May I ask what does the error code (517) means? Where can I find the list of error code for the fieldtripbuffer? Thanks a lot! Best regards, Teris ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.gross at PSY.GLA.AC.UK Tue Feb 23 14:52:55 2010 From: j.gross at PSY.GLA.AC.UK (Joachim Gross) Date: Tue, 23 Feb 2010 13:52:55 +0000 Subject: website and email list Message-ID: Dear researcher, We are in the process of building a website for the MEG community. Please have a look at megcommunity.org. There is also a mailing list associated with the website. The mailing list will be used for exchanging essential information on workshops, courses, jobs etc and for general discussion. If you do MEG research you are strongly encouraged to join the list. Please encourage other colleagues to join as well (including PhD students). Beyond members of your own group we propose that you forward this message to (say three) MEG researchers you know about in a different country/state than yours. We will make an effort to keep spam low. All the best, Joachim Gross and Ole Jensen ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.gross at PSY.GLA.AC.UK Tue Feb 23 14:55:20 2010 From: j.gross at PSY.GLA.AC.UK (Joachim Gross) Date: Tue, 23 Feb 2010 13:55:20 +0000 Subject: website and email list, + instructions Message-ID: Dear researcher, We are in the process of building a website for the MEG community. Please have a look at megcommunity.org. There is also a mailing list associated with the website. The mailing list will be used for exchanging essential information on workshops, courses, jobs etc and for general discussion. If you do MEG research you are strongly encouraged to join the list. Please encourage other colleagues to join as well (including PhD students). Beyond members of your own group we propose that you forward this message to (say three) MEG researchers you know about in a different country/state than yours. We will make an effort to keep spam low. All the best, Joachim Gross and Ole Jensen To join the list: Send following one line message to < jiscmail at jiscmail.ac.uk >: join megcommunity firstname lastname or have a look at http://megcommunity.org/index.php?option=com_content&view=article&id=13&Itemid=26 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From gianpaolo.demarchi at UNITN.IT Tue Feb 23 17:19:23 2010 From: gianpaolo.demarchi at UNITN.IT (Gianpaolo Demarchi) Date: Tue, 23 Feb 2010 17:19:23 +0100 Subject: multiplotER and Neuromag data Message-ID: Dear all, I tried recently to "multiplotER" some data coming from a Elekta Neuromag system, and what I get is just a "grey" plot (see attachment), without any scale and/or data, and no errors on the stdout. All the labels are fine, and if I go in the interactive mode, I can zoom and see correct "singleplotERs" ... So, all the info seems to be there, just the "big" multiplotER is wrong. I did some homework, and the thing doesn't seem to happen with (very!) older versions of fieldtrip, i.e. I tried with a recent version (fieldtrip-20100209) and a older one (fieldtrip-20091201), and the multiplot is still grey, whereas with and old (fieldtrip-20090318 !! that was somewhere in my HD ;-)) the multiplotER is displayed correctly. Any hint? Am I doing any silly mistake? Thanks in advance, Gianpaolo PS: I'm using Matlab (64bit) 2009b on Linux-64, if relevant ... PPS: here is the code I'm using ... and yes, I tried also with the "ft_" version of the commands cfg = []; cfg.dataset = 'raw.fif'; cfg.trialdef.eventtype = 'STI101'; cfg.trialdef.eventvalue = 32768; cfg.trialdef.prestim = 0.1; cfg.trialdef.poststim = 0.25; cfg = definetrial(cfg); cfg.channel = {'MEG'}; cfg.blc = 'yes'; cfg.blcwindow = [-0.1 0]; cfg.lpfilter = 'yes'; cfg.lpfreq = 35; data_raw = preprocessing(cfg); cfg = []; data_avg = timelockanalysis(cfg,data_raw) cfg = []; % cfg.showlabels = 'yes'; % cfg.fontsize = 6; % cfg.interactive = 'yes'; cfg.ylim = [-3e-12 3e-12]; cfg.interactive = 'yes'; multiplotER(cfg, data_avg); ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: multiploeERgrey.jpg Type: image/jpeg Size: 45301 bytes Desc: not available URL: From moratti at MED.UCM.ES Wed Feb 24 11:23:29 2010 From: moratti at MED.UCM.ES (Stephan Moratti) Date: Wed, 24 Feb 2010 11:23:29 +0100 Subject: multiplotER and Neuromag data Message-ID: Hola Gianpaolo, I had the same problem as you. The probel lies in the ft_prepare_layout.m function. It calculates the minimum distance between sensors. As the neuromag sensor has different types of sensors, the layout puts the 3 different sensors at the same place. So calculating the min(d(:)) results in 0 values. Please find below the modified subfunction sens2lay that is located in ft_prepare_layout.m that prevents this error. With that, the topoplots (and multiplots) should work out. Maybe this error can be prevented in a more elegant way that I did. Best, Stephan %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % SUBFUNCTION % convert 3D electrode positions into 2D layout %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% function lay = sens2lay(sens, rz, method, style) fprintf('creating layout for %s system\n', senstype(sens)); % apply rotation if isempty(rz) switch senstype(sens) case {'ctf151', 'ctf275', 'bti148', 'bti248', 'ctf151_planar', 'ctf275_planar', 'bti148_pla nar', 'bti248_planar'} rz = 90; case {'neuromag122', 'neuromag306'} rz = 0; case 'electrode' rz = 90; otherwise rz = 0; end end sens.pnt = warp_apply(rotate([0 0 rz]), sens.pnt, 'homogenous'); % use helper function for 3D layout [pnt, label] = channelposition(sens); if strcmpi(style, '3d') lay.pos = pnt; lay.label = label; else if strcmp(senstype(sens),'neuromag306') %this is to prevent distance of 0 prj = elproj(pnt(1:102,:), method); n=3; else prj = elproj(pnt, method); n=0; end d = dist(prj'); d(find(eye(size(d)))) = inf; mindist = min(d(:)); % this is to fix the planar layouts, which cannot be plotted anyway if n>1 %this is to prevent confusion when lab happens to be a row array prj = repmat(prj, n, 1); end X = prj(:,1); Y = prj(:,2); Width = ones(size(X)) * mindist * 0.8; Height = ones(size(X)) * mindist * 0.6; lay.pos = [X Y]; lay.width = Width; lay.height = Height; lay.label = label; end ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From v.litvak at ION.UCL.AC.UK Wed Feb 24 12:39:18 2010 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Wed, 24 Feb 2010 11:39:18 +0000 Subject: New 'Statistical Parametric Mapping for MEG/EEG' course, London May 10-12, 2010 Message-ID: Dear colleagues, We are happy to advertise the new Statistical Parametric Mapping MEG/EEG course presented by the Wellcome Trust Centre for Neuroimaging. The course will take place on Monday 10th May – Wednesday 12th May 2010 at the Wellcome Trust Centre for Neuroimaging in London. This newly established course will present instruction on the analysis of EEG and MEG data. The first two days will combine theoretical presentations with practical demonstrations of the different data analysis methods implemented in SPM. On the last day participants will have the opportunity to work on SPM tutorial data sets under the supervision of the course faculty. We also invite students to bring their own data for analysis. The course will cover (1) data pre-processing, (2) statistical analysis of sensor-space maps using GLMs and Random Field theory, (3) source reconstruction and (4) Dynamic Causal Modelling for EEG/MEG. The course will be followed by the long-established three-day course on ‘SPM for fMRI’ so it is possible to attend both courses. The course is suitable for beginners and more advanced users. We advise students to gain at least some minimal familiarity with the methodology, for example, from reading introductory articles available from the SPM web page or by following data analysis examples in the SPM manual. The detailed schedule and booking forms can be found at http://www.ion.ucl.ac.uk/articles/events/SPM . For further details and registration please contact Jean Reynolds (j.reynolds at ion.ucl.ac.uk). With best wishes, Vladimir Litvak Ph.D. Senior Research Associate Wellcome Trust Centre for Neuroimaging -------------------------------------------------------------------------------------------------- SPM (http://www.fil.ion.ucl.ac.uk/spm/) is a free and open-source Matlab toolbox in which many widely used methods for the analysis of PET and fMRI data; and for computational neuroanatomy were originally developed. In the recent years SPM has been extended to include M/EEG analysis and, in the most recent version, SPM8, extensive changes have made the software more stable, generic and accessible to researchers with data from wide range of recording systems. In addition to standard M/EEG pre-processing we presently offer three main analysis tools: (1) statistical analysis of scalp maps, time-frequency images and volumetric 3D source reconstruction images based on the general linear model with correction for multiple comparisons using random field theory (2) Bayesian M/EEG source reconstruction including support for group studies, simultaneous EEG and MEG and fMRI priors (3) Dynamic Causal Modelling (DCM) an approach combining neural modelling with data analysis for which there are several variants dealing with evoked responses, steady state responses (power spectra and cross-spectra), induced responses and phase coupling. SPM8 is integrated with the Fieldtrip toolbox (http://www.ru.nl/neuroimaging/fieldtrip/) making it possible for users to combine a variety of standard analysis methods with the new methods implemented in SPM and build custom analysis tools using powerful GUI and batching tools. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From gianpaolo.demarchi at UNITN.IT Wed Feb 24 15:06:25 2010 From: gianpaolo.demarchi at UNITN.IT (Gianpaolo Demarchi) Date: Wed, 24 Feb 2010 15:06:25 +0100 Subject: multiplotER and Neuromag data In-Reply-To: Message-ID: Dear Stephan, thanks for your 'patch' ! It works, i.e. I get a multiplotER graph with some data in it! With "your version" at least we get back a multiplot, with sadly the gradiometers and magnetometers data overlapped. The 'old' way was plotting them arranged in triplets, with one magnetometer and the two gradiometers 'clustered' together. I checked the 'old' prepare_layout.m, and in fact in the grad2lay() function there was a 'finer grained' check of the sensor type, including a different/better layout for 'neuromag306' case. Anyway, there must be a reason for choosing this option (probably the old arrangement with mag+2grads sublopts was too crowded, and probably useless), and in case we can still make two different multiplotERs for magnetometers and gradiometers ... Thanks again, Gianpaolo PS: should this one be considered a 'patch' for a 'bug', and go upstream in the official fieldtrip release? > I had the same problem as you. The probel lies in the ft_prepare_layout.m > function. It calculates the minimum distance between sensors. As the > neuromag sensor has different types of sensors, the layout puts the 3 > different sensors at the same place. So calculating the min(d(:)) results > in 0 values. Please find below the modified subfunction sens2lay that is > located in ft_prepare_layout.m that prevents this error. With that, the > topoplots (and multiplots) should work out. Maybe this error can be > prevented in a more elegant way that I did. > > Best, > > Stephan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From moratti at MED.UCM.ES Thu Feb 25 09:03:30 2010 From: moratti at MED.UCM.ES (Stephan Moratti) Date: Thu, 25 Feb 2010 09:03:30 +0100 Subject: multiplotER and Neuromag data Message-ID: Hello again, I would plot magneto- and gradiometers seperately anyway. You can choose them by using cfg.channel. Best, Stephan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From karl.doron at GMAIL.COM Thu Feb 25 18:35:42 2010 From: karl.doron at GMAIL.COM (Karl Doron) Date: Thu, 25 Feb 2010 18:35:42 +0100 Subject: read events Message-ID: My apologies if this is redundant - I believe I sent to it the megcommunity list and meant to send it here, so I am reposting. Hello, I've recently collect MEG data and had to edit trigger values. I've read in my BTi data using preprocessing() and inserted triggers at appropriate times in sub1.trial{1}(1,:). Now I would like to use definetrial. However, the cfg file references the original data, with the incorrect trigger onsets and information. What should I list as cfg.dataset to have my imported data read? Thanks for any help. karl doron Ph.D. Candidate UC, Santa Barbara ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From chesharm at STANFORD.EDU Sat Feb 27 08:15:21 2010 From: chesharm at STANFORD.EDU (Chetan Sharma) Date: Fri, 26 Feb 2010 23:15:21 -0800 Subject: clusterstats empty cfg.neighbours, cfg.neighbours example Message-ID: Hello everyone, I'm trying to run the coherence Z nonparametric test to detect synchrony between two channels of MEG data. Because of how restrictive bonferoni, FDR, and all are, we wanted to use the 'cluster' function for cfg.correctm. This call to statistics_montecarlo.m, which says in the description that to do clustering in frequency and time, as we want to do, we should use an empty cfg.neighbours structure. However, when the function calls clusterstats.m, it looks like there is a bug in the code. The relevant code is at line 38 in clusterstats.m, and is: if isfield(cfg, 'neighbours') && ~isempty(cfg.neighbours) channeighbstructmat = makechanneighbstructmat(cfg); issource = 0; else issource = 1; % cfg contains dim and inside that are needed for reshaping the data to a volume, and inside should behave as a index vector cfg = fixinside(cfg, 'index'); end The issue is that the case for an empty cfg.neighbours isn't handled. Running the function with an empty cfg.neighbours leads to a bug when calculating the clusters, and makes issource=1, when it should be zero for freq_time data. The function runs through when I manually set issource=0, but I don't know if that is the intended purpose. Has anyone else run into this problem? Without an example of what cfg.neighbours should look like, it's hard to determine if we are doing a correct setup. Could someone either send an example of cfg.neighbours, or verify this bug and suggest solutions? thanks and regards, -chetan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Sat Feb 27 14:21:03 2010 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Sat, 27 Feb 2010 14:21:03 +0100 Subject: read events In-Reply-To: Message-ID: Dear Karl, Definetrial is usually called before preprocessing, not after preprocessing. Definetrial determines the trial structure, i.e. the segments that subsequently are read with the preprocessing function. Often the interesting data segments (the trials) are much shorter than the complete continuous data, so reading only the trials saves memory. Since you have already read in all data into memory, you should use "redefinetrial" to segment your data into the trials. That also requires the trial definition to be specified in cfg.trl. The only purpose of definetrial function is t oconstruct this cfg.trl field based on the events. Since you manually added the triggers after reading the data in memory, you have to emulate the behaviour of definetrial. You should look at it's help and manually construct a cfg.trl field which you can hand over to redefinetrial together with the data. best, Robert On 25 Feb 2010, at 18:35, Karl Doron wrote: > My apologies if this is redundant - I believe I sent to it the megcommunity > list and meant to send it here, so I am reposting. > > Hello, > > I've recently collect MEG data and had to edit trigger values. I've read in > my BTi data using preprocessing() and inserted triggers at appropriate times > in sub1.trial{1}(1,:). > > Now I would like to use definetrial. However, the cfg file references the > original data, with the incorrect trigger onsets and information. What > should I list as cfg.dataset to have my imported data read? > > Thanks for any help. > > karl doron > Ph.D. Candidate > UC, Santa Barbara > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Sat Feb 27 14:27:09 2010 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Sat, 27 Feb 2010 14:27:09 +0100 Subject: Invalid MEX file /Question re: ft_clusterplot In-Reply-To: <6B7D05EBBB224D9F93C9E1F0905EE2DC@LAT6500Andrea> Message-ID: Dear Andrea > On 22 Feb 2010, at 8:55, Andrea Ostendorf wrote: > When trying to use read_mri, I encountered the error > "??? Invalid MEX-file > 'D:\FieldTrip\fieldtrip-20100219\external\spm2\spm_slice_vol.dll': The > specified procedure could not be found. > > Proceeding along the lines suggested in the FAQ - changing to the SPM2 > subdirectory and trying to compile the mex file again (using the MATLAB > compiler) - I get a long list of error messages, starting with a complaint > about a missing header file. I attach the complete error messages below. It turns out that the set of *.c files in the fieldtrip/external/spm2 directory is incomplete. You should compile the mex files from a complete spm2 version, which you can hget from the FIl website. > Regarding ft_clusterplot: I have got the impression that during the check > for the existence of clusters, ft_clusterplot assumes the existence of both > positive and negative clusters, provided that there are any at all > (l.113-115). If there are just positive or negative clusters - as may happen > in the case of one-sided tests - this can lead to an error such as > > ??? Reference to non-existent field 'negclusters'. > > Error in ==> ft_clusterplot at 119 > for iNeg = 1:length(stat.negclusters) You are right. I have made that optional on the presence of positive or negative clusters like this: if haspos == 0 && hasneg == 0 fprintf('%s\n','no significant clusters in data; nothing to plot') else if haspos for iPos = 1:length(stat.posclusters) sigpos(iPos) = stat.posclusters(iPos).prob < cfg.alpha; end end if hasneg for iNeg = 1:length(stat.negclusters) signeg(iNeg) = stat.negclusters(iNeg).prob < cfg.alpha; end end ... thanks, Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From nicolas.robitaille at UMONTREAL.CA Sat Feb 27 14:55:18 2010 From: nicolas.robitaille at UMONTREAL.CA (Nicolas Robitaille) Date: Sat, 27 Feb 2010 13:55:18 +0000 Subject: read events In-Reply-To: <1CAE6B41-DB17-4A88-BD6E-F4F231DB18C1@fcdonders.ru.nl> Message-ID: Dear Karl, dear Robert, I would suggest, alternatively, to modify the trialfun_general (or wathever trialfun you are using, Karl), in order to use the event definition found in the cfg structure, if any. This would have the advantage of allowing multiple call to definetrial (for multiple conditions; I once had 30 of them) without having to read all the events in the datafile over and over again. I think such change in behavior could be incorporated in the normal distribution of FT, according that it's already the case of the trial definition (i.e. if there is already a .trl field, definetrial.m just use it). This would look like: starting at line 49 of trialfun_general: % read the header and event information hdr = read_header(cfg.headerfile); try event = read_event(cfg.headerfile); catch event = []; end should become something like: % read the header and event information hdr = read_header(cfg.headerfile); if isfield(cfg, 'event') event = cfg.event; else try event = read_event(cfg.headerfile); catch event = []; end end Karl, note that I haven't test that. Best, Nicolas ************************* Nicolas Robitaille, Ph.D. Stagiaire post-doctoral Brams ************************* > Date: Sat, 27 Feb 2010 14:21:03 +0100 > From: r.oostenveld at FCDONDERS.RU.NL > Subject: Re: [FIELDTRIP] read events > To: FIELDTRIP at NIC.SURFNET.NL > > Dear Karl, > > Definetrial is usually called before preprocessing, not after preprocessing. Definetrial determines the trial structure, i.e. the segments that subsequently are read with the preprocessing function. Often the interesting data segments (the trials) are much shorter than the complete continuous data, so reading only the trials saves memory. > > Since you have already read in all data into memory, you should use "redefinetrial" to segment your data into the trials. That also requires the trial definition to be specified in cfg.trl. The only purpose of definetrial function is t oconstruct this cfg.trl field based on the events. > > Since you manually added the triggers after reading the data in memory, you have to emulate the behaviour of definetrial. You should look at it's help and manually construct a cfg.trl field which you can hand over to redefinetrial together with the data. > > best, > Robert > > > > > > On 25 Feb 2010, at 18:35, Karl Doron wrote: > > > My apologies if this is redundant - I believe I sent to it the megcommunity > > list and meant to send it here, so I am reposting. > > > > Hello, > > > > I've recently collect MEG data and had to edit trigger values. I've read in > > my BTi data using preprocessing() and inserted triggers at appropriate times > > in sub1.trial{1}(1,:). > > > > Now I would like to use definetrial. However, the cfg file references the > > original data, with the incorrect trigger onsets and information. What > > should I list as cfg.dataset to have my imported data read? > > > > Thanks for any help. > > > > karl doron > > Ph.D. Candidate > > UC, Santa Barbara > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. _________________________________________________________________ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Sat Feb 27 15:06:54 2010 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Sat, 27 Feb 2010 15:06:54 +0100 Subject: fieldtripbuffer error code In-Reply-To: Message-ID: Hi Teris On 22 Feb 2010, at 10:00, teris tam wrote: > Dear Fieldtrip experts, > I am trying to read event data from fieldtripbuffer in matlab using read_event(), but I receive the following error: > > ??? ERROR: the buffer returned an error (517) > > Matlab reported that the error occurred at the line: > > evt = buffer('get_evt', [], host, port); This is an error that happens if there are no events in the buffer. In more recent versions, read_event returns an empty array (i.e. []), which is what you woudl expect. I suggest that you upgrade to the most recent version. > May I ask what does the error code (517) means? Where can I find the list of error code for the fieldtripbuffer? They are defined (in hexadecimal representation, and not in decimal representation as it is printed) in fieldtrip/realtime/buffer/src/message.h. You can convert them for example here http://easycalculation.com/hex-converter.php?hex=0x0205&hexDeci=NaN&hexBin=0001 The error 517 (decimal) is 0205 (hexadecimal), which means GET_ERR. best regards, Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Sat Feb 27 15:11:22 2010 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Sat, 27 Feb 2010 15:11:22 +0100 Subject: read events In-Reply-To: Message-ID: Hi Nicolas That is a good suggestion, I have incorporated it into the code. This evenings version on the ftp server will include it. thanks, Robert ----------------------------------------------------------- Robert Oostenveld, PhD Senior Researcher Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen tel.: +31 (0)24 3619695 e-mail: r.oostenveld at donders.ru.nl web: http://www.ru.nl/neuroimaging skype: r.oostenveld ----------------------------------------------------------- On 27 Feb 2010, at 14:55, Nicolas Robitaille wrote: > Dear Karl, dear Robert, > > I would suggest, alternatively, to modify the trialfun_general (or wathever trialfun you are using, Karl), in order to use the event definition found in the cfg structure, if any. This would have the advantage of allowing multiple call to definetrial (for multiple conditions; I once had 30 of them) without having to read all the events in the datafile over and over again. I think such change in behavior could be incorporated in the normal distribution of FT, according that it's already the case of the trial definition (i.e. if there is already a .trl field, definetrial.m just use it). > > This would look like: > > starting at line 49 of trialfun_general: > > % read the header and event information > hdr = read_header(cfg.headerfile); > try > event = read_event(cfg.headerfile); > catch > event = []; > end > > should become something like: > > % read the header and event information > hdr = read_header(cfg.headerfile); > if isfield(cfg, 'event') > event = cfg.event; > else > try > event = read_event(cfg.headerfile); > catch > event = []; > end > end > > Karl, note that I haven't test that. > > Best, > > Nicolas > > ************************* > Nicolas Robitaille, Ph.D. > Stagiaire post-doctoral > Brams > ************************* > > > > > > Date: Sat, 27 Feb 2010 14:21:03 +0100 > > From: r.oostenveld at FCDONDERS.RU.NL > > Subject: Re: [FIELDTRIP] read events > > To: FIELDTRIP at NIC.SURFNET.NL > > > > Dear Karl, > > > > Definetrial is usually called before preprocessing, not after preprocessing. Definetrial determines the trial structure, i.e. the segments that subsequently are read with the preprocessing function. Often the interesting data segments (the trials) are much shorter than the complete continuous data, so reading only the trials saves memory. > > > > Since you have already read in all data into memory, you should use "redefinetrial" to segment your data into the trials. That also requires the trial definition to be specified in cfg.trl. The only purpose of definetrial function is t oconstruct this cfg.trl field based on the events. > > > > Since you manually added the triggers after reading the data in memory, you have to emulate the behaviour of definetrial. You should look at it's help and manually construct a cfg.trl field which you can hand over to redefinetrial together with the data. > > > > best, > > Robert > > > > > > > > > > > > On 25 Feb 2010, at 18:35, Karl Doron wrote: > > > > > My apologies if this is redundant - I believe I sent to it the megcommunity > > > list and meant to send it here, so I am reposting. > > > > > > Hello, > > > > > > I've recently collect MEG data and had to edit trigger values. I've read in > > > my BTi data using preprocessing() and inserted triggers at appropriate times > > > in sub1.trial{1}(1,:). > > > > > > Now I would like to use definetrial. However, the cfg file references the > > > original data, with the incorrect trigger onsets and information. What > > > should I list as cfg.dataset to have my imported data read? > > > > > > Thanks for any help. > > > > > > karl doron > > > Ph.D. Candidate > > > UC, Santa Barbara > > > > > > ---------------------------------- > > > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html andhttp://www.ru.nl/neuroimaging/fieldtrip. > > > > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html andhttp://www.ru.nl/neuroimaging/fieldtrip. > > Vous n'utilisez pas Hotmail sur votre téléphone? Mais pourquoi pas? Obtenez-le maintenant! > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. > http://listserv.surfnet.nl/archives/fieldtrip.html > http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From tomh at KURAGE.NIMH.NIH.GOV Sun Feb 28 00:12:10 2010 From: tomh at KURAGE.NIMH.NIH.GOV (Tom Holroyd) Date: Sat, 27 Feb 2010 18:12:10 -0500 Subject: clusterstats empty cfg.neighbours, cfg.neighbours example Message-ID: >I'm trying to run the coherence Z nonparametric test to detect synchrony >between two channels of MEG data. Because of how restrictive bonferoni, FDR, >and all are project source channels into dual space get independent components look at coherence differences shuffle get max look at angles between source space beamformers ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE Tue Feb 2 11:16:40 2010 From: Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE (Hanneke Van Dijk) Date: Tue, 2 Feb 2010 11:16:40 +0100 Subject: BUG in ft_topoplotER (cfg.xlim) version 20100127 Message-ID: Dear all, I wanted to report a bug in ft_topoplotER (Fieldtrip version 20100127), regarding the use of cfg.xlim. It doesn't seem to use cfg.xlim when you choose one, but just to use the 'maxmin'. When I average the data over xlim myself I get a completely different topoplot then when I use cfg.xlim for the same range. I wouldn't have known if I didn't need to average over xlim for other reasons. It seems to happen between lines 445 and 452. The data are selected for cfg.ylim and cfg.component but not for cfg.xlim. This changes the outlook on my data completely, and I think this could be important for all users of this version. Therefore I send it to the entire mailing list. I have changed it now to: 444 % make dat structure with one value for each channel 445 dat = getsubfield(data, cfg.zparam); 446 if ~isempty(cfg.yparam), 447 dat = dat(:, ymin:ymax, xmin:xmax); 448 dat = nanmean(nanmean(dat, 2), 3); 449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part Hanneke added 450 dat = dat(:, xmin:xmax); 451 dat = nanmean(dat, 2); 452 end 453 454 dat = dat(:); This helps for me and it is very important for me as well, my data looks meaningfull now! Best and good luck! Hanneke -------------------------------------------------- Institut für Klinische Neurowissenschaften und Medizinische Psychologie Gebäude-Nr.: 23.02 Ebene: 03 Zimmer-Nr.: 47 Tel.: 0211-81-13074 Mail : hanneke.vandijk at med.uni-duesseldorf.de http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at FCDONDERS.RU.NL Tue Feb 2 12:03:09 2010 From: a.stolk at FCDONDERS.RU.NL (a.stolk@fcdonders.ru.nl) Date: Tue, 2 Feb 2010 12:03:09 +0100 Subject: BUG in ft_topoplotER (cfg.xlim) version 20100127 In-Reply-To: <12550216.2564201265108507127.JavaMail.root@watertor.uci.ru.nl> Message-ID: Hi Hanneke, Thank you for your report. Could you specify some more details to help locating the problem? Are you trying to plot event-related fields or components (I'm asking this because of our earlier mail exchanges)? For the latter, I could recommend the ft_topoplotIC function. This one has maxmin values for the z-axis by default, but is more intuitive. An example: cfg = []; cfg.layout = 'NM122_ver.lay'; cfg.component = 1; ft_topoplotIC(cfg,comp); Best, Arjen ----- Original Message ----- From: "Hanneke Van Dijk" To: FIELDTRIP at NIC.SURFNET.NL Sent: Tuesday, February 2, 2010 11:16:40 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 Dear all, I wanted to report a bug in ft_topoplotER (Fieldtrip version 20100127), regarding the use of cfg.xlim. It doesn't seem to use cfg.xlim when you choose one, but just to use the 'maxmin'. When I average the data over xlim myself I get a completely different topoplot then when I use cfg.xlim for the same range. I wouldn't have known if I didn't need to average over xlim for other reasons. It seems to happen between lines 445 and 452. The data are selected for cfg.ylim and cfg.component but not for cfg.xlim. This changes the outlook on my data completely, and I think this could be important for all users of this version. Therefore I send it to the entire mailing list. I have changed it now to: 444 % make dat structure with one value for each channel 445 dat = getsubfield(data, cfg.zparam); 446 if ~isempty(cfg.yparam), 447 dat = dat(:, ymin:ymax, xmin:xmax); 448 dat = nanmean(nanmean(dat, 2), 3); 449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part Hanneke added 450 dat = dat(:, xmin:xmax); 451 dat = nanmean(dat, 2); 452 end 453 454 dat = dat(:); This helps for me and it is very important for me as well, my data looks meaningfull now! Best and good luck! Hanneke -------------------------------------------------- Institut für Klinische Neurowissenschaften und Medizinische Psychologie Gebäude-Nr.: 23.02 Ebene: 03 Zimmer-Nr.: 47 Tel.: 0211-81-13074 Mail : hanneke.vandijk at med.uni-duesseldorf.de http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE Tue Feb 2 12:40:14 2010 From: Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE (Hanneke Van Dijk) Date: Tue, 2 Feb 2010 12:40:14 +0100 Subject: AW: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 Message-ID: Hi Arjen, This time I am plotting cortico-muscular coherence obtained from ft_freqanalysis_mtmfft with fourier output and then using ft_connectivityanalysis. I wanted to plot the coherence on helmet-level only for 8-12 Hz. I attached the figures; When I do the average over the .cohspctrm field myself (or add the line I reported before) I get the left plot (figure 2) and if I say cfg.xlim I get the right plot (figure 1). Groetjes Hanneke -------------------------------------------------- Institut für Klinische Neurowissenschaften und Medizinische Psychologie Gebäude-Nr.: 23.02 Ebene: 03 Zimmer-Nr.: 47 Tel.: 0211-81-13074 Mail : hanneke.vandijk at med.uni-duesseldorf.de http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html -----Ursprüngliche Nachricht----- Von: FieldTrip discussion list im Auftrag von a.stolk at fcdonders.ru.nl Gesendet: Di 02.02.2010 12:03 An: FIELDTRIP at NIC.SURFNET.NL Betreff: Re: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 Hi Hanneke, Thank you for your report. Could you specify some more details to help locating the problem? Are you trying to plot event-related fields or components (I'm asking this because of our earlier mail exchanges)? For the latter, I could recommend the ft_topoplotIC function. This one has maxmin values for the z-axis by default, but is more intuitive. An example: cfg = []; cfg.layout = 'NM122_ver.lay'; cfg.component = 1; ft_topoplotIC(cfg,comp); Best, Arjen ----- Original Message ----- From: "Hanneke Van Dijk" To: FIELDTRIP at NIC.SURFNET.NL Sent: Tuesday, February 2, 2010 11:16:40 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 Dear all, I wanted to report a bug in ft_topoplotER (Fieldtrip version 20100127), regarding the use of cfg.xlim. It doesn't seem to use cfg.xlim when you choose one, but just to use the 'maxmin'. When I average the data over xlim myself I get a completely different topoplot then when I use cfg.xlim for the same range. I wouldn't have known if I didn't need to average over xlim for other reasons. It seems to happen between lines 445 and 452. The data are selected for cfg.ylim and cfg.component but not for cfg.xlim. This changes the outlook on my data completely, and I think this could be important for all users of this version. Therefore I send it to the entire mailing list. I have changed it now to: 444 % make dat structure with one value for each channel 445 dat = getsubfield(data, cfg.zparam); 446 if ~isempty(cfg.yparam), 447 dat = dat(:, ymin:ymax, xmin:xmax); 448 dat = nanmean(nanmean(dat, 2), 3); 449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part Hanneke added 450 dat = dat(:, xmin:xmax); 451 dat = nanmean(dat, 2); 452 end 453 454 dat = dat(:); This helps for me and it is very important for me as well, my data looks meaningfull now! Best and good luck! Hanneke -------------------------------------------------- Institut für Klinische Neurowissenschaften und Medizinische Psychologie Gebäude-Nr.: 23.02 Ebene: 03 Zimmer-Nr.: 47 Tel.: 0211-81-13074 Mail : hanneke.vandijk at med.uni-duesseldorf.de http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. figure; cfgp=[]; cfgp.cohrefchannel = {'MEG063+064'}; cfgp.xparam = 'freq'; cfgp.zparam = 'cohspctrm'; cfgp.layout = 'NM122combined_test.lay'; cfgp.showlabels = 'yes'; cfgp.xlim = [8 12]; %cfgp.zlim = [0 1]; ft_topoplotER(cfgp,fd_ccc_off);colorbar ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE Tue Feb 2 12:41:32 2010 From: Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE (Hanneke Van Dijk) Date: Tue, 2 Feb 2010 12:41:32 +0100 Subject: BUG in ft_topoplotER (cfg.xlim) version 20100127 Message-ID: Sorry, somehow the attachment didn't go allright, I'll try it again. -------------------------------------------------- Institut für Klinische Neurowissenschaften und Medizinische Psychologie Gebäude-Nr.: 23.02 Ebene: 03 Zimmer-Nr.: 47 Tel.: 0211-81-13074 Mail : hanneke.vandijk at med.uni-duesseldorf.de http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html -----Ursprüngliche Nachricht----- Von: FieldTrip discussion list im Auftrag von Hanneke Van Dijk Gesendet: Di 02.02.2010 12:40 An: FIELDTRIP at NIC.SURFNET.NL Betreff: [FIELDTRIP] AW: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 Hi Arjen, This time I am plotting cortico-muscular coherence obtained from ft_freqanalysis_mtmfft with fourier output and then using ft_connectivityanalysis. I wanted to plot the coherence on helmet-level only for 8-12 Hz. I attached the figures; When I do the average over the .cohspctrm field myself (or add the line I reported before) I get the left plot (figure 2) and if I say cfg.xlim I get the right plot (figure 1). Groetjes Hanneke -------------------------------------------------- Institut für Klinische Neurowissenschaften und Medizinische Psychologie Gebäude-Nr.: 23.02 Ebene: 03 Zimmer-Nr.: 47 Tel.: 0211-81-13074 Mail : hanneke.vandijk at med.uni-duesseldorf.de http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html -----Ursprüngliche Nachricht----- Von: FieldTrip discussion list im Auftrag von a.stolk at fcdonders.ru.nl Gesendet: Di 02.02.2010 12:03 An: FIELDTRIP at NIC.SURFNET.NL Betreff: Re: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 Hi Hanneke, Thank you for your report. Could you specify some more details to help locating the problem? Are you trying to plot event-related fields or components (I'm asking this because of our earlier mail exchanges)? For the latter, I could recommend the ft_topoplotIC function. This one has maxmin values for the z-axis by default, but is more intuitive. An example: cfg = []; cfg.layout = 'NM122_ver.lay'; cfg.component = 1; ft_topoplotIC(cfg,comp); Best, Arjen ----- Original Message ----- From: "Hanneke Van Dijk" To: FIELDTRIP at NIC.SURFNET.NL Sent: Tuesday, February 2, 2010 11:16:40 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 Dear all, I wanted to report a bug in ft_topoplotER (Fieldtrip version 20100127), regarding the use of cfg.xlim. It doesn't seem to use cfg.xlim when you choose one, but just to use the 'maxmin'. When I average the data over xlim myself I get a completely different topoplot then when I use cfg.xlim for the same range. I wouldn't have known if I didn't need to average over xlim for other reasons. It seems to happen between lines 445 and 452. The data are selected for cfg.ylim and cfg.component but not for cfg.xlim. This changes the outlook on my data completely, and I think this could be important for all users of this version. Therefore I send it to the entire mailing list. I have changed it now to: 444 % make dat structure with one value for each channel 445 dat = getsubfield(data, cfg.zparam); 446 if ~isempty(cfg.yparam), 447 dat = dat(:, ymin:ymax, xmin:xmax); 448 dat = nanmean(nanmean(dat, 2), 3); 449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part Hanneke added 450 dat = dat(:, xmin:xmax); 451 dat = nanmean(dat, 2); 452 end 453 454 dat = dat(:); This helps for me and it is very important for me as well, my data looks meaningfull now! Best and good luck! Hanneke -------------------------------------------------- Institut für Klinische Neurowissenschaften und Medizinische Psychologie Gebäude-Nr.: 23.02 Ebene: 03 Zimmer-Nr.: 47 Tel.: 0211-81-13074 Mail : hanneke.vandijk at med.uni-duesseldorf.de http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. figure; cfgp=[]; cfgp.cohrefchannel = {'MEG063+064'}; cfgp.xparam = 'freq'; cfgp.zparam = 'cohspctrm'; cfgp.layout = 'NM122combined_test.lay'; cfgp.showlabels = 'yes'; cfgp.xlim = [8 12]; %cfgp.zlim = [0 1]; ft_topoplotER(cfgp,fd_ccc_off);colorbar ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE Tue Feb 2 12:43:05 2010 From: Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE (Hanneke van Dijk) Date: Tue, 2 Feb 2010 12:43:05 +0100 Subject: AW: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8B0F358C@Mail2-UKD.VMED.UKD> Message-ID: Maybe like this then sorry for the large amount of mails... On Tue, Feb 2, 2010 at 12:40 PM, Hanneke Van Dijk < Hanneke.vanDijk at med.uni-duesseldorf.de> wrote: > Hi Arjen, > > This time I am plotting cortico-muscular coherence obtained from > ft_freqanalysis_mtmfft with fourier output and then using > ft_connectivityanalysis. I wanted to plot the coherence on helmet-level only > for 8-12 Hz. I attached the figures; When I do the average over the > .cohspctrm field myself (or add the line I reported before) I get the left > plot (figure 2) and if I say cfg.xlim I get the right plot (figure 1). > > Groetjes Hanneke > > > > -------------------------------------------------- > Institut für Klinische Neurowissenschaften und Medizinische Psychologie > Gebäude-Nr.: 23.02 > Ebene: 03 Zimmer-Nr.: 47 > Tel.: 0211-81-13074 > Mail : hanneke.vandijk at med.uni-duesseldorf.de > > http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html > > > > -----Ursprüngliche Nachricht----- > Von: FieldTrip discussion list im Auftrag von a.stolk at fcdonders.ru.nl > Gesendet: Di 02.02.2010 12:03 > An: FIELDTRIP at NIC.SURFNET.NL > Betreff: Re: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 > > Hi Hanneke, > > Thank you for your report. Could you specify some more details to help > locating the problem? > > Are you trying to plot event-related fields or components (I'm asking this > because of our earlier mail exchanges)? For the latter, I could recommend > the ft_topoplotIC function. This one has maxmin values for the z-axis by > default, but is more intuitive. > > An example: > > cfg = []; > cfg.layout = 'NM122_ver.lay'; > cfg.component = 1; > ft_topoplotIC(cfg,comp); > > > Best, > Arjen > > > > > > > > > > > ----- Original Message ----- > From: "Hanneke Van Dijk" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Tuesday, February 2, 2010 11:16:40 AM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 > > Dear all, > > I wanted to report a bug in ft_topoplotER (Fieldtrip version 20100127), > regarding the use of cfg.xlim. It doesn't seem to use cfg.xlim when you > choose one, but just to use the 'maxmin'. When I average the data over xlim > myself I get a completely different topoplot then when I use cfg.xlim for > the same range. I wouldn't have known if I didn't need to average over xlim > for other reasons. > > It seems to happen between lines 445 and 452. The data are selected for > cfg.ylim and cfg.component but not for cfg.xlim. This changes the outlook on > my data completely, and I think this could be important for all users of > this version. Therefore I send it to the entire mailing list. > > I have changed it now to: > 444 % make dat structure with one value for each channel > 445 dat = getsubfield(data, cfg.zparam); > 446 if ~isempty(cfg.yparam), > 447 dat = dat(:, ymin:ymax, xmin:xmax); > 448 dat = nanmean(nanmean(dat, 2), 3); > 449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part Hanneke > added > 450 dat = dat(:, xmin:xmax); > 451 dat = nanmean(dat, 2); > 452 end > 453 > 454 dat = dat(:); > > This helps for me and it is very important for me as well, my data looks > meaningfull now! > > Best and good luck! > > Hanneke > > > > > -------------------------------------------------- > Institut für Klinische Neurowissenschaften und Medizinische Psychologie > Gebäude-Nr.: 23.02 > Ebene: 03 Zimmer-Nr.: 47 > Tel.: 0211-81-13074 > Mail : hanneke.vandijk at med.uni-duesseldorf.de > > http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > figure; > cfgp=[]; > cfgp.cohrefchannel = {'MEG063+064'}; > cfgp.xparam = 'freq'; > cfgp.zparam = 'cohspctrm'; > cfgp.layout = 'NM122combined_test.lay'; > cfgp.showlabels = 'yes'; > cfgp.xlim = [8 12]; > %cfgp.zlim = [0 1]; > ft_topoplotER(cfgp,fd_ccc_off);colorbar > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: cfgxlimplots.jpeg Type: image/jpeg Size: 114815 bytes Desc: not available URL: From jean-michel.badier at UNIVMED.FR Tue Feb 2 14:43:46 2010 From: jean-michel.badier at UNIVMED.FR (Jean-Michel Badier) Date: Tue, 2 Feb 2010 14:43:46 +0100 Subject: reading mri from ASA format Message-ID: Dear all, As a quite new user of fieldtrip I found that it is possible to read mri stored with ASA mri format. Two points : 1.It seems that the routine read_asa_mri will only read mri stored in uint8 data format for each voxel. Unfortunately ASA also stores the data on unit16 format. I have changed the code of the routine and it seems that the mri can be correctly read. I did not go further (model generation for localization for instance) and I do not know yet the eventual consequence of the change in the code. Note that there are two keywords in the ASA mri header “BytesPerPixel” (1 or 2 in my examples) and PixelDataType (unsigned in y examples) that should help to correctly read the files. 2.As a ASA user I already have the segmentation done by this commercial software. Is there any way to retrieve directly the segmentation that have been already made? The segmentation file is read by the read_asa_mri but it is not use in the read_mri program that call it. Thanks a lot Jean-Michel ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Tue Feb 2 16:28:23 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Tue, 2 Feb 2010 16:28:23 +0100 Subject: AW: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 In-Reply-To: Message-ID: Dear Hanneke, Just to follow up: it seems there was a discrepancy between the part of code you copied (and adjusted) into one of your previous e-mails, and the code of the latest ft_topoplotER. > 444 % make dat structure with one value for each channel > 445 dat = getsubfield(data, cfg.zparam); > 446 if ~isempty(cfg.yparam), > 447 dat = dat(:, ymin:ymax, xmin:xmax); > 448 dat = nanmean(nanmean(dat, 2), 3); > 449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part > Hanneke added > 450 dat = dat(:, xmin:xmax); > 451 dat = nanmean(dat, 2); > 452 end > 453 > 454 dat = dat(:); There seems to be an 'else' missing after line 449. I guess your problem will be solved when you upgrade to the latest fieldtrip version. Sorry for the inconvenience, Jan-Mathijs On Feb 2, 2010, at 12:43 PM, Hanneke van Dijk wrote: > Maybe like this then sorry for the large amount of mails... > > On Tue, Feb 2, 2010 at 12:40 PM, Hanneke Van Dijk > wrote: > Hi Arjen, > > This time I am plotting cortico-muscular coherence obtained from > ft_freqanalysis_mtmfft with fourier output and then using > ft_connectivityanalysis. I wanted to plot the coherence on helmet- > level only for 8-12 Hz. I attached the figures; When I do the > average over the .cohspctrm field myself (or add the line I reported > before) I get the left plot (figure 2) and if I say cfg.xlim I get > the right plot (figure 1). > > Groetjes Hanneke > > > > -------------------------------------------------- > Institut für Klinische Neurowissenschaften und Medizinische > Psychologie > Gebäude-Nr.: 23.02 > Ebene: 03 Zimmer-Nr.: 47 > Tel.: 0211-81-13074 > Mail : hanneke.vandijk at med.uni-duesseldorf.de > http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html > > > > -----Ursprüngliche Nachricht----- > Von: FieldTrip discussion list im Auftrag von a.stolk at fcdonders.ru.nl > Gesendet: Di 02.02.2010 12:03 > An: FIELDTRIP at NIC.SURFNET.NL > Betreff: Re: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version > 20100127 > > Hi Hanneke, > > Thank you for your report. Could you specify some more details to > help locating the problem? > > Are you trying to plot event-related fields or components (I'm > asking this because of our earlier mail exchanges)? For the latter, > I could recommend the ft_topoplotIC function. This one has maxmin > values for the z-axis by default, but is more intuitive. > > An example: > > cfg = []; > cfg.layout = 'NM122_ver.lay'; > cfg.component = 1; > ft_topoplotIC(cfg,comp); > > > Best, > Arjen > > > > > > > > > > > ----- Original Message ----- > From: "Hanneke Van Dijk" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Tuesday, February 2, 2010 11:16:40 AM GMT +01:00 Amsterdam / > Berlin / Bern / Rome / Stockholm / Vienna > Subject: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 > > Dear all, > > I wanted to report a bug in ft_topoplotER (Fieldtrip version > 20100127), regarding the use of cfg.xlim. It doesn't seem to use > cfg.xlim when you choose one, but just to use the 'maxmin'. When I > average the data over xlim myself I get a completely different > topoplot then when I use cfg.xlim for the same range. I wouldn't > have known if I didn't need to average over xlim for other reasons. > > It seems to happen between lines 445 and 452. The data are selected > for cfg.ylim and cfg.component but not for cfg.xlim. This changes > the outlook on my data completely, and I think this could be > important for all users of this version. Therefore I send it to the > entire mailing list. > > I have changed it now to: > 444 % make dat structure with one value for each channel > 445 dat = getsubfield(data, cfg.zparam); > 446 if ~isempty(cfg.yparam), > 447 dat = dat(:, ymin:ymax, xmin:xmax); > 448 dat = nanmean(nanmean(dat, 2), 3); > 449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part > Hanneke added > 450 dat = dat(:, xmin:xmax); > 451 dat = nanmean(dat, 2); > 452 end > 453 > 454 dat = dat(:); > > This helps for me and it is very important for me as well, my data > looks meaningfull now! > > Best and good luck! > > Hanneke > > > > > -------------------------------------------------- > Institut für Klinische Neurowissenschaften und Medizinische > Psychologie > Gebäude-Nr.: 23.02 > Ebene: 03 Zimmer-Nr.: 47 > Tel.: 0211-81-13074 > Mail : hanneke.vandijk at med.uni-duesseldorf.de > http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > > figure; > cfgp=[]; > cfgp.cohrefchannel = {'MEG063+064'}; > cfgp.xparam = 'freq'; > cfgp.zparam = 'cohspctrm'; > cfgp.layout = 'NM122combined_test.lay'; > cfgp.showlabels = 'yes'; > cfgp.xlim = [8 12]; > %cfgp.zlim = [0 1]; > ft_topoplotER(cfgp,fd_ccc_off);colorbar > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sangita.dandekar at GMAIL.COM Tue Feb 2 18:22:30 2010 From: sangita.dandekar at GMAIL.COM (Sangita Dandekar) Date: Tue, 2 Feb 2010 12:22:30 -0500 Subject: beamformer on yokogawa data, megplanar.m Message-ID: Hi, Am hoping to apply beamforming based source localization to MEG data from a Yokogawa system. Think I've managed to coregister MRI and sensor coordinate systems, so that part of the problem is pretty much under control. What I'm wondering about is what the assumptions are of the prepare_leadfield and other source localization scripts about the input gradiometer data. Haven't looked at it too closely yet, but does it assume that the input sensor data is planar gradient data? If so am assuming that inputting the raw data from the Yokogawa system (axial gradiometers) is incorrect? Or does fieldtrip distinguish between different types of gradiometers using the input .grad structure? I tried to convert the axial gradiometer data from the yokogawa system to planar gradient data by using the megplanar function as shown below, and receive the following error: (Even if it isn't necessary for source localization, it would be nice to be able to view the data as planar gradient data) >> cfg=[]; >> cfg.planarmethod='sincos'; >> megplanar(cfg, righttrials); the input is raw data with 156 channels and 46 trials ??? Error using ==> checkdata at 478 This function requires ctf151, ctf275, bti148 or bti248 data as input, but you are giving meg data. Error in ==> megplanar at 228 data = checkdata(data, 'datatype', {'raw' 'freq'}, 'feedback', 'yes', 'ismeg', 'yes', 'senstype', {'ctf151', 'ctf275', 'bti148', 'bti248'}); >> Some background information: used the ft yokogawa2grad.m function (stored in private FT directory) to create the gradient structure. Here is what data structure for one set of trials looks like: >> righttrials righttrials = trial: {1x46 cell} label: {1x156 cell} time: {1x46 cell} fsample: 500 grad: [1x1 struct] offset: [46x46 double] cfg: [1x1 struct] >> righttrials.grad ans = pnt: [314x3 double] ori: [314x3 double] tra: [157x314 double] label: {157x1 cell} unit: 'cm' >> Thanks in advance for any help! Sangi ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.litvak at ION.UCL.AC.UK Tue Feb 2 19:07:41 2010 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Tue, 2 Feb 2010 18:07:41 +0000 Subject: beamformer on yokogawa data, megplanar.m In-Reply-To: Message-ID: Dear Sangi, There is no need to convert your data to planar gradient. The assumption is that the relation between coils and channels is described by the grad.tra matrix. You can look at it and make sure it is correct for your system (write back if not). The megplanar function as apparent from the error message has explicit support for some particular MEG systems and Yokogawa is not one of those. I'm not sure how easy it would be to support it generically as there might be several variants of Yokogawa systems which can be quite hard to distinguish. But for your particular system you can try to implement it yourself. Best, Vladimir On Tue, Feb 2, 2010 at 5:22 PM, Sangita Dandekar wrote: > Hi, > Am hoping to apply beamforming based source localization to MEG data from a > Yokogawa system.   Think I've managed to coregister MRI and sensor > coordinate systems, so that part of the problem is pretty much under > control. > What I'm wondering about is what the assumptions are of the > prepare_leadfield and other source localization scripts about the input > gradiometer data.  Haven't looked at it too closely yet, but does it assume > that the input sensor data is planar gradient data?  If so am assuming that > inputting the raw data from the Yokogawa system (axial gradiometers) is > incorrect?   Or does fieldtrip distinguish between different types of > gradiometers using the input .grad structure? > I tried to convert the axial gradiometer data from the yokogawa system to > planar gradient data by using the megplanar function as shown below, and > receive the following error: > (Even if it isn't necessary for source localization, it would be nice to be > able to view the data as planar gradient data) >>> cfg=[]; >>> cfg.planarmethod='sincos'; >>> megplanar(cfg, righttrials); > the input is raw data with 156 channels and 46 trials > ??? Error using ==> checkdata at 478 > This function requires ctf151, ctf275, bti148 or bti248 data as input, but > you are giving meg data. > Error in ==> megplanar at 228 > data  = checkdata(data, 'datatype', {'raw' 'freq'}, 'feedback', 'yes', > 'ismeg', 'yes', 'senstype', {'ctf151', 'ctf275', > 'bti148', 'bti248'}); >>> > Some background information:  used the ft yokogawa2grad.m function (stored > in private FT directory) to create the gradient structure.  Here is what > data structure for > one set of trials looks like: >>> righttrials > righttrials = >       trial: {1x46 cell} >       label: {1x156 cell} >        time: {1x46 cell} >     fsample: 500 >        grad: [1x1 struct] >      offset: [46x46 double] >         cfg: [1x1 struct] >>> righttrials.grad > ans = >       pnt: [314x3 double] >       ori: [314x3 double] >       tra: [157x314 double] >     label: {157x1 cell} >      unit: 'cm' >>> > > > Thanks in advance for any help! > Sangi > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From chintan_student at YAHOO.CO.IN Thu Feb 4 17:22:02 2010 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Thu, 4 Feb 2010 21:52:02 +0530 Subject: regarding besa format and freq analysis Message-ID: Hi everyone,   I am relatively new to fieldtrip.  Can you tell me, once u import .tfc file using besa2fieldtrip. how to process it further and get the analysis data??   Best Regards,   Chintan Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! http://downloads.yahoo.com/in/internetexplorer/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Juergen.Fell at UKB.UNI-BONN.DE Fri Feb 5 04:03:48 2010 From: Juergen.Fell at UKB.UNI-BONN.DE (Juergen Fell) Date: Fri, 5 Feb 2010 04:03:48 +0100 Subject: J.F. is out of the office. Message-ID: Ich werde ab 05.02.2010 nicht im Büro sein. Ich kehre zurück am 16.02.2010. Bitte wenden Sie sich in dringenden Personal- und Finanzangelegenheiten an meine Vertreterin, Frau Ruth Bender (19366). Starting 5.02.2010 I am out of the office and will be back 16.2.2010. I will answer your message after my return. Mit freundlichem Gruss/ kind regards, Juergen Fell. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From aostendorf at BESA.DE Fri Feb 5 11:07:47 2010 From: aostendorf at BESA.DE (Andrea Ostendorf) Date: Fri, 5 Feb 2010 11:07:47 +0100 Subject: regarding besa format and freq analysis In-Reply-To: <974836.26521.qm@web95402.mail.in2.yahoo.com> Message-ID: Dear Chintan, Depending on what you would like to do with your data - possibly plotting and statistical evaluation -, you may find the example script on the Fieldtrip homepage very useful: http://fieldtrip.fcdonders.nl/example/apply_clusterrandanalysis_on_tfrs_of_p ower_that_were_computed_with_besa . besa2fieldtrip converts the tfc files to a structure similar to the output of ft_freqanalysis so freqanalysis itself is not needed. The script shows you how to perform a grand average and how to carry out a statistical test. (It compares the output of the function clusterrandanalysis with the new function freqstatistics - you only need the latter.) As explained in http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq, which may also be of interest to you, Fieldtrip offers several methods for addressing the multiple-comparisons problem. In the script, the method cfg.correctm = 'cluster' is selected. For this, you will currently need some functions from the Image Processing Toolbox although I understand that in the long run, Fieldtrip will include some free functions for the benefit of those who do not have this toolbox. Also, for some options the Statistics toolbox may be required. I suppose that you are working with a BESA version prior to the BESA Research 5.3 that has just been released? The new version 5.3 features a comfortable direct MATLAB interface so you can transfer directly from BESA Research to a MATLAB structure - e.g. automatically by batch commands - and bypass export to and reading from tfc files. To facilitate Fieldtrip use for BESA users, besa2fieldtrip will soon be modified to process the new BESA MATLAB structures as well. On the BESA website (www.besa.de , link ‘Download / MATLAB Scripts’) you can find some easy-to-use sample MATLAB scripts, and shortly, sample scripts using Fieldtrip for TFC and image statistics will be added there as well. Hope this helps you All the best Andrea Dr. Andrea Ostendorf Research & Development MEGIS Software GmbH Freihamer Str. 18 82166 Gräfelfing/Germany HRB München 109956 CEOs: Dr. Michael Scherg, Theodor Scherg _____ From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of shah chintan Sent: Donnerstag, 4. Februar 2010 17:22 To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] regarding besa format and freq analysis Hi everyone, I am relatively new to fieldtrip. Can you tell me, once u import .tfc file using besa2fieldtrip. how to process it further and get the analysis data?? Best Regards, Chintan _____ The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From masaki.maruyama at CEA.FR Fri Feb 5 18:58:34 2010 From: masaki.maruyama at CEA.FR (MARUYAMA Masaki INSERM) Date: Fri, 5 Feb 2010 18:58:34 +0100 Subject: Image_Toolbox requirement in segmentation analysis Message-ID: Hello, Is it possible to remove the absolute requirement of Image_Toolbox in the segmentation analysis? The segmentation had been possible without the toolbox until the version of 2009July06, but it is absolutely necessary in the recent fieldtrip versions. I attached below the error message that I receive in my environment of no Image_Toolbox. I would appreciate your kind help in advance. With best regards, Masaki Maruyama -- Inserm U.992 - Neuroimagerie Cognitive CEA/SAC/DSV/I2BM/NeuroSpin Bât 145, Point Courrier 156 F-91191 GIF/YVETTE, FRANCE Diagnostic Information: Feature: Image_Toolbox FLEXnet Licensing error: -4,132. Error in ==> prepare_mesh_segmentation at 53 seg = imfill((mri.seg==cfg.tissue(i)), 'holes'); Error in ==> ft_prepare_mesh at 70 bnd = prepare_mesh_segmentation(cfg, mri); Error in ==> prepare_mesh at 17 [varargout{1:nargout}] = funhandle(varargin{:}); Error in ==> ft_prepare_singleshell at 58 vol.bnd = prepare_mesh(cfg, mri); Error in ==> prepare_singleshell at 17 [varargout{1:nargout}] = funhandle(varargin{:}); Error in ==> Neurospin_MRI_Preprocessing_V2 at 133 hdm = prepare_singleshell(cfg, segmentedmri); ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bps231 at NYU.EDU Sun Feb 7 19:35:30 2010 From: bps231 at NYU.EDU (Bernhard Staresina) Date: Sun, 7 Feb 2010 19:35:30 +0100 Subject: strange TFR effects Message-ID: Dear Fieldtrip experts, I've come across a strange effect during the calculation of TFRs using multitaper convolution. When I put in the raw data (no preprocessing at all), I get TFRs that look very weird. However, if I use a bandpass filter (preproc_bandpassfilter from 1 to 150 Hz with default settings) just prior to calculating the TFRs, the results look perfectly normal. I'm attaching figures of both versions so you can see the difference. The settings for the TFR calculation are identical for both cases: cfg = []; cfg.channel = 'all'; cfg.output = 'pow'; cfg.pad = 'maxperlen'; cfg.keeptrials = 'yes'; cfg.toi = -0.75:.01:2.0; cfg.method = 'mtmconvol'; cfg.foi = 2:1:120; cfg.t_ftimwin = ones(length(cfg.foi),1); cfg.t_ftimwin(cfg.foi < 30) = .500; cfg.t_ftimwin(cfg.foi >= 30) = .200; cfg.tapsmofrq = linspace(2,20,length(cfg.foi)); cfg.keeptapers = 'no'; The plots represent relative power changes, calculated by subtracting and dividing through the power from -.450 to -.250 ms before stimulus onset. Do you have any clue what's the reason for this difference? Thanks for your help, Bernhard ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: A_unfiltered.jpg Type: image/jpeg Size: 35829 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: B_bp_filtered.jpg Type: image/jpeg Size: 28425 bytes Desc: not available URL: From g.piantoni at NIN.KNAW.NL Mon Feb 8 15:38:15 2010 From: g.piantoni at NIN.KNAW.NL (Giovanni Piantoni) Date: Mon, 8 Feb 2010 15:38:15 +0100 Subject: probability zero Message-ID: Dear FieldTrip users, I am using statistics_montecarlo, which works really well, and I have a theoretical question. After using clustering correction for multiple comparisons, some clusters have a probability of 0. I don't know how to interpret this zero, as the lowest p-value you can get with a nonparametric method is 1/number_of_randomizations (see Nichols & Holmes, 2002). Shouldn't the observed cluster statistic be included in the reference probability distribution? Or has '>=' (greater than or equal to) maybe become a '>' (greater than)? Thanks, Giovanni ------ Giovanni Piantoni, Ph.D. student Dept. Sleep & Cognition Netherlands Institute for Neuroscience Meibergdreef 47 1105 BA Amsterdam (NL) +31 (0)20 5665492 g.piantoni at nin.knaw.nl www.nin.knaw.nl/research_groups/van_someren_group/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From cmuehl at GMAIL.COM Wed Feb 10 09:19:09 2010 From: cmuehl at GMAIL.COM (Christian Muehl) Date: Wed, 10 Feb 2010 09:19:09 +0100 Subject: Special Issue on Affective and Adaptive BCI Interfaces Message-ID: ============================================================== CALL FOR PAPERS ----------------------------------------------------------------------------------------------------- Special Issue on Affective Brain-Computer Interfaces of the International Journal of Autonomous and Adaptive Communication Systems http://www.inderscience.com/browse/index.php?journalCODE=ijaacs Editors: Anton Nijholt et al. ----------------------------------------------------------------------------------------------------- Special Issue ------------------ This Special Issue of the International Journal of Autonomous and Adaptive Communication Systems (IJAACS) is a follow-up of the aBCI satellite workshop of the International Conference on Affective Computing and Intelligent Interaction (ACII), held in Amsterdam in September 2009. This Special Issue, is meant to explore the advantages and limitations of using neurophysiological signals as a modality for the automatic recognition of affective and cognitive states, as well as the possibilities to use this information about the user state in innovative and adaptive applications. Background ---------------- Recent research efforts in brain-computer interfaces (BCI) show that brain activity can be used as an active/voluntary, or passive/involuntary control modality in man-machine interaction. While active BCI paradigms received a lot of attention in recent years, research on passive approaches to BCI is still lacking 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. We encourage submissions exploring one or more of the following topics: * emotion elicitation and data collection for affective BCI * detection of affective and cognitive states with BCI and other modalities * adaptive interfaces and affective BCI, affective BCI applications * embedding affective BCI in active and passive BCI approaches (Revised) Time Schedule ----------------- * February 15 : Deadline for Abstracts * February 18 : Invitation for Full Paper Submission * March 20: Full Paper Deadline Paper submissions ---------------------- Potential authors should first submit a title and a one-page abstract. Please submit them in PDF format to anijholt at cs.utwente.nl. Final papers should be at most 20 pages long and in the format of the IJAACS Journal (see http://www.inderscience.com/mapper.php?id=31). ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From psowman at MACCS.MQ.EDU.AU Fri Feb 12 04:44:35 2010 From: psowman at MACCS.MQ.EDU.AU (Paul Sowman) Date: Fri, 12 Feb 2010 04:44:35 +0100 Subject: Coherence MEG Message-ID: Hi, I'm trying to perform coherence analysis on a data set with 2 channels (source waveforms). I have followed the tute example. All is fine with the frequency analysis however when I attempt the coherence using: cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'all' 'all'}; fd = ft_connectivityanalysis(cfg, freq); I get: averaging crsspctrm over rpt removing dimension rpt from crsspctrm ??? Undefined function or variable "siz". Error in ==> ft_connectivityanalysis>coupling_corr at 485 n = siz(1); Error in ==> ft_connectivityanalysis at 188 [datout, varout, nrpt] = coupling_corr(tmpcfg, data.(inparam), hasrpt, hasjack);I get: Any ideas on where I am going wrong? Regards, Paul ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Fri Feb 12 09:11:47 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Fri, 12 Feb 2010 09:11:47 +0100 Subject: Coherence MEG In-Reply-To: Message-ID: Dear Paul, This was an issue in a past version of fieldtrip. Please download and use the latest version from the ftp-server. Best, Jan-Mathijs On Feb 12, 2010, at 4:44 AM, Paul Sowman wrote: > Hi, I'm trying to perform coherence analysis on a data set with 2 > channels > (source waveforms). I have followed the tute example. All is fine > with the > frequency analysis however when I attempt the coherence using: > > cfg = []; > cfg.method = 'coh'; > cfg.channelcmb = {'all' 'all'}; > fd = ft_connectivityanalysis(cfg, freq); > > I get: > > averaging crsspctrm over rpt > removing dimension rpt from crsspctrm > > ??? Undefined function or variable "siz". > > Error in ==> ft_connectivityanalysis>coupling_corr at 485 > n = siz(1); > > Error in ==> ft_connectivityanalysis at 188 > [datout, varout, nrpt] = coupling_corr(tmpcfg, data.(inparam), > hasrpt, > hasjack);I get: > > Any ideas on where I am going wrong? > > Regards, Paul > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/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: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From e.maris at DONDERS.RU.NL Fri Feb 12 09:35:59 2010 From: e.maris at DONDERS.RU.NL (Eric Maris) Date: Fri, 12 Feb 2010 09:35:59 +0100 Subject: probability zero In-Reply-To: <83ebc8b0934aea8da5243d487e331999.squirrel@ssl.nin.knaw.nl> Message-ID: Hi Giovanni, It is good to know that you would not have this question if the support of the permutation distribution was continuous instead of discrete, because in that case >= and > would produce the same p-value. In most situations, the number of replications is so large that the difference between >= and > is very small. I am aware that this answer is not acceptable for someone who appreciates the discrete nature of the support of the permutation distribution. To those neuroscientists, I can only say that whether you use >= or > is a matter of choice. This choice is of the same type as choosing for 0.05 or 0.01 as your significance level. Best, Eric -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Giovanni Piantoni Sent: maandag 8 februari 2010 15:38 To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] probability zero Dear FieldTrip users, I am using statistics_montecarlo, which works really well, and I have a theoretical question. After using clustering correction for multiple comparisons, some clusters have a probability of 0. I don't know how to interpret this zero, as the lowest p-value you can get with a nonparametric method is 1/number_of_randomizations (see Nichols & Holmes, 2002). Shouldn't the observed cluster statistic be included in the reference probability distribution? Or has '>=' (greater than or equal to) maybe become a '>' (greater than)? Thanks, Giovanni ------ Giovanni Piantoni, Ph.D. student Dept. Sleep & Cognition Netherlands Institute for Neuroscience Meibergdreef 47 1105 BA Amsterdam (NL) +31 (0)20 5665492 g.piantoni at nin.knaw.nl www.nin.knaw.nl/research_groups/van_someren_group/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From gbirot at GMAIL.COM Fri Feb 12 14:54:29 2010 From: gbirot at GMAIL.COM (Gwenael Birot) Date: Fri, 12 Feb 2010 14:54:29 +0100 Subject: function prepare_bemmodel: resulting BEM system matrix is NaN Message-ID: Hello, I am a new user of fieldtrip. I am trying to generate BEM system matrix using the function 'prepare_bemmodel' and the 'bemcp' method. The system matrix 'vol.mat' I obtained using the following code is a 'NaN' matrix. %% -------------- Begin -------------- % ---- load brain mesh % load_bnd is a function to load brainvisa mesh [vol.bnd(1).pnt vol.bnd(1).tri] = load_bnd('../data/mesh/colin_ no_artef.eeg-3.bnd'); vol.bnd(1).tri = vol.bnd(1).tri + 1; vol.bnd(1).pnt = vol.bnd(1).pnt; % ---- load skull mesh [vol.bnd(2).pnt vol.bnd(2).tri] = load_bnd('../data/mesh/colin_no_artef.eeg-2.bnd'); vol.bnd(2).tri = vol.bnd(2).tri + 1; vol.bnd(2).pnt = vol.bnd(2).pnt/1000; % ---- load skin mesh [vol.bnd(3).pnt vol.bnd(3).tri] = load_bnd('../data/mesh/colin_no_artef.eeg-1.bnd'); vol.bnd(3).tri = vol.bnd(3).tri + 1; vol.bnd(3).pnt = vol.bnd(3).pnt; % ---- check meshes figure; triplot(vol.bnd(1).pnt, vol.bnd(1).tri, [], 'faces_skin'); rotate3d figure; triplot(vol.bnd(2).pnt, vol.bnd(2).tri, [], 'faces_skin'); rotate3d figure; triplot(vol.bnd(3).pnt, vol.bnd(3).tri, [], 'faces_skin'); rotate3d % this gives good results, so meshes are correctly loaded % ---- prepare BEM model vol.cond = [0.3300 0.0825 0.3300]; % conductivities vol.skin = 3; % index of skin surface cfg = []; cfg.method = 'bemcp'; vol = prepare_bemmodel(cfg, vol); %% ------------------- End ------------------------ When executing this code I've got the following result in the matlab prompt using the mesh specified in the input volume conductor determining source compartment (1) determining skin compartment (3) not using the isolated source approach Nvert = 1222 Ntri = 2440 weight = 0.095493 , defl = 0.000000 Nverta = 1222 Ntrib = 2440 Nverta = 1222 Ntrib = 2440 Nvert = 1222 Ntri = 2440 weight = -0.095493 , defl = 0.000000 Nverta = 1222 Ntrib = 2440 Warning: Matrix is singular, close to singular or badly scaled. Results may be inaccurate. RCOND = NaN. > In prepare_bemmodel at 187 In test_fieldtrip at 166 Nverta = 1222 Ntrib = 2440 Warning: Matrix is singular, close to singular or badly scaled. Results may be inaccurate. RCOND = NaN. > In prepare_bemmodel at 194 In test_fieldtrip at 166 Nverta = 1222 Ntrib = 2440 Nverta = 1222 Ntrib = 2440 Nvert = 1222 Ntri = 2440 weight = 0.159155 , defl = 0.000818 Warning: Matrix is singular, close to singular or badly scaled. Results may be inaccurate. RCOND = NaN. > In prepare_bemmodel at 220 In test_fieldtrip at 166 and as I mentionned the resulting BEM system matrix vol.mat is a 'NaN' matrix. I guess the problem occurs in this part of the prepare_bemmodel function (beginning at line 152): % -------------------------------------------- % Deal first with surface 1 and 2 (inner and outer skull % NOTE: % C11st/C22st/C33st are simply the matrix C11/C22/C33 minus the identity % matrix, i.e. C11st = C11-eye(N) weight = (vol.cond(1)-vol.cond(2))/((vol.cond(1)+vol.cond(2))*2*pi); C11st = bem_Cii_lin(vol.bnd(1).tri,vol.bnd(1).pnt, weight,defl(1),vol.bnd(1).pnt4); weight = (vol.cond(1)-vol.cond(2))/((vol.cond(2)+vol.cond(3))*2*pi); C21 = bem_Cij_lin(vol.bnd(2).pnt,vol.bnd(1).pnt,vol.bnd(1).tri, weight,defl(1)); tmp1 = C21/C11st; weight = (vol.cond(2)-vol.cond(3))/((vol.cond(1)+vol.cond(2))*2*pi); C12 = bem_Cij_lin(vol.bnd(1).pnt,vol.bnd(2).pnt,vol.bnd(2).tri, weight,defl(2)); weight = (vol.cond(2)-vol.cond(3))/((vol.cond(2)+vol.cond(3))*2*pi); C22st = bem_Cii_lin(vol.bnd(2).tri,vol.bnd(2).pnt, weight,defl(2),vol.bnd(2).pnt4); tmp2 = C12/C22st; % ------------------------------------------------ where the matrix C11st contains three elements equal to NaN. Since C11st is then inverted, the result is a 'NaN' matrix. I'll would very much appreciate your help Thanks Gwenael ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From zaifengg at GMAIL.COM Sun Feb 14 11:16:31 2010 From: zaifengg at GMAIL.COM (gao zai) Date: Sun, 14 Feb 2010 18:16:31 +0800 Subject: Questions on freqanalysis Message-ID: Dear all, I am now trying to do the frequencyanalysis in Fieldtrip. Since the data is analyzed in EEGlab before, thus I first convert the data from EEGlab to Fieldtrip using eeglab2fieldtrip: *data = eeglab2fieldtrip(EEG, 'preprocessing' )*. The data was epoched from -200 ms to 1400ms time-locked to the onset of the stimuli. Then I run the following scripts: cfg = []; cfg.output = 'pow'; cfg.method = 'mtmconvol'; cfg.taper = 'hanning'; cfg.foi = 5:1:30; cfg.t_ftimwin = 7./cfg.foi; % 7 cycles per time window cfg.toi = -0.15:0.05:1.35; % to reduce boundary effects TFRhann = freqanalysis(cfg, data); However, part of the result in TFRhann.*powspctrm* is *NaN*. And I didn't see any problem in the parameters I use. I wonder whether someone can give me some suggestions to fix it? Many thanks. Best, Feng ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at FCDONDERS.RU.NL Sun Feb 14 12:16:24 2010 From: a.stolk at FCDONDERS.RU.NL (a.stolk@fcdonders.ru.nl) Date: Sun, 14 Feb 2010 12:16:24 +0100 Subject: Questions on freqanalysis In-Reply-To: <23712806.130831266146100104.JavaMail.root@watertor.uci.ru.nl> Message-ID: Hi Feng, ft_freqanalysis; method mtmconvol can be considered as a frequency estimation shifting over time (in your case: -0.15 til 1.35 seconds). More specifically, every 0.05 seconds it makes an estimation of the powerspectrum. In order to so, one needs a certain timewindow to base the estimation on. The larger the timewindow, the better the estimation as one then averages over more cycles. You can either specify your timewindow with a steady length or let it be a function of the frequency. You chose the latter, which is fine. But when we consider timepoint "-0.15", frequency "5", and window "7 cycles"; the timewindow is 7 * 1/5 (5 hertz) = 1400 ms. At timepoint -0.15, this ranges from 700 ms before (-0.85 s) until 700 ms after. However, your data begins at -0.2 s and an estimation, therefore, can not be performed for this timepoint (-0.15 s) resulting in a NaN. You'll need to adjust one or more of the parameter settings (according to what is written above), or export more data from eeglab (with offsets), or live with the NaN's (they're displayed in white in ft_singleplotTFR). Also check out the TFR section in fieldtrip's tutorial section. Best, Arjen ----- Original Message ----- From: "gao zai" To: FIELDTRIP at NIC.SURFNET.NL Sent: Sunday, February 14, 2010 11:16:31 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: [FIELDTRIP] Questions on freqanalysis Dear all, I am now trying to do the frequencyanalysis in Fieldtrip. Since the data is analyzed in EEGlab before, thus I first convert the data from EEGlab to Fieldtrip using eeglab2fieldtrip: *data = eeglab2fieldtrip(EEG, 'preprocessing' )*. The data was epoched from -200 ms to 1400ms time-locked to the onset of the stimuli. Then I run the following scripts: cfg = []; cfg.output = 'pow'; cfg.method = 'mtmconvol'; cfg.taper = 'hanning'; cfg.foi = 5:1:30; cfg.t_ftimwin = 7./cfg.foi; % 7 cycles per time window cfg.toi = -0.15:0.05:1.35; % to reduce boundary effects TFRhann = freqanalysis(cfg, data); However, part of the result in TFRhann.*powspctrm* is *NaN*. And I didn't see any problem in the parameters I use. I wonder whether someone can give me some suggestions to fix it? Many thanks. Best, Feng ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From zaifengg at GMAIL.COM Sun Feb 14 12:26:54 2010 From: zaifengg at GMAIL.COM (gao zai) Date: Sun, 14 Feb 2010 19:26:54 +0800 Subject: Questions on freqanalysis In-Reply-To: <21332973.130871266146184356.JavaMail.root@watertor.uci.ru.nl> Message-ID: Dear Arjen, Thanks for your great answer. Have a nice day. Best, Feng On Sun, Feb 14, 2010 at 7:16 PM, a.stolk at fcdonders.ru.nl < a.stolk at fcdonders.ru.nl> wrote: > Hi Feng, > > ft_freqanalysis; method mtmconvol can be considered as a frequency > estimation shifting over time (in your case: -0.15 til 1.35 seconds). More > specifically, every 0.05 seconds it makes an estimation of the > powerspectrum. In order to so, one needs a certain timewindow to base the > estimation on. The larger the timewindow, the better the estimation as one > then averages over more cycles. > > You can either specify your timewindow with a steady length or let it be a > function of the frequency. You chose the latter, which is fine. But when we > consider timepoint "-0.15", frequency "5", and window "7 cycles"; the > timewindow is 7 * 1/5 (5 hertz) = 1400 ms. At timepoint -0.15, this ranges > from 700 ms before (-0.85 s) until 700 ms after. However, your data begins > at -0.2 s and an estimation, therefore, can not be performed for this > timepoint (-0.15 s) resulting in a NaN. > > You'll need to adjust one or more of the parameter settings (according to > what is written above), or export more data from eeglab (with offsets), or > live with the NaN's (they're displayed in white in ft_singleplotTFR). Also > check out the TFR section in fieldtrip's tutorial section. > > Best, > > Arjen > > ----- Original Message ----- > From: "gao zai" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Sunday, February 14, 2010 11:16:31 AM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: [FIELDTRIP] Questions on freqanalysis > > Dear all, > > I am now trying to do the frequencyanalysis in Fieldtrip. Since the data is > analyzed in EEGlab before, thus I first convert the data from EEGlab to > Fieldtrip using eeglab2fieldtrip: *data = eeglab2fieldtrip(EEG, > 'preprocessing' )*. The data was epoched from -200 ms to 1400ms time-locked > to the onset of the stimuli. > > Then I run the following scripts: > > cfg = []; > cfg.output = 'pow'; > cfg.method = 'mtmconvol'; > cfg.taper = 'hanning'; > cfg.foi = 5:1:30; > cfg.t_ftimwin = 7./cfg.foi; % 7 cycles per time window > cfg.toi = -0.15:0.05:1.35; % to reduce boundary effects > TFRhann = freqanalysis(cfg, data); > > However, part of the result in TFRhann.*powspctrm* is *NaN*. And I didn't > see any problem in the parameters I use. I wonder whether someone can give > me some suggestions to fix it? Many thanks. > > Best, > Feng > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sreenivasan.r.nadar at GMAIL.COM Mon Feb 15 01:11:12 2010 From: sreenivasan.r.nadar at GMAIL.COM (Sreenivasan Rajamoni Nadar) Date: Sun, 14 Feb 2010 19:11:12 -0500 Subject: coordinates outside brain volume Message-ID: Dear Users, I am using the FieldTrip to extract single trial source signals using the CTF coordinates. Although I have been successful but for some coordinates the Fieldtrip is giving error as coordinates are outside the brain volume. The same coordinates are very much inside brain volume and the CTF software does not report error to extract the virtual source signals. An expert suggested to "inflate" the sphere model so that coordinates are within brain volume to do the source estimation. Anybody has a better idea to deal the problem in FieldTrip? Thank you Vasan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From psowman at MACCS.MQ.EDU.AU Mon Feb 15 02:03:35 2010 From: psowman at MACCS.MQ.EDU.AU (Paul Sowman) Date: Mon, 15 Feb 2010 02:03:35 +0100 Subject: Coherence MEG Message-ID: Dear Jan-Mathijs, thanks for your reply. You suggest that my problem was confined to the previous version however I have the latest version installed. I am using the fieldtrip-20100210.zip version and have just tried with the fieldtrip-20100214.zip version but still the same message. I don't have any other versions on my path. Any ideas? Thanks in advance. Paul ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Mon Feb 15 09:29:21 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Mon, 15 Feb 2010 09:29:21 +0100 Subject: Coherence MEG In-Reply-To: Message-ID: Dear Paul, Once again I tried to reproduce your error. I downloaded fieldtrip-20100214.zip and ran the tutorial. No error in my case. Are you sure that you removed the old fieldtrip from your path? You can check which version of ft_connectivityanalysis was used (to produce your error) by typing which ft_connectivityanalysis from the command line. Best, Jan-Mathijs On Feb 15, 2010, at 2:03 AM, Paul Sowman wrote: > Dear Jan-Mathijs, thanks for your reply. You suggest that my problem > was > confined to the previous version however I have the latest version > installed. I am using the fieldtrip-20100210.zip version and have > just tried > with the fieldtrip-20100214.zip version but still the same message. > I don't > have any other versions on my path. Any ideas? Thanks in advance. Paul > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/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: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Mon Feb 15 10:16:46 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Mon, 15 Feb 2010 10:16:46 +0100 Subject: Toolkit of Cognitive Neuroscience: advanced data analysis and source modelling of EEG and MEG data Message-ID: Dear all, I would like to point you to our yearly toolkit for EEG and MEG data analysis at the Donders Institute. This year's toolkit will take place from April 12 to April 15. Registration is now open. Have a look at: http://www.ru.nl/neuroimaging/toolkit/ for a preliminary programme and to register. 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: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From rajamonis at MAIL.NIH.GOV Mon Feb 15 13:58:41 2010 From: rajamonis at MAIL.NIH.GOV (Rajamoni Nadar, Sreenivasan (NIH/NIMH) [E]) Date: Mon, 15 Feb 2010 07:58:41 -0500 Subject: coordinates outside brain volume Message-ID: Dear Users, I am using the FieldTrip to extract single trial source signals using the CTF coordinates. Although I have been successful but for some coordinates the Fieldtrip is giving error as coordinates are outside the brain volume. The same coordinates are very much inside brain volume and the CTF software does not report error to extract the virtual source signals. An expert suggested to "inflate" the sphere model so that coordinates are within brain volume to do the source estimation. Anybody has a better idea to deal the problem in FieldTrip? Thank you Vasan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Mon Feb 15 14:25:56 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Mon, 15 Feb 2010 14:25:56 +0100 Subject: coordinates outside brain volume In-Reply-To: Message-ID: Dear Vasan, If you don't fully specify a 'grid' (i.e. the locations of your virtual channels and an assignment whether they are inside the brain volume or not) fieldtrip tries to automatically detect whether the locations (either specified by you, or specified by some semi-clever algorithm) fall inside the volume conductor model. For a single sphere which is fitted to the headsurface (or to the inside of the skull) this could lead to many points being excluded. I think generally there are two ways to deal with it: 1 either explicitly specify your virtual channel locations to be 'inside'. In other words: provide fieldtrip's ft_sourceanalysis with a cfg structure containing a grid, in which you state grid.inside = 1:size(grid.pos,1) and grid.outside = []; 2 alternatively, as already mentioned to you, inflate the single sphere, because for a single sphere volume conductor it's the origin that counts. Alternatively, if you have the anatomical scan of your subject, use a volume conductor model which is more 'realistic', taking the geometry of the inside of the skull into account. Cheers, Jan-Mathijs On Feb 15, 2010, at 1:58 PM, Rajamoni Nadar, Sreenivasan (NIH/NIMH) [E] wrote: > Dear Users, > > I am using the FieldTrip to extract single trial source signals > using the CTF coordinates. Although I have been successful but for > some coordinates the Fieldtrip is giving error as coordinates are > outside the brain volume. The same coordinates are very much inside > brain volume and the CTF software does not report error to extract > the virtual source signals. An expert suggested to "inflate" the > sphere model so that coordinates are within brain volume to do the > source estimation. Anybody has a better idea to deal the problem in > FieldTrip? > > Thank you > > Vasan > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/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: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From ole.jensen at DONDERS.RU.NL Mon Feb 15 17:27:49 2010 From: ole.jensen at DONDERS.RU.NL (Ole Jensen) Date: Mon, 15 Feb 2010 17:27:49 +0100 Subject: megcommunity.org: editors wanted Message-ID: Dear all, We are in the processing of constructing a website for the MEG community (megcommunity.org). Clearly there is a strong need for a forum for providing technical information, conferences/courses, teaching material etc. So far this site has been developed by researchers at the Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen (Ole Jensen and Esther Meeuwissen) and Department of Psychology, Glasgow University (Joachim Gross). We are searching for editors to maintain part of the website. If you are interested or would like to suggest candidates (e.g. assign a student/postdoc) please contact us at megcommunity at gmail.com This e-mail address is being protected from spambots. You need JavaScript enabled to view it To be filled: Editor: research groups and software. Maintain list over research groups and software packages. Would require an initial proactive effort, but long-term maintenance is simple. Note that specifics on groups and software are not intended for the megcommunity.org site but we will link to groups/developers sites. Editor: Education and teacing material We hope to collect representative information to facilitate the teaching of MEG research. Thus a strong proactive effort is required in organizing and collecting teaching material (including ppt slides, links and [references to] articles). We hope to collected material from university courses, toolkits and workshops. The aim is to have comprehensive but sufficient information - i.e. content should be edited. Editor: Peripherals Build and organize a comprehensive list of peripherals used for MEG. This includes visual projectors, auditory devices, somatosensory stimulators, button boxes, presentation software, .... Key characteristics could be listed. This would require a proactive and technically knowledgeable editor. Other ideas are of course most welcome! All the best, Ole Jensen -- Ole Jensen Principal Investigator Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Office : +31 24 36 10884 MEG lab : +31 24 36 10988 Fax : +31 24 36 10989 e-mail : ole.jensen at donders.ru.nl URL : http://ojensen.ruhosting.nl/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bibi.raquel at GMAIL.COM Mon Feb 15 20:44:30 2010 From: bibi.raquel at GMAIL.COM (Raquel Bibi) Date: Mon, 15 Feb 2010 14:44:30 -0500 Subject: Coherence MEG In-Reply-To: Message-ID: Dear Jan-Mathijs, I thouth I'd let you know that I have the same problem. Best, Raquel On Mon, Feb 15, 2010 at 3:29 AM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Dear Paul, > > Once again I tried to reproduce your error. I downloaded > fieldtrip-20100214.zip and ran the tutorial. No error in my case. Are you > sure that you removed the old fieldtrip from your path? You can check which > version of ft_connectivityanalysis was used (to produce your error) by > typing which ft_connectivityanalysis from the command line. > > Best, > > Jan-Mathijs > > > > On Feb 15, 2010, at 2:03 AM, Paul Sowman wrote: > > Dear Jan-Mathijs, thanks for your reply. You suggest that my problem was >> confined to the previous version however I have the latest version >> installed. I am using the fieldtrip-20100210.zip version and have just >> tried >> with the fieldtrip-20100214.zip version but still the same message. I >> don't >> have any other versions on my path. Any ideas? Thanks in advance. Paul >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG >> and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/neuroimaging/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: 0031-24-3668063 > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at DONDERS.RU.NL Tue Feb 16 09:05:10 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Tue, 16 Feb 2010 09:05:10 +0100 Subject: Coherence MEG In-Reply-To: <742c550b1002151144h4d6d091dr1513b336ee48837c@mail.gmail.com> Message-ID: Dear Paul, dear Raquel, I apologize. I misread Paul's e-mail in the first instance, when I thought he was working on the coherence tutorial on the fieldtrip website. I now know what's causing the crash. I noted the error and will think of a solution. For the time being I think you could work around this by calling ft_freqanalysis with cfg.output = 'fourier' (rather than 'powandcsd') and calling ft_connectivityanalysis using the output to the call to ft_freqanalysis. Best wishes, Jan-Mathijs On Feb 15, 2010, at 8:44 PM, Raquel Bibi wrote: > Dear Jan-Mathijs, > I thouth I'd let you know that I have the same problem. > > Best, > > Raquel > > On Mon, Feb 15, 2010 at 3:29 AM, jan-mathijs schoffelen > wrote: > Dear Paul, > > Once again I tried to reproduce your error. I downloaded > fieldtrip-20100214.zip and ran the tutorial. No error in my case. > Are you sure that you removed the old fieldtrip from your path? You > can check which version of ft_connectivityanalysis was used (to > produce your error) by typing which ft_connectivityanalysis from the > command line. > > Best, > > Jan-Mathijs > > > > On Feb 15, 2010, at 2:03 AM, Paul Sowman wrote: > > Dear Jan-Mathijs, thanks for your reply. You suggest that my problem > was > confined to the previous version however I have the latest version > installed. I am using the fieldtrip-20100210.zip version and have > just tried > with the fieldtrip-20100214.zip version but still the same message. > I don't > have any other versions on my path. Any ideas? Thanks in advance. Paul > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/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: 0031-24-3668063 > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/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: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.litvak at ION.UCL.AC.UK Wed Feb 17 11:48:13 2010 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Wed, 17 Feb 2010 10:48:13 +0000 Subject: function prepare_bemmodel: resulting BEM system matrix is NaN In-Reply-To: <4B7BBFD1.30302@ulg.ac.be> Message-ID: FYI ---------- Forwarded message ---------- From: Christophe Phillips Date: Wed, Feb 17, 2010 at 10:07 AM Subject: Re: Fwd: [FIELDTRIP] function prepare_bemmodel: resulting BEM system matrix is NaN To: Vladimir Litvak , gbirot at gmail.com Dear Gwenael, Vladimir, feel free to forward my response to the FieldTrip mailing list though a few emails may be needed to sort out this error... If there are NaN in the 1st BEM matrix generated, C11st, then these will indeed propagate throughout the rest of calculation... This C11st matrix is created by a compiled C-routine to speed up things. The details of the numerical implementation are available here: http://www.fil.ion.ucl.ac.uk/~chrisp/Thesis/these_ch3_numBEM.zip Since the code seems to be working for most people but not on your data, I suspect there is a problem in your mesh. Are you using a mesh you generated yourself ? Or the (deformed) template mesh from SPM ? I assume it's the former. Sometimes, when meshes are generated, there remain "errors" in the mesh, like one triangle becoming infinitely small because 3 vertices collapsed to one single point. I suspect this is the case here. Could you check which vertices lead to a NaN in C11st? Something like [ii,jj] = find(isNaN(C11st)) should give you the index of those vertices. Then check their actual location in 3D (in vol.bnd(1).pnt) and the triangles that use this/those vertices (in vol.bnd(1).tri). If you find something dodgy, then you should correct the mesh... like removing the collapsed vertex/triangle. Best, Chris PS: You should also check that the other matrices Cij don't contain any NaN. ---------- Forwarded message ---------- From: Gwenael Birot Date: Fri, Feb 12, 2010 at 1:54 PM Subject: [FIELDTRIP] function prepare_bemmodel: resulting BEM system matrix is NaN To: FIELDTRIP at nic.surfnet.nl Hello, I am a new user of fieldtrip. I am trying to generate BEM system matrix using the function 'prepare_bemmodel' and the 'bemcp' method. The system matrix 'vol.mat' I obtained using the following code is a 'NaN' matrix. %% -------------- Begin -------------- % ---- load brain mesh % load_bnd is a function to load brainvisa mesh [vol.bnd(1).pnt vol.bnd(1).tri] = load_bnd('../data/mesh/colin_ no_artef.eeg-3.bnd'); vol.bnd(1).tri = vol.bnd(1).tri + 1; vol.bnd(1).pnt = vol.bnd(1).pnt; % ---- load skull mesh [vol.bnd(2).pnt vol.bnd(2).tri] = load_bnd('../data/mesh/colin_no_artef.eeg-2.bnd'); vol.bnd(2).tri = vol.bnd(2).tri + 1; vol.bnd(2).pnt = vol.bnd(2).pnt/1000; % ---- load skin mesh [vol.bnd(3).pnt vol.bnd(3).tri] = load_bnd('../data/mesh/colin_no_artef.eeg-1.bnd'); vol.bnd(3).tri = vol.bnd(3).tri + 1; vol.bnd(3).pnt = vol.bnd(3).pnt; % ---- check meshes figure; triplot(vol.bnd(1).pnt, vol.bnd(1).tri, [], 'faces_skin'); rotate3d figure; triplot(vol.bnd(2).pnt, vol.bnd(2).tri, [], 'faces_skin'); rotate3d figure; triplot(vol.bnd(3).pnt, vol.bnd(3).tri, [], 'faces_skin'); rotate3d % this gives good results, so meshes are correctly loaded % ---- prepare BEM model vol.cond   = [0.3300 0.0825 0.3300]; % conductivities vol.skin   = 3; % index of skin surface cfg = []; cfg.method = 'bemcp'; vol = prepare_bemmodel(cfg, vol); %% ------------------- End ------------------------ When executing this code I've got the following result in the matlab prompt using the mesh specified in the input volume conductor determining source compartment (1) determining skin compartment (3) not using the isolated source approach Nvert = 1222 Ntri = 2440 weight = 0.095493 , defl =  0.000000 Nverta = 1222 Ntrib = 2440 Nverta = 1222 Ntrib = 2440 Nvert = 1222 Ntri = 2440 weight = -0.095493 , defl =  0.000000 Nverta = 1222 Ntrib = 2440 Warning: Matrix is singular, close to singular or badly scaled.          Results may be inaccurate. RCOND = NaN. In prepare_bemmodel at 187   In test_fieldtrip at 166 Nverta = 1222 Ntrib = 2440 Warning: Matrix is singular, close to singular or badly scaled.          Results may be inaccurate. RCOND = NaN. In prepare_bemmodel at 194   In test_fieldtrip at 166 Nverta = 1222 Ntrib = 2440 Nverta = 1222 Ntrib = 2440 Nvert = 1222 Ntri = 2440 weight = 0.159155 , defl =  0.000818 Warning: Matrix is singular, close to singular or badly scaled.          Results may be inaccurate. RCOND = NaN. In prepare_bemmodel at 220   In test_fieldtrip at 166 and as I mentionned the resulting BEM system matrix vol.mat is a 'NaN' matrix. I guess the problem occurs in this part of the prepare_bemmodel function (beginning at line 152):   % --------------------------------------------   % Deal first with surface 1 and 2 (inner and outer skull   % NOTE:   % C11st/C22st/C33st are simply the matrix C11/C22/C33 minus the identity   % matrix, i.e. C11st = C11-eye(N)   weight = (vol.cond(1)-vol.cond(2))/((vol.cond(1)+vol.cond(2))*2*pi);   C11st  = bem_Cii_lin(vol.bnd(1).tri,vol.bnd(1).pnt, weight,defl(1),vol.bnd(1).pnt4);   weight = (vol.cond(1)-vol.cond(2))/((vol.cond(2)+vol.cond(3))*2*pi);   C21    = bem_Cij_lin(vol.bnd(2).pnt,vol.bnd(1).pnt,vol.bnd(1).tri, weight,defl(1));   tmp1   = C21/C11st;   weight = (vol.cond(2)-vol.cond(3))/((vol.cond(1)+vol.cond(2))*2*pi);   C12    = bem_Cij_lin(vol.bnd(1).pnt,vol.bnd(2).pnt,vol.bnd(2).tri, weight,defl(2));   weight = (vol.cond(2)-vol.cond(3))/((vol.cond(2)+vol.cond(3))*2*pi);   C22st  = bem_Cii_lin(vol.bnd(2).tri,vol.bnd(2).pnt, weight,defl(2),vol.bnd(2).pnt4);   tmp2   = C12/C22st;   % ------------------------------------------------ where the matrix C11st contains three elements equal to NaN. Since C11st is then inverted, the result is a 'NaN' matrix. I'll would very much appreciate your help Thanks Gwenael ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From A.Stancak at LIVERPOOL.AC.UK Sat Feb 20 11:38:27 2010 From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej) Date: Sat, 20 Feb 2010 10:38:27 +0000 Subject: EGI 129 electrode layout file Message-ID: Dear FieldTrip community, I was not able to find the *.lay file for the 129-channel EGI net in the FieldTrip/SPM8/EEGlab directories. We plan to plot the 2D topographic maps and I assume plotting will not work without appropriate *.lay file. Would anyone have it? Best wishes Andrej Stancak School of Psychology University of Liverpool ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From arno at CERCO.UPS-TLSE.FR Sat Feb 20 11:52:10 2010 From: arno at CERCO.UPS-TLSE.FR (Arnaud Delorme) Date: Sat, 20 Feb 2010 11:52:10 +0100 Subject: EGI 129 electrode layout file In-Reply-To: <0813B54A9D2C494CACBD693C6A2D4D4C1468F6D038@STAFFMBX2.livad.liv.ac.uk> Message-ID: Dear Andrej, the ".sfp" files are enough. They are in EEGLAB "sample_locs" folder and are automatically imported with any binary or Matlab EGI file (since only 2 weeks ago so in case you are using EEGLAB, download the latest version). You may then save the EEGLAB dataset (.set EEGLAB format) and import it within Fieldtrip or SPM8 using the FILEIO module (the defalt import module for Fieldtrip and SPM8). You may also find the channel location files on the EGI FTP sites. Best, Arno On Feb 20, 2010, at 11:38 AM, Stancak, Andrej wrote: > Dear FieldTrip community, > > I was not able to find the *.lay file for the 129-channel EGI net > in the FieldTrip/SPM8/EEGlab directories. We plan to plot the 2D > topographic maps and I assume plotting will not work without > appropriate *.lay file. > Would anyone have it? > > Best wishes > Andrej Stancak > > School of Psychology > University of Liverpool > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From aostendorf at BESA.DE Mon Feb 22 08:55:05 2010 From: aostendorf at BESA.DE (Andrea Ostendorf) Date: Mon, 22 Feb 2010 08:55:05 +0100 Subject: Invalid MEX file /Question re: ft_clusterplot In-Reply-To: <31A51C77-8960-435E-88F0-79E8851D3D37@cerco.ups-tlse.fr> Message-ID: Dear Fieldtrip community, When trying to use read_mri, I encountered the error "??? Invalid MEX-file 'D:\FieldTrip\fieldtrip-20100219\external\spm2\spm_slice_vol.dll': The specified procedure could not be found. Proceeding along the lines suggested in the FAQ - changing to the SPM2 subdirectory and trying to compile the mex file again (using the MATLAB compiler) - I get a long list of error messages, starting with a complaint about a missing header file. I attach the complete error messages below. As the error messages show, I use MATLAB R2007A and a new Fieldtrip version. I have to admit to not having looked up this topic in the discussion list because of the message that there is a problem with the security certificate. Does anyone have an idea? Any help would be very much appreciated. Regarding ft_clusterplot: I have got the impression that during the check for the existence of clusters, ft_clusterplot assumes the existence of both positive and negative clusters, provided that there are any at all (l.113-115). If there are just positive or negative clusters - as may happen in the case of one-sided tests - this can lead to an error such as ??? Reference to non-existent field 'negclusters'. Error in ==> ft_clusterplot at 119 for iNeg = 1:length(stat.negclusters) All the best Andrea ------------- >> cd D:\FieldTrip\fieldtrip-20100219\external\spm2 >> mex spm_slice_vol.c lcc preprocessor error: spm_slice_vol.c:5 Could not find include file "spm_mapping.h" Error spm_slice_vol.c: 6 missing parameter type Error spm_slice_vol.c: 6 syntax error; found `*' expecting `)' Error spm_slice_vol.c: 6 skipping `*' `plhs' `[' `]' `,' Error spm_slice_vol.c: 6 syntax error; found `int' expecting `{' Error spm_slice_vol.c: 6 missing identifier Error spm_slice_vol.c: 6 syntax error; found `const' expecting `;' Error spm_slice_vol.c: 6 redeclaration of `mxArray' previously declared at spm_slice_vol.c 6 Error spm_slice_vol.c: 6 syntax error; found `*' expecting `;' Error spm_slice_vol.c: 6 undeclared identifier `prhs' Error spm_slice_vol.c: 6 illegal expression Error spm_slice_vol.c: 6 syntax error; found `)' expecting `]' Error spm_slice_vol.c: 6 skipping `)' Error spm_slice_vol.c: 7 type error: pointer expected Error spm_slice_vol.c: 7 type error: pointer expected Warning spm_slice_vol.c: 7 Statement has no effect Error spm_slice_vol.c: 7 syntax error; found `{' expecting `;' Error spm_slice_vol.c: 8 undeclared identifier `MAPTYPE' Error spm_slice_vol.c: 8 undeclared identifier `map' Error spm_slice_vol.c: 8 type error: pointer expected Error spm_slice_vol.c: 9 illegal statement termination Error spm_slice_vol.c: 9 too many errors C:\PROGRA~1\MATLAB\R2007A\BIN\MEX.PL: Error: Compile of 'spm_slice_vol.c' failed. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From teristam at GMAIL.COM Mon Feb 22 10:00:09 2010 From: teristam at GMAIL.COM (teris tam) Date: Mon, 22 Feb 2010 17:00:09 +0800 Subject: fieldtripbuffer error code Message-ID: Dear Fieldtrip experts, I am trying to read event data from fieldtripbuffer in matlab using read_event(), but I receive the following error: ??? ERROR: the buffer returned an error (517) Matlab reported that the error occurred at the line: evt = buffer('get_evt', [], host, port); May I ask what does the error code (517) means? Where can I find the list of error code for the fieldtripbuffer? Thanks a lot! Best regards, Teris ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.gross at PSY.GLA.AC.UK Tue Feb 23 14:52:55 2010 From: j.gross at PSY.GLA.AC.UK (Joachim Gross) Date: Tue, 23 Feb 2010 13:52:55 +0000 Subject: website and email list Message-ID: Dear researcher, We are in the process of building a website for the MEG community. Please have a look at megcommunity.org. There is also a mailing list associated with the website. The mailing list will be used for exchanging essential information on workshops, courses, jobs etc and for general discussion. If you do MEG research you are strongly encouraged to join the list. Please encourage other colleagues to join as well (including PhD students). Beyond members of your own group we propose that you forward this message to (say three) MEG researchers you know about in a different country/state than yours. We will make an effort to keep spam low. All the best, Joachim Gross and Ole Jensen ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.gross at PSY.GLA.AC.UK Tue Feb 23 14:55:20 2010 From: j.gross at PSY.GLA.AC.UK (Joachim Gross) Date: Tue, 23 Feb 2010 13:55:20 +0000 Subject: website and email list, + instructions Message-ID: Dear researcher, We are in the process of building a website for the MEG community. Please have a look at megcommunity.org. There is also a mailing list associated with the website. The mailing list will be used for exchanging essential information on workshops, courses, jobs etc and for general discussion. If you do MEG research you are strongly encouraged to join the list. Please encourage other colleagues to join as well (including PhD students). Beyond members of your own group we propose that you forward this message to (say three) MEG researchers you know about in a different country/state than yours. We will make an effort to keep spam low. All the best, Joachim Gross and Ole Jensen To join the list: Send following one line message to < jiscmail at jiscmail.ac.uk >: join megcommunity firstname lastname or have a look at http://megcommunity.org/index.php?option=com_content&view=article&id=13&Itemid=26 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From gianpaolo.demarchi at UNITN.IT Tue Feb 23 17:19:23 2010 From: gianpaolo.demarchi at UNITN.IT (Gianpaolo Demarchi) Date: Tue, 23 Feb 2010 17:19:23 +0100 Subject: multiplotER and Neuromag data Message-ID: Dear all, I tried recently to "multiplotER" some data coming from a Elekta Neuromag system, and what I get is just a "grey" plot (see attachment), without any scale and/or data, and no errors on the stdout. All the labels are fine, and if I go in the interactive mode, I can zoom and see correct "singleplotERs" ... So, all the info seems to be there, just the "big" multiplotER is wrong. I did some homework, and the thing doesn't seem to happen with (very!) older versions of fieldtrip, i.e. I tried with a recent version (fieldtrip-20100209) and a older one (fieldtrip-20091201), and the multiplot is still grey, whereas with and old (fieldtrip-20090318 !! that was somewhere in my HD ;-)) the multiplotER is displayed correctly. Any hint? Am I doing any silly mistake? Thanks in advance, Gianpaolo PS: I'm using Matlab (64bit) 2009b on Linux-64, if relevant ... PPS: here is the code I'm using ... and yes, I tried also with the "ft_" version of the commands cfg = []; cfg.dataset = 'raw.fif'; cfg.trialdef.eventtype = 'STI101'; cfg.trialdef.eventvalue = 32768; cfg.trialdef.prestim = 0.1; cfg.trialdef.poststim = 0.25; cfg = definetrial(cfg); cfg.channel = {'MEG'}; cfg.blc = 'yes'; cfg.blcwindow = [-0.1 0]; cfg.lpfilter = 'yes'; cfg.lpfreq = 35; data_raw = preprocessing(cfg); cfg = []; data_avg = timelockanalysis(cfg,data_raw) cfg = []; % cfg.showlabels = 'yes'; % cfg.fontsize = 6; % cfg.interactive = 'yes'; cfg.ylim = [-3e-12 3e-12]; cfg.interactive = 'yes'; multiplotER(cfg, data_avg); ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: multiploeERgrey.jpg Type: image/jpeg Size: 45301 bytes Desc: not available URL: From moratti at MED.UCM.ES Wed Feb 24 11:23:29 2010 From: moratti at MED.UCM.ES (Stephan Moratti) Date: Wed, 24 Feb 2010 11:23:29 +0100 Subject: multiplotER and Neuromag data Message-ID: Hola Gianpaolo, I had the same problem as you. The probel lies in the ft_prepare_layout.m function. It calculates the minimum distance between sensors. As the neuromag sensor has different types of sensors, the layout puts the 3 different sensors at the same place. So calculating the min(d(:)) results in 0 values. Please find below the modified subfunction sens2lay that is located in ft_prepare_layout.m that prevents this error. With that, the topoplots (and multiplots) should work out. Maybe this error can be prevented in a more elegant way that I did. Best, Stephan %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % SUBFUNCTION % convert 3D electrode positions into 2D layout %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% function lay = sens2lay(sens, rz, method, style) fprintf('creating layout for %s system\n', senstype(sens)); % apply rotation if isempty(rz) switch senstype(sens) case {'ctf151', 'ctf275', 'bti148', 'bti248', 'ctf151_planar', 'ctf275_planar', 'bti148_pla nar', 'bti248_planar'} rz = 90; case {'neuromag122', 'neuromag306'} rz = 0; case 'electrode' rz = 90; otherwise rz = 0; end end sens.pnt = warp_apply(rotate([0 0 rz]), sens.pnt, 'homogenous'); % use helper function for 3D layout [pnt, label] = channelposition(sens); if strcmpi(style, '3d') lay.pos = pnt; lay.label = label; else if strcmp(senstype(sens),'neuromag306') %this is to prevent distance of 0 prj = elproj(pnt(1:102,:), method); n=3; else prj = elproj(pnt, method); n=0; end d = dist(prj'); d(find(eye(size(d)))) = inf; mindist = min(d(:)); % this is to fix the planar layouts, which cannot be plotted anyway if n>1 %this is to prevent confusion when lab happens to be a row array prj = repmat(prj, n, 1); end X = prj(:,1); Y = prj(:,2); Width = ones(size(X)) * mindist * 0.8; Height = ones(size(X)) * mindist * 0.6; lay.pos = [X Y]; lay.width = Width; lay.height = Height; lay.label = label; end ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From v.litvak at ION.UCL.AC.UK Wed Feb 24 12:39:18 2010 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Wed, 24 Feb 2010 11:39:18 +0000 Subject: New 'Statistical Parametric Mapping for MEG/EEG' course, London May 10-12, 2010 Message-ID: Dear colleagues, We are happy to advertise the new Statistical Parametric Mapping MEG/EEG course presented by the Wellcome Trust Centre for Neuroimaging. The course will take place on Monday 10th May – Wednesday 12th May 2010 at the Wellcome Trust Centre for Neuroimaging in London. This newly established course will present instruction on the analysis of EEG and MEG data. The first two days will combine theoretical presentations with practical demonstrations of the different data analysis methods implemented in SPM. On the last day participants will have the opportunity to work on SPM tutorial data sets under the supervision of the course faculty. We also invite students to bring their own data for analysis. The course will cover (1) data pre-processing, (2) statistical analysis of sensor-space maps using GLMs and Random Field theory, (3) source reconstruction and (4) Dynamic Causal Modelling for EEG/MEG. The course will be followed by the long-established three-day course on ‘SPM for fMRI’ so it is possible to attend both courses. The course is suitable for beginners and more advanced users. We advise students to gain at least some minimal familiarity with the methodology, for example, from reading introductory articles available from the SPM web page or by following data analysis examples in the SPM manual. The detailed schedule and booking forms can be found at http://www.ion.ucl.ac.uk/articles/events/SPM . For further details and registration please contact Jean Reynolds (j.reynolds at ion.ucl.ac.uk). With best wishes, Vladimir Litvak Ph.D. Senior Research Associate Wellcome Trust Centre for Neuroimaging -------------------------------------------------------------------------------------------------- SPM (http://www.fil.ion.ucl.ac.uk/spm/) is a free and open-source Matlab toolbox in which many widely used methods for the analysis of PET and fMRI data; and for computational neuroanatomy were originally developed. In the recent years SPM has been extended to include M/EEG analysis and, in the most recent version, SPM8, extensive changes have made the software more stable, generic and accessible to researchers with data from wide range of recording systems. In addition to standard M/EEG pre-processing we presently offer three main analysis tools: (1) statistical analysis of scalp maps, time-frequency images and volumetric 3D source reconstruction images based on the general linear model with correction for multiple comparisons using random field theory (2) Bayesian M/EEG source reconstruction including support for group studies, simultaneous EEG and MEG and fMRI priors (3) Dynamic Causal Modelling (DCM) an approach combining neural modelling with data analysis for which there are several variants dealing with evoked responses, steady state responses (power spectra and cross-spectra), induced responses and phase coupling. SPM8 is integrated with the Fieldtrip toolbox (http://www.ru.nl/neuroimaging/fieldtrip/) making it possible for users to combine a variety of standard analysis methods with the new methods implemented in SPM and build custom analysis tools using powerful GUI and batching tools. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From gianpaolo.demarchi at UNITN.IT Wed Feb 24 15:06:25 2010 From: gianpaolo.demarchi at UNITN.IT (Gianpaolo Demarchi) Date: Wed, 24 Feb 2010 15:06:25 +0100 Subject: multiplotER and Neuromag data In-Reply-To: Message-ID: Dear Stephan, thanks for your 'patch' ! It works, i.e. I get a multiplotER graph with some data in it! With "your version" at least we get back a multiplot, with sadly the gradiometers and magnetometers data overlapped. The 'old' way was plotting them arranged in triplets, with one magnetometer and the two gradiometers 'clustered' together. I checked the 'old' prepare_layout.m, and in fact in the grad2lay() function there was a 'finer grained' check of the sensor type, including a different/better layout for 'neuromag306' case. Anyway, there must be a reason for choosing this option (probably the old arrangement with mag+2grads sublopts was too crowded, and probably useless), and in case we can still make two different multiplotERs for magnetometers and gradiometers ... Thanks again, Gianpaolo PS: should this one be considered a 'patch' for a 'bug', and go upstream in the official fieldtrip release? > I had the same problem as you. The probel lies in the ft_prepare_layout.m > function. It calculates the minimum distance between sensors. As the > neuromag sensor has different types of sensors, the layout puts the 3 > different sensors at the same place. So calculating the min(d(:)) results > in 0 values. Please find below the modified subfunction sens2lay that is > located in ft_prepare_layout.m that prevents this error. With that, the > topoplots (and multiplots) should work out. Maybe this error can be > prevented in a more elegant way that I did. > > Best, > > Stephan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From moratti at MED.UCM.ES Thu Feb 25 09:03:30 2010 From: moratti at MED.UCM.ES (Stephan Moratti) Date: Thu, 25 Feb 2010 09:03:30 +0100 Subject: multiplotER and Neuromag data Message-ID: Hello again, I would plot magneto- and gradiometers seperately anyway. You can choose them by using cfg.channel. Best, Stephan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From karl.doron at GMAIL.COM Thu Feb 25 18:35:42 2010 From: karl.doron at GMAIL.COM (Karl Doron) Date: Thu, 25 Feb 2010 18:35:42 +0100 Subject: read events Message-ID: My apologies if this is redundant - I believe I sent to it the megcommunity list and meant to send it here, so I am reposting. Hello, I've recently collect MEG data and had to edit trigger values. I've read in my BTi data using preprocessing() and inserted triggers at appropriate times in sub1.trial{1}(1,:). Now I would like to use definetrial. However, the cfg file references the original data, with the incorrect trigger onsets and information. What should I list as cfg.dataset to have my imported data read? Thanks for any help. karl doron Ph.D. Candidate UC, Santa Barbara ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From chesharm at STANFORD.EDU Sat Feb 27 08:15:21 2010 From: chesharm at STANFORD.EDU (Chetan Sharma) Date: Fri, 26 Feb 2010 23:15:21 -0800 Subject: clusterstats empty cfg.neighbours, cfg.neighbours example Message-ID: Hello everyone, I'm trying to run the coherence Z nonparametric test to detect synchrony between two channels of MEG data. Because of how restrictive bonferoni, FDR, and all are, we wanted to use the 'cluster' function for cfg.correctm. This call to statistics_montecarlo.m, which says in the description that to do clustering in frequency and time, as we want to do, we should use an empty cfg.neighbours structure. However, when the function calls clusterstats.m, it looks like there is a bug in the code. The relevant code is at line 38 in clusterstats.m, and is: if isfield(cfg, 'neighbours') && ~isempty(cfg.neighbours) channeighbstructmat = makechanneighbstructmat(cfg); issource = 0; else issource = 1; % cfg contains dim and inside that are needed for reshaping the data to a volume, and inside should behave as a index vector cfg = fixinside(cfg, 'index'); end The issue is that the case for an empty cfg.neighbours isn't handled. Running the function with an empty cfg.neighbours leads to a bug when calculating the clusters, and makes issource=1, when it should be zero for freq_time data. The function runs through when I manually set issource=0, but I don't know if that is the intended purpose. Has anyone else run into this problem? Without an example of what cfg.neighbours should look like, it's hard to determine if we are doing a correct setup. Could someone either send an example of cfg.neighbours, or verify this bug and suggest solutions? thanks and regards, -chetan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Sat Feb 27 14:21:03 2010 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Sat, 27 Feb 2010 14:21:03 +0100 Subject: read events In-Reply-To: Message-ID: Dear Karl, Definetrial is usually called before preprocessing, not after preprocessing. Definetrial determines the trial structure, i.e. the segments that subsequently are read with the preprocessing function. Often the interesting data segments (the trials) are much shorter than the complete continuous data, so reading only the trials saves memory. Since you have already read in all data into memory, you should use "redefinetrial" to segment your data into the trials. That also requires the trial definition to be specified in cfg.trl. The only purpose of definetrial function is t oconstruct this cfg.trl field based on the events. Since you manually added the triggers after reading the data in memory, you have to emulate the behaviour of definetrial. You should look at it's help and manually construct a cfg.trl field which you can hand over to redefinetrial together with the data. best, Robert On 25 Feb 2010, at 18:35, Karl Doron wrote: > My apologies if this is redundant - I believe I sent to it the megcommunity > list and meant to send it here, so I am reposting. > > Hello, > > I've recently collect MEG data and had to edit trigger values. I've read in > my BTi data using preprocessing() and inserted triggers at appropriate times > in sub1.trial{1}(1,:). > > Now I would like to use definetrial. However, the cfg file references the > original data, with the incorrect trigger onsets and information. What > should I list as cfg.dataset to have my imported data read? > > Thanks for any help. > > karl doron > Ph.D. Candidate > UC, Santa Barbara > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Sat Feb 27 14:27:09 2010 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Sat, 27 Feb 2010 14:27:09 +0100 Subject: Invalid MEX file /Question re: ft_clusterplot In-Reply-To: <6B7D05EBBB224D9F93C9E1F0905EE2DC@LAT6500Andrea> Message-ID: Dear Andrea > On 22 Feb 2010, at 8:55, Andrea Ostendorf wrote: > When trying to use read_mri, I encountered the error > "??? Invalid MEX-file > 'D:\FieldTrip\fieldtrip-20100219\external\spm2\spm_slice_vol.dll': The > specified procedure could not be found. > > Proceeding along the lines suggested in the FAQ - changing to the SPM2 > subdirectory and trying to compile the mex file again (using the MATLAB > compiler) - I get a long list of error messages, starting with a complaint > about a missing header file. I attach the complete error messages below. It turns out that the set of *.c files in the fieldtrip/external/spm2 directory is incomplete. You should compile the mex files from a complete spm2 version, which you can hget from the FIl website. > Regarding ft_clusterplot: I have got the impression that during the check > for the existence of clusters, ft_clusterplot assumes the existence of both > positive and negative clusters, provided that there are any at all > (l.113-115). If there are just positive or negative clusters - as may happen > in the case of one-sided tests - this can lead to an error such as > > ??? Reference to non-existent field 'negclusters'. > > Error in ==> ft_clusterplot at 119 > for iNeg = 1:length(stat.negclusters) You are right. I have made that optional on the presence of positive or negative clusters like this: if haspos == 0 && hasneg == 0 fprintf('%s\n','no significant clusters in data; nothing to plot') else if haspos for iPos = 1:length(stat.posclusters) sigpos(iPos) = stat.posclusters(iPos).prob < cfg.alpha; end end if hasneg for iNeg = 1:length(stat.negclusters) signeg(iNeg) = stat.negclusters(iNeg).prob < cfg.alpha; end end ... thanks, Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From nicolas.robitaille at UMONTREAL.CA Sat Feb 27 14:55:18 2010 From: nicolas.robitaille at UMONTREAL.CA (Nicolas Robitaille) Date: Sat, 27 Feb 2010 13:55:18 +0000 Subject: read events In-Reply-To: <1CAE6B41-DB17-4A88-BD6E-F4F231DB18C1@fcdonders.ru.nl> Message-ID: Dear Karl, dear Robert, I would suggest, alternatively, to modify the trialfun_general (or wathever trialfun you are using, Karl), in order to use the event definition found in the cfg structure, if any. This would have the advantage of allowing multiple call to definetrial (for multiple conditions; I once had 30 of them) without having to read all the events in the datafile over and over again. I think such change in behavior could be incorporated in the normal distribution of FT, according that it's already the case of the trial definition (i.e. if there is already a .trl field, definetrial.m just use it). This would look like: starting at line 49 of trialfun_general: % read the header and event information hdr = read_header(cfg.headerfile); try event = read_event(cfg.headerfile); catch event = []; end should become something like: % read the header and event information hdr = read_header(cfg.headerfile); if isfield(cfg, 'event') event = cfg.event; else try event = read_event(cfg.headerfile); catch event = []; end end Karl, note that I haven't test that. Best, Nicolas ************************* Nicolas Robitaille, Ph.D. Stagiaire post-doctoral Brams ************************* > Date: Sat, 27 Feb 2010 14:21:03 +0100 > From: r.oostenveld at FCDONDERS.RU.NL > Subject: Re: [FIELDTRIP] read events > To: FIELDTRIP at NIC.SURFNET.NL > > Dear Karl, > > Definetrial is usually called before preprocessing, not after preprocessing. Definetrial determines the trial structure, i.e. the segments that subsequently are read with the preprocessing function. Often the interesting data segments (the trials) are much shorter than the complete continuous data, so reading only the trials saves memory. > > Since you have already read in all data into memory, you should use "redefinetrial" to segment your data into the trials. That also requires the trial definition to be specified in cfg.trl. The only purpose of definetrial function is t oconstruct this cfg.trl field based on the events. > > Since you manually added the triggers after reading the data in memory, you have to emulate the behaviour of definetrial. You should look at it's help and manually construct a cfg.trl field which you can hand over to redefinetrial together with the data. > > best, > Robert > > > > > > On 25 Feb 2010, at 18:35, Karl Doron wrote: > > > My apologies if this is redundant - I believe I sent to it the megcommunity > > list and meant to send it here, so I am reposting. > > > > Hello, > > > > I've recently collect MEG data and had to edit trigger values. I've read in > > my BTi data using preprocessing() and inserted triggers at appropriate times > > in sub1.trial{1}(1,:). > > > > Now I would like to use definetrial. However, the cfg file references the > > original data, with the incorrect trigger onsets and information. What > > should I list as cfg.dataset to have my imported data read? > > > > Thanks for any help. > > > > karl doron > > Ph.D. Candidate > > UC, Santa Barbara > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. _________________________________________________________________ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Sat Feb 27 15:06:54 2010 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Sat, 27 Feb 2010 15:06:54 +0100 Subject: fieldtripbuffer error code In-Reply-To: Message-ID: Hi Teris On 22 Feb 2010, at 10:00, teris tam wrote: > Dear Fieldtrip experts, > I am trying to read event data from fieldtripbuffer in matlab using read_event(), but I receive the following error: > > ??? ERROR: the buffer returned an error (517) > > Matlab reported that the error occurred at the line: > > evt = buffer('get_evt', [], host, port); This is an error that happens if there are no events in the buffer. In more recent versions, read_event returns an empty array (i.e. []), which is what you woudl expect. I suggest that you upgrade to the most recent version. > May I ask what does the error code (517) means? Where can I find the list of error code for the fieldtripbuffer? They are defined (in hexadecimal representation, and not in decimal representation as it is printed) in fieldtrip/realtime/buffer/src/message.h. You can convert them for example here http://easycalculation.com/hex-converter.php?hex=0x0205&hexDeci=NaN&hexBin=0001 The error 517 (decimal) is 0205 (hexadecimal), which means GET_ERR. best regards, Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Sat Feb 27 15:11:22 2010 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Sat, 27 Feb 2010 15:11:22 +0100 Subject: read events In-Reply-To: Message-ID: Hi Nicolas That is a good suggestion, I have incorporated it into the code. This evenings version on the ftp server will include it. thanks, Robert ----------------------------------------------------------- Robert Oostenveld, PhD Senior Researcher Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen tel.: +31 (0)24 3619695 e-mail: r.oostenveld at donders.ru.nl web: http://www.ru.nl/neuroimaging skype: r.oostenveld ----------------------------------------------------------- On 27 Feb 2010, at 14:55, Nicolas Robitaille wrote: > Dear Karl, dear Robert, > > I would suggest, alternatively, to modify the trialfun_general (or wathever trialfun you are using, Karl), in order to use the event definition found in the cfg structure, if any. This would have the advantage of allowing multiple call to definetrial (for multiple conditions; I once had 30 of them) without having to read all the events in the datafile over and over again. I think such change in behavior could be incorporated in the normal distribution of FT, according that it's already the case of the trial definition (i.e. if there is already a .trl field, definetrial.m just use it). > > This would look like: > > starting at line 49 of trialfun_general: > > % read the header and event information > hdr = read_header(cfg.headerfile); > try > event = read_event(cfg.headerfile); > catch > event = []; > end > > should become something like: > > % read the header and event information > hdr = read_header(cfg.headerfile); > if isfield(cfg, 'event') > event = cfg.event; > else > try > event = read_event(cfg.headerfile); > catch > event = []; > end > end > > Karl, note that I haven't test that. > > Best, > > Nicolas > > ************************* > Nicolas Robitaille, Ph.D. > Stagiaire post-doctoral > Brams > ************************* > > > > > > Date: Sat, 27 Feb 2010 14:21:03 +0100 > > From: r.oostenveld at FCDONDERS.RU.NL > > Subject: Re: [FIELDTRIP] read events > > To: FIELDTRIP at NIC.SURFNET.NL > > > > Dear Karl, > > > > Definetrial is usually called before preprocessing, not after preprocessing. Definetrial determines the trial structure, i.e. the segments that subsequently are read with the preprocessing function. Often the interesting data segments (the trials) are much shorter than the complete continuous data, so reading only the trials saves memory. > > > > Since you have already read in all data into memory, you should use "redefinetrial" to segment your data into the trials. That also requires the trial definition to be specified in cfg.trl. The only purpose of definetrial function is t oconstruct this cfg.trl field based on the events. > > > > Since you manually added the triggers after reading the data in memory, you have to emulate the behaviour of definetrial. You should look at it's help and manually construct a cfg.trl field which you can hand over to redefinetrial together with the data. > > > > best, > > Robert > > > > > > > > > > > > On 25 Feb 2010, at 18:35, Karl Doron wrote: > > > > > My apologies if this is redundant - I believe I sent to it the megcommunity > > > list and meant to send it here, so I am reposting. > > > > > > Hello, > > > > > > I've recently collect MEG data and had to edit trigger values. I've read in > > > my BTi data using preprocessing() and inserted triggers at appropriate times > > > in sub1.trial{1}(1,:). > > > > > > Now I would like to use definetrial. However, the cfg file references the > > > original data, with the incorrect trigger onsets and information. What > > > should I list as cfg.dataset to have my imported data read? > > > > > > Thanks for any help. > > > > > > karl doron > > > Ph.D. Candidate > > > UC, Santa Barbara > > > > > > ---------------------------------- > > > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html andhttp://www.ru.nl/neuroimaging/fieldtrip. > > > > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html andhttp://www.ru.nl/neuroimaging/fieldtrip. > > Vous n'utilisez pas Hotmail sur votre téléphone? Mais pourquoi pas? Obtenez-le maintenant! > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. > http://listserv.surfnet.nl/archives/fieldtrip.html > http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From tomh at KURAGE.NIMH.NIH.GOV Sun Feb 28 00:12:10 2010 From: tomh at KURAGE.NIMH.NIH.GOV (Tom Holroyd) Date: Sat, 27 Feb 2010 18:12:10 -0500 Subject: clusterstats empty cfg.neighbours, cfg.neighbours example Message-ID: >I'm trying to run the coherence Z nonparametric test to detect synchrony >between two channels of MEG data. Because of how restrictive bonferoni, FDR, >and all are project source channels into dual space get independent components look at coherence differences shuffle get max look at angles between source space beamformers ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE Tue Feb 2 11:16:40 2010 From: Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE (Hanneke Van Dijk) Date: Tue, 2 Feb 2010 11:16:40 +0100 Subject: BUG in ft_topoplotER (cfg.xlim) version 20100127 Message-ID: Dear all, I wanted to report a bug in ft_topoplotER (Fieldtrip version 20100127), regarding the use of cfg.xlim. It doesn't seem to use cfg.xlim when you choose one, but just to use the 'maxmin'. When I average the data over xlim myself I get a completely different topoplot then when I use cfg.xlim for the same range. I wouldn't have known if I didn't need to average over xlim for other reasons. It seems to happen between lines 445 and 452. The data are selected for cfg.ylim and cfg.component but not for cfg.xlim. This changes the outlook on my data completely, and I think this could be important for all users of this version. Therefore I send it to the entire mailing list. I have changed it now to: 444 % make dat structure with one value for each channel 445 dat = getsubfield(data, cfg.zparam); 446 if ~isempty(cfg.yparam), 447 dat = dat(:, ymin:ymax, xmin:xmax); 448 dat = nanmean(nanmean(dat, 2), 3); 449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part Hanneke added 450 dat = dat(:, xmin:xmax); 451 dat = nanmean(dat, 2); 452 end 453 454 dat = dat(:); This helps for me and it is very important for me as well, my data looks meaningfull now! Best and good luck! Hanneke -------------------------------------------------- Institut für Klinische Neurowissenschaften und Medizinische Psychologie Gebäude-Nr.: 23.02 Ebene: 03 Zimmer-Nr.: 47 Tel.: 0211-81-13074 Mail : hanneke.vandijk at med.uni-duesseldorf.de http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at FCDONDERS.RU.NL Tue Feb 2 12:03:09 2010 From: a.stolk at FCDONDERS.RU.NL (a.stolk@fcdonders.ru.nl) Date: Tue, 2 Feb 2010 12:03:09 +0100 Subject: BUG in ft_topoplotER (cfg.xlim) version 20100127 In-Reply-To: <12550216.2564201265108507127.JavaMail.root@watertor.uci.ru.nl> Message-ID: Hi Hanneke, Thank you for your report. Could you specify some more details to help locating the problem? Are you trying to plot event-related fields or components (I'm asking this because of our earlier mail exchanges)? For the latter, I could recommend the ft_topoplotIC function. This one has maxmin values for the z-axis by default, but is more intuitive. An example: cfg = []; cfg.layout = 'NM122_ver.lay'; cfg.component = 1; ft_topoplotIC(cfg,comp); Best, Arjen ----- Original Message ----- From: "Hanneke Van Dijk" To: FIELDTRIP at NIC.SURFNET.NL Sent: Tuesday, February 2, 2010 11:16:40 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 Dear all, I wanted to report a bug in ft_topoplotER (Fieldtrip version 20100127), regarding the use of cfg.xlim. It doesn't seem to use cfg.xlim when you choose one, but just to use the 'maxmin'. When I average the data over xlim myself I get a completely different topoplot then when I use cfg.xlim for the same range. I wouldn't have known if I didn't need to average over xlim for other reasons. It seems to happen between lines 445 and 452. The data are selected for cfg.ylim and cfg.component but not for cfg.xlim. This changes the outlook on my data completely, and I think this could be important for all users of this version. Therefore I send it to the entire mailing list. I have changed it now to: 444 % make dat structure with one value for each channel 445 dat = getsubfield(data, cfg.zparam); 446 if ~isempty(cfg.yparam), 447 dat = dat(:, ymin:ymax, xmin:xmax); 448 dat = nanmean(nanmean(dat, 2), 3); 449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part Hanneke added 450 dat = dat(:, xmin:xmax); 451 dat = nanmean(dat, 2); 452 end 453 454 dat = dat(:); This helps for me and it is very important for me as well, my data looks meaningfull now! Best and good luck! Hanneke -------------------------------------------------- Institut für Klinische Neurowissenschaften und Medizinische Psychologie Gebäude-Nr.: 23.02 Ebene: 03 Zimmer-Nr.: 47 Tel.: 0211-81-13074 Mail : hanneke.vandijk at med.uni-duesseldorf.de http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE Tue Feb 2 12:40:14 2010 From: Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE (Hanneke Van Dijk) Date: Tue, 2 Feb 2010 12:40:14 +0100 Subject: AW: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 Message-ID: Hi Arjen, This time I am plotting cortico-muscular coherence obtained from ft_freqanalysis_mtmfft with fourier output and then using ft_connectivityanalysis. I wanted to plot the coherence on helmet-level only for 8-12 Hz. I attached the figures; When I do the average over the .cohspctrm field myself (or add the line I reported before) I get the left plot (figure 2) and if I say cfg.xlim I get the right plot (figure 1). Groetjes Hanneke -------------------------------------------------- Institut für Klinische Neurowissenschaften und Medizinische Psychologie Gebäude-Nr.: 23.02 Ebene: 03 Zimmer-Nr.: 47 Tel.: 0211-81-13074 Mail : hanneke.vandijk at med.uni-duesseldorf.de http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html -----Ursprüngliche Nachricht----- Von: FieldTrip discussion list im Auftrag von a.stolk at fcdonders.ru.nl Gesendet: Di 02.02.2010 12:03 An: FIELDTRIP at NIC.SURFNET.NL Betreff: Re: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 Hi Hanneke, Thank you for your report. Could you specify some more details to help locating the problem? Are you trying to plot event-related fields or components (I'm asking this because of our earlier mail exchanges)? For the latter, I could recommend the ft_topoplotIC function. This one has maxmin values for the z-axis by default, but is more intuitive. An example: cfg = []; cfg.layout = 'NM122_ver.lay'; cfg.component = 1; ft_topoplotIC(cfg,comp); Best, Arjen ----- Original Message ----- From: "Hanneke Van Dijk" To: FIELDTRIP at NIC.SURFNET.NL Sent: Tuesday, February 2, 2010 11:16:40 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 Dear all, I wanted to report a bug in ft_topoplotER (Fieldtrip version 20100127), regarding the use of cfg.xlim. It doesn't seem to use cfg.xlim when you choose one, but just to use the 'maxmin'. When I average the data over xlim myself I get a completely different topoplot then when I use cfg.xlim for the same range. I wouldn't have known if I didn't need to average over xlim for other reasons. It seems to happen between lines 445 and 452. The data are selected for cfg.ylim and cfg.component but not for cfg.xlim. This changes the outlook on my data completely, and I think this could be important for all users of this version. Therefore I send it to the entire mailing list. I have changed it now to: 444 % make dat structure with one value for each channel 445 dat = getsubfield(data, cfg.zparam); 446 if ~isempty(cfg.yparam), 447 dat = dat(:, ymin:ymax, xmin:xmax); 448 dat = nanmean(nanmean(dat, 2), 3); 449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part Hanneke added 450 dat = dat(:, xmin:xmax); 451 dat = nanmean(dat, 2); 452 end 453 454 dat = dat(:); This helps for me and it is very important for me as well, my data looks meaningfull now! Best and good luck! Hanneke -------------------------------------------------- Institut für Klinische Neurowissenschaften und Medizinische Psychologie Gebäude-Nr.: 23.02 Ebene: 03 Zimmer-Nr.: 47 Tel.: 0211-81-13074 Mail : hanneke.vandijk at med.uni-duesseldorf.de http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. figure; cfgp=[]; cfgp.cohrefchannel = {'MEG063+064'}; cfgp.xparam = 'freq'; cfgp.zparam = 'cohspctrm'; cfgp.layout = 'NM122combined_test.lay'; cfgp.showlabels = 'yes'; cfgp.xlim = [8 12]; %cfgp.zlim = [0 1]; ft_topoplotER(cfgp,fd_ccc_off);colorbar ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE Tue Feb 2 12:41:32 2010 From: Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE (Hanneke Van Dijk) Date: Tue, 2 Feb 2010 12:41:32 +0100 Subject: BUG in ft_topoplotER (cfg.xlim) version 20100127 Message-ID: Sorry, somehow the attachment didn't go allright, I'll try it again. -------------------------------------------------- Institut für Klinische Neurowissenschaften und Medizinische Psychologie Gebäude-Nr.: 23.02 Ebene: 03 Zimmer-Nr.: 47 Tel.: 0211-81-13074 Mail : hanneke.vandijk at med.uni-duesseldorf.de http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html -----Ursprüngliche Nachricht----- Von: FieldTrip discussion list im Auftrag von Hanneke Van Dijk Gesendet: Di 02.02.2010 12:40 An: FIELDTRIP at NIC.SURFNET.NL Betreff: [FIELDTRIP] AW: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 Hi Arjen, This time I am plotting cortico-muscular coherence obtained from ft_freqanalysis_mtmfft with fourier output and then using ft_connectivityanalysis. I wanted to plot the coherence on helmet-level only for 8-12 Hz. I attached the figures; When I do the average over the .cohspctrm field myself (or add the line I reported before) I get the left plot (figure 2) and if I say cfg.xlim I get the right plot (figure 1). Groetjes Hanneke -------------------------------------------------- Institut für Klinische Neurowissenschaften und Medizinische Psychologie Gebäude-Nr.: 23.02 Ebene: 03 Zimmer-Nr.: 47 Tel.: 0211-81-13074 Mail : hanneke.vandijk at med.uni-duesseldorf.de http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html -----Ursprüngliche Nachricht----- Von: FieldTrip discussion list im Auftrag von a.stolk at fcdonders.ru.nl Gesendet: Di 02.02.2010 12:03 An: FIELDTRIP at NIC.SURFNET.NL Betreff: Re: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 Hi Hanneke, Thank you for your report. Could you specify some more details to help locating the problem? Are you trying to plot event-related fields or components (I'm asking this because of our earlier mail exchanges)? For the latter, I could recommend the ft_topoplotIC function. This one has maxmin values for the z-axis by default, but is more intuitive. An example: cfg = []; cfg.layout = 'NM122_ver.lay'; cfg.component = 1; ft_topoplotIC(cfg,comp); Best, Arjen ----- Original Message ----- From: "Hanneke Van Dijk" To: FIELDTRIP at NIC.SURFNET.NL Sent: Tuesday, February 2, 2010 11:16:40 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 Dear all, I wanted to report a bug in ft_topoplotER (Fieldtrip version 20100127), regarding the use of cfg.xlim. It doesn't seem to use cfg.xlim when you choose one, but just to use the 'maxmin'. When I average the data over xlim myself I get a completely different topoplot then when I use cfg.xlim for the same range. I wouldn't have known if I didn't need to average over xlim for other reasons. It seems to happen between lines 445 and 452. The data are selected for cfg.ylim and cfg.component but not for cfg.xlim. This changes the outlook on my data completely, and I think this could be important for all users of this version. Therefore I send it to the entire mailing list. I have changed it now to: 444 % make dat structure with one value for each channel 445 dat = getsubfield(data, cfg.zparam); 446 if ~isempty(cfg.yparam), 447 dat = dat(:, ymin:ymax, xmin:xmax); 448 dat = nanmean(nanmean(dat, 2), 3); 449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part Hanneke added 450 dat = dat(:, xmin:xmax); 451 dat = nanmean(dat, 2); 452 end 453 454 dat = dat(:); This helps for me and it is very important for me as well, my data looks meaningfull now! Best and good luck! Hanneke -------------------------------------------------- Institut für Klinische Neurowissenschaften und Medizinische Psychologie Gebäude-Nr.: 23.02 Ebene: 03 Zimmer-Nr.: 47 Tel.: 0211-81-13074 Mail : hanneke.vandijk at med.uni-duesseldorf.de http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. figure; cfgp=[]; cfgp.cohrefchannel = {'MEG063+064'}; cfgp.xparam = 'freq'; cfgp.zparam = 'cohspctrm'; cfgp.layout = 'NM122combined_test.lay'; cfgp.showlabels = 'yes'; cfgp.xlim = [8 12]; %cfgp.zlim = [0 1]; ft_topoplotER(cfgp,fd_ccc_off);colorbar ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE Tue Feb 2 12:43:05 2010 From: Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE (Hanneke van Dijk) Date: Tue, 2 Feb 2010 12:43:05 +0100 Subject: AW: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8B0F358C@Mail2-UKD.VMED.UKD> Message-ID: Maybe like this then sorry for the large amount of mails... On Tue, Feb 2, 2010 at 12:40 PM, Hanneke Van Dijk < Hanneke.vanDijk at med.uni-duesseldorf.de> wrote: > Hi Arjen, > > This time I am plotting cortico-muscular coherence obtained from > ft_freqanalysis_mtmfft with fourier output and then using > ft_connectivityanalysis. I wanted to plot the coherence on helmet-level only > for 8-12 Hz. I attached the figures; When I do the average over the > .cohspctrm field myself (or add the line I reported before) I get the left > plot (figure 2) and if I say cfg.xlim I get the right plot (figure 1). > > Groetjes Hanneke > > > > -------------------------------------------------- > Institut für Klinische Neurowissenschaften und Medizinische Psychologie > Gebäude-Nr.: 23.02 > Ebene: 03 Zimmer-Nr.: 47 > Tel.: 0211-81-13074 > Mail : hanneke.vandijk at med.uni-duesseldorf.de > > http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html > > > > -----Ursprüngliche Nachricht----- > Von: FieldTrip discussion list im Auftrag von a.stolk at fcdonders.ru.nl > Gesendet: Di 02.02.2010 12:03 > An: FIELDTRIP at NIC.SURFNET.NL > Betreff: Re: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 > > Hi Hanneke, > > Thank you for your report. Could you specify some more details to help > locating the problem? > > Are you trying to plot event-related fields or components (I'm asking this > because of our earlier mail exchanges)? For the latter, I could recommend > the ft_topoplotIC function. This one has maxmin values for the z-axis by > default, but is more intuitive. > > An example: > > cfg = []; > cfg.layout = 'NM122_ver.lay'; > cfg.component = 1; > ft_topoplotIC(cfg,comp); > > > Best, > Arjen > > > > > > > > > > > ----- Original Message ----- > From: "Hanneke Van Dijk" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Tuesday, February 2, 2010 11:16:40 AM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 > > Dear all, > > I wanted to report a bug in ft_topoplotER (Fieldtrip version 20100127), > regarding the use of cfg.xlim. It doesn't seem to use cfg.xlim when you > choose one, but just to use the 'maxmin'. When I average the data over xlim > myself I get a completely different topoplot then when I use cfg.xlim for > the same range. I wouldn't have known if I didn't need to average over xlim > for other reasons. > > It seems to happen between lines 445 and 452. The data are selected for > cfg.ylim and cfg.component but not for cfg.xlim. This changes the outlook on > my data completely, and I think this could be important for all users of > this version. Therefore I send it to the entire mailing list. > > I have changed it now to: > 444 % make dat structure with one value for each channel > 445 dat = getsubfield(data, cfg.zparam); > 446 if ~isempty(cfg.yparam), > 447 dat = dat(:, ymin:ymax, xmin:xmax); > 448 dat = nanmean(nanmean(dat, 2), 3); > 449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part Hanneke > added > 450 dat = dat(:, xmin:xmax); > 451 dat = nanmean(dat, 2); > 452 end > 453 > 454 dat = dat(:); > > This helps for me and it is very important for me as well, my data looks > meaningfull now! > > Best and good luck! > > Hanneke > > > > > -------------------------------------------------- > Institut für Klinische Neurowissenschaften und Medizinische Psychologie > Gebäude-Nr.: 23.02 > Ebene: 03 Zimmer-Nr.: 47 > Tel.: 0211-81-13074 > Mail : hanneke.vandijk at med.uni-duesseldorf.de > > http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > figure; > cfgp=[]; > cfgp.cohrefchannel = {'MEG063+064'}; > cfgp.xparam = 'freq'; > cfgp.zparam = 'cohspctrm'; > cfgp.layout = 'NM122combined_test.lay'; > cfgp.showlabels = 'yes'; > cfgp.xlim = [8 12]; > %cfgp.zlim = [0 1]; > ft_topoplotER(cfgp,fd_ccc_off);colorbar > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: cfgxlimplots.jpeg Type: image/jpeg Size: 114815 bytes Desc: not available URL: From jean-michel.badier at UNIVMED.FR Tue Feb 2 14:43:46 2010 From: jean-michel.badier at UNIVMED.FR (Jean-Michel Badier) Date: Tue, 2 Feb 2010 14:43:46 +0100 Subject: reading mri from ASA format Message-ID: Dear all, As a quite new user of fieldtrip I found that it is possible to read mri stored with ASA mri format. Two points : 1.It seems that the routine read_asa_mri will only read mri stored in uint8 data format for each voxel. Unfortunately ASA also stores the data on unit16 format. I have changed the code of the routine and it seems that the mri can be correctly read. I did not go further (model generation for localization for instance) and I do not know yet the eventual consequence of the change in the code. Note that there are two keywords in the ASA mri header “BytesPerPixel” (1 or 2 in my examples) and PixelDataType (unsigned in y examples) that should help to correctly read the files. 2.As a ASA user I already have the segmentation done by this commercial software. Is there any way to retrieve directly the segmentation that have been already made? The segmentation file is read by the read_asa_mri but it is not use in the read_mri program that call it. Thanks a lot Jean-Michel ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Tue Feb 2 16:28:23 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Tue, 2 Feb 2010 16:28:23 +0100 Subject: AW: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 In-Reply-To: Message-ID: Dear Hanneke, Just to follow up: it seems there was a discrepancy between the part of code you copied (and adjusted) into one of your previous e-mails, and the code of the latest ft_topoplotER. > 444 % make dat structure with one value for each channel > 445 dat = getsubfield(data, cfg.zparam); > 446 if ~isempty(cfg.yparam), > 447 dat = dat(:, ymin:ymax, xmin:xmax); > 448 dat = nanmean(nanmean(dat, 2), 3); > 449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part > Hanneke added > 450 dat = dat(:, xmin:xmax); > 451 dat = nanmean(dat, 2); > 452 end > 453 > 454 dat = dat(:); There seems to be an 'else' missing after line 449. I guess your problem will be solved when you upgrade to the latest fieldtrip version. Sorry for the inconvenience, Jan-Mathijs On Feb 2, 2010, at 12:43 PM, Hanneke van Dijk wrote: > Maybe like this then sorry for the large amount of mails... > > On Tue, Feb 2, 2010 at 12:40 PM, Hanneke Van Dijk > wrote: > Hi Arjen, > > This time I am plotting cortico-muscular coherence obtained from > ft_freqanalysis_mtmfft with fourier output and then using > ft_connectivityanalysis. I wanted to plot the coherence on helmet- > level only for 8-12 Hz. I attached the figures; When I do the > average over the .cohspctrm field myself (or add the line I reported > before) I get the left plot (figure 2) and if I say cfg.xlim I get > the right plot (figure 1). > > Groetjes Hanneke > > > > -------------------------------------------------- > Institut für Klinische Neurowissenschaften und Medizinische > Psychologie > Gebäude-Nr.: 23.02 > Ebene: 03 Zimmer-Nr.: 47 > Tel.: 0211-81-13074 > Mail : hanneke.vandijk at med.uni-duesseldorf.de > http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html > > > > -----Ursprüngliche Nachricht----- > Von: FieldTrip discussion list im Auftrag von a.stolk at fcdonders.ru.nl > Gesendet: Di 02.02.2010 12:03 > An: FIELDTRIP at NIC.SURFNET.NL > Betreff: Re: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version > 20100127 > > Hi Hanneke, > > Thank you for your report. Could you specify some more details to > help locating the problem? > > Are you trying to plot event-related fields or components (I'm > asking this because of our earlier mail exchanges)? For the latter, > I could recommend the ft_topoplotIC function. This one has maxmin > values for the z-axis by default, but is more intuitive. > > An example: > > cfg = []; > cfg.layout = 'NM122_ver.lay'; > cfg.component = 1; > ft_topoplotIC(cfg,comp); > > > Best, > Arjen > > > > > > > > > > > ----- Original Message ----- > From: "Hanneke Van Dijk" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Tuesday, February 2, 2010 11:16:40 AM GMT +01:00 Amsterdam / > Berlin / Bern / Rome / Stockholm / Vienna > Subject: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127 > > Dear all, > > I wanted to report a bug in ft_topoplotER (Fieldtrip version > 20100127), regarding the use of cfg.xlim. It doesn't seem to use > cfg.xlim when you choose one, but just to use the 'maxmin'. When I > average the data over xlim myself I get a completely different > topoplot then when I use cfg.xlim for the same range. I wouldn't > have known if I didn't need to average over xlim for other reasons. > > It seems to happen between lines 445 and 452. The data are selected > for cfg.ylim and cfg.component but not for cfg.xlim. This changes > the outlook on my data completely, and I think this could be > important for all users of this version. Therefore I send it to the > entire mailing list. > > I have changed it now to: > 444 % make dat structure with one value for each channel > 445 dat = getsubfield(data, cfg.zparam); > 446 if ~isempty(cfg.yparam), > 447 dat = dat(:, ymin:ymax, xmin:xmax); > 448 dat = nanmean(nanmean(dat, 2), 3); > 449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part > Hanneke added > 450 dat = dat(:, xmin:xmax); > 451 dat = nanmean(dat, 2); > 452 end > 453 > 454 dat = dat(:); > > This helps for me and it is very important for me as well, my data > looks meaningfull now! > > Best and good luck! > > Hanneke > > > > > -------------------------------------------------- > Institut für Klinische Neurowissenschaften und Medizinische > Psychologie > Gebäude-Nr.: 23.02 > Ebene: 03 Zimmer-Nr.: 47 > Tel.: 0211-81-13074 > Mail : hanneke.vandijk at med.uni-duesseldorf.de > http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > > figure; > cfgp=[]; > cfgp.cohrefchannel = {'MEG063+064'}; > cfgp.xparam = 'freq'; > cfgp.zparam = 'cohspctrm'; > cfgp.layout = 'NM122combined_test.lay'; > cfgp.showlabels = 'yes'; > cfgp.xlim = [8 12]; > %cfgp.zlim = [0 1]; > ft_topoplotER(cfgp,fd_ccc_off);colorbar > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sangita.dandekar at GMAIL.COM Tue Feb 2 18:22:30 2010 From: sangita.dandekar at GMAIL.COM (Sangita Dandekar) Date: Tue, 2 Feb 2010 12:22:30 -0500 Subject: beamformer on yokogawa data, megplanar.m Message-ID: Hi, Am hoping to apply beamforming based source localization to MEG data from a Yokogawa system. Think I've managed to coregister MRI and sensor coordinate systems, so that part of the problem is pretty much under control. What I'm wondering about is what the assumptions are of the prepare_leadfield and other source localization scripts about the input gradiometer data. Haven't looked at it too closely yet, but does it assume that the input sensor data is planar gradient data? If so am assuming that inputting the raw data from the Yokogawa system (axial gradiometers) is incorrect? Or does fieldtrip distinguish between different types of gradiometers using the input .grad structure? I tried to convert the axial gradiometer data from the yokogawa system to planar gradient data by using the megplanar function as shown below, and receive the following error: (Even if it isn't necessary for source localization, it would be nice to be able to view the data as planar gradient data) >> cfg=[]; >> cfg.planarmethod='sincos'; >> megplanar(cfg, righttrials); the input is raw data with 156 channels and 46 trials ??? Error using ==> checkdata at 478 This function requires ctf151, ctf275, bti148 or bti248 data as input, but you are giving meg data. Error in ==> megplanar at 228 data = checkdata(data, 'datatype', {'raw' 'freq'}, 'feedback', 'yes', 'ismeg', 'yes', 'senstype', {'ctf151', 'ctf275', 'bti148', 'bti248'}); >> Some background information: used the ft yokogawa2grad.m function (stored in private FT directory) to create the gradient structure. Here is what data structure for one set of trials looks like: >> righttrials righttrials = trial: {1x46 cell} label: {1x156 cell} time: {1x46 cell} fsample: 500 grad: [1x1 struct] offset: [46x46 double] cfg: [1x1 struct] >> righttrials.grad ans = pnt: [314x3 double] ori: [314x3 double] tra: [157x314 double] label: {157x1 cell} unit: 'cm' >> Thanks in advance for any help! Sangi ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.litvak at ION.UCL.AC.UK Tue Feb 2 19:07:41 2010 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Tue, 2 Feb 2010 18:07:41 +0000 Subject: beamformer on yokogawa data, megplanar.m In-Reply-To: Message-ID: Dear Sangi, There is no need to convert your data to planar gradient. The assumption is that the relation between coils and channels is described by the grad.tra matrix. You can look at it and make sure it is correct for your system (write back if not). The megplanar function as apparent from the error message has explicit support for some particular MEG systems and Yokogawa is not one of those. I'm not sure how easy it would be to support it generically as there might be several variants of Yokogawa systems which can be quite hard to distinguish. But for your particular system you can try to implement it yourself. Best, Vladimir On Tue, Feb 2, 2010 at 5:22 PM, Sangita Dandekar wrote: > Hi, > Am hoping to apply beamforming based source localization to MEG data from a > Yokogawa system.   Think I've managed to coregister MRI and sensor > coordinate systems, so that part of the problem is pretty much under > control. > What I'm wondering about is what the assumptions are of the > prepare_leadfield and other source localization scripts about the input > gradiometer data.  Haven't looked at it too closely yet, but does it assume > that the input sensor data is planar gradient data?  If so am assuming that > inputting the raw data from the Yokogawa system (axial gradiometers) is > incorrect?   Or does fieldtrip distinguish between different types of > gradiometers using the input .grad structure? > I tried to convert the axial gradiometer data from the yokogawa system to > planar gradient data by using the megplanar function as shown below, and > receive the following error: > (Even if it isn't necessary for source localization, it would be nice to be > able to view the data as planar gradient data) >>> cfg=[]; >>> cfg.planarmethod='sincos'; >>> megplanar(cfg, righttrials); > the input is raw data with 156 channels and 46 trials > ??? Error using ==> checkdata at 478 > This function requires ctf151, ctf275, bti148 or bti248 data as input, but > you are giving meg data. > Error in ==> megplanar at 228 > data  = checkdata(data, 'datatype', {'raw' 'freq'}, 'feedback', 'yes', > 'ismeg', 'yes', 'senstype', {'ctf151', 'ctf275', > 'bti148', 'bti248'}); >>> > Some background information:  used the ft yokogawa2grad.m function (stored > in private FT directory) to create the gradient structure.  Here is what > data structure for > one set of trials looks like: >>> righttrials > righttrials = >       trial: {1x46 cell} >       label: {1x156 cell} >        time: {1x46 cell} >     fsample: 500 >        grad: [1x1 struct] >      offset: [46x46 double] >         cfg: [1x1 struct] >>> righttrials.grad > ans = >       pnt: [314x3 double] >       ori: [314x3 double] >       tra: [157x314 double] >     label: {157x1 cell} >      unit: 'cm' >>> > > > Thanks in advance for any help! > Sangi > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From chintan_student at YAHOO.CO.IN Thu Feb 4 17:22:02 2010 From: chintan_student at YAHOO.CO.IN (shah chintan) Date: Thu, 4 Feb 2010 21:52:02 +0530 Subject: regarding besa format and freq analysis Message-ID: Hi everyone,   I am relatively new to fieldtrip.  Can you tell me, once u import .tfc file using besa2fieldtrip. how to process it further and get the analysis data??   Best Regards,   Chintan Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! http://downloads.yahoo.com/in/internetexplorer/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Juergen.Fell at UKB.UNI-BONN.DE Fri Feb 5 04:03:48 2010 From: Juergen.Fell at UKB.UNI-BONN.DE (Juergen Fell) Date: Fri, 5 Feb 2010 04:03:48 +0100 Subject: J.F. is out of the office. Message-ID: Ich werde ab 05.02.2010 nicht im Büro sein. Ich kehre zurück am 16.02.2010. Bitte wenden Sie sich in dringenden Personal- und Finanzangelegenheiten an meine Vertreterin, Frau Ruth Bender (19366). Starting 5.02.2010 I am out of the office and will be back 16.2.2010. I will answer your message after my return. Mit freundlichem Gruss/ kind regards, Juergen Fell. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From aostendorf at BESA.DE Fri Feb 5 11:07:47 2010 From: aostendorf at BESA.DE (Andrea Ostendorf) Date: Fri, 5 Feb 2010 11:07:47 +0100 Subject: regarding besa format and freq analysis In-Reply-To: <974836.26521.qm@web95402.mail.in2.yahoo.com> Message-ID: Dear Chintan, Depending on what you would like to do with your data - possibly plotting and statistical evaluation -, you may find the example script on the Fieldtrip homepage very useful: http://fieldtrip.fcdonders.nl/example/apply_clusterrandanalysis_on_tfrs_of_p ower_that_were_computed_with_besa . besa2fieldtrip converts the tfc files to a structure similar to the output of ft_freqanalysis so freqanalysis itself is not needed. The script shows you how to perform a grand average and how to carry out a statistical test. (It compares the output of the function clusterrandanalysis with the new function freqstatistics - you only need the latter.) As explained in http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq, which may also be of interest to you, Fieldtrip offers several methods for addressing the multiple-comparisons problem. In the script, the method cfg.correctm = 'cluster' is selected. For this, you will currently need some functions from the Image Processing Toolbox although I understand that in the long run, Fieldtrip will include some free functions for the benefit of those who do not have this toolbox. Also, for some options the Statistics toolbox may be required. I suppose that you are working with a BESA version prior to the BESA Research 5.3 that has just been released? The new version 5.3 features a comfortable direct MATLAB interface so you can transfer directly from BESA Research to a MATLAB structure - e.g. automatically by batch commands - and bypass export to and reading from tfc files. To facilitate Fieldtrip use for BESA users, besa2fieldtrip will soon be modified to process the new BESA MATLAB structures as well. On the BESA website (www.besa.de , link ‘Download / MATLAB Scripts’) you can find some easy-to-use sample MATLAB scripts, and shortly, sample scripts using Fieldtrip for TFC and image statistics will be added there as well. Hope this helps you All the best Andrea Dr. Andrea Ostendorf Research & Development MEGIS Software GmbH Freihamer Str. 18 82166 Gräfelfing/Germany HRB München 109956 CEOs: Dr. Michael Scherg, Theodor Scherg _____ From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of shah chintan Sent: Donnerstag, 4. Februar 2010 17:22 To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] regarding besa format and freq analysis Hi everyone, I am relatively new to fieldtrip. Can you tell me, once u import .tfc file using besa2fieldtrip. how to process it further and get the analysis data?? Best Regards, Chintan _____ The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From masaki.maruyama at CEA.FR Fri Feb 5 18:58:34 2010 From: masaki.maruyama at CEA.FR (MARUYAMA Masaki INSERM) Date: Fri, 5 Feb 2010 18:58:34 +0100 Subject: Image_Toolbox requirement in segmentation analysis Message-ID: Hello, Is it possible to remove the absolute requirement of Image_Toolbox in the segmentation analysis? The segmentation had been possible without the toolbox until the version of 2009July06, but it is absolutely necessary in the recent fieldtrip versions. I attached below the error message that I receive in my environment of no Image_Toolbox. I would appreciate your kind help in advance. With best regards, Masaki Maruyama -- Inserm U.992 - Neuroimagerie Cognitive CEA/SAC/DSV/I2BM/NeuroSpin Bât 145, Point Courrier 156 F-91191 GIF/YVETTE, FRANCE Diagnostic Information: Feature: Image_Toolbox FLEXnet Licensing error: -4,132. Error in ==> prepare_mesh_segmentation at 53 seg = imfill((mri.seg==cfg.tissue(i)), 'holes'); Error in ==> ft_prepare_mesh at 70 bnd = prepare_mesh_segmentation(cfg, mri); Error in ==> prepare_mesh at 17 [varargout{1:nargout}] = funhandle(varargin{:}); Error in ==> ft_prepare_singleshell at 58 vol.bnd = prepare_mesh(cfg, mri); Error in ==> prepare_singleshell at 17 [varargout{1:nargout}] = funhandle(varargin{:}); Error in ==> Neurospin_MRI_Preprocessing_V2 at 133 hdm = prepare_singleshell(cfg, segmentedmri); ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bps231 at NYU.EDU Sun Feb 7 19:35:30 2010 From: bps231 at NYU.EDU (Bernhard Staresina) Date: Sun, 7 Feb 2010 19:35:30 +0100 Subject: strange TFR effects Message-ID: Dear Fieldtrip experts, I've come across a strange effect during the calculation of TFRs using multitaper convolution. When I put in the raw data (no preprocessing at all), I get TFRs that look very weird. However, if I use a bandpass filter (preproc_bandpassfilter from 1 to 150 Hz with default settings) just prior to calculating the TFRs, the results look perfectly normal. I'm attaching figures of both versions so you can see the difference. The settings for the TFR calculation are identical for both cases: cfg = []; cfg.channel = 'all'; cfg.output = 'pow'; cfg.pad = 'maxperlen'; cfg.keeptrials = 'yes'; cfg.toi = -0.75:.01:2.0; cfg.method = 'mtmconvol'; cfg.foi = 2:1:120; cfg.t_ftimwin = ones(length(cfg.foi),1); cfg.t_ftimwin(cfg.foi < 30) = .500; cfg.t_ftimwin(cfg.foi >= 30) = .200; cfg.tapsmofrq = linspace(2,20,length(cfg.foi)); cfg.keeptapers = 'no'; The plots represent relative power changes, calculated by subtracting and dividing through the power from -.450 to -.250 ms before stimulus onset. Do you have any clue what's the reason for this difference? Thanks for your help, Bernhard ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: A_unfiltered.jpg Type: image/jpeg Size: 35829 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: B_bp_filtered.jpg Type: image/jpeg Size: 28425 bytes Desc: not available URL: From g.piantoni at NIN.KNAW.NL Mon Feb 8 15:38:15 2010 From: g.piantoni at NIN.KNAW.NL (Giovanni Piantoni) Date: Mon, 8 Feb 2010 15:38:15 +0100 Subject: probability zero Message-ID: Dear FieldTrip users, I am using statistics_montecarlo, which works really well, and I have a theoretical question. After using clustering correction for multiple comparisons, some clusters have a probability of 0. I don't know how to interpret this zero, as the lowest p-value you can get with a nonparametric method is 1/number_of_randomizations (see Nichols & Holmes, 2002). Shouldn't the observed cluster statistic be included in the reference probability distribution? Or has '>=' (greater than or equal to) maybe become a '>' (greater than)? Thanks, Giovanni ------ Giovanni Piantoni, Ph.D. student Dept. Sleep & Cognition Netherlands Institute for Neuroscience Meibergdreef 47 1105 BA Amsterdam (NL) +31 (0)20 5665492 g.piantoni at nin.knaw.nl www.nin.knaw.nl/research_groups/van_someren_group/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From cmuehl at GMAIL.COM Wed Feb 10 09:19:09 2010 From: cmuehl at GMAIL.COM (Christian Muehl) Date: Wed, 10 Feb 2010 09:19:09 +0100 Subject: Special Issue on Affective and Adaptive BCI Interfaces Message-ID: ============================================================== CALL FOR PAPERS ----------------------------------------------------------------------------------------------------- Special Issue on Affective Brain-Computer Interfaces of the International Journal of Autonomous and Adaptive Communication Systems http://www.inderscience.com/browse/index.php?journalCODE=ijaacs Editors: Anton Nijholt et al. ----------------------------------------------------------------------------------------------------- Special Issue ------------------ This Special Issue of the International Journal of Autonomous and Adaptive Communication Systems (IJAACS) is a follow-up of the aBCI satellite workshop of the International Conference on Affective Computing and Intelligent Interaction (ACII), held in Amsterdam in September 2009. This Special Issue, is meant to explore the advantages and limitations of using neurophysiological signals as a modality for the automatic recognition of affective and cognitive states, as well as the possibilities to use this information about the user state in innovative and adaptive applications. Background ---------------- Recent research efforts in brain-computer interfaces (BCI) show that brain activity can be used as an active/voluntary, or passive/involuntary control modality in man-machine interaction. While active BCI paradigms received a lot of attention in recent years, research on passive approaches to BCI is still lacking 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. We encourage submissions exploring one or more of the following topics: * emotion elicitation and data collection for affective BCI * detection of affective and cognitive states with BCI and other modalities * adaptive interfaces and affective BCI, affective BCI applications * embedding affective BCI in active and passive BCI approaches (Revised) Time Schedule ----------------- * February 15 : Deadline for Abstracts * February 18 : Invitation for Full Paper Submission * March 20: Full Paper Deadline Paper submissions ---------------------- Potential authors should first submit a title and a one-page abstract. Please submit them in PDF format to anijholt at cs.utwente.nl. Final papers should be at most 20 pages long and in the format of the IJAACS Journal (see http://www.inderscience.com/mapper.php?id=31). ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From psowman at MACCS.MQ.EDU.AU Fri Feb 12 04:44:35 2010 From: psowman at MACCS.MQ.EDU.AU (Paul Sowman) Date: Fri, 12 Feb 2010 04:44:35 +0100 Subject: Coherence MEG Message-ID: Hi, I'm trying to perform coherence analysis on a data set with 2 channels (source waveforms). I have followed the tute example. All is fine with the frequency analysis however when I attempt the coherence using: cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'all' 'all'}; fd = ft_connectivityanalysis(cfg, freq); I get: averaging crsspctrm over rpt removing dimension rpt from crsspctrm ??? Undefined function or variable "siz". Error in ==> ft_connectivityanalysis>coupling_corr at 485 n = siz(1); Error in ==> ft_connectivityanalysis at 188 [datout, varout, nrpt] = coupling_corr(tmpcfg, data.(inparam), hasrpt, hasjack);I get: Any ideas on where I am going wrong? Regards, Paul ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Fri Feb 12 09:11:47 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Fri, 12 Feb 2010 09:11:47 +0100 Subject: Coherence MEG In-Reply-To: Message-ID: Dear Paul, This was an issue in a past version of fieldtrip. Please download and use the latest version from the ftp-server. Best, Jan-Mathijs On Feb 12, 2010, at 4:44 AM, Paul Sowman wrote: > Hi, I'm trying to perform coherence analysis on a data set with 2 > channels > (source waveforms). I have followed the tute example. All is fine > with the > frequency analysis however when I attempt the coherence using: > > cfg = []; > cfg.method = 'coh'; > cfg.channelcmb = {'all' 'all'}; > fd = ft_connectivityanalysis(cfg, freq); > > I get: > > averaging crsspctrm over rpt > removing dimension rpt from crsspctrm > > ??? Undefined function or variable "siz". > > Error in ==> ft_connectivityanalysis>coupling_corr at 485 > n = siz(1); > > Error in ==> ft_connectivityanalysis at 188 > [datout, varout, nrpt] = coupling_corr(tmpcfg, data.(inparam), > hasrpt, > hasjack);I get: > > Any ideas on where I am going wrong? > > Regards, Paul > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/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: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From e.maris at DONDERS.RU.NL Fri Feb 12 09:35:59 2010 From: e.maris at DONDERS.RU.NL (Eric Maris) Date: Fri, 12 Feb 2010 09:35:59 +0100 Subject: probability zero In-Reply-To: <83ebc8b0934aea8da5243d487e331999.squirrel@ssl.nin.knaw.nl> Message-ID: Hi Giovanni, It is good to know that you would not have this question if the support of the permutation distribution was continuous instead of discrete, because in that case >= and > would produce the same p-value. In most situations, the number of replications is so large that the difference between >= and > is very small. I am aware that this answer is not acceptable for someone who appreciates the discrete nature of the support of the permutation distribution. To those neuroscientists, I can only say that whether you use >= or > is a matter of choice. This choice is of the same type as choosing for 0.05 or 0.01 as your significance level. Best, Eric -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Giovanni Piantoni Sent: maandag 8 februari 2010 15:38 To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] probability zero Dear FieldTrip users, I am using statistics_montecarlo, which works really well, and I have a theoretical question. After using clustering correction for multiple comparisons, some clusters have a probability of 0. I don't know how to interpret this zero, as the lowest p-value you can get with a nonparametric method is 1/number_of_randomizations (see Nichols & Holmes, 2002). Shouldn't the observed cluster statistic be included in the reference probability distribution? Or has '>=' (greater than or equal to) maybe become a '>' (greater than)? Thanks, Giovanni ------ Giovanni Piantoni, Ph.D. student Dept. Sleep & Cognition Netherlands Institute for Neuroscience Meibergdreef 47 1105 BA Amsterdam (NL) +31 (0)20 5665492 g.piantoni at nin.knaw.nl www.nin.knaw.nl/research_groups/van_someren_group/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From gbirot at GMAIL.COM Fri Feb 12 14:54:29 2010 From: gbirot at GMAIL.COM (Gwenael Birot) Date: Fri, 12 Feb 2010 14:54:29 +0100 Subject: function prepare_bemmodel: resulting BEM system matrix is NaN Message-ID: Hello, I am a new user of fieldtrip. I am trying to generate BEM system matrix using the function 'prepare_bemmodel' and the 'bemcp' method. The system matrix 'vol.mat' I obtained using the following code is a 'NaN' matrix. %% -------------- Begin -------------- % ---- load brain mesh % load_bnd is a function to load brainvisa mesh [vol.bnd(1).pnt vol.bnd(1).tri] = load_bnd('../data/mesh/colin_ no_artef.eeg-3.bnd'); vol.bnd(1).tri = vol.bnd(1).tri + 1; vol.bnd(1).pnt = vol.bnd(1).pnt; % ---- load skull mesh [vol.bnd(2).pnt vol.bnd(2).tri] = load_bnd('../data/mesh/colin_no_artef.eeg-2.bnd'); vol.bnd(2).tri = vol.bnd(2).tri + 1; vol.bnd(2).pnt = vol.bnd(2).pnt/1000; % ---- load skin mesh [vol.bnd(3).pnt vol.bnd(3).tri] = load_bnd('../data/mesh/colin_no_artef.eeg-1.bnd'); vol.bnd(3).tri = vol.bnd(3).tri + 1; vol.bnd(3).pnt = vol.bnd(3).pnt; % ---- check meshes figure; triplot(vol.bnd(1).pnt, vol.bnd(1).tri, [], 'faces_skin'); rotate3d figure; triplot(vol.bnd(2).pnt, vol.bnd(2).tri, [], 'faces_skin'); rotate3d figure; triplot(vol.bnd(3).pnt, vol.bnd(3).tri, [], 'faces_skin'); rotate3d % this gives good results, so meshes are correctly loaded % ---- prepare BEM model vol.cond = [0.3300 0.0825 0.3300]; % conductivities vol.skin = 3; % index of skin surface cfg = []; cfg.method = 'bemcp'; vol = prepare_bemmodel(cfg, vol); %% ------------------- End ------------------------ When executing this code I've got the following result in the matlab prompt using the mesh specified in the input volume conductor determining source compartment (1) determining skin compartment (3) not using the isolated source approach Nvert = 1222 Ntri = 2440 weight = 0.095493 , defl = 0.000000 Nverta = 1222 Ntrib = 2440 Nverta = 1222 Ntrib = 2440 Nvert = 1222 Ntri = 2440 weight = -0.095493 , defl = 0.000000 Nverta = 1222 Ntrib = 2440 Warning: Matrix is singular, close to singular or badly scaled. Results may be inaccurate. RCOND = NaN. > In prepare_bemmodel at 187 In test_fieldtrip at 166 Nverta = 1222 Ntrib = 2440 Warning: Matrix is singular, close to singular or badly scaled. Results may be inaccurate. RCOND = NaN. > In prepare_bemmodel at 194 In test_fieldtrip at 166 Nverta = 1222 Ntrib = 2440 Nverta = 1222 Ntrib = 2440 Nvert = 1222 Ntri = 2440 weight = 0.159155 , defl = 0.000818 Warning: Matrix is singular, close to singular or badly scaled. Results may be inaccurate. RCOND = NaN. > In prepare_bemmodel at 220 In test_fieldtrip at 166 and as I mentionned the resulting BEM system matrix vol.mat is a 'NaN' matrix. I guess the problem occurs in this part of the prepare_bemmodel function (beginning at line 152): % -------------------------------------------- % Deal first with surface 1 and 2 (inner and outer skull % NOTE: % C11st/C22st/C33st are simply the matrix C11/C22/C33 minus the identity % matrix, i.e. C11st = C11-eye(N) weight = (vol.cond(1)-vol.cond(2))/((vol.cond(1)+vol.cond(2))*2*pi); C11st = bem_Cii_lin(vol.bnd(1).tri,vol.bnd(1).pnt, weight,defl(1),vol.bnd(1).pnt4); weight = (vol.cond(1)-vol.cond(2))/((vol.cond(2)+vol.cond(3))*2*pi); C21 = bem_Cij_lin(vol.bnd(2).pnt,vol.bnd(1).pnt,vol.bnd(1).tri, weight,defl(1)); tmp1 = C21/C11st; weight = (vol.cond(2)-vol.cond(3))/((vol.cond(1)+vol.cond(2))*2*pi); C12 = bem_Cij_lin(vol.bnd(1).pnt,vol.bnd(2).pnt,vol.bnd(2).tri, weight,defl(2)); weight = (vol.cond(2)-vol.cond(3))/((vol.cond(2)+vol.cond(3))*2*pi); C22st = bem_Cii_lin(vol.bnd(2).tri,vol.bnd(2).pnt, weight,defl(2),vol.bnd(2).pnt4); tmp2 = C12/C22st; % ------------------------------------------------ where the matrix C11st contains three elements equal to NaN. Since C11st is then inverted, the result is a 'NaN' matrix. I'll would very much appreciate your help Thanks Gwenael ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From zaifengg at GMAIL.COM Sun Feb 14 11:16:31 2010 From: zaifengg at GMAIL.COM (gao zai) Date: Sun, 14 Feb 2010 18:16:31 +0800 Subject: Questions on freqanalysis Message-ID: Dear all, I am now trying to do the frequencyanalysis in Fieldtrip. Since the data is analyzed in EEGlab before, thus I first convert the data from EEGlab to Fieldtrip using eeglab2fieldtrip: *data = eeglab2fieldtrip(EEG, 'preprocessing' )*. The data was epoched from -200 ms to 1400ms time-locked to the onset of the stimuli. Then I run the following scripts: cfg = []; cfg.output = 'pow'; cfg.method = 'mtmconvol'; cfg.taper = 'hanning'; cfg.foi = 5:1:30; cfg.t_ftimwin = 7./cfg.foi; % 7 cycles per time window cfg.toi = -0.15:0.05:1.35; % to reduce boundary effects TFRhann = freqanalysis(cfg, data); However, part of the result in TFRhann.*powspctrm* is *NaN*. And I didn't see any problem in the parameters I use. I wonder whether someone can give me some suggestions to fix it? Many thanks. Best, Feng ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at FCDONDERS.RU.NL Sun Feb 14 12:16:24 2010 From: a.stolk at FCDONDERS.RU.NL (a.stolk@fcdonders.ru.nl) Date: Sun, 14 Feb 2010 12:16:24 +0100 Subject: Questions on freqanalysis In-Reply-To: <23712806.130831266146100104.JavaMail.root@watertor.uci.ru.nl> Message-ID: Hi Feng, ft_freqanalysis; method mtmconvol can be considered as a frequency estimation shifting over time (in your case: -0.15 til 1.35 seconds). More specifically, every 0.05 seconds it makes an estimation of the powerspectrum. In order to so, one needs a certain timewindow to base the estimation on. The larger the timewindow, the better the estimation as one then averages over more cycles. You can either specify your timewindow with a steady length or let it be a function of the frequency. You chose the latter, which is fine. But when we consider timepoint "-0.15", frequency "5", and window "7 cycles"; the timewindow is 7 * 1/5 (5 hertz) = 1400 ms. At timepoint -0.15, this ranges from 700 ms before (-0.85 s) until 700 ms after. However, your data begins at -0.2 s and an estimation, therefore, can not be performed for this timepoint (-0.15 s) resulting in a NaN. You'll need to adjust one or more of the parameter settings (according to what is written above), or export more data from eeglab (with offsets), or live with the NaN's (they're displayed in white in ft_singleplotTFR). Also check out the TFR section in fieldtrip's tutorial section. Best, Arjen ----- Original Message ----- From: "gao zai" To: FIELDTRIP at NIC.SURFNET.NL Sent: Sunday, February 14, 2010 11:16:31 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: [FIELDTRIP] Questions on freqanalysis Dear all, I am now trying to do the frequencyanalysis in Fieldtrip. Since the data is analyzed in EEGlab before, thus I first convert the data from EEGlab to Fieldtrip using eeglab2fieldtrip: *data = eeglab2fieldtrip(EEG, 'preprocessing' )*. The data was epoched from -200 ms to 1400ms time-locked to the onset of the stimuli. Then I run the following scripts: cfg = []; cfg.output = 'pow'; cfg.method = 'mtmconvol'; cfg.taper = 'hanning'; cfg.foi = 5:1:30; cfg.t_ftimwin = 7./cfg.foi; % 7 cycles per time window cfg.toi = -0.15:0.05:1.35; % to reduce boundary effects TFRhann = freqanalysis(cfg, data); However, part of the result in TFRhann.*powspctrm* is *NaN*. And I didn't see any problem in the parameters I use. I wonder whether someone can give me some suggestions to fix it? Many thanks. Best, Feng ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From zaifengg at GMAIL.COM Sun Feb 14 12:26:54 2010 From: zaifengg at GMAIL.COM (gao zai) Date: Sun, 14 Feb 2010 19:26:54 +0800 Subject: Questions on freqanalysis In-Reply-To: <21332973.130871266146184356.JavaMail.root@watertor.uci.ru.nl> Message-ID: Dear Arjen, Thanks for your great answer. Have a nice day. Best, Feng On Sun, Feb 14, 2010 at 7:16 PM, a.stolk at fcdonders.ru.nl < a.stolk at fcdonders.ru.nl> wrote: > Hi Feng, > > ft_freqanalysis; method mtmconvol can be considered as a frequency > estimation shifting over time (in your case: -0.15 til 1.35 seconds). More > specifically, every 0.05 seconds it makes an estimation of the > powerspectrum. In order to so, one needs a certain timewindow to base the > estimation on. The larger the timewindow, the better the estimation as one > then averages over more cycles. > > You can either specify your timewindow with a steady length or let it be a > function of the frequency. You chose the latter, which is fine. But when we > consider timepoint "-0.15", frequency "5", and window "7 cycles"; the > timewindow is 7 * 1/5 (5 hertz) = 1400 ms. At timepoint -0.15, this ranges > from 700 ms before (-0.85 s) until 700 ms after. However, your data begins > at -0.2 s and an estimation, therefore, can not be performed for this > timepoint (-0.15 s) resulting in a NaN. > > You'll need to adjust one or more of the parameter settings (according to > what is written above), or export more data from eeglab (with offsets), or > live with the NaN's (they're displayed in white in ft_singleplotTFR). Also > check out the TFR section in fieldtrip's tutorial section. > > Best, > > Arjen > > ----- Original Message ----- > From: "gao zai" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Sunday, February 14, 2010 11:16:31 AM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: [FIELDTRIP] Questions on freqanalysis > > Dear all, > > I am now trying to do the frequencyanalysis in Fieldtrip. Since the data is > analyzed in EEGlab before, thus I first convert the data from EEGlab to > Fieldtrip using eeglab2fieldtrip: *data = eeglab2fieldtrip(EEG, > 'preprocessing' )*. The data was epoched from -200 ms to 1400ms time-locked > to the onset of the stimuli. > > Then I run the following scripts: > > cfg = []; > cfg.output = 'pow'; > cfg.method = 'mtmconvol'; > cfg.taper = 'hanning'; > cfg.foi = 5:1:30; > cfg.t_ftimwin = 7./cfg.foi; % 7 cycles per time window > cfg.toi = -0.15:0.05:1.35; % to reduce boundary effects > TFRhann = freqanalysis(cfg, data); > > However, part of the result in TFRhann.*powspctrm* is *NaN*. And I didn't > see any problem in the parameters I use. I wonder whether someone can give > me some suggestions to fix it? Many thanks. > > Best, > Feng > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sreenivasan.r.nadar at GMAIL.COM Mon Feb 15 01:11:12 2010 From: sreenivasan.r.nadar at GMAIL.COM (Sreenivasan Rajamoni Nadar) Date: Sun, 14 Feb 2010 19:11:12 -0500 Subject: coordinates outside brain volume Message-ID: Dear Users, I am using the FieldTrip to extract single trial source signals using the CTF coordinates. Although I have been successful but for some coordinates the Fieldtrip is giving error as coordinates are outside the brain volume. The same coordinates are very much inside brain volume and the CTF software does not report error to extract the virtual source signals. An expert suggested to "inflate" the sphere model so that coordinates are within brain volume to do the source estimation. Anybody has a better idea to deal the problem in FieldTrip? Thank you Vasan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From psowman at MACCS.MQ.EDU.AU Mon Feb 15 02:03:35 2010 From: psowman at MACCS.MQ.EDU.AU (Paul Sowman) Date: Mon, 15 Feb 2010 02:03:35 +0100 Subject: Coherence MEG Message-ID: Dear Jan-Mathijs, thanks for your reply. You suggest that my problem was confined to the previous version however I have the latest version installed. I am using the fieldtrip-20100210.zip version and have just tried with the fieldtrip-20100214.zip version but still the same message. I don't have any other versions on my path. Any ideas? Thanks in advance. Paul ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Mon Feb 15 09:29:21 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Mon, 15 Feb 2010 09:29:21 +0100 Subject: Coherence MEG In-Reply-To: Message-ID: Dear Paul, Once again I tried to reproduce your error. I downloaded fieldtrip-20100214.zip and ran the tutorial. No error in my case. Are you sure that you removed the old fieldtrip from your path? You can check which version of ft_connectivityanalysis was used (to produce your error) by typing which ft_connectivityanalysis from the command line. Best, Jan-Mathijs On Feb 15, 2010, at 2:03 AM, Paul Sowman wrote: > Dear Jan-Mathijs, thanks for your reply. You suggest that my problem > was > confined to the previous version however I have the latest version > installed. I am using the fieldtrip-20100210.zip version and have > just tried > with the fieldtrip-20100214.zip version but still the same message. > I don't > have any other versions on my path. Any ideas? Thanks in advance. Paul > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/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: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Mon Feb 15 10:16:46 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Mon, 15 Feb 2010 10:16:46 +0100 Subject: Toolkit of Cognitive Neuroscience: advanced data analysis and source modelling of EEG and MEG data Message-ID: Dear all, I would like to point you to our yearly toolkit for EEG and MEG data analysis at the Donders Institute. This year's toolkit will take place from April 12 to April 15. Registration is now open. Have a look at: http://www.ru.nl/neuroimaging/toolkit/ for a preliminary programme and to register. 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: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From rajamonis at MAIL.NIH.GOV Mon Feb 15 13:58:41 2010 From: rajamonis at MAIL.NIH.GOV (Rajamoni Nadar, Sreenivasan (NIH/NIMH) [E]) Date: Mon, 15 Feb 2010 07:58:41 -0500 Subject: coordinates outside brain volume Message-ID: Dear Users, I am using the FieldTrip to extract single trial source signals using the CTF coordinates. Although I have been successful but for some coordinates the Fieldtrip is giving error as coordinates are outside the brain volume. The same coordinates are very much inside brain volume and the CTF software does not report error to extract the virtual source signals. An expert suggested to "inflate" the sphere model so that coordinates are within brain volume to do the source estimation. Anybody has a better idea to deal the problem in FieldTrip? Thank you Vasan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Mon Feb 15 14:25:56 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Mon, 15 Feb 2010 14:25:56 +0100 Subject: coordinates outside brain volume In-Reply-To: Message-ID: Dear Vasan, If you don't fully specify a 'grid' (i.e. the locations of your virtual channels and an assignment whether they are inside the brain volume or not) fieldtrip tries to automatically detect whether the locations (either specified by you, or specified by some semi-clever algorithm) fall inside the volume conductor model. For a single sphere which is fitted to the headsurface (or to the inside of the skull) this could lead to many points being excluded. I think generally there are two ways to deal with it: 1 either explicitly specify your virtual channel locations to be 'inside'. In other words: provide fieldtrip's ft_sourceanalysis with a cfg structure containing a grid, in which you state grid.inside = 1:size(grid.pos,1) and grid.outside = []; 2 alternatively, as already mentioned to you, inflate the single sphere, because for a single sphere volume conductor it's the origin that counts. Alternatively, if you have the anatomical scan of your subject, use a volume conductor model which is more 'realistic', taking the geometry of the inside of the skull into account. Cheers, Jan-Mathijs On Feb 15, 2010, at 1:58 PM, Rajamoni Nadar, Sreenivasan (NIH/NIMH) [E] wrote: > Dear Users, > > I am using the FieldTrip to extract single trial source signals > using the CTF coordinates. Although I have been successful but for > some coordinates the Fieldtrip is giving error as coordinates are > outside the brain volume. The same coordinates are very much inside > brain volume and the CTF software does not report error to extract > the virtual source signals. An expert suggested to "inflate" the > sphere model so that coordinates are within brain volume to do the > source estimation. Anybody has a better idea to deal the problem in > FieldTrip? > > Thank you > > Vasan > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/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: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From ole.jensen at DONDERS.RU.NL Mon Feb 15 17:27:49 2010 From: ole.jensen at DONDERS.RU.NL (Ole Jensen) Date: Mon, 15 Feb 2010 17:27:49 +0100 Subject: megcommunity.org: editors wanted Message-ID: Dear all, We are in the processing of constructing a website for the MEG community (megcommunity.org). Clearly there is a strong need for a forum for providing technical information, conferences/courses, teaching material etc. So far this site has been developed by researchers at the Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen (Ole Jensen and Esther Meeuwissen) and Department of Psychology, Glasgow University (Joachim Gross). We are searching for editors to maintain part of the website. If you are interested or would like to suggest candidates (e.g. assign a student/postdoc) please contact us at megcommunity at gmail.com This e-mail address is being protected from spambots. You need JavaScript enabled to view it To be filled: Editor: research groups and software. Maintain list over research groups and software packages. Would require an initial proactive effort, but long-term maintenance is simple. Note that specifics on groups and software are not intended for the megcommunity.org site but we will link to groups/developers sites. Editor: Education and teacing material We hope to collect representative information to facilitate the teaching of MEG research. Thus a strong proactive effort is required in organizing and collecting teaching material (including ppt slides, links and [references to] articles). We hope to collected material from university courses, toolkits and workshops. The aim is to have comprehensive but sufficient information - i.e. content should be edited. Editor: Peripherals Build and organize a comprehensive list of peripherals used for MEG. This includes visual projectors, auditory devices, somatosensory stimulators, button boxes, presentation software, .... Key characteristics could be listed. This would require a proactive and technically knowledgeable editor. Other ideas are of course most welcome! All the best, Ole Jensen -- Ole Jensen Principal Investigator Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Office : +31 24 36 10884 MEG lab : +31 24 36 10988 Fax : +31 24 36 10989 e-mail : ole.jensen at donders.ru.nl URL : http://ojensen.ruhosting.nl/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bibi.raquel at GMAIL.COM Mon Feb 15 20:44:30 2010 From: bibi.raquel at GMAIL.COM (Raquel Bibi) Date: Mon, 15 Feb 2010 14:44:30 -0500 Subject: Coherence MEG In-Reply-To: Message-ID: Dear Jan-Mathijs, I thouth I'd let you know that I have the same problem. Best, Raquel On Mon, Feb 15, 2010 at 3:29 AM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Dear Paul, > > Once again I tried to reproduce your error. I downloaded > fieldtrip-20100214.zip and ran the tutorial. No error in my case. Are you > sure that you removed the old fieldtrip from your path? You can check which > version of ft_connectivityanalysis was used (to produce your error) by > typing which ft_connectivityanalysis from the command line. > > Best, > > Jan-Mathijs > > > > On Feb 15, 2010, at 2:03 AM, Paul Sowman wrote: > > Dear Jan-Mathijs, thanks for your reply. You suggest that my problem was >> confined to the previous version however I have the latest version >> installed. I am using the fieldtrip-20100210.zip version and have just >> tried >> with the fieldtrip-20100214.zip version but still the same message. I >> don't >> have any other versions on my path. Any ideas? Thanks in advance. Paul >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG >> and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/neuroimaging/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: 0031-24-3668063 > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at DONDERS.RU.NL Tue Feb 16 09:05:10 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Tue, 16 Feb 2010 09:05:10 +0100 Subject: Coherence MEG In-Reply-To: <742c550b1002151144h4d6d091dr1513b336ee48837c@mail.gmail.com> Message-ID: Dear Paul, dear Raquel, I apologize. I misread Paul's e-mail in the first instance, when I thought he was working on the coherence tutorial on the fieldtrip website. I now know what's causing the crash. I noted the error and will think of a solution. For the time being I think you could work around this by calling ft_freqanalysis with cfg.output = 'fourier' (rather than 'powandcsd') and calling ft_connectivityanalysis using the output to the call to ft_freqanalysis. Best wishes, Jan-Mathijs On Feb 15, 2010, at 8:44 PM, Raquel Bibi wrote: > Dear Jan-Mathijs, > I thouth I'd let you know that I have the same problem. > > Best, > > Raquel > > On Mon, Feb 15, 2010 at 3:29 AM, jan-mathijs schoffelen > wrote: > Dear Paul, > > Once again I tried to reproduce your error. I downloaded > fieldtrip-20100214.zip and ran the tutorial. No error in my case. > Are you sure that you removed the old fieldtrip from your path? You > can check which version of ft_connectivityanalysis was used (to > produce your error) by typing which ft_connectivityanalysis from the > command line. > > Best, > > Jan-Mathijs > > > > On Feb 15, 2010, at 2:03 AM, Paul Sowman wrote: > > Dear Jan-Mathijs, thanks for your reply. You suggest that my problem > was > confined to the previous version however I have the latest version > installed. I am using the fieldtrip-20100210.zip version and have > just tried > with the fieldtrip-20100214.zip version but still the same message. > I don't > have any other versions on my path. Any ideas? Thanks in advance. Paul > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/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: 0031-24-3668063 > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/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: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.litvak at ION.UCL.AC.UK Wed Feb 17 11:48:13 2010 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Wed, 17 Feb 2010 10:48:13 +0000 Subject: function prepare_bemmodel: resulting BEM system matrix is NaN In-Reply-To: <4B7BBFD1.30302@ulg.ac.be> Message-ID: FYI ---------- Forwarded message ---------- From: Christophe Phillips Date: Wed, Feb 17, 2010 at 10:07 AM Subject: Re: Fwd: [FIELDTRIP] function prepare_bemmodel: resulting BEM system matrix is NaN To: Vladimir Litvak , gbirot at gmail.com Dear Gwenael, Vladimir, feel free to forward my response to the FieldTrip mailing list though a few emails may be needed to sort out this error... If there are NaN in the 1st BEM matrix generated, C11st, then these will indeed propagate throughout the rest of calculation... This C11st matrix is created by a compiled C-routine to speed up things. The details of the numerical implementation are available here: http://www.fil.ion.ucl.ac.uk/~chrisp/Thesis/these_ch3_numBEM.zip Since the code seems to be working for most people but not on your data, I suspect there is a problem in your mesh. Are you using a mesh you generated yourself ? Or the (deformed) template mesh from SPM ? I assume it's the former. Sometimes, when meshes are generated, there remain "errors" in the mesh, like one triangle becoming infinitely small because 3 vertices collapsed to one single point. I suspect this is the case here. Could you check which vertices lead to a NaN in C11st? Something like [ii,jj] = find(isNaN(C11st)) should give you the index of those vertices. Then check their actual location in 3D (in vol.bnd(1).pnt) and the triangles that use this/those vertices (in vol.bnd(1).tri). If you find something dodgy, then you should correct the mesh... like removing the collapsed vertex/triangle. Best, Chris PS: You should also check that the other matrices Cij don't contain any NaN. ---------- Forwarded message ---------- From: Gwenael Birot Date: Fri, Feb 12, 2010 at 1:54 PM Subject: [FIELDTRIP] function prepare_bemmodel: resulting BEM system matrix is NaN To: FIELDTRIP at nic.surfnet.nl Hello, I am a new user of fieldtrip. I am trying to generate BEM system matrix using the function 'prepare_bemmodel' and the 'bemcp' method. The system matrix 'vol.mat' I obtained using the following code is a 'NaN' matrix. %% -------------- Begin -------------- % ---- load brain mesh % load_bnd is a function to load brainvisa mesh [vol.bnd(1).pnt vol.bnd(1).tri] = load_bnd('../data/mesh/colin_ no_artef.eeg-3.bnd'); vol.bnd(1).tri = vol.bnd(1).tri + 1; vol.bnd(1).pnt = vol.bnd(1).pnt; % ---- load skull mesh [vol.bnd(2).pnt vol.bnd(2).tri] = load_bnd('../data/mesh/colin_no_artef.eeg-2.bnd'); vol.bnd(2).tri = vol.bnd(2).tri + 1; vol.bnd(2).pnt = vol.bnd(2).pnt/1000; % ---- load skin mesh [vol.bnd(3).pnt vol.bnd(3).tri] = load_bnd('../data/mesh/colin_no_artef.eeg-1.bnd'); vol.bnd(3).tri = vol.bnd(3).tri + 1; vol.bnd(3).pnt = vol.bnd(3).pnt; % ---- check meshes figure; triplot(vol.bnd(1).pnt, vol.bnd(1).tri, [], 'faces_skin'); rotate3d figure; triplot(vol.bnd(2).pnt, vol.bnd(2).tri, [], 'faces_skin'); rotate3d figure; triplot(vol.bnd(3).pnt, vol.bnd(3).tri, [], 'faces_skin'); rotate3d % this gives good results, so meshes are correctly loaded % ---- prepare BEM model vol.cond   = [0.3300 0.0825 0.3300]; % conductivities vol.skin   = 3; % index of skin surface cfg = []; cfg.method = 'bemcp'; vol = prepare_bemmodel(cfg, vol); %% ------------------- End ------------------------ When executing this code I've got the following result in the matlab prompt using the mesh specified in the input volume conductor determining source compartment (1) determining skin compartment (3) not using the isolated source approach Nvert = 1222 Ntri = 2440 weight = 0.095493 , defl =  0.000000 Nverta = 1222 Ntrib = 2440 Nverta = 1222 Ntrib = 2440 Nvert = 1222 Ntri = 2440 weight = -0.095493 , defl =  0.000000 Nverta = 1222 Ntrib = 2440 Warning: Matrix is singular, close to singular or badly scaled.          Results may be inaccurate. RCOND = NaN. In prepare_bemmodel at 187   In test_fieldtrip at 166 Nverta = 1222 Ntrib = 2440 Warning: Matrix is singular, close to singular or badly scaled.          Results may be inaccurate. RCOND = NaN. In prepare_bemmodel at 194   In test_fieldtrip at 166 Nverta = 1222 Ntrib = 2440 Nverta = 1222 Ntrib = 2440 Nvert = 1222 Ntri = 2440 weight = 0.159155 , defl =  0.000818 Warning: Matrix is singular, close to singular or badly scaled.          Results may be inaccurate. RCOND = NaN. In prepare_bemmodel at 220   In test_fieldtrip at 166 and as I mentionned the resulting BEM system matrix vol.mat is a 'NaN' matrix. I guess the problem occurs in this part of the prepare_bemmodel function (beginning at line 152):   % --------------------------------------------   % Deal first with surface 1 and 2 (inner and outer skull   % NOTE:   % C11st/C22st/C33st are simply the matrix C11/C22/C33 minus the identity   % matrix, i.e. C11st = C11-eye(N)   weight = (vol.cond(1)-vol.cond(2))/((vol.cond(1)+vol.cond(2))*2*pi);   C11st  = bem_Cii_lin(vol.bnd(1).tri,vol.bnd(1).pnt, weight,defl(1),vol.bnd(1).pnt4);   weight = (vol.cond(1)-vol.cond(2))/((vol.cond(2)+vol.cond(3))*2*pi);   C21    = bem_Cij_lin(vol.bnd(2).pnt,vol.bnd(1).pnt,vol.bnd(1).tri, weight,defl(1));   tmp1   = C21/C11st;   weight = (vol.cond(2)-vol.cond(3))/((vol.cond(1)+vol.cond(2))*2*pi);   C12    = bem_Cij_lin(vol.bnd(1).pnt,vol.bnd(2).pnt,vol.bnd(2).tri, weight,defl(2));   weight = (vol.cond(2)-vol.cond(3))/((vol.cond(2)+vol.cond(3))*2*pi);   C22st  = bem_Cii_lin(vol.bnd(2).tri,vol.bnd(2).pnt, weight,defl(2),vol.bnd(2).pnt4);   tmp2   = C12/C22st;   % ------------------------------------------------ where the matrix C11st contains three elements equal to NaN. Since C11st is then inverted, the result is a 'NaN' matrix. I'll would very much appreciate your help Thanks Gwenael ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From A.Stancak at LIVERPOOL.AC.UK Sat Feb 20 11:38:27 2010 From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej) Date: Sat, 20 Feb 2010 10:38:27 +0000 Subject: EGI 129 electrode layout file Message-ID: Dear FieldTrip community, I was not able to find the *.lay file for the 129-channel EGI net in the FieldTrip/SPM8/EEGlab directories. We plan to plot the 2D topographic maps and I assume plotting will not work without appropriate *.lay file. Would anyone have it? Best wishes Andrej Stancak School of Psychology University of Liverpool ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From arno at CERCO.UPS-TLSE.FR Sat Feb 20 11:52:10 2010 From: arno at CERCO.UPS-TLSE.FR (Arnaud Delorme) Date: Sat, 20 Feb 2010 11:52:10 +0100 Subject: EGI 129 electrode layout file In-Reply-To: <0813B54A9D2C494CACBD693C6A2D4D4C1468F6D038@STAFFMBX2.livad.liv.ac.uk> Message-ID: Dear Andrej, the ".sfp" files are enough. They are in EEGLAB "sample_locs" folder and are automatically imported with any binary or Matlab EGI file (since only 2 weeks ago so in case you are using EEGLAB, download the latest version). You may then save the EEGLAB dataset (.set EEGLAB format) and import it within Fieldtrip or SPM8 using the FILEIO module (the defalt import module for Fieldtrip and SPM8). You may also find the channel location files on the EGI FTP sites. Best, Arno On Feb 20, 2010, at 11:38 AM, Stancak, Andrej wrote: > Dear FieldTrip community, > > I was not able to find the *.lay file for the 129-channel EGI net > in the FieldTrip/SPM8/EEGlab directories. We plan to plot the 2D > topographic maps and I assume plotting will not work without > appropriate *.lay file. > Would anyone have it? > > Best wishes > Andrej Stancak > > School of Psychology > University of Liverpool > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From aostendorf at BESA.DE Mon Feb 22 08:55:05 2010 From: aostendorf at BESA.DE (Andrea Ostendorf) Date: Mon, 22 Feb 2010 08:55:05 +0100 Subject: Invalid MEX file /Question re: ft_clusterplot In-Reply-To: <31A51C77-8960-435E-88F0-79E8851D3D37@cerco.ups-tlse.fr> Message-ID: Dear Fieldtrip community, When trying to use read_mri, I encountered the error "??? Invalid MEX-file 'D:\FieldTrip\fieldtrip-20100219\external\spm2\spm_slice_vol.dll': The specified procedure could not be found. Proceeding along the lines suggested in the FAQ - changing to the SPM2 subdirectory and trying to compile the mex file again (using the MATLAB compiler) - I get a long list of error messages, starting with a complaint about a missing header file. I attach the complete error messages below. As the error messages show, I use MATLAB R2007A and a new Fieldtrip version. I have to admit to not having looked up this topic in the discussion list because of the message that there is a problem with the security certificate. Does anyone have an idea? Any help would be very much appreciated. Regarding ft_clusterplot: I have got the impression that during the check for the existence of clusters, ft_clusterplot assumes the existence of both positive and negative clusters, provided that there are any at all (l.113-115). If there are just positive or negative clusters - as may happen in the case of one-sided tests - this can lead to an error such as ??? Reference to non-existent field 'negclusters'. Error in ==> ft_clusterplot at 119 for iNeg = 1:length(stat.negclusters) All the best Andrea ------------- >> cd D:\FieldTrip\fieldtrip-20100219\external\spm2 >> mex spm_slice_vol.c lcc preprocessor error: spm_slice_vol.c:5 Could not find include file "spm_mapping.h" Error spm_slice_vol.c: 6 missing parameter type Error spm_slice_vol.c: 6 syntax error; found `*' expecting `)' Error spm_slice_vol.c: 6 skipping `*' `plhs' `[' `]' `,' Error spm_slice_vol.c: 6 syntax error; found `int' expecting `{' Error spm_slice_vol.c: 6 missing identifier Error spm_slice_vol.c: 6 syntax error; found `const' expecting `;' Error spm_slice_vol.c: 6 redeclaration of `mxArray' previously declared at spm_slice_vol.c 6 Error spm_slice_vol.c: 6 syntax error; found `*' expecting `;' Error spm_slice_vol.c: 6 undeclared identifier `prhs' Error spm_slice_vol.c: 6 illegal expression Error spm_slice_vol.c: 6 syntax error; found `)' expecting `]' Error spm_slice_vol.c: 6 skipping `)' Error spm_slice_vol.c: 7 type error: pointer expected Error spm_slice_vol.c: 7 type error: pointer expected Warning spm_slice_vol.c: 7 Statement has no effect Error spm_slice_vol.c: 7 syntax error; found `{' expecting `;' Error spm_slice_vol.c: 8 undeclared identifier `MAPTYPE' Error spm_slice_vol.c: 8 undeclared identifier `map' Error spm_slice_vol.c: 8 type error: pointer expected Error spm_slice_vol.c: 9 illegal statement termination Error spm_slice_vol.c: 9 too many errors C:\PROGRA~1\MATLAB\R2007A\BIN\MEX.PL: Error: Compile of 'spm_slice_vol.c' failed. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From teristam at GMAIL.COM Mon Feb 22 10:00:09 2010 From: teristam at GMAIL.COM (teris tam) Date: Mon, 22 Feb 2010 17:00:09 +0800 Subject: fieldtripbuffer error code Message-ID: Dear Fieldtrip experts, I am trying to read event data from fieldtripbuffer in matlab using read_event(), but I receive the following error: ??? ERROR: the buffer returned an error (517) Matlab reported that the error occurred at the line: evt = buffer('get_evt', [], host, port); May I ask what does the error code (517) means? Where can I find the list of error code for the fieldtripbuffer? Thanks a lot! Best regards, Teris ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.gross at PSY.GLA.AC.UK Tue Feb 23 14:52:55 2010 From: j.gross at PSY.GLA.AC.UK (Joachim Gross) Date: Tue, 23 Feb 2010 13:52:55 +0000 Subject: website and email list Message-ID: Dear researcher, We are in the process of building a website for the MEG community. Please have a look at megcommunity.org. There is also a mailing list associated with the website. The mailing list will be used for exchanging essential information on workshops, courses, jobs etc and for general discussion. If you do MEG research you are strongly encouraged to join the list. Please encourage other colleagues to join as well (including PhD students). Beyond members of your own group we propose that you forward this message to (say three) MEG researchers you know about in a different country/state than yours. We will make an effort to keep spam low. All the best, Joachim Gross and Ole Jensen ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.gross at PSY.GLA.AC.UK Tue Feb 23 14:55:20 2010 From: j.gross at PSY.GLA.AC.UK (Joachim Gross) Date: Tue, 23 Feb 2010 13:55:20 +0000 Subject: website and email list, + instructions Message-ID: Dear researcher, We are in the process of building a website for the MEG community. Please have a look at megcommunity.org. There is also a mailing list associated with the website. The mailing list will be used for exchanging essential information on workshops, courses, jobs etc and for general discussion. If you do MEG research you are strongly encouraged to join the list. Please encourage other colleagues to join as well (including PhD students). Beyond members of your own group we propose that you forward this message to (say three) MEG researchers you know about in a different country/state than yours. We will make an effort to keep spam low. All the best, Joachim Gross and Ole Jensen To join the list: Send following one line message to < jiscmail at jiscmail.ac.uk >: join megcommunity firstname lastname or have a look at http://megcommunity.org/index.php?option=com_content&view=article&id=13&Itemid=26 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From gianpaolo.demarchi at UNITN.IT Tue Feb 23 17:19:23 2010 From: gianpaolo.demarchi at UNITN.IT (Gianpaolo Demarchi) Date: Tue, 23 Feb 2010 17:19:23 +0100 Subject: multiplotER and Neuromag data Message-ID: Dear all, I tried recently to "multiplotER" some data coming from a Elekta Neuromag system, and what I get is just a "grey" plot (see attachment), without any scale and/or data, and no errors on the stdout. All the labels are fine, and if I go in the interactive mode, I can zoom and see correct "singleplotERs" ... So, all the info seems to be there, just the "big" multiplotER is wrong. I did some homework, and the thing doesn't seem to happen with (very!) older versions of fieldtrip, i.e. I tried with a recent version (fieldtrip-20100209) and a older one (fieldtrip-20091201), and the multiplot is still grey, whereas with and old (fieldtrip-20090318 !! that was somewhere in my HD ;-)) the multiplotER is displayed correctly. Any hint? Am I doing any silly mistake? Thanks in advance, Gianpaolo PS: I'm using Matlab (64bit) 2009b on Linux-64, if relevant ... PPS: here is the code I'm using ... and yes, I tried also with the "ft_" version of the commands cfg = []; cfg.dataset = 'raw.fif'; cfg.trialdef.eventtype = 'STI101'; cfg.trialdef.eventvalue = 32768; cfg.trialdef.prestim = 0.1; cfg.trialdef.poststim = 0.25; cfg = definetrial(cfg); cfg.channel = {'MEG'}; cfg.blc = 'yes'; cfg.blcwindow = [-0.1 0]; cfg.lpfilter = 'yes'; cfg.lpfreq = 35; data_raw = preprocessing(cfg); cfg = []; data_avg = timelockanalysis(cfg,data_raw) cfg = []; % cfg.showlabels = 'yes'; % cfg.fontsize = 6; % cfg.interactive = 'yes'; cfg.ylim = [-3e-12 3e-12]; cfg.interactive = 'yes'; multiplotER(cfg, data_avg); ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: multiploeERgrey.jpg Type: image/jpeg Size: 45301 bytes Desc: not available URL: From moratti at MED.UCM.ES Wed Feb 24 11:23:29 2010 From: moratti at MED.UCM.ES (Stephan Moratti) Date: Wed, 24 Feb 2010 11:23:29 +0100 Subject: multiplotER and Neuromag data Message-ID: Hola Gianpaolo, I had the same problem as you. The probel lies in the ft_prepare_layout.m function. It calculates the minimum distance between sensors. As the neuromag sensor has different types of sensors, the layout puts the 3 different sensors at the same place. So calculating the min(d(:)) results in 0 values. Please find below the modified subfunction sens2lay that is located in ft_prepare_layout.m that prevents this error. With that, the topoplots (and multiplots) should work out. Maybe this error can be prevented in a more elegant way that I did. Best, Stephan %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % SUBFUNCTION % convert 3D electrode positions into 2D layout %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% function lay = sens2lay(sens, rz, method, style) fprintf('creating layout for %s system\n', senstype(sens)); % apply rotation if isempty(rz) switch senstype(sens) case {'ctf151', 'ctf275', 'bti148', 'bti248', 'ctf151_planar', 'ctf275_planar', 'bti148_pla nar', 'bti248_planar'} rz = 90; case {'neuromag122', 'neuromag306'} rz = 0; case 'electrode' rz = 90; otherwise rz = 0; end end sens.pnt = warp_apply(rotate([0 0 rz]), sens.pnt, 'homogenous'); % use helper function for 3D layout [pnt, label] = channelposition(sens); if strcmpi(style, '3d') lay.pos = pnt; lay.label = label; else if strcmp(senstype(sens),'neuromag306') %this is to prevent distance of 0 prj = elproj(pnt(1:102,:), method); n=3; else prj = elproj(pnt, method); n=0; end d = dist(prj'); d(find(eye(size(d)))) = inf; mindist = min(d(:)); % this is to fix the planar layouts, which cannot be plotted anyway if n>1 %this is to prevent confusion when lab happens to be a row array prj = repmat(prj, n, 1); end X = prj(:,1); Y = prj(:,2); Width = ones(size(X)) * mindist * 0.8; Height = ones(size(X)) * mindist * 0.6; lay.pos = [X Y]; lay.width = Width; lay.height = Height; lay.label = label; end ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From v.litvak at ION.UCL.AC.UK Wed Feb 24 12:39:18 2010 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Wed, 24 Feb 2010 11:39:18 +0000 Subject: New 'Statistical Parametric Mapping for MEG/EEG' course, London May 10-12, 2010 Message-ID: Dear colleagues, We are happy to advertise the new Statistical Parametric Mapping MEG/EEG course presented by the Wellcome Trust Centre for Neuroimaging. The course will take place on Monday 10th May – Wednesday 12th May 2010 at the Wellcome Trust Centre for Neuroimaging in London. This newly established course will present instruction on the analysis of EEG and MEG data. The first two days will combine theoretical presentations with practical demonstrations of the different data analysis methods implemented in SPM. On the last day participants will have the opportunity to work on SPM tutorial data sets under the supervision of the course faculty. We also invite students to bring their own data for analysis. The course will cover (1) data pre-processing, (2) statistical analysis of sensor-space maps using GLMs and Random Field theory, (3) source reconstruction and (4) Dynamic Causal Modelling for EEG/MEG. The course will be followed by the long-established three-day course on ‘SPM for fMRI’ so it is possible to attend both courses. The course is suitable for beginners and more advanced users. We advise students to gain at least some minimal familiarity with the methodology, for example, from reading introductory articles available from the SPM web page or by following data analysis examples in the SPM manual. The detailed schedule and booking forms can be found at http://www.ion.ucl.ac.uk/articles/events/SPM . For further details and registration please contact Jean Reynolds (j.reynolds at ion.ucl.ac.uk). With best wishes, Vladimir Litvak Ph.D. Senior Research Associate Wellcome Trust Centre for Neuroimaging -------------------------------------------------------------------------------------------------- SPM (http://www.fil.ion.ucl.ac.uk/spm/) is a free and open-source Matlab toolbox in which many widely used methods for the analysis of PET and fMRI data; and for computational neuroanatomy were originally developed. In the recent years SPM has been extended to include M/EEG analysis and, in the most recent version, SPM8, extensive changes have made the software more stable, generic and accessible to researchers with data from wide range of recording systems. In addition to standard M/EEG pre-processing we presently offer three main analysis tools: (1) statistical analysis of scalp maps, time-frequency images and volumetric 3D source reconstruction images based on the general linear model with correction for multiple comparisons using random field theory (2) Bayesian M/EEG source reconstruction including support for group studies, simultaneous EEG and MEG and fMRI priors (3) Dynamic Causal Modelling (DCM) an approach combining neural modelling with data analysis for which there are several variants dealing with evoked responses, steady state responses (power spectra and cross-spectra), induced responses and phase coupling. SPM8 is integrated with the Fieldtrip toolbox (http://www.ru.nl/neuroimaging/fieldtrip/) making it possible for users to combine a variety of standard analysis methods with the new methods implemented in SPM and build custom analysis tools using powerful GUI and batching tools. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From gianpaolo.demarchi at UNITN.IT Wed Feb 24 15:06:25 2010 From: gianpaolo.demarchi at UNITN.IT (Gianpaolo Demarchi) Date: Wed, 24 Feb 2010 15:06:25 +0100 Subject: multiplotER and Neuromag data In-Reply-To: Message-ID: Dear Stephan, thanks for your 'patch' ! It works, i.e. I get a multiplotER graph with some data in it! With "your version" at least we get back a multiplot, with sadly the gradiometers and magnetometers data overlapped. The 'old' way was plotting them arranged in triplets, with one magnetometer and the two gradiometers 'clustered' together. I checked the 'old' prepare_layout.m, and in fact in the grad2lay() function there was a 'finer grained' check of the sensor type, including a different/better layout for 'neuromag306' case. Anyway, there must be a reason for choosing this option (probably the old arrangement with mag+2grads sublopts was too crowded, and probably useless), and in case we can still make two different multiplotERs for magnetometers and gradiometers ... Thanks again, Gianpaolo PS: should this one be considered a 'patch' for a 'bug', and go upstream in the official fieldtrip release? > I had the same problem as you. The probel lies in the ft_prepare_layout.m > function. It calculates the minimum distance between sensors. As the > neuromag sensor has different types of sensors, the layout puts the 3 > different sensors at the same place. So calculating the min(d(:)) results > in 0 values. Please find below the modified subfunction sens2lay that is > located in ft_prepare_layout.m that prevents this error. With that, the > topoplots (and multiplots) should work out. Maybe this error can be > prevented in a more elegant way that I did. > > Best, > > Stephan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From moratti at MED.UCM.ES Thu Feb 25 09:03:30 2010 From: moratti at MED.UCM.ES (Stephan Moratti) Date: Thu, 25 Feb 2010 09:03:30 +0100 Subject: multiplotER and Neuromag data Message-ID: Hello again, I would plot magneto- and gradiometers seperately anyway. You can choose them by using cfg.channel. Best, Stephan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From karl.doron at GMAIL.COM Thu Feb 25 18:35:42 2010 From: karl.doron at GMAIL.COM (Karl Doron) Date: Thu, 25 Feb 2010 18:35:42 +0100 Subject: read events Message-ID: My apologies if this is redundant - I believe I sent to it the megcommunity list and meant to send it here, so I am reposting. Hello, I've recently collect MEG data and had to edit trigger values. I've read in my BTi data using preprocessing() and inserted triggers at appropriate times in sub1.trial{1}(1,:). Now I would like to use definetrial. However, the cfg file references the original data, with the incorrect trigger onsets and information. What should I list as cfg.dataset to have my imported data read? Thanks for any help. karl doron Ph.D. Candidate UC, Santa Barbara ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From chesharm at STANFORD.EDU Sat Feb 27 08:15:21 2010 From: chesharm at STANFORD.EDU (Chetan Sharma) Date: Fri, 26 Feb 2010 23:15:21 -0800 Subject: clusterstats empty cfg.neighbours, cfg.neighbours example Message-ID: Hello everyone, I'm trying to run the coherence Z nonparametric test to detect synchrony between two channels of MEG data. Because of how restrictive bonferoni, FDR, and all are, we wanted to use the 'cluster' function for cfg.correctm. This call to statistics_montecarlo.m, which says in the description that to do clustering in frequency and time, as we want to do, we should use an empty cfg.neighbours structure. However, when the function calls clusterstats.m, it looks like there is a bug in the code. The relevant code is at line 38 in clusterstats.m, and is: if isfield(cfg, 'neighbours') && ~isempty(cfg.neighbours) channeighbstructmat = makechanneighbstructmat(cfg); issource = 0; else issource = 1; % cfg contains dim and inside that are needed for reshaping the data to a volume, and inside should behave as a index vector cfg = fixinside(cfg, 'index'); end The issue is that the case for an empty cfg.neighbours isn't handled. Running the function with an empty cfg.neighbours leads to a bug when calculating the clusters, and makes issource=1, when it should be zero for freq_time data. The function runs through when I manually set issource=0, but I don't know if that is the intended purpose. Has anyone else run into this problem? Without an example of what cfg.neighbours should look like, it's hard to determine if we are doing a correct setup. Could someone either send an example of cfg.neighbours, or verify this bug and suggest solutions? thanks and regards, -chetan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Sat Feb 27 14:21:03 2010 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Sat, 27 Feb 2010 14:21:03 +0100 Subject: read events In-Reply-To: Message-ID: Dear Karl, Definetrial is usually called before preprocessing, not after preprocessing. Definetrial determines the trial structure, i.e. the segments that subsequently are read with the preprocessing function. Often the interesting data segments (the trials) are much shorter than the complete continuous data, so reading only the trials saves memory. Since you have already read in all data into memory, you should use "redefinetrial" to segment your data into the trials. That also requires the trial definition to be specified in cfg.trl. The only purpose of definetrial function is t oconstruct this cfg.trl field based on the events. Since you manually added the triggers after reading the data in memory, you have to emulate the behaviour of definetrial. You should look at it's help and manually construct a cfg.trl field which you can hand over to redefinetrial together with the data. best, Robert On 25 Feb 2010, at 18:35, Karl Doron wrote: > My apologies if this is redundant - I believe I sent to it the megcommunity > list and meant to send it here, so I am reposting. > > Hello, > > I've recently collect MEG data and had to edit trigger values. I've read in > my BTi data using preprocessing() and inserted triggers at appropriate times > in sub1.trial{1}(1,:). > > Now I would like to use definetrial. However, the cfg file references the > original data, with the incorrect trigger onsets and information. What > should I list as cfg.dataset to have my imported data read? > > Thanks for any help. > > karl doron > Ph.D. Candidate > UC, Santa Barbara > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Sat Feb 27 14:27:09 2010 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Sat, 27 Feb 2010 14:27:09 +0100 Subject: Invalid MEX file /Question re: ft_clusterplot In-Reply-To: <6B7D05EBBB224D9F93C9E1F0905EE2DC@LAT6500Andrea> Message-ID: Dear Andrea > On 22 Feb 2010, at 8:55, Andrea Ostendorf wrote: > When trying to use read_mri, I encountered the error > "??? Invalid MEX-file > 'D:\FieldTrip\fieldtrip-20100219\external\spm2\spm_slice_vol.dll': The > specified procedure could not be found. > > Proceeding along the lines suggested in the FAQ - changing to the SPM2 > subdirectory and trying to compile the mex file again (using the MATLAB > compiler) - I get a long list of error messages, starting with a complaint > about a missing header file. I attach the complete error messages below. It turns out that the set of *.c files in the fieldtrip/external/spm2 directory is incomplete. You should compile the mex files from a complete spm2 version, which you can hget from the FIl website. > Regarding ft_clusterplot: I have got the impression that during the check > for the existence of clusters, ft_clusterplot assumes the existence of both > positive and negative clusters, provided that there are any at all > (l.113-115). If there are just positive or negative clusters - as may happen > in the case of one-sided tests - this can lead to an error such as > > ??? Reference to non-existent field 'negclusters'. > > Error in ==> ft_clusterplot at 119 > for iNeg = 1:length(stat.negclusters) You are right. I have made that optional on the presence of positive or negative clusters like this: if haspos == 0 && hasneg == 0 fprintf('%s\n','no significant clusters in data; nothing to plot') else if haspos for iPos = 1:length(stat.posclusters) sigpos(iPos) = stat.posclusters(iPos).prob < cfg.alpha; end end if hasneg for iNeg = 1:length(stat.negclusters) signeg(iNeg) = stat.negclusters(iNeg).prob < cfg.alpha; end end ... thanks, Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From nicolas.robitaille at UMONTREAL.CA Sat Feb 27 14:55:18 2010 From: nicolas.robitaille at UMONTREAL.CA (Nicolas Robitaille) Date: Sat, 27 Feb 2010 13:55:18 +0000 Subject: read events In-Reply-To: <1CAE6B41-DB17-4A88-BD6E-F4F231DB18C1@fcdonders.ru.nl> Message-ID: Dear Karl, dear Robert, I would suggest, alternatively, to modify the trialfun_general (or wathever trialfun you are using, Karl), in order to use the event definition found in the cfg structure, if any. This would have the advantage of allowing multiple call to definetrial (for multiple conditions; I once had 30 of them) without having to read all the events in the datafile over and over again. I think such change in behavior could be incorporated in the normal distribution of FT, according that it's already the case of the trial definition (i.e. if there is already a .trl field, definetrial.m just use it). This would look like: starting at line 49 of trialfun_general: % read the header and event information hdr = read_header(cfg.headerfile); try event = read_event(cfg.headerfile); catch event = []; end should become something like: % read the header and event information hdr = read_header(cfg.headerfile); if isfield(cfg, 'event') event = cfg.event; else try event = read_event(cfg.headerfile); catch event = []; end end Karl, note that I haven't test that. Best, Nicolas ************************* Nicolas Robitaille, Ph.D. Stagiaire post-doctoral Brams ************************* > Date: Sat, 27 Feb 2010 14:21:03 +0100 > From: r.oostenveld at FCDONDERS.RU.NL > Subject: Re: [FIELDTRIP] read events > To: FIELDTRIP at NIC.SURFNET.NL > > Dear Karl, > > Definetrial is usually called before preprocessing, not after preprocessing. Definetrial determines the trial structure, i.e. the segments that subsequently are read with the preprocessing function. Often the interesting data segments (the trials) are much shorter than the complete continuous data, so reading only the trials saves memory. > > Since you have already read in all data into memory, you should use "redefinetrial" to segment your data into the trials. That also requires the trial definition to be specified in cfg.trl. The only purpose of definetrial function is t oconstruct this cfg.trl field based on the events. > > Since you manually added the triggers after reading the data in memory, you have to emulate the behaviour of definetrial. You should look at it's help and manually construct a cfg.trl field which you can hand over to redefinetrial together with the data. > > best, > Robert > > > > > > On 25 Feb 2010, at 18:35, Karl Doron wrote: > > > My apologies if this is redundant - I believe I sent to it the megcommunity > > list and meant to send it here, so I am reposting. > > > > Hello, > > > > I've recently collect MEG data and had to edit trigger values. I've read in > > my BTi data using preprocessing() and inserted triggers at appropriate times > > in sub1.trial{1}(1,:). > > > > Now I would like to use definetrial. However, the cfg file references the > > original data, with the incorrect trigger onsets and information. What > > should I list as cfg.dataset to have my imported data read? > > > > Thanks for any help. > > > > karl doron > > Ph.D. Candidate > > UC, Santa Barbara > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. _________________________________________________________________ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Sat Feb 27 15:06:54 2010 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Sat, 27 Feb 2010 15:06:54 +0100 Subject: fieldtripbuffer error code In-Reply-To: Message-ID: Hi Teris On 22 Feb 2010, at 10:00, teris tam wrote: > Dear Fieldtrip experts, > I am trying to read event data from fieldtripbuffer in matlab using read_event(), but I receive the following error: > > ??? ERROR: the buffer returned an error (517) > > Matlab reported that the error occurred at the line: > > evt = buffer('get_evt', [], host, port); This is an error that happens if there are no events in the buffer. In more recent versions, read_event returns an empty array (i.e. []), which is what you woudl expect. I suggest that you upgrade to the most recent version. > May I ask what does the error code (517) means? Where can I find the list of error code for the fieldtripbuffer? They are defined (in hexadecimal representation, and not in decimal representation as it is printed) in fieldtrip/realtime/buffer/src/message.h. You can convert them for example here http://easycalculation.com/hex-converter.php?hex=0x0205&hexDeci=NaN&hexBin=0001 The error 517 (decimal) is 0205 (hexadecimal), which means GET_ERR. best regards, Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Sat Feb 27 15:11:22 2010 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Sat, 27 Feb 2010 15:11:22 +0100 Subject: read events In-Reply-To: Message-ID: Hi Nicolas That is a good suggestion, I have incorporated it into the code. This evenings version on the ftp server will include it. thanks, Robert ----------------------------------------------------------- Robert Oostenveld, PhD Senior Researcher Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen tel.: +31 (0)24 3619695 e-mail: r.oostenveld at donders.ru.nl web: http://www.ru.nl/neuroimaging skype: r.oostenveld ----------------------------------------------------------- On 27 Feb 2010, at 14:55, Nicolas Robitaille wrote: > Dear Karl, dear Robert, > > I would suggest, alternatively, to modify the trialfun_general (or wathever trialfun you are using, Karl), in order to use the event definition found in the cfg structure, if any. This would have the advantage of allowing multiple call to definetrial (for multiple conditions; I once had 30 of them) without having to read all the events in the datafile over and over again. I think such change in behavior could be incorporated in the normal distribution of FT, according that it's already the case of the trial definition (i.e. if there is already a .trl field, definetrial.m just use it). > > This would look like: > > starting at line 49 of trialfun_general: > > % read the header and event information > hdr = read_header(cfg.headerfile); > try > event = read_event(cfg.headerfile); > catch > event = []; > end > > should become something like: > > % read the header and event information > hdr = read_header(cfg.headerfile); > if isfield(cfg, 'event') > event = cfg.event; > else > try > event = read_event(cfg.headerfile); > catch > event = []; > end > end > > Karl, note that I haven't test that. > > Best, > > Nicolas > > ************************* > Nicolas Robitaille, Ph.D. > Stagiaire post-doctoral > Brams > ************************* > > > > > > Date: Sat, 27 Feb 2010 14:21:03 +0100 > > From: r.oostenveld at FCDONDERS.RU.NL > > Subject: Re: [FIELDTRIP] read events > > To: FIELDTRIP at NIC.SURFNET.NL > > > > Dear Karl, > > > > Definetrial is usually called before preprocessing, not after preprocessing. Definetrial determines the trial structure, i.e. the segments that subsequently are read with the preprocessing function. Often the interesting data segments (the trials) are much shorter than the complete continuous data, so reading only the trials saves memory. > > > > Since you have already read in all data into memory, you should use "redefinetrial" to segment your data into the trials. That also requires the trial definition to be specified in cfg.trl. The only purpose of definetrial function is t oconstruct this cfg.trl field based on the events. > > > > Since you manually added the triggers after reading the data in memory, you have to emulate the behaviour of definetrial. You should look at it's help and manually construct a cfg.trl field which you can hand over to redefinetrial together with the data. > > > > best, > > Robert > > > > > > > > > > > > On 25 Feb 2010, at 18:35, Karl Doron wrote: > > > > > My apologies if this is redundant - I believe I sent to it the megcommunity > > > list and meant to send it here, so I am reposting. > > > > > > Hello, > > > > > > I've recently collect MEG data and had to edit trigger values. I've read in > > > my BTi data using preprocessing() and inserted triggers at appropriate times > > > in sub1.trial{1}(1,:). > > > > > > Now I would like to use definetrial. However, the cfg file references the > > > original data, with the incorrect trigger onsets and information. What > > > should I list as cfg.dataset to have my imported data read? > > > > > > Thanks for any help. > > > > > > karl doron > > > Ph.D. Candidate > > > UC, Santa Barbara > > > > > > ---------------------------------- > > > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html andhttp://www.ru.nl/neuroimaging/fieldtrip. > > > > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html andhttp://www.ru.nl/neuroimaging/fieldtrip. > > Vous n'utilisez pas Hotmail sur votre téléphone? Mais pourquoi pas? Obtenez-le maintenant! > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. > http://listserv.surfnet.nl/archives/fieldtrip.html > http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From tomh at KURAGE.NIMH.NIH.GOV Sun Feb 28 00:12:10 2010 From: tomh at KURAGE.NIMH.NIH.GOV (Tom Holroyd) Date: Sat, 27 Feb 2010 18:12:10 -0500 Subject: clusterstats empty cfg.neighbours, cfg.neighbours example Message-ID: >I'm trying to run the coherence Z nonparametric test to detect synchrony >between two channels of MEG data. Because of how restrictive bonferoni, FDR, >and all are project source channels into dual space get independent components look at coherence differences shuffle get max look at angles between source space beamformers ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.