From mcoskun at mail.uh.edu Wed Feb 1 13:55:15 2012 From: mcoskun at mail.uh.edu (Mehmet-Akif Coskun) Date: Wed, 01 Feb 2012 06:55:15 -0600 Subject: [FieldTrip] Error -> ft_databrowser Message-ID: <7220b947bb8f3.4f28e1d3@mail.uh.edu> Dear Fieldtrippers, I am encountering a strange error while i try to use ft_databrowser. The error code is as below. I have never seen this error earlier. I used ft_databrowser many times and its only last 2 days that i am getting the error. I downloaded a newer version of fieldtrip (fieldtrip-20120130) and used the newer version but still the same error. Strangely, i dont get this error when i tried with other computers (same matlab version (R2010a), same operating system (windows 7) on both computers. Has anyone got this error before? what may cause this error? fieldtrip version 20120130, matlab version R2010a, operating system windows 7. Thanks in advance for any suggestions. ??? Error using ==> ft_fetch_data at 57 data does not contain a consistent trial definition, fetching data is not possible Error in ==> ft_databrowser>redraw_cb at 1159 art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', endsample); Error in ==> ft_databrowser at 535 redraw_cb(h); -------------- next part -------------- An HTML attachment was scrubbed... URL: From Ulrich.Pomper at charite.de Wed Feb 1 14:44:44 2012 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Wed, 1 Feb 2012 14:44:44 +0100 Subject: [FieldTrip] Defining cfg.neighbourdist at source level In-Reply-To: References: <4F22C422.4080906@charite.de> <4F26B91E.2050200@donders.ru.nl> <4F26BE42.5030204@charite.de> Message-ID: <4F2941CC.6030609@charite.de> Dear Robert and Stephan, Thank you for your replies. I guess I use what Robert called the 'regular' 3D grid, but I'm not quite sure. The structures of my headmodel and leadfield matrix are the following (based on data from a BEM standard file): vol = bnd: [1x3 struct] cond: [0.3300 0.0041 0.3300] mat: [3000x3000 double] type: 'dipoli' ldf = xgrid: [-65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68] ygrid: [-107 -100 -93 -86 -79 -72 -65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68 75] zgrid: [-52 -45 -38 -31 -24 -17 -10 -3 4 11 18 25 32 39 46 53 60 67 74 81] dim: [20 27 20] pos: [10800x3 double] inside: [1x5739 double] outside: [1x5061 double] leadfield: {1x10800 cell} cfg: [1x1 struct] In any case, I still don't quite understand how to calculate the neighbours to each voxel. By saying that the "neighbours are trivial to find and you do not have to specify a structure", do you mean that I don't need to define the cfg.neighbours property at all (given that I do use a regular 3D grid)? Thanks again for your help, cheers, Ulrich On 31.01.2012 21:48, smoratti at psi.ucm.es wrote: Dear Robert, To do clustering on a 3D source surface I always had to "trick" field trip and squeezed the 3D source surface data into a ERF structure treating the 3D surface points as sensors. Then by triangulation I found the neighbors. However, if there is a more elegant method implemented in ft_sourcestatistc, I would be very interested to know how to do it. Where can I find some hints on that? Best, Stephan ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 28223 Pozuelo de Alarcón (Madrid) Spain and Center for Biomedical Technology Laboratory for Cognitive and Computational Neuroscience Parque Científico y Tecnológico de la Universidad Politecnica de Madrid Campus Montegancedo 28223 Pozuelo de Alarcón (Madrid) Spain email: smoratti at psi.ucm.es Tel.: +34 679219982 El 31/01/2012, a las 15:37, Robert Oostenveld escribió: Dear Ulrich If your source locations are defined on a regular 3D grid that can be represented as volume, then the neighbours are trivial to find and you do not have to specify a structure for the neighbours. If you have done source reconstruction on a 3D folded cortical sheet that is defined by a triangulated surface, then it is also possible to cluster along the surface. I don't know the details for the cortical sheet clustering from the top of my head, if you are interested please let me know and I'll look them up. best Robert On 30 Jan 2012, at 16:58, Pomper, Ulrich wrote: Dear Jörn, Thanks for you reply. I did mean source-level, so like you said, I am trying to define the neighbouring voxels for each voxel. As far as I understand, leaving cfg.neighbours blank means that the clustering is done over the time and frequency dimensions only, not over space. The FT help reads: %If you specify an empty neighbourhood structure, clustering will only be done in frequency and time (if available) and not over neighbouring channels. Has anybody done clustering in source space using all three dimensions and could explain how this works? Cheers, Ulrich _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus -------------- next part -------------- An HTML attachment was scrubbed... URL: From MEpstein at NKI.RFMH.ORG Wed Feb 1 20:44:47 2012 From: MEpstein at NKI.RFMH.ORG (Epstein, Michael) Date: Wed, 1 Feb 2012 14:44:47 -0500 Subject: [FieldTrip] rereferencing after preproc Message-ID: <2586A1048152BE4D861E64A98700AD420A601176@nki-mail.NKI.rfmh.org> Hi all, I'm trying to analyze a dataset using multiple reference points - is there a way to re-reference the data after the whole preprocessing step? I'm using ft_rejectvisual to clean the data, so I want to reference after that, in order to preserve as much consistency between the two sets as is possible. I was trying to use ft_preproc_rereference to achieve this goal, but that only takes in channel x time data, not trial data or freq data. Is there a different way to rereference? Thanks, -Michael Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Wed Feb 1 21:00:33 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Wed, 1 Feb 2012 21:00:33 +0100 Subject: [FieldTrip] rereferencing after preproc In-Reply-To: <2586A1048152BE4D861E64A98700AD420A601176@nki-mail.NKI.rfmh.org> References: <2586A1048152BE4D861E64A98700AD420A601176@nki-mail.NKI.rfmh.org> Message-ID: Hi Michael, Probably ft_preprocessing with the options cfg.reref = 'yes' and cfg.refchannel = '' is what you are looking for. ft_preproc_rereference is a lower-level FieldTrip function, which indeed operates directly on a channel x time matrix. ft_preprocessing contains all the necessary bookkeeping wrappers around ft_preproc_* so that you can conveniently apply the preprocessing functions on FieldTrip-style data structures. Hope this helps. Eelke On 1 February 2012 20:44, Epstein, Michael wrote: > Hi all, > > > > I’m trying to analyze a dataset using multiple reference points – is there a > way to re-reference the data after the whole preprocessing step? I’m using > ft_rejectvisual to clean the data, so I want to reference after that, in > order to preserve as much consistency between the two sets as is possible. > > > > I was trying to use ft_preproc_rereference to achieve this goal, but that > only takes in channel x time data, not trial data or freq data. Is there a > different way to rereference? > > > > Thanks, > > > > -Michael > > > > ________________________________ > Conserve Resources. Print only when necessary. > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended > recipient. It may contain confidential information which is legally > privilegedor otherwise protected by law. If you received this e-mail in > error or from someone who is not authorized to send it to you, you are > strictly prohibited from reviewing, using, disseminating, distributing or > copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN > E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your > cooperation. > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From MEpstein at NKI.RFMH.ORG Wed Feb 1 21:05:49 2012 From: MEpstein at NKI.RFMH.ORG (Epstein, Michael) Date: Wed, 1 Feb 2012 15:05:49 -0500 Subject: [FieldTrip] rereferencing after preproc In-Reply-To: References: <2586A1048152BE4D861E64A98700AD420A601176@nki-mail.NKI.rfmh.org> Message-ID: <2586A1048152BE4D861E64A98700AD420A601194@nki-mail.NKI.rfmh.org> Oh I see - I didn't realize you could use that function on data you had already preprocessed once. Thank you, that's useful. -Michael -----Original Message----- From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Eelke Spaak Sent: Wednesday, February 01, 2012 3:01 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] rereferencing after preproc Hi Michael, Probably ft_preprocessing with the options cfg.reref = 'yes' and cfg.refchannel = '' is what you are looking for. ft_preproc_rereference is a lower-level FieldTrip function, which indeed operates directly on a channel x time matrix. ft_preprocessing contains all the necessary bookkeeping wrappers around ft_preproc_* so that you can conveniently apply the preprocessing functions on FieldTrip-style data structures. Hope this helps. Eelke On 1 February 2012 20:44, Epstein, Michael wrote: > Hi all, > > > > I'm trying to analyze a dataset using multiple reference points - is there a > way to re-reference the data after the whole preprocessing step? I'm using > ft_rejectvisual to clean the data, so I want to reference after that, in > order to preserve as much consistency between the two sets as is possible. > > > > I was trying to use ft_preproc_rereference to achieve this goal, but that > only takes in channel x time data, not trial data or freq data. Is there a > different way to rereference? > > > > Thanks, > > > > -Michael > > > > ________________________________ > Conserve Resources. Print only when necessary. > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended > recipient. It may contain confidential information which is legally > privilegedor otherwise protected by law. If you received this e-mail in > error or from someone who is not authorized to send it to you, you are > strictly prohibited from reviewing, using, disseminating, distributing or > copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN > E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your > cooperation. > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. From inieuwenhuis at berkeley.edu Wed Feb 1 21:20:20 2012 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Wed, 01 Feb 2012 12:20:20 -0800 Subject: [FieldTrip] rereferencing after preproc In-Reply-To: <2586A1048152BE4D861E64A98700AD420A601194@nki-mail.NKI.rfmh.org> References: <2586A1048152BE4D861E64A98700AD420A601176@nki-mail.NKI.rfmh.org> <2586A1048152BE4D861E64A98700AD420A601194@nki-mail.NKI.rfmh.org> Message-ID: <4F299E84.7040804@berkeley.edu> Hi, just a little addition. You mention freq data, but you can't re-reference after freq analysis. Has to take place before. (Just in case you meant that) Good luck, Ingrid -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 On 2/1/2012 12:05 PM, Epstein, Michael wrote: > Oh I see - I didn't realize you could use that function on data you had > already preprocessed once. > > Thank you, that's useful. > > -Michael > > -----Original Message----- > From: fieldtrip-bounces at donders.ru.nl > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Eelke Spaak > Sent: Wednesday, February 01, 2012 3:01 PM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] rereferencing after preproc > > Hi Michael, > > Probably ft_preprocessing with the options cfg.reref = 'yes' and > cfg.refchannel = '' is what you are looking for. > > ft_preproc_rereference is a lower-level FieldTrip function, which > indeed operates directly on a channel x time matrix. ft_preprocessing > contains all the necessary bookkeeping wrappers around ft_preproc_* so > that you can conveniently apply the preprocessing functions on > FieldTrip-style data structures. > > Hope this helps. > > Eelke > > On 1 February 2012 20:44, Epstein, Michael > wrote: >> Hi all, >> >> >> >> I'm trying to analyze a dataset using multiple reference points - is > there a >> way to re-reference the data after the whole preprocessing step? I'm > using >> ft_rejectvisual to clean the data, so I want to reference after that, > in >> order to preserve as much consistency between the two sets as is > possible. >> >> >> I was trying to use ft_preproc_rereference to achieve this goal, but > that >> only takes in channel x time data, not trial data or freq data. Is > there a >> different way to rereference? >> >> >> >> Thanks, >> >> >> >> -Michael >> >> >> >> ________________________________ >> Conserve Resources. Print only when necessary. >> >> IMPORTANT NOTICE: This e-mail is meant only for the use of the > intended >> recipient. It may contain confidential information which is legally >> privilegedor otherwise protected by law. If you received this e-mail > in >> error or from someone who is not authorized to send it to you, you are >> strictly prohibited from reviewing, using, disseminating, distributing > or >> copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY > RETURN >> E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your >> cooperation. >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Conserve Resources. Print only when necessary. > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 From jm.horschig at donders.ru.nl Thu Feb 2 09:30:37 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 02 Feb 2012 09:30:37 +0100 Subject: [FieldTrip] rereferencing after preproc In-Reply-To: <4F299E84.7040804@berkeley.edu> References: <2586A1048152BE4D861E64A98700AD420A601176@nki-mail.NKI.rfmh.org> <2586A1048152BE4D861E64A98700AD420A601194@nki-mail.NKI.rfmh.org> <4F299E84.7040804@berkeley.edu> Message-ID: <4F2A49AD.1050303@donders.ru.nl> Hi, another addition: ft_apply_montage is doing the same (ft_preprocessing also calls this function), but it also changes the labels. This is useful when, for example, wanting to construct bipolar channels like hEOG and vEOG. Best, Jörn On 2/1/2012 9:20 PM, Ingrid Nieuwenhuis wrote: > Hi, just a little addition. You mention freq data, but you can't > re-reference after freq analysis. Has to take place before. (Just in > case you meant that) > Good luck, > Ingrid > -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From sysoevao at psychiatry.wustl.edu Thu Feb 2 23:49:41 2012 From: sysoevao at psychiatry.wustl.edu (Sysoeva, Olga Vladimirovna) Date: Thu, 2 Feb 2012 16:49:41 -0600 Subject: [FieldTrip] channels interpolation Message-ID: <76DC57362137854CB9592B496182D5FA09D909A83B@wusmexmbx2.medpriv.wucon.wustl.edu> Dear group, Am I doing something wrong or is it a bug? I needed to do some bad channel interpolation for my dataset (epoched data). So I found out that there is a ft_channel_repair function. And I tried to use it in the following way. cfg = []; cfg.method = 'distance'%, 'triangulation' or 'template' (default = 'distance') cfg.neighbourdist = 4; % number, maximum distance between neighbouring sensors (only for 'distance') cfg.layout = 'C:\Matlab_programs\Fieldtrip\My_Fieldtrip\EEG1010_modified32.lay'; [neighbours] = ft_prepare_neighbours(cfg, data) cfg = []; cfg.badchannel = {'F4'};%cell-array, see FT_CHANNELSELECTION for details cfg.neighbours = neighbours; [interp] = ft_channelrepair(cfg, data) But I'm getting the error ??? Reference to non-existent field 'pnt'. It seems to me that I'm not preparing the sensor(electrode) structure correctly, but I couldn't find mistake. I do follow the tutorial. There are a link that I need to prepare the electrode structure as in ft_fetch_sens function, but I my version of Fieldtrip I do not have this function. I'll appreciate any help, Best Regards, Olga. __________________________________________________________ Olga Sysoeva, Research Associate, PhD Psychiatry Department, Washington University School of Medicine Campus Box 8134 660 South Euclid Ave Saint Louis, MO 63110-9909 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Fri Feb 3 09:50:26 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Fri, 03 Feb 2012 09:50:26 +0100 Subject: [FieldTrip] channels interpolation In-Reply-To: <76DC57362137854CB9592B496182D5FA09D909A83B@wusmexmbx2.medpriv.wucon.wustl.edu> References: <76DC57362137854CB9592B496182D5FA09D909A83B@wusmexmbx2.medpriv.wucon.wustl.edu> Message-ID: <4F2B9FD2.7070003@donders.ru.nl> Dear Olga, indeed that there is a problem with the sensor definition. In addition to specifying neighbours, the channelrepair function needs to know the distance between channels. Therefore, you need to provide a definition of the sensor position additionally. However, the error message you get is not the one you should see - there should be one that is more elaborate and intuitively understandable ;) Could you send me (outside the mailinglist) the whole error message, including the lines where this goes wrong? I will then fix the problem asap. Btw, the ft_fetch_sens function has recently been moved to the FieldTrip/private folder, that means Matlab prevents you from seeing or calling the function directly, but if you just cd to that directory, you can access the file. Also, I just changed the error message that you should have seen to be more elaborate (will be available from tomorrow on). Best, Jörn On 2/2/2012 11:49 PM, Sysoeva, Olga Vladimirovna wrote: > > Dear group, > > Am I doing something wrong or is it a bug? > > I needed to do some bad channel interpolation for my dataset (epoched > data). > > So I found out that there is a ft_channel_repair function. And I tried > to use it in the following way. > > cfg = []; > > cfg.method = 'distance'%, 'triangulation' or 'template' > (default = 'distance') > > cfg.neighbourdist = 4; % number, maximum distance between neighbouring > sensors (only for 'distance') > > cfg.layout = > 'C:\Matlab_programs\Fieldtrip\My_Fieldtrip\EEG1010_modified32.lay'; > > [neighbours] = ft_prepare_neighbours(cfg, data) > > cfg = []; > > cfg.badchannel = {'F4'};%cell-array, see FT_CHANNELSELECTION for > details > > cfg.neighbours = neighbours; > > [interp] = ft_channelrepair(cfg, data) > > But I'm getting the error ??? Reference to non-existent field 'pnt'. > > It seems to me that I'm not preparing the sensor(electrode) structure > correctly, but I couldn't find mistake. I do follow the tutorial. > There are a link that I need to prepare the electrode structure as in > ft_fetch_sens function, but I my version of Fieldtrip I do not have > this function. > > I'll appreciate any help, > > Best Regards, > > Olga. > > __________________________________________________________ > > Olga Sysoeva, > > Research Associate, PhD > > Psychiatry Department, > > Washington University School of Medicine > > Campus Box 8134 > > 660 South Euclid Ave > > Saint Louis, MO 63110-9909 > > > ------------------------------------------------------------------------ > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying or the taking of any action in reliance on > the contents of this information is strictly prohibited. If you have > received this email in error, please immediately notify the sender via > telephone or return mail. > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From chadbircher at yahoo.com Fri Feb 3 17:06:45 2012 From: chadbircher at yahoo.com (Chad Bircher) Date: Fri, 3 Feb 2012 08:06:45 -0800 (PST) Subject: [FieldTrip] Pthread install Message-ID: <1328285205.47747.YahooMailNeo@web162006.mail.bf1.yahoo.com> I am trying to install the peer directories, but cannot run peercompile('VC') on my Windows7 64bit machine using Microsoft Visual C++ express 2012.  I am getting an error that it cannot find pthread.h  I am not a systems developer, and do not know how to install this correctly.  Every attempt I have made still does not allow peercompile to run. How do I install pthread on this sort of a system? Thank you Chad -------------- next part -------------- An HTML attachment was scrubbed... URL: From Ulrich.Pomper at charite.de Mon Feb 6 14:05:38 2012 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Mon, 6 Feb 2012 14:05:38 +0100 Subject: [FieldTrip] Fwd: Re: Defining cfg.neighbourdist at source level In-Reply-To: <2594dc0d96864f1a8d49694602e55bce@EXCCAHT-2.mail.uke.ads> References: <2594dc0d96864f1a8d49694602e55bce@EXCCAHT-2.mail.uke.ads> Message-ID: <4F2FD022.3000407@charite.de> Dear fieldtrippers, I'm still in need of an advise on the issue below. Any help would be greatly appreciated!! Dear Robert and Stephan, Thank you for your replies. I guess I use what Robert called the 'regular' 3D grid, but I'm not quite sure. The structures of my headmodel and leadfield matrix are the following (based on data from a BEM standard file): vol = bnd: [1x3 struct] cond: [0.3300 0.0041 0.3300] mat: [3000x3000 double] type: 'dipoli' ldf = xgrid: [-65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68] ygrid: [-107 -100 -93 -86 -79 -72 -65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68 75] zgrid: [-52 -45 -38 -31 -24 -17 -10 -3 4 11 18 25 32 39 46 53 60 67 74 81] dim: [20 27 20] pos: [10800x3 double] inside: [1x5739 double] outside: [1x5061 double] leadfield: {1x10800 cell} cfg: [1x1 struct] In any case, I still don't quite understand how to calculate the neighbours to each voxel. By saying that the "neighbours are trivial to find and you do not have to specify a structure", do you mean that I don't need to define the cfg.neighbours property at all (given that I do use a regular 3D grid)? Thanks again for your help, cheers, Ulrich On 31.01.2012 21:48, smoratti at psi.ucm.es wrote: Dear Robert, To do clustering on a 3D source surface I always had to "trick" field trip and squeezed the 3D source surface data into a ERF structure treating the 3D surface points as sensors. Then by triangulation I found the neighbors. However, if there is a more elegant method implemented in ft_sourcestatistc, I would be very interested to know how to do it. Where can I find some hints on that? Best, Stephan ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 28223 Pozuelo de Alarcón (Madrid) Spain and Center for Biomedical Technology Laboratory for Cognitive and Computational Neuroscience Parque Científico y Tecnológico de la Universidad Politecnica de Madrid Campus Montegancedo 28223 Pozuelo de Alarcón (Madrid) Spain email: smoratti at psi.ucm.es Tel.: +34 679219982 El 31/01/2012, a las 15:37, Robert Oostenveld escribió: Dear Ulrich If your source locations are defined on a regular 3D grid that can be represented as volume, then the neighbours are trivial to find and you do not have to specify a structure for the neighbours. If you have done source reconstruction on a 3D folded cortical sheet that is defined by a triangulated surface, then it is also possible to cluster along the surface. I don't know the details for the cortical sheet clustering from the top of my head, if you are interested please let me know and I'll look them up. best Robert On 30 Jan 2012, at 16:58, Pomper, Ulrich wrote: Dear Jörn, Thanks for you reply. I did mean source-level, so like you said, I am trying to define the neighbouring voxels for each voxel. As far as I understand, leaving cfg.neighbours blank means that the clustering is done over the time and frequency dimensions only, not over space. The FT help reads: %If you specify an empty neighbourhood structure, clustering will only be done in frequency and time (if available) and not over neighbouring channels. Has anybody done clustering in source space using all three dimensions and could explain how this works? Cheers, Ulrich _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus -------------- next part -------------- An HTML attachment was scrubbed... URL: From phc5 at georgetown.edu Tue Feb 7 05:56:09 2012 From: phc5 at georgetown.edu (patrick cox) Date: Mon, 6 Feb 2012 23:56:09 -0500 Subject: [FieldTrip] Computing the system matrix in a the forward model? Message-ID: Hi, I have just started using feildtrip, and I am trying to do some source localization using beamforming. I am working with EEG data and would like to anatomically constrain the forward model, so I am trying out the various BEM methods in fieldtrip. As a first pass I have been using the SPM T1 template, but I also have anatomical scans of my subjects. My problem is that when I try to calculate the model for the volume conductor using most of the methods (openmeeg, dipoli), my vol structure does not contain a vol.mat field (which I believe is the system matrix). The one BEM method that actully returns a vol with a system matrix is the BEMCP method, but the vol.mat file is all NaNs! I have tracked the problem to the calculation of the Cij's, particularly C12 and C21, in the ft_headmodel_bemcp.m which contain a large number of NaN entries. Does anyone have a fix for this, or a advice on how to producing vol structures with system matrices/vol.mat fields using the other BEM methods? Thanks! Patrick Cox -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue Feb 7 11:26:24 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 7 Feb 2012 10:26:24 +0000 Subject: [FieldTrip] Pthread install In-Reply-To: <1328285205.47747.YahooMailNeo@web162006.mail.bf1.yahoo.com> References: <1328285205.47747.YahooMailNeo@web162006.mail.bf1.yahoo.com> Message-ID: Dear Chad All peer functions rely on a single mex file. That mex file implements a TCP server and client in a seperate thread, which allows MATLAB to receive data while at the same time busy with computations. The TCP networking details are slightly different between operating systems. The computers we work with most are unix-bases (linux, os x), therefore those are the ones that we primarily target with out code. Stefan, a former colleague at the Donders has compiled it once on windows32 and 64, but that mex file has not been kept up to date since then. The peer TCP server and client are derived from the FieldTrip buffer (see http://fieldtrip.fcdonders.nl/development/realtime) which is the result of a project to allow MATLAB to do efficient and easy computations on real-time streamed EEG and MEG data. The fieldtrip realtime buffer works well on all operating systems, so as such there is no reason to assume that peer would also not work. The TCP server and the other peer threads (i.e. announce, discover, expire) are all implemented with posix threads, which is the default on unix-like operating systems (linux, os x). On MS Windows there is another threading system, but there is a port of pthreads for windows (see http://sourceware.org/pthreads-win32/). At the time we implemented this stuff, there was only a version available for 32-bit windows, whereas nowadays most Windows computers are 64 bit. Stefan made a 64-bit version of the "ptherads-win32" library himself, that is the one we also use for the fieldtrip buffer. That library and header files can be found in fieldtrip/realtime/buffer/pthreads-win64. It might also be that there is an official release of the pthreads library for win64, if there is, I suggest you use that instead of the fieldtrip version. An alternative might be to use mingw as a compiler: if I recall correctly it also includes pthreads. But then, I don't know how easy or hard it is to use the mingw compiler in combination with MATLAB. hope this helps, Robert PS yet another aspect is the peerslave.exe command line application that allows to start a slave prior to starting MATLAB. Although also for that one Stefan managed to get a version compiled, but I know that that version is buggy. Even the linux version is not 100% stable. At the time Stefan worked with us, it was decided not to spend time on resolving the windows bugs in command-line version. Therefore I suggest that you first focus on getting the mex file to work, and only then start thinking on whether you need the peerslave.exe command-line version. On 3 Feb 2012, at 16:06, Chad Bircher wrote: > I am trying to install the peer directories, but cannot run peercompile('VC') on my Windows7 64bit machine using Microsoft Visual C++ express 2012. I am getting an error that it cannot find pthread.h > I am not a systems developer, and do not know how to install this correctly. Every attempt I have made still does not allow peercompile to run. > How do I install pthread on this sort of a system? > Thank you > Chad > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue Feb 7 11:34:20 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 7 Feb 2012 10:34:20 +0000 Subject: [FieldTrip] Defining cfg.neighbourdist at source level In-Reply-To: <4F2941CC.6030609@charite.de> References: <4F22C422.4080906@charite.de> <4F26B91E.2050200@donders.ru.nl> <4F26BE42.5030204@charite.de> <4F2941CC.6030609@charite.de> Message-ID: <93BEC2B0-B372-4EA9-BE41-1D0606B217FF@donders.ru.nl> Dear Ulrich On 1 Feb 2012, at 13:44, Pomper, Ulrich wrote: > Dear Robert and Stephan, > Thank you for your replies. > I guess I use what Robert called the 'regular' 3D grid, but I'm not quite sure. ... > ldf = > > xgrid: [-65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68] > ygrid: [-107 -100 -93 -86 -79 -72 -65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68 75] > zgrid: [-52 -45 -38 -31 -24 -17 -10 -3 4 11 18 25 32 39 46 53 60 67 74 81] > dim: [20 27 20] > pos: [10800x3 double] ... > > In any case, I still don't quite understand how to calculate the neighbours to each voxel. Yes, you are using a regular 3D grid with dipole positions that are placed at the center of a large number of voxels which jointly fill a cube that spans the head. Just like an MRI. If you look in ldf.pos you will see all positions. Those positions form a 20x27x20 regular grid, with the x-, y, and z-values according to xgrid/ygrid/zgrid. You have a grid spacing of 7mm in each direction. The first positions is [-65 -107 -52] and its neighbours are the grid points that are 7mm to the right, top and front. Just think of it as functional_data = rand(20, 27, 20) i.e. a cube. It is clear for each voxel what the neighbours are. FieldTrip makes use of vectorization, i.e. the 3d matrix with the functional data can also be represented by MATLAB as a vector. functional_data = functional_data(:) What you then get is a vector of length 10800, i.e. matching all the [x y z] positions as they are specified in ldf.pos. > By saying that the "neighbours are trivial to find and you do not have to specify a structure", do you mean that I don't need to define the cfg.neighbours property at all (given that I do use a regular 3D grid)? correct. Robert From Ulrich.Pomper at charite.de Tue Feb 7 11:40:27 2012 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Tue, 7 Feb 2012 11:40:27 +0100 Subject: [FieldTrip] Defining cfg.neighbourdist at source level In-Reply-To: <93BEC2B0-B372-4EA9-BE41-1D0606B217FF@donders.ru.nl> References: <4F22C422.4080906@charite.de> <4F26B91E.2050200@donders.ru.nl> <4F26BE42.5030204@charite.de> <4F2941CC.6030609@charite.de> <93BEC2B0-B372-4EA9-BE41-1D0606B217FF@donders.ru.nl> Message-ID: <4F30FF9B.8080300@charite.de> Thanks a lot Robert, now I get it! Best, Ulrich On 07.02.2012 11:34, Robert Oostenveld wrote: Dear Ulrich On 1 Feb 2012, at 13:44, Pomper, Ulrich wrote: > Dear Robert and Stephan, > Thank you for your replies. > I guess I use what Robert called the 'regular' 3D grid, but I'm not quite sure. ... > ldf = > > xgrid: [-65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68] > ygrid: [-107 -100 -93 -86 -79 -72 -65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68 75] > zgrid: [-52 -45 -38 -31 -24 -17 -10 -3 4 11 18 25 32 39 46 53 60 67 74 81] > dim: [20 27 20] > pos: [10800x3 double] ... > > In any case, I still don't quite understand how to calculate the neighbours to each voxel. Yes, you are using a regular 3D grid with dipole positions that are placed at the center of a large number of voxels which jointly fill a cube that spans the head. Just like an MRI. If you look in ldf.pos you will see all positions. Those positions form a 20x27x20 regular grid, with the x-, y, and z-values according to xgrid/ygrid/zgrid. You have a grid spacing of 7mm in each direction. The first positions is [-65 -107 -52] and its neighbours are the grid points that are 7mm to the right, top and front. Just think of it as functional_data = rand(20, 27, 20) i.e. a cube. It is clear for each voxel what the neighbours are. FieldTrip makes use of vectorization, i.e. the 3d matrix with the functional data can also be represented by MATLAB as a vector. functional_data = functional_data(:) What you then get is a vector of length 10800, i.e. matching all the [x y z] positions as they are specified in ldf.pos. > By saying that the "neighbours are trivial to find and you do not have to specify a structure", do you mean that I don't need to define the cfg.neighbours property at all (given that I do use a regular 3D grid)? correct. Robert _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue Feb 7 11:42:57 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 7 Feb 2012 10:42:57 +0000 Subject: [FieldTrip] Defining cfg.neighbourdist at source level In-Reply-To: <61FDD8CB-F79B-48A6-BC19-015F778A4945@psi.ucm.es> References: <4F22C422.4080906@charite.de> <4F26B91E.2050200@donders.ru.nl> <4F26BE42.5030204@charite.de> <61FDD8CB-F79B-48A6-BC19-015F778A4945@psi.ucm.es> Message-ID: <8AD16232-88F0-4C2E-87FA-03D22928B940@donders.ru.nl> Dear Stephan In fieldtrip/rpivate/clusterstat around line 194 you can see posclusobs = findcluster(reshape(postailobs, [cfg.dim,1]),channeighbstructmat,cfg.minnbchan); that is the section that should get used (the present code still thinks that source is always a 3d regular grid, which is not the case for a surface grid) Furthermore, in ft_prepare_neighbours there is the subfunction "compneighbstructfromtri" that is of relevance. This is a section of the code that needs to be cleaned up and the clustering along the sheet should become a standard feature instead of something that can be managed by a hack. Concrete code suggestions (evt. through bugzilla.fcdonders.nl) are welcome. best Robert On 31 Jan 2012, at 20:48, smoratti at psi.ucm.es wrote: > Dear Robert, > > To do clustering on a 3D source surface I always had to "trick" field trip and squeezed the 3D source surface data into a ERF structure treating the 3D surface points as sensors. Then by triangulation I found the neighbors. However, if there is a more elegant method implemented in ft_sourcestatistc, I would be very interested to know how to do it. Where can I find some hints on that? > > Best, > > Stephan > > ________________________________________________________ > Stephan Moratti, PhD > > see also: http://web.me.com/smoratti/ > > Universidad Complutense de Madrid > Facultad de Psicología > Departamento de Psicología Básica I > Campus de Somosaguas > 28223 Pozuelo de Alarcón (Madrid) > Spain > > and > > Center for Biomedical Technology > Laboratory for Cognitive and Computational Neuroscience > Parque Científico y Tecnológico de la Universidad Politecnica de Madrid > Campus Montegancedo > 28223 Pozuelo de Alarcón (Madrid) > Spain > > > email: smoratti at psi.ucm.es > Tel.: +34 679219982 > > El 31/01/2012, a las 15:37, Robert Oostenveld escribió: > >> Dear Ulrich >> >> If your source locations are defined on a regular 3D grid that can be represented as volume, then the neighbours are trivial to find and you do not have to specify a structure for the neighbours. >> >> If you have done source reconstruction on a 3D folded cortical sheet that is defined by a triangulated surface, then it is also possible to cluster along the surface. I don't know the details for the cortical sheet clustering from the top of my head, if you are interested please let me know and I'll look them up. >> >> best >> Robert >> >> >> >> >> On 30 Jan 2012, at 16:58, Pomper, Ulrich wrote: >> >>> Dear Jörn, >>> Thanks for you reply. I did mean source-level, so like you said, I am trying to define the neighbouring voxels for each voxel. >>> As far as I understand, leaving cfg.neighbours blank means that the clustering is done over the time and frequency dimensions only, not over space. >>> The FT help reads: >>> %If you specify an empty neighbourhood structure, clustering will only be done in frequency and time (if available) and not over neighbouring channels. >>> >>> Has anybody done clustering in source space using all three dimensions and could explain how this works? >>> Cheers, >>> Ulrich >>> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Wed Feb 8 17:14:17 2012 From: lihqih at gmail.com (qi li) Date: Wed, 8 Feb 2012 11:14:17 -0500 Subject: [FieldTrip] coordinate transform Message-ID: Hi, I want to do a coordinate transformation of the sensor positions by knowing the fiducial point(na,lpa,rpa). Is there any function can do this? More specifically I want to know the 3 translational and 3 rotational degree changes between the original coordinate and the changed one. Thanks a lot! Qi From adama.sophie at gmail.com Wed Feb 8 18:03:12 2012 From: adama.sophie at gmail.com (Sophie ADAMA) Date: Wed, 8 Feb 2012 18:03:12 +0100 Subject: [FieldTrip] signal acquisition with Biosemi Message-ID: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> Hi, I am trying to use the acquisition program acquire.m with Biosemi but I get the following error. ??? Undefined function or method 'gdfdatatype' for input arguments of type 'char'. Error in ==> acquire at 51 [datatyp,limits,datatypes,HDR.Bits,HDR.GDFTYP]=gdfdatatype('int32'); There is no gdfdatatype function in the toolbox. What should I do? Can somebody help me, please ? Sophie -------------- next part -------------- An HTML attachment was scrubbed... URL: From tomh at kurage.nimh.nih.gov Wed Feb 8 18:17:53 2012 From: tomh at kurage.nimh.nih.gov (Tom Holroyd (NIH/NIMH) [E]) Date: Wed, 08 Feb 2012 12:17:53 -0500 Subject: [FieldTrip] coordinate transform In-Reply-To: References: Message-ID: <4F32AE41.1030907@kurage.nimh.nih.gov> Here is a function that creates the fiducial basis. You can use it to transform the sensor coordinates into head coordinates. There are lots of comments. Oh, it's written in Python. qi li wrote: > Hi, > > I want to do a coordinate transformation of the sensor positions by > knowing the fiducial point(na,lpa,rpa). Is there any function can do > this? More specifically I want to know the 3 translational and 3 > rotational degree changes between the original coordinate and the > changed one. > > Thanks a lot! > > Qi > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- "The test of a first-rate intelligence is the ability to hold two opposed ideas in the mind at the same time, and still retain the ability to function." — F. Scott Fitzgerald -------------- next part -------------- A non-text attachment was scrubbed... Name: fid.py Type: application/x-python Size: 1651 bytes Desc: not available URL: From gonzalo.rojas.costa at gmail.com Wed Feb 8 20:13:13 2012 From: gonzalo.rojas.costa at gmail.com (Gonzalo Rojas Costa) Date: Wed, 8 Feb 2012 16:13:13 -0300 Subject: [FieldTrip] Cadwell EASY 3 (.ez3) format Message-ID: Hi: How can I read some Cadwell Easy 3 (.ez3) format files that I have ?... Any converter ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Clinica Las Condes Santiago Chile From hamzaf at sabanciuniv.edu Thu Feb 9 06:16:26 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Thu, 9 Feb 2012 07:16:26 +0200 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> Message-ID: Yes, I faced that problem before. I searched for the function and found it in https://sccn.ucsd.edu/svn/software/tags/EEGLAB7_0_1_5beta/external/fieldtrip-20090727/external/biosig/gdfdatatype.m But also I did face another problem after that as I remember. Could you check and tell us the result? Best, Hamza On Wed, Feb 8, 2012 at 7:03 PM, Sophie ADAMA wrote: > Hi,**** > > ** ** > > I am trying to use the acquisition program *acquire.m* with Biosemi but I > get the following error.**** > > ** ** > > ** ** > > *??? Undefined function or method 'gdfdatatype' for input arguments of > type 'char'.* > > * * > > *Error in ==> acquire at 51* > > *[datatyp,limits,datatypes,HDR.Bits,HDR.GDFTYP]=gdfdatatype('int32');* > > ** ** > > There is no *gdfdatatype* function in the toolbox.**** > > **** > > What should I do? Can somebody help me, please ?**** > > ** ** > > Sophie**** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Feb 9 09:23:45 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 9 Feb 2012 09:23:45 +0100 Subject: [FieldTrip] coordinate transform In-Reply-To: References: Message-ID: <83467D5B-606E-40AF-B407-D8CD0F3F2AC1@donders.ru.nl> Hi Qi, Could you be a bit more specific? In what coordinate system are the fiducials defined? MRI-voxel space? MEG-dewar space? Something else? There is a headcoordinates function in fieldtrip/private, which is computing a 4x4 affine transformation matrix for you (from which the rotation and translation can be determined). The high level fieldtrip functions you may want to look into are ft_electroderealign, or ft_volumerealign. Best, Jan-Mathijs On Feb 8, 2012, at 5:14 PM, qi li wrote: > Hi, > > I want to do a coordinate transformation of the sensor positions by > knowing the fiducial point(na,lpa,rpa). Is there any function can do > this? More specifically I want to know the 3 translational and 3 > rotational degree changes between the original coordinate and the > changed one. > > Thanks a lot! > > Qi > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Feb 9 15:41:23 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 9 Feb 2012 14:41:23 +0000 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> Message-ID: Dear Sophie and Hamza the acquire script that is present in the fieldtrip/realtime/acquisition/biosemi directory is only an example script that was written for initial testing. It acquires data in MATLAB, processes it and writes to a file. I believe that the normal way of acquiring data for biosemi is to run the biosemi2ft.exe application, i.e. not in MATLAB. Philip (CC) should be able to tell what the the normal use is, they do this in their lab every day. best Robert On 9 Feb 2012, at 5:16, Hamza Fawzi Altakroury (Student) wrote: > Yes, I faced that problem before. > > I searched for the function and found it in > > https://sccn.ucsd.edu/svn/software/tags/EEGLAB7_0_1_5beta/external/fieldtrip-20090727/external/biosig/gdfdatatype.m > > But also I did face another problem after that as I remember. Could you check and tell us the result? > > Best, > > Hamza > > On Wed, Feb 8, 2012 at 7:03 PM, Sophie ADAMA wrote: > Hi, > > > > I am trying to use the acquisition program acquire.m with Biosemi but I get the following error. > > > > > > ??? Undefined function or method 'gdfdatatype' for input arguments of type 'char'. > > > > Error in ==> acquire at 51 > > [datatyp,limits,datatypes,HDR.Bits,HDR.GDFTYP]=gdfdatatype('int32'); > > > > There is no gdfdatatype function in the toolbox. > > > What should I do? Can somebody help me, please ? > > > > Sophie > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Feb 9 17:56:06 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 9 Feb 2012 16:56:06 +0000 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> <09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl> Message-ID: <8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl> On behalf of Philip... On 9 Feb 2012, at 15:31, Philip van den Broek wrote: > Dear Sophie and Hamza, > > The connection between the Biosemi Active2 system and the FieldTrip buffer is handled by interfacing software biosemi2ft (part of fieldtrip), and should be started from the terminal (mac) or command prompt (windows). > > The interfacing software is located in the FieldTrip folder: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > > The BioSemi system needs a configuration (.cfg) file in which some acquisition-related settings are specified. Configuration files for the BioSemi system specify for example from how many channels data should be streamed and/or recorded, and whether the data should be downsampled. For more information about configuration files for different acquisition systems, see the Fieldtrip website. > > To start the buffer that connects to the Biosemi Active2, open the terminal (Mac) or command prompt (PC) and in the folder where you would like to save your data execute (change path according to your system and location of fieldtrip toolbox): > > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > > : configuration file > : base name of the gdf file. The suffix .gdf and session counters will be added automatically. > : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) > : optional, default is 1972 > an example: > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 > Note that the manually specified name of the file will overwrite any existing file, so make sure myfile.gdf doesn't exist. > > Once this is running, you get access to the data through the fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip fileio functions give you access to the data: > ft_read_header('buffer://localhost:1972'), or > ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100,........ > For further information, see fieldtrip website. > (more info on how we use the system at our department can be found here: http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) > > Hope this helps you to get things running in your place. If you have any further questions, just let me know. > > Best regards, > > > Philip van den Broek > Radboud University Nijmegen > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > > P.O. Box 9104, 6500 HE Nijmegen > Montessorilaan 3, 6525 HR Nijmegen > The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From adama.sophie at gmail.com Thu Feb 9 20:37:09 2012 From: adama.sophie at gmail.com (Sophie ADAMA) Date: Thu, 09 Feb 2012 20:37:09 +0100 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> <09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl> <8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl> Message-ID: <4F342065.8050707@gmail.com> Hi, Thanks for your response. I tried that but I get this: *command not found*. I am using Mac OS Lion. Any suggestions? Thanks Sophie Le 09.02.12 17:56, Robert Oostenveld a écrit : > On behalf of Philip... > > > On 9 Feb 2012, at 15:31, Philip van den Broek wrote: > >> Dear Sophie and Hamza, >> >> The connection between the Biosemi Active2 system and the FieldTrip >> buffer is handled by interfacing software biosemi2ft (part of >> fieldtrip), and should be started from the terminal (mac) or command >> prompt (windows). >> >> The interfacing software is located in the FieldTrip folder: >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft >> >> The BioSemi system needs a configuration (.cfg) file in which some >> acquisition-related settings are specified. Configuration files for >> the BioSemi system specify for example from how many channels data >> should be streamed and/or recorded, and whether the data should be >> downsampled. For more information about configuration files for >> different acquisition systems, see the Fieldtrip website >> . >> >> To start the buffer that connects to the Biosemi Active2, open the >> terminal (Mac) or command prompt (PC) and in the folder where you >> would like to save your data execute (change path according to your >> system and location of fieldtrip toolbox): >> >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft >> >> : configuration file >> : base name of the gdf file. The suffix .gdf and session counters will be added automatically. >> : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) >> : optional, default is 1972 >> an example: >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 >> >> Note that the manually specified name of the file will overwrite any >> existing file, so make sure myfile.gdf doesn't exist. >> >> Once this is running, you get access to the data through the >> fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip >> fileio functions give you access to the data: >> ft_read_header('buffer://localhost:1972' >> ), or >> ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100 >> ,........ >> For further information, see fieldtrip website. >> >> (more info on how we use the system at our department can be found >> here: >> http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) >> >> Hope this helps you to get things running in your place. If you have >> any further questions, just let me know. >> >> Best regards, >> >> >> Philip van den Broek >> Radboud University Nijmegen >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognition >> >> P.O. Box 9104, 6500 HE Nijmegen >> Montessorilaan 3, 6525 HR Nijmegen >> The Netherlands > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From akiko.ikkai at gmail.com Thu Feb 9 23:04:30 2012 From: akiko.ikkai at gmail.com (Akiko Ikkai) Date: Thu, 9 Feb 2012 17:04:30 -0500 Subject: [FieldTrip] volume conduction model missing .mat Message-ID: Hi, I'm trying to create a volume conduction model for my EEG study based on anatomical MRI, and having trouble with ft_prepare_bemmodel when I run cfg = []; cfg.tissue = [7 4 1]; % value for brain, skull, and scalp cfg.conductivity = [1 1/80 1]*.33; % after standard_BEM.zip data cfg.isolatedsource = true; cfg.method = 'dipoli'; cfg.sourceunits = 'mm'; cfg.mriunits = 'mm'; vol = ft_prepare_bemmodel(cfg, seg4bem); I get the following error message while ft_prepare_bemmodel is running: Fatal error in dipoli: interface /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect at vertex 1402 of /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri Warning: an error ocurred while running dipoli > In dipoli at 94 In ft_prepare_bemmodel at 112 Error using ==> fread Invalid file identifier. Use fopen to generate a valid file identifier. Warning: File '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' not found. > In dipoli at 102 In ft_prepare_bemmodel at 112 and the output vol is missing .mat, which causes an error during ft_sourceanalysis. >> vol vol = cond: [0.3300 0.0041 0.3300] bnd: [1x3 struct] source: 3 skin_surface: 3 skin: 1 type: 'dipoli' Does anyone know how to correct for "fatal error" so that ft_prepare_bemmodel creates the correct volume conduction model? I opened .tri file and removed line 1402, but got the same results. Thanks in advance! Akiko -- Akiko Ikkai, Ph.D. Postdoctoral Fellow Department of Psychological and Brain Sciences Johns Hopkins University Ames Hall, 3400 N. Charles St. Baltimore, MD 21218 -------------- next part -------------- An HTML attachment was scrubbed... URL: From phc5 at georgetown.edu Thu Feb 9 23:15:30 2012 From: phc5 at georgetown.edu (patrick cox) Date: Thu, 9 Feb 2012 17:15:30 -0500 Subject: [FieldTrip] volume conduction model missing .mat In-Reply-To: References: Message-ID: Hi Akiko, I had that same problem and also tried using the 'bemcp' which gave me a vol.mat file that was all NaNs. I did not figure out how to solve the problem in FT directly, but have been having some success creating the head model in SPM and loading that into FeildTrip. The SPM manual helped me. Hope that is somewhat helpful, Pat Patrick Cox Prethesis Student Lab For Computational Cognitive Science Georgetown University Medical Center 3970 Reservoir Rd. NW Washington, DC 20007 On Thu, Feb 9, 2012 at 5:04 PM, Akiko Ikkai wrote: > Hi, > > I'm trying to create a volume conduction model for my EEG study based on > anatomical MRI, and having trouble with ft_prepare_bemmodel > > when I run > cfg = []; > cfg.tissue = [7 4 1]; % value for brain, skull, and scalp > cfg.conductivity = [1 1/80 1]*.33; % after standard_BEM.zip data > cfg.isolatedsource = true; > cfg.method = 'dipoli'; > cfg.sourceunits = 'mm'; > cfg.mriunits = 'mm'; > vol = ft_prepare_bemmodel(cfg, seg4bem); > > I get the following error message while ft_prepare_bemmodel is running: > > Fatal error in dipoli: interface > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and > /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect > at vertex 1402 of /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri > > Warning: an error ocurred while running dipoli > > In dipoli at 94 > In ft_prepare_bemmodel at 112 > Error using ==> fread > Invalid file identifier. Use fopen to generate a valid file identifier. > Warning: File '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' not > found. > > In dipoli at 102 > In ft_prepare_bemmodel at 112 > > > and the output vol is missing .mat, which causes an error > during ft_sourceanalysis. > >> vol > vol = > cond: [0.3300 0.0041 0.3300] > bnd: [1x3 struct] > source: 3 > skin_surface: 3 > skin: 1 > type: 'dipoli' > > Does anyone know how to correct for "fatal error" so > that ft_prepare_bemmodel creates the correct volume conduction model? I > opened .tri file and removed line 1402, but got the same results. > > Thanks in advance! Akiko > > -- > Akiko Ikkai, Ph.D. > Postdoctoral Fellow > Department of Psychological and Brain Sciences > Johns Hopkins University > Ames Hall, 3400 N. Charles St. > Baltimore, MD 21218 > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Fri Feb 10 06:26:22 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Fri, 10 Feb 2012 07:26:22 +0200 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <4F342065.8050707@gmail.com> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> <09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl> <8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl> <4F342065.8050707@gmail.com> Message-ID: Hello, I tried the biosemi2tf.exe command it works well on Windows. But, unfortunately I don't know about the Mac OS. Best, Hamza On Thu, Feb 9, 2012 at 9:37 PM, Sophie ADAMA wrote: > Hi, > > Thanks for your response. > > I tried that but I get this: *command not found*. I am using Mac OS Lion. > > Any suggestions? > > Thanks > > Sophie > > Le 09.02.12 17:56, Robert Oostenveld a écrit : > > On behalf of Philip... > > > On 9 Feb 2012, at 15:31, Philip van den Broek wrote: > > Dear Sophie and Hamza, > > The connection between the Biosemi Active2 system and the FieldTrip buffer > is handled by interfacing software biosemi2ft (part of fieldtrip), and > should be started from the terminal (mac) or command prompt (windows). > > The interfacing software is located in the FieldTrip folder: > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > > The BioSemi system needs a configuration (.cfg) file in which some > acquisition-related settings are specified. Configuration files for the > BioSemi system specify for example from how many channels data should be > streamed and/or recorded, and whether the data should be downsampled. For > more information about configuration files for different acquisition > systems, see the Fieldtrip website > . > > To start the buffer that connects to the Biosemi Active2, open the > terminal (Mac) or command prompt (PC) and in the folder where you would > like to save your data execute (change path according to your system and > location of fieldtrip toolbox): > > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > > : configuration file > : base name of the gdf file. The suffix .gdf and session counters will be added automatically. > : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) > : optional, default is 1972 > > an example: > > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 > > Note that the manually specified name of the file will overwrite any > existing file, so make sure myfile.gdf doesn't exist. > Once this is running, you get access to the data through the fieldtrip > buffer filled with data by biosemi2ft, i.e., fieldtrip fileio functions > give you access to the data: > ft_read_header('buffer://localhost:1972'), or > ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100 > ,........ > For further information, see fieldtrip website. > > (more info on how we use the system at our department can be found here: > http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation > ) > > Hope this helps you to get things running in your place. If you have any > further questions, just let me know. > > Best regards, > > Philip van den Broek > Radboud University Nijmegen > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > > P.O. Box 9104, 6500 HE Nijmegen > Montessorilaan 3, 6525 HR Nijmegen > The Netherlands > > > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at mac.com Fri Feb 10 09:00:44 2012 From: nathanweisz at mac.com (Nathan Weisz) Date: Fri, 10 Feb 2012 09:00:44 +0100 Subject: [FieldTrip] volume conduction model missing .mat In-Reply-To: References: Message-ID: <2341406D-6422-4FD3-AD3C-73D1BF70B6CF@mac.com> Hi Akiki, I am not a headmodel expert. but looking at the output message, it seems your segementation did not go too well (see the "intersect" message). my intuition is then then the next temporary file *.ama is not created and ft_prepare_bemmodel then simply says ciao. perhaps you want to check / redo the segmentation? good luck, nathan On 09.02.2012, at 23:04, Akiko Ikkai wrote: > Hi, > > I'm trying to create a volume conduction model for my EEG study based on anatomical MRI, and having trouble with ft_prepare_bemmodel > > when I run > cfg = []; > cfg.tissue = [7 4 1]; % value for brain, skull, and scalp > cfg.conductivity = [1 1/80 1]*.33; % after standard_BEM.zip data > cfg.isolatedsource = true; > cfg.method = 'dipoli'; > cfg.sourceunits = 'mm'; > cfg.mriunits = 'mm'; > vol = ft_prepare_bemmodel(cfg, seg4bem); > > I get the following error message while ft_prepare_bemmodel is running: > > Fatal error in dipoli: interface /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect > at vertex 1402 of /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri > > Warning: an error ocurred while running dipoli > > In dipoli at 94 > In ft_prepare_bemmodel at 112 > Error using ==> fread > Invalid file identifier. Use fopen to generate a valid file identifier. > Warning: File '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' not > found. > > In dipoli at 102 > In ft_prepare_bemmodel at 112 > > > and the output vol is missing .mat, which causes an error during ft_sourceanalysis. > >> vol > vol = > cond: [0.3300 0.0041 0.3300] > bnd: [1x3 struct] > source: 3 > skin_surface: 3 > skin: 1 > type: 'dipoli' > > Does anyone know how to correct for "fatal error" so that ft_prepare_bemmodel creates the correct volume conduction model? I opened .tri file and removed line 1402, but got the same results. > > Thanks in advance! Akiko > > -- > Akiko Ikkai, Ph.D. > Postdoctoral Fellow > Department of Psychological and Brain Sciences > Johns Hopkins University > Ames Hall, 3400 N. Charles St. > Baltimore, MD 21218 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.piantoni at nin.knaw.nl Fri Feb 10 10:36:20 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Fri, 10 Feb 2012 10:36:20 +0100 Subject: [FieldTrip] volume conduction model missing .mat In-Reply-To: <2341406D-6422-4FD3-AD3C-73D1BF70B6CF@mac.com> References: <2341406D-6422-4FD3-AD3C-73D1BF70B6CF@mac.com> Message-ID: Hi Akiki and Patrick, I agree with Nathan about segmentation problems. I had the same problem when two of the three meshes intersected each other. Before you run the forward model, you should check the segmentation (bnd) using ft_plot_mesh. ft_plot_mesh(bnd(1), 'facealpha', .5) hold on ft_plot_mesh(bnd(2), 'facecolor', 'r') You will see that the two meshes intersect with each other. Depending on how you created the meshes, you should fix the parameters in such a way that they don't intersect. For example, ft_volumesegment has a cfg.threshold option (you can check how the segmentation went with ft_sourceplot) and ft_prepare_mesh_new has cfg.thresholdseg and cfg.smoothseg. I think that the meshes in SPM are computed on an (affine-transformed) template and not on the anatomically derived meshes. The template is more robust and that's why the two surfaces do not intersect. In general, the segmentation depends on the quality of your MRIs and you should really visually check the segmentation and meshes. When those look ok, the BEM forward model usually works. Hope this helps. Cheers, Gio On Fri, Feb 10, 2012 at 09:00, Nathan Weisz wrote: > Hi Akiki, > > I am not a headmodel expert. > but looking at the output message, it seems your segementation did not go > too well (see the "intersect" message). my intuition is then then the next > temporary file *.ama is not created and ft_prepare_bemmodel then simply says > ciao. > > perhaps you want to check / redo the segmentation? > > good luck, > nathan > > > On 09.02.2012, at 23:04, Akiko Ikkai wrote: > > Hi, > > I'm trying to create a volume conduction model for my EEG study based on > anatomical MRI, and having trouble with ft_prepare_bemmodel > > when I run > cfg                = []; > cfg.tissue         = [7 4 1]; % value for brain, skull, and scalp > cfg.conductivity   = [1 1/80 1]*.33; % after standard_BEM.zip data > cfg.isolatedsource = true; > cfg.method         = 'dipoli'; > cfg.sourceunits = 'mm'; > cfg.mriunits = 'mm'; > vol = ft_prepare_bemmodel(cfg, seg4bem); > > I get the following error message while ft_prepare_bemmodel is running: > > Fatal error in dipoli:  interface > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and > /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect >  at vertex 1402 of /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri > > Warning: an error ocurred while running dipoli >> In dipoli at 94 >   In ft_prepare_bemmodel at 112 > Error using ==> fread > Invalid file identifier.  Use fopen to generate a valid file identifier. > Warning: File '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' not > found. >> In dipoli at 102 >   In ft_prepare_bemmodel at 112 > > > and the output vol is missing .mat, which causes an error > during ft_sourceanalysis. >>> vol > vol = >             cond: [0.3300 0.0041 0.3300] >              bnd: [1x3 struct] >           source: 3 >     skin_surface: 3 >             skin: 1 >             type: 'dipoli' > > Does anyone know how to correct for "fatal error" so > that ft_prepare_bemmodel creates the correct volume conduction model? I > opened .tri file and removed line 1402, but got the same results. > > Thanks in advance! Akiko > > -- > Akiko Ikkai, Ph.D. > Postdoctoral Fellow > Department of Psychological and Brain Sciences > Johns Hopkins University > Ames Hall, 3400 N. Charles St. > Baltimore, MD 21218 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From adama.sophie at gmail.com Fri Feb 10 14:53:48 2012 From: adama.sophie at gmail.com (Sophie ADAMA) Date: Fri, 10 Feb 2012 14:53:48 +0100 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> <09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl> <8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl> <4F342065.8050707@gmail.com> Message-ID: <016201cce7fb$6a4b9e90$3ee2dbb0$@gmail.com> Hi, I tried it on Windows too, and it works perfectly. But I’m a Mac girl J and I will be happy if someone could help me. Thank you From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) Sent: vendredi 10 février 2012 06:26 To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] signal acquisition with Biosemi Hello, I tried the biosemi2tf.exe command it works well on Windows. But, unfortunately I don't know about the Mac OS. Best, Hamza On Thu, Feb 9, 2012 at 9:37 PM, Sophie ADAMA wrote: Hi, Thanks for your response. I tried that but I get this: command not found. I am using Mac OS Lion. Any suggestions? Thanks Sophie Le 09.02.12 17:56, Robert Oostenveld a écrit : On behalf of Philip... On 9 Feb 2012, at 15:31, Philip van den Broek wrote: Dear Sophie and Hamza, The connection between the Biosemi Active2 system and the FieldTrip buffer is handled by interfacing software biosemi2ft (part of fieldtrip), and should be started from the terminal (mac) or command prompt (windows). The interfacing software is located in the FieldTrip folder: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft The BioSemi system needs a configuration (.cfg) file in which some acquisition-related settings are specified. Configuration files for the BioSemi system specify for example from how many channels data should be streamed and/or recorded, and whether the data should be downsampled. For more information about configuration files for different acquisition systems, see the Fieldtrip website . To start the buffer that connects to the Biosemi Active2, open the terminal (Mac) or command prompt (PC) and in the folder where you would like to save your data execute (change path according to your system and location of fieldtrip toolbox): ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft : configuration file : base name of the gdf file. The suffix .gdf and session counters will be added automatically. : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) : optional, default is 1972 an example: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 Note that the manually specified name of the file will overwrite any existing file, so make sure myfile.gdf doesn't exist. Once this is running, you get access to the data through the fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip fileio functions give you access to the data: ft_read_header('buffer://localhost:1972'), or ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100,........ For further information, see fieldtrip website. (more info on how we use the system at our department can be found here: http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) Hope this helps you to get things running in your place. If you have any further questions, just let me know. Best regards, Philip van den Broek Radboud University Nijmegen Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104, 6500 HE Nijmegen Montessorilaan 3, 6525 HR Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From elilife at gmail.com Fri Feb 10 15:34:45 2012 From: elilife at gmail.com (Eliana Garcia) Date: Fri, 10 Feb 2012 15:34:45 +0100 Subject: [FieldTrip] elilife@gmail.com Message-ID: -- Eliana García Cossio Applied Neurotechnology Lab. Graduate School of Neural and Behavioral Science - Max Planck Research School Institute of Medical Psychology and Behavioral Neurobiology Universität Tübingen (+0049) 01 577-8587604 Otfried-Müller-Str. 47, 72076 Tübingen- Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.severens at maartenskliniek.nl Fri Feb 10 15:46:07 2012 From: m.severens at maartenskliniek.nl (Severens, Marianne) Date: Fri, 10 Feb 2012 15:46:07 +0100 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <016201cce7fb$6a4b9e90$3ee2dbb0$@gmail.com> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com><09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl><8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl><4F342065.8050707@gmail.com> <016201cce7fb$6a4b9e90$3ee2dbb0$@gmail.com> Message-ID: <70FC3ACFFB46314EBEAF9101EA45F50E06D8EC7A0C@smkexch02.maartenskliniek.nl> Hi Sophie Are you sure that the correct version of the biosemi2ft (so the one for the mac) is in the folder that you are specifying? Maybe you can try it first without the optional parameters, so just ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft Best, Marianne From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Sophie ADAMA Sent: vrijdag 10 februari 2012 14:54 To: 'Email discussion list for the FieldTrip project' Subject: Re: [FieldTrip] signal acquisition with Biosemi Hi, I tried it on Windows too, and it works perfectly. But I’m a Mac girl ☺ and I will be happy if someone could help me. Thank you From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) Sent: vendredi 10 février 2012 06:26 To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] signal acquisition with Biosemi Hello, I tried the biosemi2tf.exe command it works well on Windows. But, unfortunately I don't know about the Mac OS. Best, Hamza On Thu, Feb 9, 2012 at 9:37 PM, Sophie ADAMA > wrote: Hi, Thanks for your response. I tried that but I get this: command not found. I am using Mac OS Lion. Any suggestions? Thanks Sophie Le 09.02.12 17:56, Robert Oostenveld a écrit : On behalf of Philip... On 9 Feb 2012, at 15:31, Philip van den Broek wrote: Dear Sophie and Hamza, The connection between the Biosemi Active2 system and the FieldTrip buffer is handled by interfacing software biosemi2ft (part of fieldtrip), and should be started from the terminal (mac) or command prompt (windows). The interfacing software is located in the FieldTrip folder: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft The BioSemi system needs a configuration (.cfg) file in which some acquisition-related settings are specified. Configuration files for the BioSemi system specify for example from how many channels data should be streamed and/or recorded, and whether the data should be downsampled. For more information about configuration files for different acquisition systems, see the Fieldtrip website. To start the buffer that connects to the Biosemi Active2, open the terminal (Mac) or command prompt (PC) and in the folder where you would like to save your data execute (change path according to your system and location of fieldtrip toolbox): ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft : configuration file : base name of the gdf file. The suffix .gdf and session counters will be added automatically. : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) : optional, default is 1972 an example: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 Note that the manually specified name of the file will overwrite any existing file, so make sure myfile.gdf doesn't exist. Once this is running, you get access to the data through the fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip fileio functions give you access to the data: ft_read_header('buffer://localhost:1972'), or ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100,........ For further information, see fieldtrip website. (more info on how we use the system at our department can be found here: http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) Hope this helps you to get things running in your place. If you have any further questions, just let me know. Best regards, Philip van den Broek Radboud University Nijmegen Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104, 6500 HE Nijmegen Montessorilaan 3, 6525 HR Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University ________________________________ Disclaimer Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. Sint Maartenskliniek Hengstdal 3, 6574 NA Ubbergen (bij Nijmegen) Telefoon 024-3659 911 Telefax 024-3659 204 KvK nummer 41055111 -------------- next part -------------- An HTML attachment was scrubbed... URL: From isabella.premoli at gmail.com Fri Feb 10 15:48:24 2012 From: isabella.premoli at gmail.com (isabella premoli) Date: Fri, 10 Feb 2012 15:48:24 +0100 Subject: [FieldTrip] TMS-EEG data analysis Message-ID: Dear FieldTrip community, My name is Isabella and I have just started using FieldTrip to analyze TMS-EEG data. I was wondering whether the Donders Institute will provide courses on FieldTrip regarding this specific analysis. In case the answer is positive, I would be very happy to join. Cheers, Isabella -- Isabella Premoli, PhD student Motor Cortex Laboratory Schleusenweg 2-16 D-60528 Frankfurt am Main Tel: +49-69-6301-83826 -------------- next part -------------- An HTML attachment was scrubbed... URL: From elilife at gmail.com Fri Feb 10 16:26:46 2012 From: elilife at gmail.com (Eliana Garcia) Date: Fri, 10 Feb 2012 16:26:46 +0100 Subject: [FieldTrip] wPLI and analysis of band frequencies Message-ID: Hello! I am currently trying to analyze my data using the wPLI. However I would like to do a band frequency analysis i.e calculate a wPLI value for example for the beta band, but this is not possible since the wPLI is calculated for a time window (according to the time-frequency transformation resolution) and for a certain specific frequency across trials. Guggisberg et al ('Mapping functional connectivity in Patients with Brain lesions') solved this problem in the case of coherence, calculating the sum of autospectra and sum of cross-spectra of the corresponding frequency bins. However, I think that this approach will influence a lot false negatives in the case of the wPLI, since the shifts of phases for the components of the certain band can somehow cancel to each other. Another idea could be to calculate the wPLI for each frequency bin and then average across the band frequency, but I am not sure if this will be really representative of functional connectivity for this band. I still have no clue and what could be the best approach. Thank you so much, -- Eliana García Cossio Applied Neurotechnology Lab. Graduate School of Neural and Behavioral Science - Max Planck Research School Institute of Medical Psychology and Behavioral Neurobiology Universität Tübingen -------------- next part -------------- An HTML attachment was scrubbed... URL: From adama.sophie at gmail.com Sat Feb 11 18:29:33 2012 From: adama.sophie at gmail.com (Sophie ADAMA) Date: Sat, 11 Feb 2012 18:29:33 +0100 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <70FC3ACFFB46314EBEAF9101EA45F50E06D8EC7A0C@smkexch02.maartenskliniek.nl> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com><09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl><8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl><4F342065.8050707@gmail.com> <016201cce7fb$6a4b9e90$3ee2dbb0$@gmail.com> <70FC3ACFFB46314EBEAF9101EA45F50E06D8EC7A0C@smkexch02.maartenskliniek.nl> Message-ID: <002101cce8e2$bb478060$31d68120$@gmail.com> Hi Marianne, There are 3 biosemi2ft in that folder : biosemi2ft.cc, biosemi2ft.exe and biosemi2ft.maci; but when I type ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft in the command line, it says No such file or directory. Sophie From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Severens, Marianne Sent: vendredi 10 février 2012 15:46 To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] signal acquisition with Biosemi Hi Sophie Are you sure that the correct version of the biosemi2ft (so the one for the mac) is in the folder that you are specifying? Maybe you can try it first without the optional parameters, so just ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft Best, Marianne From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Sophie ADAMA Sent: vrijdag 10 februari 2012 14:54 To: 'Email discussion list for the FieldTrip project' Subject: Re: [FieldTrip] signal acquisition with Biosemi Hi, I tried it on Windows too, and it works perfectly. But I’m a Mac girl J and I will be happy if someone could help me. Thank you From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) Sent: vendredi 10 février 2012 06:26 To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] signal acquisition with Biosemi Hello, I tried the biosemi2tf.exe command it works well on Windows. But, unfortunately I don't know about the Mac OS. Best, Hamza On Thu, Feb 9, 2012 at 9:37 PM, Sophie ADAMA wrote: Hi, Thanks for your response. I tried that but I get this: command not found. I am using Mac OS Lion. Any suggestions? Thanks Sophie Le 09.02.12 17:56, Robert Oostenveld a écrit : On behalf of Philip... On 9 Feb 2012, at 15:31, Philip van den Broek wrote: Dear Sophie and Hamza, The connection between the Biosemi Active2 system and the FieldTrip buffer is handled by interfacing software biosemi2ft (part of fieldtrip), and should be started from the terminal (mac) or command prompt (windows). The interfacing software is located in the FieldTrip folder: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft The BioSemi system needs a configuration (.cfg) file in which some acquisition-related settings are specified. Configuration files for the BioSemi system specify for example from how many channels data should be streamed and/or recorded, and whether the data should be downsampled. For more information about configuration files for different acquisition systems, see the Fieldtrip website . To start the buffer that connects to the Biosemi Active2, open the terminal (Mac) or command prompt (PC) and in the folder where you would like to save your data execute (change path according to your system and location of fieldtrip toolbox): ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft : configuration file : base name of the gdf file. The suffix .gdf and session counters will be added automatically. : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) : optional, default is 1972 an example: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 Note that the manually specified name of the file will overwrite any existing file, so make sure myfile.gdf doesn't exist. Once this is running, you get access to the data through the fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip fileio functions give you access to the data: ft_read_header('buffer://localhost:1972'), or ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100,........ For further information, see fieldtrip website. (more info on how we use the system at our department can be found here: http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) Hope this helps you to get things running in your place. If you have any further questions, just let me know. Best regards, Philip van den Broek Radboud University Nijmegen Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104, 6500 HE Nijmegen Montessorilaan 3, 6525 HR Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University _____ Disclaimer Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. Sint Maartenskliniek Hengstdal 3, 6574 NA Ubbergen (bij Nijmegen) Telefoon 024-3659 911 Telefax 024-3659 204 KvK nummer 41055111 -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.severens at maartenskliniek.nl Mon Feb 13 15:52:29 2012 From: m.severens at maartenskliniek.nl (Severens, Marianne) Date: Mon, 13 Feb 2012 15:52:29 +0100 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <002101cce8e2$bb478060$31d68120$@gmail.com> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com><09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl><8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl><4F342065.8050707@gmail.com><016201cce7fb$6a4b9e90$3ee2dbb0$@gmail.com><70FC3ACFFB46314EBEAF9101EA45F50E06D8EC7A0C@smkexch02.maartenskliniek.nl>, <002101cce8e2$bb478060$31d68120$@gmail.com> Message-ID: <70FC3ACFFB46314EBEAF9101EA45F50E06D145F312@smkexch02.maartenskliniek.nl> Hi Sophie I've checked the script that we use to startup the buffer in our lab. Apparently you need to type ./ before the command. This is what our script looks like: cd to the /fieldtrip/realtime/acquisition/biosemi/ folder. Then run the biosemi2ft: ./biosemi2ft (with optional parameters) I think you can also put a path in the gdf filename, so it does not save it in the fieldtrip folder, but you will have to check that. I hope this works for you! Best, Marianne ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Sophie ADAMA [adama.sophie at gmail.com] Sent: Saturday, February 11, 2012 6:29 PM To: 'Email discussion list for the FieldTrip project' Subject: Re: [FieldTrip] signal acquisition with Biosemi Hi Marianne, There are 3 biosemi2ft in that folder : biosemi2ft.cc, biosemi2ft.exe and biosemi2ft.maci; but when I type ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft in the command line, it says No such file or directory. Sophie From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Severens, Marianne Sent: vendredi 10 février 2012 15:46 To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] signal acquisition with Biosemi Hi Sophie Are you sure that the correct version of the biosemi2ft (so the one for the mac) is in the folder that you are specifying? Maybe you can try it first without the optional parameters, so just ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft Best, Marianne From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Sophie ADAMA Sent: vrijdag 10 februari 2012 14:54 To: 'Email discussion list for the FieldTrip project' Subject: Re: [FieldTrip] signal acquisition with Biosemi Hi, I tried it on Windows too, and it works perfectly. But I’m a Mac girl ☺ and I will be happy if someone could help me. Thank you From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) Sent: vendredi 10 février 2012 06:26 To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] signal acquisition with Biosemi Hello, I tried the biosemi2tf.exe command it works well on Windows. But, unfortunately I don't know about the Mac OS. Best, Hamza On Thu, Feb 9, 2012 at 9:37 PM, Sophie ADAMA > wrote: Hi, Thanks for your response. I tried that but I get this: command not found. I am using Mac OS Lion. Any suggestions? Thanks Sophie Le 09.02.12 17:56, Robert Oostenveld a écrit : On behalf of Philip... On 9 Feb 2012, at 15:31, Philip van den Broek wrote: Dear Sophie and Hamza, The connection between the Biosemi Active2 system and the FieldTrip buffer is handled by interfacing software biosemi2ft (part of fieldtrip), and should be started from the terminal (mac) or command prompt (windows). The interfacing software is located in the FieldTrip folder: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft The BioSemi system needs a configuration (.cfg) file in which some acquisition-related settings are specified. Configuration files for the BioSemi system specify for example from how many channels data should be streamed and/or recorded, and whether the data should be downsampled. For more information about configuration files for different acquisition systems, see the Fieldtrip website. To start the buffer that connects to the Biosemi Active2, open the terminal (Mac) or command prompt (PC) and in the folder where you would like to save your data execute (change path according to your system and location of fieldtrip toolbox): ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft : configuration file : base name of the gdf file. The suffix .gdf and session counters will be added automatically. : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) : optional, default is 1972 an example: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 Note that the manually specified name of the file will overwrite any existing file, so make sure myfile.gdf doesn't exist. Once this is running, you get access to the data through the fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip fileio functions give you access to the data: ft_read_header('buffer://localhost:1972'), or ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100,........ For further information, see fieldtrip website. (more info on how we use the system at our department can be found here: http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) Hope this helps you to get things running in your place. If you have any further questions, just let me know. Best regards, Philip van den Broek Radboud University Nijmegen Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104, 6500 HE Nijmegen Montessorilaan 3, 6525 HR Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University ________________________________ Disclaimer Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. Sint Maartenskliniek Hengstdal 3, 6574 NA Ubbergen (bij Nijmegen) Telefoon 024-3659 911 Telefax 024-3659 204 KvK nummer 41055111 Disclaimer Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. Sint Maartenskliniek Hengstdal 3, 6574 NA Ubbergen (bij Nijmegen) Telefoon 024-3659 911 Telefax 024-3659 204 KvK nummer 41055111 From p.vandenbroek at donders.ru.nl Mon Feb 13 19:08:15 2012 From: p.vandenbroek at donders.ru.nl (Philip van den Broek) Date: Mon, 13 Feb 2012 19:08:15 +0100 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <70FC3ACFFB46314EBEAF9101EA45F50E06D145F312@smkexch02.maartenskliniek.nl> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> <09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl> <8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl> <4F342065.8050707@gmail.com> <016201cce7fb$6a4b9e90$3ee2dbb0$@gmail.com> <70FC3ACFFB46314EBEAF9101EA45F50E06D8EC7A0C@smkexch02.maartenskliniek.nl> <002101cce8e2$bb478060$31d68120$@gmail.com> <70FC3ACFFB46314EBEAF9101EA45F50E06D145F312@smkexch02.maartenskliniek.nl> Message-ID: Hi Sophie, If you specify a file and path, you don't need ./ in front of it, only when you try to execute a file in the current folder. In our local fieldtrip distribution for biosemi2ft, contrary to yours, apparently the extension .maci is missing so you need to specify the extension as well: If you are in the folder: ./biosemi2ft.maci (with optional parameters) or from anywhere else: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft.maci (with optional parameters) Gr. Philip On Feb 13, 2012, at 3:52 PM, Severens, Marianne wrote: > Hi Sophie > > I've checked the script that we use to startup the buffer in our lab. Apparently you need to type ./ before the command. This is what our script looks like: > cd to the /fieldtrip/realtime/acquisition/biosemi/ folder. > Then run the biosemi2ft: ./biosemi2ft (with optional parameters) > > I think you can also put a path in the gdf filename, so it does not save it in the fieldtrip folder, but you will have to check that. > > I hope this works for you! > Best, Marianne > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Sophie ADAMA [adama.sophie at gmail.com] > Sent: Saturday, February 11, 2012 6:29 PM > To: 'Email discussion list for the FieldTrip project' > Subject: Re: [FieldTrip] signal acquisition with Biosemi > > Hi Marianne, > > There are 3 biosemi2ft in that folder : biosemi2ft.cc, biosemi2ft.exe and biosemi2ft.maci; but when I type ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > in the command line, it says No such file or directory. > > Sophie > > From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Severens, Marianne > Sent: vendredi 10 février 2012 15:46 > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] signal acquisition with Biosemi > > Hi Sophie > > Are you sure that the correct version of the biosemi2ft (so the one for the mac) is in the folder that you are specifying? Maybe you can try it first without the optional parameters, so just > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > > Best, Marianne > > From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Sophie ADAMA > Sent: vrijdag 10 februari 2012 14:54 > To: 'Email discussion list for the FieldTrip project' > Subject: Re: [FieldTrip] signal acquisition with Biosemi > > Hi, > > I tried it on Windows too, and it works perfectly. > > But I’m a Mac girl ☺ and I will be happy if someone could help me. > > Thank you > > > From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) > Sent: vendredi 10 février 2012 06:26 > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] signal acquisition with Biosemi > > Hello, > > I tried the biosemi2tf.exe command it works well on Windows. > > But, unfortunately I don't know about the Mac OS. > > Best, > > Hamza > On Thu, Feb 9, 2012 at 9:37 PM, Sophie ADAMA > wrote: > Hi, > > Thanks for your response. > > I tried that but I get this: command not found. I am using Mac OS Lion. > > Any suggestions? > > Thanks > > Sophie > Le 09.02.12 17:56, Robert Oostenveld a écrit : > On behalf of Philip... > > > On 9 Feb 2012, at 15:31, Philip van den Broek wrote: > > > Dear Sophie and Hamza, > > The connection between the Biosemi Active2 system and the FieldTrip buffer is handled by interfacing software biosemi2ft (part of fieldtrip), and should be started from the terminal (mac) or command prompt (windows). > > The interfacing software is located in the FieldTrip folder: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > > The BioSemi system needs a configuration (.cfg) file in which some acquisition-related settings are specified. Configuration files for the BioSemi system specify for example from how many channels data should be streamed and/or recorded, and whether the data should be downsampled. For more information about configuration files for different acquisition systems, see the Fieldtrip website. > > To start the buffer that connects to the Biosemi Active2, open the terminal (Mac) or command prompt (PC) and in the folder where you would like to save your data execute (change path according to your system and location of fieldtrip toolbox): > > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > > > > : configuration file > > : base name of the gdf file. The suffix .gdf and session counters will be added automatically. > > : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) > > : optional, default is 1972 > > an example: > > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 > > Note that the manually specified name of the file will overwrite any existing file, so make sure myfile.gdf doesn't exist. > Once this is running, you get access to the data through the fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip fileio functions give you access to the data: > ft_read_header('buffer://localhost:1972'), or > ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100,........ > For further information, see fieldtrip website. > > (more info on how we use the system at our department can be found here: http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) > > Hope this helps you to get things running in your place. If you have any further questions, just let me know. > > Best regards, > > Philip van den Broek > Radboud University Nijmegen > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > > P.O. Box 9104, 6500 HE Nijmegen > Montessorilaan 3, 6525 HR Nijmegen > The Netherlands > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > ________________________________ > Disclaimer > Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. > > Sint Maartenskliniek > Hengstdal 3, > 6574 NA Ubbergen (bij Nijmegen) > Telefoon 024-3659 911 > Telefax 024-3659 204 > KvK nummer 41055111 > > Disclaimer > Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. > > Sint Maartenskliniek > Hengstdal 3, > 6574 NA Ubbergen (bij Nijmegen) > Telefoon 024-3659 911 > Telefax 024-3659 204 > KvK nummer 41055111 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From sysoevao at psychiatry.wustl.edu Mon Feb 13 21:49:17 2012 From: sysoevao at psychiatry.wustl.edu (Sysoeva, Olga Vladimirovna) Date: Mon, 13 Feb 2012 14:49:17 -0600 Subject: [FieldTrip] one/two-tails analysis Message-ID: <76DC57362137854CB9592B496182D5FA09D91CC315@wusmexmbx2.medpriv.wucon.wustl.edu> Dear group, I do face some weird results during my analysis. Usually I do t-test analysis to compare 2 condions/groups and use 2-tails, as far as I do not have any preliminary hypothesis about the direction of the effect. So my script looks something like Script 1 (see below). Important here is that I do keep the default parameters, cfg.tail = 0; cfg.clustertail = 0; To my understanding of statistic, if you have the two-tail effect, and group 1 has bigger mean than gr2, you should have the effect with one-tail as well and even more significant. But what I discovered just today that if I change this parameter to 1, cfg.tail = 1; cfg.clustertail = 1; in order to look spesifically for the one-tail effect (gr1 is bigger than gr2), my very significant 2 tail effect just disappeared completely. Is it a bug? Your comments are appreciated. Best reGards, Olga. Script 1 cfg = []; cfg.method = 'montecarlo'; % use the Monte Carlo Method to calculate the significance probability cfg.statistic = 'indepsamplesT'; % use the independent samples T-statistic as a measure to evaluate % the effect at the sample level % cfg.statistic = 'indepsamplesF'; % use the independent samples T-statistic as a measure to evaluate % cfg.computecritval = 'yes' % the effect at the sample level cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; % alpha level of the sample-specific test statistic that will be used for thresholding cfg.clusterstatistic = 'maxsum'; % test statistic that will be evaluated under the permutation distribution. cfg.minnbchan = 1; % minimum number of neighborhood channels that is required for a selected % sample to be included in the clustering algorithm (default=0). cfg.tail = 0; % -1, 1 or 0 (default = 0); one-sided or two-sided test cfg.clustertail = 0; cfg.alpha = 0.05; % alpha level of the permutation test cfg.numrandomization = 1000; % number of draws from the permutation distribution cfg.neighbourdist = 0.2; %cfg.neighbours = cfg_n; cfg.channel = {'all', '-HEOG', '-VEOG', '-EKG'}; cfg.latency = [0. 0.5]; cfg.layout = 'C:\Matlab_programs\Fieldtrip\My_Fieldtrip\EEG1010_modified32.lay'; subj1 = length(GROUP {nGroup1,1}); subj2 = length(GROUP {nGroup2,1}); design = zeros(1,subj1+subj2); design(1,1:subj1) = 1; design(1,subj1+1:subj1+subj2) = 2; cfg.design = design; cfg.ivar = 1; [stat] = ft_timelockstatistics(cfg, peak1_gr1 , peak1_gr2 ); ____________________________________________________________________________ Olga Sysoeva, Research Associate, PhD Psychiatry Department, Washington University School of Medicine Campus Box 8134 660 South Euclid Ave Saint Louis, MO 63110-9909 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From adama.sophie at gmail.com Tue Feb 14 15:06:21 2012 From: adama.sophie at gmail.com (Sophie ADAMA) Date: Tue, 14 Feb 2012 15:06:21 +0100 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> <09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl> <8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl> <4F342065.8050707@gmail.com> <016201cce7fb$6a4b9e90$3ee2dbb0$@gmail.com> <70FC3ACFFB46314EBEAF9101EA45F50E06D8EC7A0C@smkexch02.maartenskliniek.nl> <002101cce8e2$bb478060$31d68120$@gmail.com> <70FC3ACFFB46314EBEAF9101EA45F50E06D145F312@smkexch02.maartenskliniek.nl> Message-ID: <4F3A6A5D.1050101@gmail.com> Hi everybody, I tried all this but it still doesn't work. The latest error I got was: *Access denied* Sincerly, Sophie Le 13.02.12 19:08, Philip van den Broek a écrit : > Hi Sophie, > > If you specify a file and path, you don't need ./ in front of it, only > when you try to execute a file in the current folder. In our local > fieldtrip distribution for biosemi2ft, contrary to yours, apparently > the extension .maci is missing so you need to specify the extension as > well: > If you are in the folder: > ./biosemi2ft.maci (with optional parameters) > > or from anywhere else: > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft.maci (with > optional parameters) > > Gr. Philip > > On Feb 13, 2012, at 3:52 PM, Severens, Marianne wrote: > >> Hi Sophie >> >> I've checked the script that we use to startup the buffer in our lab. >> Apparently you need to type ./ before the command. This is what our >> script looks like: >> cd to the /fieldtrip/realtime/acquisition/biosemi/ folder. >> Then run the biosemi2ft: ./biosemi2ft (with optional parameters) >> >> I think you can also put a path in the gdf filename, so it does not >> save it in the fieldtrip folder, but you will have to check that. >> >> I hope this works for you! >> Best, Marianne >> ________________________________________ >> From: fieldtrip-bounces at donders.ru.nl >> >> [fieldtrip-bounces at donders.ru.nl >> ] On Behalf Of Sophie ADAMA >> [adama.sophie at gmail.com ] >> Sent: Saturday, February 11, 2012 6:29 PM >> To: 'Email discussion list for the FieldTrip project' >> Subject: Re: [FieldTrip] signal acquisition with Biosemi >> >> Hi Marianne, >> >> There are 3 biosemi2ft in that folder : biosemi2ft.cc, biosemi2ft.exe >> and biosemi2ft.maci; but when I type >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft >> in the command line, it says No such file or directory. >> >> Sophie >> >> From: fieldtrip-bounces at donders.ru.nl >> >> [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Severens, Marianne >> Sent: vendredi 10 février 2012 15:46 >> To: Email discussion list for the FieldTrip project >> Subject: Re: [FieldTrip] signal acquisition with Biosemi >> >> Hi Sophie >> >> Are you sure that the correct version of the biosemi2ft (so the one >> for the mac) is in the folder that you are specifying? Maybe you can >> try it first without the optional parameters, so just >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft >> >> Best, Marianne >> >> From: fieldtrip-bounces at donders.ru.nl >> >> [mailto:fieldtrip-bounces at donders.ru.nl] >> On Behalf Of Sophie ADAMA >> Sent: vrijdag 10 februari 2012 14:54 >> To: 'Email discussion list for the FieldTrip project' >> Subject: Re: [FieldTrip] signal acquisition with Biosemi >> >> Hi, >> >> I tried it on Windows too, and it works perfectly. >> >> But I'm a Mac girl ? and I will be happy if someone could help me. >> >> Thank you >> >> >> From: fieldtrip-bounces at donders.ru.nl >> >> [mailto:fieldtrip-bounces at donders.ru.nl] >> On Behalf Of Hamza Fawzi Altakroury (Student) >> Sent: vendredi 10 février 2012 06:26 >> To: Email discussion list for the FieldTrip project >> Subject: Re: [FieldTrip] signal acquisition with Biosemi >> >> Hello, >> >> I tried the biosemi2tf.exe command it works well on Windows. >> >> But, unfortunately I don't know about the Mac OS. >> >> Best, >> >> Hamza >> On Thu, Feb 9, 2012 at 9:37 PM, Sophie ADAMA > > wrote: >> Hi, >> >> Thanks for your response. >> >> I tried that but I get this: command not found. I am using Mac OS Lion. >> >> Any suggestions? >> >> Thanks >> >> Sophie >> Le 09.02.12 17:56, Robert Oostenveld a écrit : >> On behalf of Philip... >> >> >> On 9 Feb 2012, at 15:31, Philip van den Broek wrote: >> >> >> Dear Sophie and Hamza, >> >> The connection between the Biosemi Active2 system and the FieldTrip >> buffer is handled by interfacing software biosemi2ft (part of >> fieldtrip), and should be started from the terminal (mac) or command >> prompt (windows). >> >> The interfacing software is located in the FieldTrip folder: >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft >> >> The BioSemi system needs a configuration (.cfg) file in which some >> acquisition-related settings are specified. Configuration files for >> the BioSemi system specify for example from how many channels data >> should be streamed and/or recorded, and whether the data should be >> downsampled. For more information about configuration files for >> different acquisition systems, see the Fieldtrip >> website. >> >> To start the buffer that connects to the Biosemi Active2, open the >> terminal (Mac) or command prompt (PC) and in the folder where you >> would like to save your data execute (change path according to your >> system and location of fieldtrip toolbox): >> >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft >> >> >> >> >> : configuration file >> >> : base name of the gdf file. The suffix .gdf and session >> counters will be added automatically. >> >> : optional, default is 'localhost', specify '-' to spawn a >> local buffer (recommended) >> >> : optional, default is 1972 >> >> an example: >> >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg >> myfile - 1972 >> >> Note that the manually specified name of the file will overwrite any >> existing file, so make sure myfile.gdf doesn't exist. >> Once this is running, you get access to the data through the >> fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip >> fileio functions give you access to the data: >> ft_read_header('buffer://localhost:1972' >> ), or >> ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100 >> ,........ >> For further information, see fieldtrip website. >> >> (more info on how we use the system at our department can be found >> here: >> http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) >> >> Hope this helps you to get things running in your place. If you have >> any further questions, just let me know. >> >> Best regards, >> >> Philip van den Broek >> Radboud University Nijmegen >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognition >> >> P.O. Box 9104, 6500 HE Nijmegen >> Montessorilaan 3, 6525 HR Nijmegen >> The Netherlands >> >> >> >> _______________________________________________ >> >> fieldtrip mailing list >> >> fieldtrip at donders.ru.nl >> >> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Hamza Fawzi Altakroury >> Graduate student - MA >> Faculty of Engineering and Natural Sciences >> Sabanc? University >> >> ________________________________ >> Disclaimer >> Vrijgave van de informatie verzonden met dit e-mail bericht is >> geaccordeerd door de ontvanger en/of zijn behandelend arts. >> Verstrekking van deze informatie is conform het Privacy reglement van >> de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de >> geadresseerde. Gebruik van deze informatie door anderen dan de >> geadresseerde is, zonder voorafgaande schriftelijke toestemming van >> de rechthebbende , verboden. De Sint Maartenskliniek staat niet in >> voor de juiste en volledige overbrenging van de inhoud van een >> gezonden e-mail, noch voor de ontvangst daarvan. >> >> Sint Maartenskliniek >> Hengstdal 3, >> 6574 NA Ubbergen (bij Nijmegen) >> Telefoon 024-3659 911 >> Telefax 024-3659 204 >> KvK nummer 41055111 >> >> Disclaimer >> Vrijgave van de informatie verzonden met dit e-mail bericht is >> geaccordeerd door de ontvanger en/of zijn behandelend arts. >> Verstrekking van deze informatie is conform het Privacy reglement van >> de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de >> geadresseerde. Gebruik van deze informatie door anderen dan de >> geadresseerde is, zonder voorafgaande schriftelijke toestemming van >> de rechthebbende , verboden. De Sint Maartenskliniek staat niet in >> voor de juiste en volledige overbrenging van de inhoud van een >> gezonden e-mail, noch voor de ontvangst daarvan. >> >> Sint Maartenskliniek >> Hengstdal 3, >> 6574 NA Ubbergen (bij Nijmegen) >> Telefoon 024-3659 911 >> Telefax 024-3659 204 >> KvK nummer 41055111 >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From sla.samiee at gmail.com Tue Feb 14 17:42:50 2012 From: sla.samiee at gmail.com (Soheila Samiee) Date: Tue, 14 Feb 2012 11:42:50 -0500 Subject: [FieldTrip] A problem in real-time processing of MEG signal using field trip buffer Message-ID: Dear group, I use FieldTrip for real-time processing of MEG signals using shared memory and field trip buffer in a machine other than acquisition system. I use matlab for reading the buffer and processing the data. During my data acquisition and sending it to other computer with *acq2ft*in linux, I face a problem. After sending some blocks of data, this message: "*Internal Converter thread does not keep up with load*" is shown in the terminal of *acq2ft* and in my matlab session I see an error : "ERROR: the buffer returned an error (517)". It does not depend on sampling rate of data in acquisition system. The problem often solve when I restart the computer which receives the data, but after some minutes of transferring the data I see the message again. Would you please help me in solving this problem? Best Wishes, Soheila -------------- next part -------------- An HTML attachment was scrubbed... URL: From akiko.ikkai at gmail.com Wed Feb 15 17:45:37 2012 From: akiko.ikkai at gmail.com (Akiko Ikkai) Date: Wed, 15 Feb 2012 11:45:37 -0500 Subject: [FieldTrip] volume conduction model missing .mat In-Reply-To: References: <2341406D-6422-4FD3-AD3C-73D1BF70B6CF@mac.com> Message-ID: Dear Fieldtrip users, Thank you Patrick, Nathan & Gio for your inputs. My MRI anatomical images need extensive cleaning (enhance contrasts, get rid of non-zero voxels outside the brain, etc...) before segmentation, as well as adjusting cfg.threshold for each tissue type during segmentation and each subject. At least testing with SPM standard MRI, segmentation and forward modeling works OK now. Individual subject's MRI, though, is still problematic, and I have a question for Fieldtrip developers: could you let me know whether "Create BEM headmodel for EEG ( http://fieldtrip.fcdonders.nl/example/create_bem_headmodel_for_eeg )" routine is what you recommend, or it's integrated into a newer function with newer cfg options? Is there a page I missed on the web? Thank you so much for your time! Akiko On Fri, Feb 10, 2012 at 4:36 AM, Gio Piantoni wrote: > Hi Akiki and Patrick, > > I agree with Nathan about segmentation problems. I had the same > problem when two of the three meshes intersected each other. Before > you run the forward model, you should check the segmentation (bnd) > using ft_plot_mesh. > ft_plot_mesh(bnd(1), 'facealpha', .5) > hold on > ft_plot_mesh(bnd(2), 'facecolor', 'r') > You will see that the two meshes intersect with each other. Depending > on how you created the meshes, you should fix the parameters in such a > way that they don't intersect. For example, ft_volumesegment has a > cfg.threshold option (you can check how the segmentation went with > ft_sourceplot) and ft_prepare_mesh_new has cfg.thresholdseg and > cfg.smoothseg. > > I think that the meshes in SPM are computed on an (affine-transformed) > template and not on the anatomically derived meshes. The template is > more robust and that's why the two surfaces do not intersect. > > In general, the segmentation depends on the quality of your MRIs and > you should really visually check the segmentation and meshes. When > those look ok, the BEM forward model usually works. Hope this helps. > > Cheers, > > Gio > > On Fri, Feb 10, 2012 at 09:00, Nathan Weisz wrote: > > Hi Akiki, > > > > I am not a headmodel expert. > > but looking at the output message, it seems your segementation did not go > > too well (see the "intersect" message). my intuition is then then the > next > > temporary file *.ama is not created and ft_prepare_bemmodel then simply > says > > ciao. > > > > perhaps you want to check / redo the segmentation? > > > > good luck, > > nathan > > > > > > On 09.02.2012, at 23:04, Akiko Ikkai wrote: > > > > Hi, > > > > I'm trying to create a volume conduction model for my EEG study based on > > anatomical MRI, and having trouble with ft_prepare_bemmodel > > > > when I run > > cfg = []; > > cfg.tissue = [7 4 1]; % value for brain, skull, and scalp > > cfg.conductivity = [1 1/80 1]*.33; % after standard_BEM.zip data > > cfg.isolatedsource = true; > > cfg.method = 'dipoli'; > > cfg.sourceunits = 'mm'; > > cfg.mriunits = 'mm'; > > vol = ft_prepare_bemmodel(cfg, seg4bem); > > > > I get the following error message while ft_prepare_bemmodel is running: > > > > Fatal error in dipoli: interface > > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and > > /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect > > at vertex 1402 of > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri > > > > Warning: an error ocurred while running dipoli > >> In dipoli at 94 > > In ft_prepare_bemmodel at 112 > > Error using ==> fread > > Invalid file identifier. Use fopen to generate a valid file identifier. > > Warning: File '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' > not > > found. > >> In dipoli at 102 > > In ft_prepare_bemmodel at 112 > > > > > > and the output vol is missing .mat, which causes an error > > during ft_sourceanalysis. > >>> vol > > vol = > > cond: [0.3300 0.0041 0.3300] > > bnd: [1x3 struct] > > source: 3 > > skin_surface: 3 > > skin: 1 > > type: 'dipoli' > > > > Does anyone know how to correct for "fatal error" so > > that ft_prepare_bemmodel creates the correct volume conduction model? I > > opened .tri file and removed line 1402, but got the same results. > > > > Thanks in advance! Akiko > > > > -- > > Akiko Ikkai, Ph.D. > > Postdoctoral Fellow > > Department of Psychological and Brain Sciences > > Johns Hopkins University > > Ames Hall, 3400 N. Charles St. > > Baltimore, MD 21218 > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Akiko Ikkai, Ph.D. Postdoctoral Fellow Department of Psychological and Brain Sciences Johns Hopkins University Ames Hall, 3400 N. Charles St. Baltimore, MD 21218 -------------- next part -------------- An HTML attachment was scrubbed... URL: From shayda.malekpour at gmail.com Wed Feb 15 21:19:50 2012 From: shayda.malekpour at gmail.com (Shayda Malekpour) Date: Wed, 15 Feb 2012 14:19:50 -0600 Subject: [FieldTrip] A question Message-ID: Dear All, I am using fieldtrip on MEG data set. I want to know if I do not remove any ICA component, will the data be the same as the original data, or is there is a filter somewhere in the software that changes the data? If so how much does it change it (What is their relative difference?) Thanks, Sheida -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu Feb 16 09:28:43 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 16 Feb 2012 09:28:43 +0100 Subject: [FieldTrip] A question In-Reply-To: References: Message-ID: Dear Sheida, You probably need to provide a bit more information before anyone is able to help you. In general, if you perform ICA, you get out component timecourses and mixing/unmixing matrices. If you keep all your components, and multiply them with the mixing matrix, you should get all your original channel timecourses out again. So: if you don't change the data, the data will not be changed :) Best, Eelke On 15 February 2012 21:19, Shayda Malekpour wrote: > Dear All, > > I am using fieldtrip on MEG data set. > I want to know if I do not remove any ICA component,  will the data be  the > same as the original data, or is there is a filter somewhere in the software > that changes the data? If so how much does it change it (What is their > relative difference?) > > Thanks, > > Sheida > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Thu Feb 16 10:36:05 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 16 Feb 2012 10:36:05 +0100 Subject: [FieldTrip] A problem in real-time processing of MEG signal using field trip buffer In-Reply-To: References: Message-ID: <4F3CCE05.4050109@donders.ru.nl> Dear Soheila, we were facing the same problem here. Presumably, there is some problem in the shared memory module that the buffer is using. Right now, however, we could not find out where the error precisely comes from, so our best work around is to restart the computer prior recording and optimize settings, such as channels and sampling/decimation rate of acq2ft. In our lab, we managed to find near-optimal settings, so that the buffer crashes only rarely (actually, I never saw it crashing when the acquisition computer was freshly restarted). Note that a lower number of channels or higher decimation does not mean that it runs more stable. It seems to be literally a trial-and-error approach :/ In order to track this down further, we need some more information, e.g. what MEG system are you using? What's your sampling rate, how many channels do you put into the buffer, and what's your decimation rate? It would be great if you could send me that information so that we can maybe try to track this down. Best regards, Jörn On 2/14/2012 5:42 PM, Soheila Samiee wrote: > Dear group, > > I use FieldTrip for real-time processing of MEG signals using shared > memory and field trip buffer in a machine other than acquisition > system. I use matlab for reading the buffer and processing the data. > During my data acquisition and sending it to other computer with > /acq2ft/ in linux, I face a problem. After sending some blocks of > data, this message: "/Internal Converter thread does not keep up with > load/" is shown in the terminal of /acq2ft/ and in my matlab session I > see an error : "ERROR: the buffer returned an error (517)". It does > not depend on sampling rate of data in acquisition system. The problem > often solve when I restart the computer which receives the data, but > after some minutes of transferring the data I see the message again. > > Would you please help me in solving this problem? > Best Wishes, > Soheila > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.piantoni at nin.knaw.nl Thu Feb 16 11:52:45 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Thu, 16 Feb 2012 11:52:45 +0100 Subject: [FieldTrip] volume conduction model missing .mat In-Reply-To: References: <2341406D-6422-4FD3-AD3C-73D1BF70B6CF@mac.com> Message-ID: Hi Akiko, What do you mean "problematic" exactly? From my understanding, there are 4 steps to get from the MRI to the forward model. 1. from MRI to segmentation 2. from segmentation to mesh (bnd) 3. from mesh to headmodel 4. from headmodel to forward model Here is the code I use. It seems to work fine, but experts might want to chip in and improve it. 1. from MRI to segmentation %-----------------% %-read MRI mrifile = '/path/to/your/mri.nii.gz'; mri = ft_read_mri(mrifile); %-----------------% %-----------------% %-segmenting the volume, Tissue Probability Maps % It takes time to run 'tpm' cfg1 = []; cfg1.threshold = []; cfg1.output = 'tpm'; cfg1.coordsys = 'spm'; tpm = ft_volumesegment(cfg1, mri); tpm.anatomy = mri.anatomy; %-----------------% %-----------------% %-segmenting the volume % this is faster after tpm cfg1 = []; cfg1.threshold = 1; % 1 is default, my MRI scalps were noisy, so I had to make it lower. cfg1.output = 'scalp'; cfg1.coordsys = 'spm'; segscalp = ft_volumesegment(cfg1, tpm); cfg1 = []; cfg1.threshold = []; cfg1.output = {'skull' 'brain'}; cfg1.coordsys = 'spm'; segment = ft_volumesegment(cfg1, tpm); segment.scalp = segscalp.scalp; %-----------------% Check the output with ft_sourceplot 2. from segmentation to mesh (bnd) %-----------------% %-prepare mesh for skull and brain (easy) cfg2 = []; cfg2.tissue = {'skull', 'brain'}; cfg2.numvertices = [1200 1000]; cfg2.transform = segment.transform; bnd = ft_prepare_mesh_new(cfg2, segment); %-----------------% %-----------------% %-prepare mesh for scalp (we need to be more liberal with threshold, bc of poor quality of MRI) cfg2 = []; cfg2.tissue = {'scalp'}; cfg2.numvertices = 2500; cfg2.thresholdseg = 0.1; cfg2.transform = segment.transform; scalp = ft_prepare_mesh_new(cfg2, segment); %-----------------% %-----------------% %-combine scalp and bnd bnd = [scalp bnd]; ft_plot_mesh(bnd(1), 'facealpha', .5) hold on ft_plot_mesh(bnd(2), 'facecolor', 'red') %-----------------% If bnd is good, no intersection between meshes and the outline looks nice, the following should run without problems. Please, do check your bnd. Segmentation and ft_prepare_mesh_new work really well. Another approach to get nice meshes is to skip step 1 and 2 and use Freesurfer/MNE. You can read the meshes in fieldtrip (ft_read_headshape, I think). The meshes are in the "bem" folder of Freesurfer, but I don't remember off the top of my head which files you should read ("outer_skull, inner_skull", I think). These meshes have a very very high resolution, you can scale them down with "reducepatch" in Matlab. 3. from mesh to headmodel %-----------------% %-headmodel cfg3 = []; cfg3.method = 'bem_dipoli'; cfg3.conductivity = [0.33 0.0042 0.33]; vol = ft_prepare_headmodel(cfg3, bnd); %-----------------% You can really pick your favorite here: dipoli, openmeeg, bemcp. This will take time (the more time, the more points on your meshes). 4. from headmodel to forward model You last problem is to get electrodes and headmodel in the same space. The template in SPM is already in MNI space, your individual MRIs probably not. You can realign them to MNI space before step 1 using SPM or FSL. elec = ft_read_sens(sensfile); elec = ft_convert_units(elec, 'mm'); %-------% %-simple transformation (based on visual realignment) % elecM is an affine matrix that you can get from ft_electroderealign % electrodes do not need to match the scalp perfectly, but they should be pretty close by. elec.chanpos = warp_apply(elecM, elec.chanpos); elec.elecpos = warp_apply(elecM, elec.elecpos); %-------% [vol, elec] = ft_prepare_vol_sens(vol, elec); % now you should check that the electrodes are on the scalp. %-----------------% %-----------------% %-prepare leadfield cfg4 = []; cfg4.elec = elec; cfg4.vol = vol; cfg4.grid.xgrid = -70:10:70; cfg4.grid.ygrid = -110:10:80; cfg4.grid.zgrid = -60:10:90; cfg4.inwardshift = 1; % to avoid dipoles on the border of bnd(3), which are very instable cfg4.grid.tight = 'no'; cfg4.feedback = 'none'; lead = ft_prepare_leadfield(cfg4, []); % use ft_plot_topo3d and ft_plot_dipole to check whether the projection of your dipole onto the scalp makes sense. %-----------------% "lead" should be your subject-specific, electrode-specific leadfield. There are quite a few parameters that you can change, but a clean segmentation and non-intersecting, smooth and realistic-looking meshes are a must. Then, using dipoli, openmeeg or bemcp should not change your forward model too much. Sorry if some points are not clear, but you should really look at your MRI/segmentation/meshes/electrodes/forward model as much as possible. Hope this will get you started. I appreciate any feedback on improving the code, this is just my personal attempt. Cheers Gio On Wed, Feb 15, 2012 at 17:45, Akiko Ikkai wrote: > Dear Fieldtrip users, > > Thank you Patrick, Nathan & Gio for your inputs. My MRI anatomical images > need extensive cleaning (enhance contrasts, get rid of non-zero voxels > outside the brain, etc...) before segmentation, as well as adjusting > cfg.threshold for each tissue type during segmentation and each subject. At > least testing with SPM standard MRI, segmentation and forward modeling works > OK now. > > Individual subject's MRI, though, is still problematic, and I have a > question for Fieldtrip developers: could you let me know whether "Create BEM > headmodel for EEG ( >  http://fieldtrip.fcdonders.nl/example/create_bem_headmodel_for_eeg )" > routine is what you recommend, or it's integrated into a newer function with > newer cfg options? Is there a page I missed on the web? > > Thank you so much for your time! > Akiko > > On Fri, Feb 10, 2012 at 4:36 AM, Gio Piantoni > wrote: >> >> Hi Akiki and Patrick, >> >> I agree with Nathan about segmentation problems. I had the same >> problem when two of the three meshes intersected each other. Before >> you run the forward model, you should check the segmentation (bnd) >> using ft_plot_mesh. >> ft_plot_mesh(bnd(1), 'facealpha', .5) >> hold on >> ft_plot_mesh(bnd(2), 'facecolor', 'r') >> You will see that the two meshes intersect with each other. Depending >> on how you created the meshes, you should fix the parameters in such a >> way that they don't intersect. For example, ft_volumesegment has a >> cfg.threshold option (you can check how the segmentation went with >> ft_sourceplot) and ft_prepare_mesh_new has cfg.thresholdseg and >> cfg.smoothseg. >> >> I think that the meshes in SPM are computed on an (affine-transformed) >> template and not on the anatomically derived meshes. The template is >> more robust and that's why the two surfaces do not intersect. >> >> In general, the segmentation depends on the quality of your MRIs and >> you should really visually check the segmentation and meshes. When >> those look ok, the BEM forward model usually works. Hope this helps. >> >> Cheers, >> >> Gio >> >> On Fri, Feb 10, 2012 at 09:00, Nathan Weisz wrote: >> > Hi Akiki, >> > >> > I am not a headmodel expert. >> > but looking at the output message, it seems your segementation did not >> > go >> > too well (see the "intersect" message). my intuition is then then the >> > next >> > temporary file *.ama is not created and ft_prepare_bemmodel then simply >> > says >> > ciao. >> > >> > perhaps you want to check / redo the segmentation? >> > >> > good luck, >> > nathan >> > >> > >> > On 09.02.2012, at 23:04, Akiko Ikkai wrote: >> > >> > Hi, >> > >> > I'm trying to create a volume conduction model for my EEG study based on >> > anatomical MRI, and having trouble with ft_prepare_bemmodel >> > >> > when I run >> > cfg                = []; >> > cfg.tissue         = [7 4 1]; % value for brain, skull, and scalp >> > cfg.conductivity   = [1 1/80 1]*.33; % after standard_BEM.zip data >> > cfg.isolatedsource = true; >> > cfg.method         = 'dipoli'; >> > cfg.sourceunits = 'mm'; >> > cfg.mriunits = 'mm'; >> > vol = ft_prepare_bemmodel(cfg, seg4bem); >> > >> > I get the following error message while ft_prepare_bemmodel is running: >> > >> > Fatal error in dipoli:  interface >> > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and >> > /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect >> >  at vertex 1402 of >> > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri >> > >> > Warning: an error ocurred while running dipoli >> >> In dipoli at 94 >> >   In ft_prepare_bemmodel at 112 >> > Error using ==> fread >> > Invalid file identifier.  Use fopen to generate a valid file identifier. >> > Warning: File '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' >> > not >> > found. >> >> In dipoli at 102 >> >   In ft_prepare_bemmodel at 112 >> > >> > >> > and the output vol is missing .mat, which causes an error >> > during ft_sourceanalysis. >> >>> vol >> > vol = >> >             cond: [0.3300 0.0041 0.3300] >> >              bnd: [1x3 struct] >> >           source: 3 >> >     skin_surface: 3 >> >             skin: 1 >> >             type: 'dipoli' >> > >> > Does anyone know how to correct for "fatal error" so >> > that ft_prepare_bemmodel creates the correct volume conduction model? I >> > opened .tri file and removed line 1402, but got the same results. >> > >> > Thanks in advance! Akiko >> > >> > -- >> > Akiko Ikkai, Ph.D. >> > Postdoctoral Fellow >> > Department of Psychological and Brain Sciences >> > Johns Hopkins University >> > Ames Hall, 3400 N. Charles St. >> > Baltimore, MD 21218 >> > >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > >> > >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Akiko Ikkai, Ph.D. > Postdoctoral Fellow > Department of Psychological and Brain Sciences > Johns Hopkins University > Ames Hall, 3400 N. Charles St. > Baltimore, MD 21218 > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From politzerahless at gmail.com Thu Feb 16 12:35:13 2012 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Thu, 16 Feb 2012 05:35:13 -0600 Subject: [FieldTrip] A question Message-ID: Hi Shayda, FieldTrip does not apply a filter by default, and I am not aware of any other 'hidden' transformations that happen. You can specify a filter when importing the data with ft_preprocessing(), and there are several different kinds of filters available, which will affect your data in different ways-- see http://fieldtrip.fcdonders.nl/reference/ft_preprocessing. The best thing to do is to import your data without using a filter and, if possible, use whatever tool comes with your MEG software to import that raw data into MATLAB as well (for example, for CTF this would be ds2txt), then you can plot them together to make sure there are no differences--when I have tried this with EEG data, fieldtrip hasn't changed them. Of course, if you want to use a filter, you can also try several filters (you can either filter within your system's software and then import straight to Fieldtrip, or use one of Fieldtrip's filters during import) and plot them to see how they affect your data. Best, Steve Politzer-Ahles > > Message: 2 > Date: Wed, 15 Feb 2012 14:19:50 -0600 > From: Shayda Malekpour > To: fieldtrip at donders.ru.nl > Subject: [FieldTrip] A question > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > Dear All, > > I am using fieldtrip on MEG data set. > I want to know if I do not remove any ICA component, will the data be the > same as the original data, or is there is a filter somewhere in the > software that changes the data? If so how much does it change it (What is > their relative difference?) > > Thanks, > > Sheida > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120215/ba4458d8/attachment-0001.html > > > > ------------------------------ > > Message: 3 > Date: Thu, 16 Feb 2012 09:28:43 +0100 > From: Eelke Spaak > To: Email discussion list for the FieldTrip project > > Subject: Re: [FieldTrip] A question > Message-ID: > > > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Sheida, > > You probably need to provide a bit more information before anyone is > able to help you. In general, if you perform ICA, you get out > component timecourses and mixing/unmixing matrices. If you keep all > your components, and multiply them with the mixing matrix, you should > get all your original channel timecourses out again. So: if you don't > change the data, the data will not be changed :) > > Best, > Eelke > > On 15 February 2012 21:19, Shayda Malekpour > wrote: > > Dear All, > > > > I am using fieldtrip on MEG data set. > > I want to know if I do not remove any ICA component,? will the data be? > the > > same as the original data, or is there is a filter somewhere in the > software > > that changes the data? If so how much does it change it (What is their > > relative difference?) > > > > Thanks, > > > > Sheida > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > ------------------------------ > > Message: 4 > Date: Thu, 16 Feb 2012 10:36:05 +0100 > From: "J?rn M. Horschig" > To: Email discussion list for the FieldTrip project > > Subject: Re: [FieldTrip] A problem in real-time processing of MEG > signal using field trip buffer > Message-ID: <4F3CCE05.4050109 at donders.ru.nl> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Dear Soheila, > > we were facing the same problem here. Presumably, there is some problem > in the shared memory module that the buffer is using. Right now, > however, we could not find out where the error precisely comes from, so > our best work around is to restart the computer prior recording and > optimize settings, such as channels and sampling/decimation rate of > acq2ft. In our lab, we managed to find near-optimal settings, so that > the buffer crashes only rarely (actually, I never saw it crashing when > the acquisition computer was freshly restarted). Note that a lower > number of channels or higher decimation does not mean that it runs more > stable. It seems to be literally a trial-and-error approach :/ > > In order to track this down further, we need some more information, e.g. > what MEG system are you using? What's your sampling rate, how many > channels do you put into the buffer, and what's your decimation rate? It > would be great if you could send me that information so that we can > maybe try to track this down. > > Best regards, > J?rn > > On 2/14/2012 5:42 PM, Soheila Samiee wrote: > > Dear group, > > > > I use FieldTrip for real-time processing of MEG signals using shared > > memory and field trip buffer in a machine other than acquisition > > system. I use matlab for reading the buffer and processing the data. > > During my data acquisition and sending it to other computer with > > /acq2ft/ in linux, I face a problem. After sending some blocks of > > data, this message: "/Internal Converter thread does not keep up with > > load/" is shown in the terminal of /acq2ft/ and in my matlab session I > > see an error : "ERROR: the buffer returned an error (517)". It does > > not depend on sampling rate of data in acquisition system. The problem > > often solve when I restart the computer which receives the data, but > > after some minutes of transferring the data I see the message again. > > > > Would you please help me in solving this problem? > > Best Wishes, > > Soheila > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > J?rn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120216/c01be767/attachment.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 15, Issue 17 > ***************************************** > -- Stephen Politzer-Ahles University of Kansas Linguistics Department http://www.linguistics.ku.edu/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Feb 16 12:39:25 2012 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 16 Feb 2012 12:39:25 +0100 Subject: [FieldTrip] A question In-Reply-To: References: Message-ID: Dear All, All true, except that ICA implemented by FT does demean the data before unmixing by default. Use cfg.demean = 'no' if you don't want to. cheers, stephen On 16 February 2012 12:35, Stephen Politzer-Ahles wrote: > Hi Shayda, > > FieldTrip does not apply a filter by default, and I am not aware of any > other 'hidden' transformations that happen. You can specify a filter when > importing the data with ft_preprocessing(), and there are several different > kinds of filters available, which will affect your data in different ways-- > see http://fieldtrip.fcdonders.nl/reference/ft_preprocessing. The best thing > to do is to import your data without using a filter and, if possible, use > whatever tool comes with your MEG software to import that raw data into > MATLAB as well (for example, for CTF this would be ds2txt), then you can > plot them together to make sure there are no differences--when I have tried > this with EEG data, fieldtrip hasn't changed them. Of course, if you want to > use a filter, you can also try several filters (you can either filter within > your system's software and then import straight to Fieldtrip, or use one of > Fieldtrip's filters during import) and plot them to see how they affect your > data. > > Best, > Steve Politzer-Ahles > > >> >> >> Message: 2 >> Date: Wed, 15 Feb 2012 14:19:50 -0600 >> From: Shayda Malekpour >> To: fieldtrip at donders.ru.nl >> Subject: [FieldTrip] A question >> Message-ID: >> >>   >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Dear All, >> >> I am using fieldtrip on MEG data set. >> I want to know if I do not remove any ICA component,  will the data be >>  the >> same as the original data, or is there is a filter somewhere in the >> software that changes the data? If so how much does it change it (What is >> their relative difference?) >> >> Thanks, >> >> Sheida >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> >> >> ------------------------------ >> >> Message: 3 >> Date: Thu, 16 Feb 2012 09:28:43 +0100 >> From: Eelke Spaak >> To: Email discussion list for the FieldTrip project >>         >> Subject: Re: [FieldTrip] A question >> Message-ID: >> >>   >> Content-Type: text/plain; charset=ISO-8859-1 >> >> >> Dear Sheida, >> >> You probably need to provide a bit more information before anyone is >> able to help you. In general, if you perform ICA, you get out >> component timecourses and mixing/unmixing matrices. If you keep all >> your components, and multiply them with the mixing matrix, you should >> get all your original channel timecourses out again. So: if you don't >> change the data, the data will not be changed :) >> >> Best, >> Eelke >> >> On 15 February 2012 21:19, Shayda Malekpour >> wrote: >> > Dear All, >> > >> > I am using fieldtrip on MEG data set. >> > I want to know if I do not remove any ICA component,? will the data be? >> > the >> >> > same as the original data, or is there is a filter somewhere in the >> > software >> > that changes the data? If so how much does it change it (What is their >> > relative difference?) >> > >> > Thanks, >> > >> > Sheida >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> ------------------------------ >> >> Message: 4 >> Date: Thu, 16 Feb 2012 10:36:05 +0100 >> From: "J?rn M. Horschig" >> To: Email discussion list for the FieldTrip project >>         >> Subject: Re: [FieldTrip] A problem in real-time processing of MEG >>        signal using field trip buffer >> Message-ID: <4F3CCE05.4050109 at donders.ru.nl> >> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" >> >> Dear Soheila, >> >> we were facing the same problem here. Presumably, there is some problem >> in the shared memory module that the buffer is using. Right now, >> however, we could not find out where the error precisely comes from, so >> our best work around is to restart the computer prior recording and >> optimize settings, such as channels and sampling/decimation rate of >> acq2ft. In our lab, we managed to find near-optimal settings, so that >> the buffer crashes only rarely (actually, I never saw it crashing when >> the acquisition computer was freshly restarted). Note that a lower >> number of channels or higher decimation does not mean that it runs more >> stable.  It seems to be literally a trial-and-error approach :/ >> >> In order to track this down further, we need some more information, e.g. >> what MEG system are you using? What's your sampling rate, how many >> channels do you put into the buffer, and what's your decimation rate? It >> would be great if you could send me that information so that we can >> maybe try to track this down. >> >> Best regards, >> J?rn >> >> On 2/14/2012 5:42 PM, Soheila Samiee wrote: >> > Dear group, >> > >> > I use FieldTrip for real-time processing of MEG signals using shared >> > memory and field trip buffer in a machine other than acquisition >> > system. I use matlab for reading the buffer and processing the data. >> > During my data acquisition and sending it to other computer with >> > /acq2ft/ in linux, I face a problem. After sending some blocks of >> > data, this message: "/Internal Converter thread does not keep up with >> > load/" is shown in the terminal of /acq2ft/ and in my matlab session I >> > see an error : "ERROR: the buffer returned an error (517)". It does >> > not depend on sampling rate of data in acquisition system. The problem >> > often solve when I restart the computer which receives the data, but >> > after some minutes of transferring the data I see the message again. >> > >> > Would you please help me in solving this problem? >> > Best Wishes, >> > Soheila >> >> > >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -- >> J?rn M. Horschig >> PhD Student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> Neuronal Oscillations Group >> >> P.O. Box 9101 >> NL-6500 HB Nijmegen >> The Netherlands >> >> Contact: >> E-Mail: jm.horschig at donders.ru.nl >> Tel:    +31-(0)24-36-68493 >> Web: http://www.ru.nl/donders >> >> Visiting address: >> Trigon, room 2.30 >> Kapittelweg 29 >> NL-6525 EN Nijmegen >> The Netherlands >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> >> >> ------------------------------ >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> End of fieldtrip Digest, Vol 15, Issue 17 >> ***************************************** > > > > > -- > Stephen Politzer-Ahles > University of Kansas > Linguistics Department > http://www.linguistics.ku.edu/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From carsten.wolters at uni-muenster.de Thu Feb 16 14:01:36 2012 From: carsten.wolters at uni-muenster.de (Dr. Carsten Wolters) Date: Thu, 16 Feb 2012 14:01:36 +0100 Subject: [FieldTrip] =?iso-8859-1?q?Postdoctoral_research_associate_positi?= =?iso-8859-1?q?on_available__at_the_University_of_M=FCnster?= Message-ID: <4F3CFE30.4050502@uni-muenster.de> Neuroscientist with focus on MR image analysis The Medical Faculty of the University of Münster is searching for a postdoctoral research associate at the 'Translational Research Imaging Center' (TRIC), where a new 3T MR-system for neuroimaging research will be put into operation soon. This position is focused on image processing and optimization to support the interdisciplinary working groups from the faculties of Medicine and Psychology. The position (TVL13) is initially limited to 3 years with possibility of extension. The area of responsibility includes the analysis of structural and functional MR data and the post-processing of fMRI- and DTI- measurements as well as the implementation of new post-processing methods for imaging and spectroscopy. Furthermore, the applicant should be interested in integration of different neuroimaging methods (multimodal integration). Besides an interdisciplinary and team-oriented working style, a high degree of mathematical and statistical knowledge is required. The applicant should possess a master degree (or equivalent) in natural or engineering sciences and a PhD and should be qualified by his scientific work and his own research that will also be pursued at the University of Münster. Applications of women and disabled applicants are explicitly welcome and will be preferred at same qualification, merits and achievements. For further questions please consult Dr. rer. nat. H. Kugel, the responsible senior physicist at the TRIC (Email: kugel at uni-muenster.de, Phone:+49/( 0)251 / 83-56145). The position will be open until filled. Applications should contain a personal statement of research background and interests, CV, list of publications and grants as well as the names of three referees and preprints of the three most important publications. Applications should be send to: *Dekan der Medizinischen Fakultät der Westfälischen Wilhelms-Universität Münster, Albert-Schweitzer-Campus 1, Gebäude D3, 48149 Münster * -- PD.Dr.rer.nat. Carsten Wolters Institute for Biomagnetism and Biosignalanalysis University of Muenster, 48149 Muenster, Germany Tel.: +49/(0)251-83-56904 Fax: +49/(0)251-83-56874 http://biomag.uni-muenster.de -------------- next part -------------- A non-text attachment was scrubbed... Name: MRTPostprocessing_Englisch.pdf Type: application/x-pdf Size: 166979 bytes Desc: not available URL: From jpnv2006 at gmail.com Thu Feb 16 17:35:28 2012 From: jpnv2006 at gmail.com (Juan Pablo Neira) Date: Thu, 16 Feb 2012 17:35:28 +0100 Subject: [FieldTrip] Align EEG electrode positions to BEM headmodel Question Message-ID: Hello, I am trying to align EEG electrodes to an individual MRI and a BEM model.  I am using the example: "Align EEG electrode positions to BEM headmodel" http://fieldtrip.fcdonders.nl/example/align_eeg_electrode_positions_to_bem_headmodel But I am having the next problem in "% align using fiducials" part: * Template structure (label, chanpos and elecpos) - sens_t structure (label, chanpos and elecpos) elec_mni.label = {'Nz', 'LPA', 'RPA'}; elec_mni.chanpos = [   head_Nas   head_Lpa   head_Rpa   ]; elec_mni.elecpos = [   head_Nas   head_Lpa   head_Rpa   ]; elec_mni.unit = 'mm'; % align using fiducials cfg = []; cfg.method = 'fiducial'; cfg.template= elec_mni; cfg.elec     = sens_t; cfg.casesensitive  = 'no';%'yes' or 'no' sens_aligned = ft_electroderealign(cfg); %Error message: %----------------------------------------------------- ??? Subscripted assignment between dissimilar structures. Error in ==> ft_electroderealign at 183     tmp(i) = ft_datatype_sens(template(i)); % ensure up-to-date sensor     descriptions (Oct 2011) %------------------------------------------------------- I have some questions that maybe can help to find the error: -  According to the example in the webpage, there are 2 functions from the private directory used:  electrodenormalize.m & warp_apply.m, but electrodenormalize.m never was used. Also in "% align using fiducials" the method used was 'realignfiducial', but that method is not available in electroderealign function. Is it possible the example is using the wrong function? - How should be the structure of the fiducials in the main sensor structure (sens_t). As 3 more electrodes (label+fid, chanpos+fid and elecpos+fid) or in a different place, for example sens_t.fid.pnt and sens_t.fid.label? By the way I am using Matlab 2011 and fieldtrip version 20120208 Best regards and thanks for the help. Jua Pablo Neira Vesga Christian Albrechts Universität Clinic Kiel, Germany From kd889 at nyu.edu Fri Feb 17 18:08:53 2012 From: kd889 at nyu.edu (Keith Doelling) Date: Fri, 17 Feb 2012 12:08:53 -0500 Subject: [FieldTrip] ft_channelrepair replaces channel data with NaNs after running PCA Message-ID: Hi guys, I'm struggling with my attempts to interpolate channel data for some bad channels. I put in the following code: cfg=[]; cfg.badchannel = 15; cfg.missingchannel = []; cfg.neighbours = neighbours; cfg.trials = 'all'; cleanchdata = ft_channelrepair(cfg,cleandata); the function the displays the following: "the input is raw data with 157 channels and 80 trials repairing channel AG015 using neighbour AG010 using neighbour AG014 using neighbour AG062 using neighbour AG092" suggesting that neighbours have been selected successfully. but a call to chdata.trial(1){15,:) just returns a bunch of NaNs rather than interpolated data I need. I found another email thread similar to this but that solution doesn't seem to apply to me as the neighbours seemed to have been selected successfully. The other interesting caveat is that ft_channelrepair seems to work fine if i run it without having run pca (to reject eyeblink and heartbeat components) beforehand. The code for the component analysis and the subsequent rejection are in separate loops. The PCA is saved into a .mat file and then loaded again when i'm ready to reject the bad components. But for simplicity's sake the important code looks like this. % principle component analysis run with 32 components cfg = []; cfg.channel = (1:157); cfg.runica.pca=32; pca_data = ft_componentanalysis(cfg,data); % view components in order to select bad ones cfg = []; cfg.layout = layout; % specify the layout file that should be used for plotting cfg.viewmode = 'component'; ft_databrowser(cfg, pca_data); waitfor(gcf); % type bad components as user input % for example: if runica002 and runica0003 should be rejected, type "2,3" into the dialogue box badcomps = inputdlg({'Bad Components:'}); badcomps = str2double(csv2cell(badcomps{1})); % reject bad components cfg = []; cfg.component = badcomps; cleandata = ft_rejectcomponent(cfg,pca_data); the variable 'cleandata' i get out from this code is the same cleandata i put in to ft_channelrepair. Are there any ideas as to what I've done wrong here? Let me know if I need to give you guys more information. Thanks for your help, Keith -- Keith Doelling Lab Manager and Research Assistant David Poeppel Lab New York University -------------- next part -------------- An HTML attachment was scrubbed... URL: From karl.doron at gmail.com Sat Feb 18 02:16:50 2012 From: karl.doron at gmail.com (Karl Doron) Date: Fri, 17 Feb 2012 17:16:50 -0800 Subject: [FieldTrip] help with channel combination In-Reply-To: References: Message-ID: Hello, I'm trying to run ft_connectivityanalysis on a reduced set of MEG channels, i.e., left and right posterior channels. Because neighboring channels are highly correlated, I'd like to exclude them and look only at "inter-hemispheric" connections. I'm having some troubling getting ft_channelcombination to produce this set of channels. I have 43 channels per hemisphere giving n(n-1)/2 connections. I made an NX2 matrix using repmat.m and passed it as cfg.channelcmb; however the output of ft_connectivityanalysis gave a vector for 'cohspctrm' rather than a chan_chan_freq matrix. Thanks for any suggestions. Karl Doron UC Santa Barbara -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Sat Feb 18 10:24:02 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Sat, 18 Feb 2012 10:24:02 +0100 Subject: [FieldTrip] help with channel combination In-Reply-To: References: Message-ID: Hi Karl, This is perfectly fine behavior. ft_connectivityanalysis either outputs a 'chan_chan_freq' matrix, or a 'chancmb_freq' matrix. The former will be the output when the input freq-structure contains fourier-spectra, and the cfg lacks a channelcmb field. Ft_connectivityanalysis then computes connectivity between all channel pairs, which can conveniently be stored in a square matrix 'chan_chan' for each frequency. If the freq-structure contains cross-spectra (and power-spectra), or if you specify a cfg.channelcmb in combination with fourierspectra in the input, you will get the connectivity data to be 'chancmb_freq', i.e. each row in the matrix contains a spectrum. The reason for this is that it is a priori unlikely that the channelcmb-array defines a set of channel pairs that can be represented in a square all-to-all matrix. If it is your intention to end up with a square matrix, you may want to consider first doing a subselection of channels, i.e. computing your fourierspectra only on the subset of channels you want to use in a later step, and then call ft_connectivityanalysis without a channelcmb field in the cfg. See for some additional information about the different representation of frequency domain data: http://fieldtrip.fcdonders.nl/faq/in_what_way_can_frequency_domain_data_be_represented_in_fieldtrip Cheers, Jan-Mathijs On Feb 18, 2012, at 2:16 AM, Karl Doron wrote: > Hello, > > I'm trying to run ft_connectivityanalysis on a reduced set of MEG channels, i.e., left and right posterior channels. Because neighboring channels are highly correlated, I'd like to exclude them and look only at "inter-hemispheric" connections. > > I'm having some troubling getting ft_channelcombination to produce this set of channels. I have 43 channels per hemisphere giving n(n-1)/2 connections. I made an NX2 matrix using repmat.m and passed it as cfg.channelcmb; however the output of ft_connectivityanalysis gave a vector for 'cohspctrm' rather than a chan_chan_freq matrix. > > Thanks for any suggestions. > > Karl Doron > UC Santa Barbara > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhaoyizhe at gmail.com Mon Feb 20 11:51:07 2012 From: zhaoyizhe at gmail.com (zhaoyizhe) Date: Mon, 20 Feb 2012 18:51:07 +0800 Subject: [FieldTrip] question about ft_sourceinterpolate Message-ID: <52DE5EF7-93B4-4261-AAC9-A1550A37C986@gmail.com> Dear all, I have a problem in function of 'ft_sourceinterpolate'. I run the scrips below, and data from the ftp sever as the test data. the result is below: ??? Error using ==> ft_checkconfig at 162 The field cfg.parameter is required cfg.parameter='all' has been tried. the result is below: ??? Reference to non-existent field 'all'. Would you mind tell me how to deal with it? Thanks a lot in advance. -------------------------------------- close clc clear load source mri = ft_read_mri('Subject01.mri'); cfg = []; cfg.downsample = 2; sourcePostInt = ft_sourceinterpolate(cfg, sourcePost , mri); -------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From mark.noordenbos at gmail.com Mon Feb 20 12:25:46 2012 From: mark.noordenbos at gmail.com (Mark Noordenbos) Date: Mon, 20 Feb 2012 12:25:46 +0100 Subject: [FieldTrip] clusterstatistics Message-ID: Dear Fieldtrippers, I have a question about how to report the findings using clusterstatistics. I used the cluster method to determine at which channels activity is significant different from zero. The cluster method revealed a significant cluster ranging from about 258-370 ms (using ft_clusterplot). If I only look at a certain channel (e.g., Fz) the activity is only significant during 272-322 ms. The time interval of the cluster is determined by the first and the last sample where the activity is significant, regardless if a certain channel shows significant activity during the complete time interval. For instance, if a certain channel shows significant activity only at sample X and another channel only at sample X+100, the cluster ranges from sample X to X+100. My problem is how to report the finding of the significant cluster. If I report that a significant cluster was found from 258-370 ms and show a plot of the activity at Fz (272-322 ms). Then the time intervals and p-values do not correspond. The stat structure contains only the p-value for the time interval of the cluster and not of the individual channels. Any suggestions or examples of how to report clusterstatistics. Regards, Mark -- Mark Noordenbos, MSc Radboud University Nijmegen Behavioural Science Institute P.O. Box 9104, Room A05.36 6500 HE Nijmegen The Netherlands Email: m.noordenbos at bsi.ru.nl Telephone: +31 24 3612070 Fax: +31 24 3616211 http://www.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From Lilla.Magyari at mpi.nl Mon Feb 20 14:44:57 2012 From: Lilla.Magyari at mpi.nl (Magyari, Lilla) Date: Mon, 20 Feb 2012 14:44:57 +0100 Subject: [FieldTrip] question about ft_sourceinterpolate In-Reply-To: <52DE5EF7-93B4-4261-AAC9-A1550A37C986@gmail.com> References: <52DE5EF7-93B4-4261-AAC9-A1550A37C986@gmail.com> Message-ID: <4F424E59.9030609@mpi.nl> Hi, ft_sourceinterpolate is probably requires the specific field of your functional data that should be interpolated. I do not know what kind of source-reconstruction you did on your data, and what kind of fields your data has (sourcePost), but it will be probably the "avg.pow" field. So, I suggest to try this: cfg.parameter = 'avg.pow'; Best, Lilla zhaoyizhe wrote: > Dear all, > > I have a problem in function of 'ft_sourceinterpolate'. > > I run the scrips below, and data from the ftp sever as the test data. > > the result is below: > ??? Error using ==> ft_checkconfig at 162 > The field cfg.parameter is required > > > cfg.parameter='all' has been tried. > the result is below: > ??? Reference to non-existent field 'all'. > > Would you mind tell me how to deal with it? Thanks a lot in advance. > > > -------------------------------------- > close > clc > clear > > > load source > mri = ft_read_mri('Subject01.mri'); > > cfg = []; > cfg.downsample = 2; > sourcePostInt = ft_sourceinterpolate(cfg, sourcePost , mri); > > -------------------------------------- > > > ------------------------------------------------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- PhD student Language and Cognition Group research assistant Neurobiology of Language Group Max Planck Institute for Psycholinguistics Nijmegen, P.O. Box 310, 6500AH, the Netherlands Phone: 0031 24 3521561 From zhaoyizhe at gmail.com Mon Feb 20 15:22:41 2012 From: zhaoyizhe at gmail.com (zhaoyizhe) Date: Mon, 20 Feb 2012 22:22:41 +0800 Subject: [FieldTrip] question about ft_sourceinterpolate In-Reply-To: <4F424E59.9030609@mpi.nl> References: <52DE5EF7-93B4-4261-AAC9-A1550A37C986@gmail.com> <4F424E59.9030609@mpi.nl> Message-ID: <64945130-6612-4591-B986-69C2A3904F69@gmail.com> Hi, Lilla, Thank you for your timely help! The problem has been solved! Cheers, Yizhe From sla.samiee at gmail.com Mon Feb 20 17:21:58 2012 From: sla.samiee at gmail.com (Soheila Samiee) Date: Mon, 20 Feb 2012 11:21:58 -0500 Subject: [FieldTrip] A problem in real-time processing of MEG signal using field trip buffer In-Reply-To: <4F3CCE05.4050109@donders.ru.nl> References: <4F3CCE05.4050109@donders.ru.nl> Message-ID: Dear Jörn, Thanks for your answer. I use CTF/VSM MedTech System. I use 364 channels and the sampling rate is 1200. The decimation rate is 1. As I saw in my recording there are two reasons for crashing in matlab session one of them is about transferring data which rarely occurs when the system is freshly restarted and the second one is related to reading data from buffer. When the number of samples of data which should be read is high we may see such problem. I wanted to check the timing of MEG System data stream and I used a m-file similar to what is published in fieldtrip website ( http://fieldtrip.fcdonders.nl/example/measuring_the_timing_delay_and_jitter_for_a_real-time_application), I attach the mfile to this email. When I run it step by step there is no problem, but when I run the whole file the problem of crashing matlab is occurred exactly when "i=2" and we are on the line of reading the data (*dat = buffer('get_dat', [s(i-1),s(i)],host,port); *). The problem occurs even if I restarted the computer just before running this file. On the other hand, although when the computer is freshly restarted we won't see any crash in matlab session during transferring data, but sometimes we see the message of "*Internal Converter thread does not keep up with load*" in the *acq2ft *terminal in acquisition system. This problem is depend on the rate of sending the data which is related to number of the channels and sampling rate, when we have more sampling rate or more number of channels we will see this message more times and when this message show on the screen, no data transfer to field trip buffer and we can't read data on the other computer. I appreciate it if you help me solve both of these problems about matlab crash and error in data transferring. All the best, Soheila On Thu, Feb 16, 2012 at 4:36 AM, "Jörn M. Horschig" < jm.horschig at donders.ru.nl> wrote: > Dear Soheila, > > we were facing the same problem here. Presumably, there is some problem in > the shared memory module that the buffer is using. Right now, however, we > could not find out where the error precisely comes from, so our best work > around is to restart the computer prior recording and optimize settings, > such as channels and sampling/decimation rate of acq2ft. In our lab, we > managed to find near-optimal settings, so that the buffer crashes only > rarely (actually, I never saw it crashing when the acquisition computer was > freshly restarted). Note that a lower number of channels or higher > decimation does not mean that it runs more stable. It seems to be > literally a trial-and-error approach :/ > > In order to track this down further, we need some more information, e.g. > what MEG system are you using? What's your sampling rate, how many channels > do you put into the buffer, and what's your decimation rate? It would be > great if you could send me that information so that we can maybe try to > track this down. > > Best regards, > Jörn > > > On 2/14/2012 5:42 PM, Soheila Samiee wrote: > > Dear group, > > I use FieldTrip for real-time processing of MEG signals using shared > memory and field trip buffer in a machine other than acquisition system. I > use matlab for reading the buffer and processing the data. > During my data acquisition and sending it to other computer with *acq2ft*in linux, I face a problem. After sending some blocks of data, this > message: "*Internal Converter thread does not keep up with load*" is > shown in the terminal of *acq2ft* and in my matlab session I see an error > : "ERROR: the buffer returned an error (517)". It does not depend on > sampling rate of data in acquisition system. The problem often solve when I > restart the computer which receives the data, but after some minutes of > transferring the data I see the message again. > > Would you please help me in solving this problem? > Best Wishes, > Soheila > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: DataStreamTiming.m Type: text/x-objcsrc Size: 1005 bytes Desc: not available URL: From g.piantoni at nin.knaw.nl Mon Feb 20 18:41:22 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Mon, 20 Feb 2012 18:41:22 +0100 Subject: [FieldTrip] clusterstatistics In-Reply-To: References: Message-ID: Hi Mark, It seems to me that clusterstatistics is giving the appropriate answer. Indeed it takes advantage of the information which can be sparse over multiple channels/frequency/time bins. The only criterion is that this activity is contiguous. I don't follow your example about significant activity at X and X+100 on two different channels. There should be some continuity between the two. As you mentioned, the cluster can span one channels between 0 and 100 and in another neighboring channel between 50 and 150. The cluster will correctly include both channels and the time window between 0 and 150. This is because there is some overlap in time between the two channels. If you think in terms of activity, you can report that activity is significantly different from baseline between 258 and 370 ms, over your channels. The p-value only belongs to the cluster, not to the single time point or channel. If you use bonferroni correction, you can attach single p-values to each timepoint/channel. If you have a priori hypothesis that you expect activity in Fz, you can specify a single channel in timelockstatistics. Depending your data, you might see more power (because you're testing fewer channels at the same time). Hope this helps, Gio -- 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.giovannipiantoni.com On Mon, Feb 20, 2012 at 12:25, Mark Noordenbos wrote: > Dear Fieldtrippers, > > > I have a question about how to report the findings using clusterstatistics. > I used the cluster method to determine at which channels activity is > significant different from zero. > > The cluster method revealed a significant cluster ranging from about 258-370 > ms (using ft_clusterplot). If I only look at a certain channel (e.g., Fz) > the activity is only significant during 272-322 ms. > > > The time interval of the cluster is determined by the first and the last > sample where the activity is significant, regardless if a certain channel > shows significant activity during the complete time interval. For instance, > if a certain channel shows significant activity only at sample X and another > channel only at sample X+100, the cluster ranges from sample X to X+100. > > > My problem is how to report the finding of the significant cluster. If I > report that a significant cluster was found from 258-370 ms and show a plot > of the activity at Fz (272-322 ms). Then the time intervals and p-values do > not correspond. The stat structure contains only the p-value for the time > interval of the cluster and not of the individual channels. > > > Any suggestions or examples of how to report clusterstatistics. > > > Regards, > Mark > > -- > Mark Noordenbos, MSc > > Radboud University Nijmegen > Behavioural Science Institute > > P.O. Box 9104, Room A05.36 > 6500 HE Nijmegen > The Netherlands > > Email: m.noordenbos at bsi.ru.nl > Telephone: +31 24 3612070 > Fax:          +31 24 3616211 > > http://www.ru.nl > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From drivolta81 at gmail.com Tue Feb 21 11:17:00 2012 From: drivolta81 at gmail.com (Davide Rivolta) Date: Tue, 21 Feb 2012 11:17:00 +0100 Subject: [FieldTrip] CTF to SPM Message-ID: Dear all, I wish to ask whether there is a way to import anatomical CTF files (.V2) into SPM. Thanks, Davide -- Davide Rivolta, PhD -------------- next part -------------- An HTML attachment was scrubbed... URL: From tomh at kurage.nimh.nih.gov Tue Feb 21 17:16:51 2012 From: tomh at kurage.nimh.nih.gov (Tom Holroyd (NIH/NIMH) [E]) Date: Tue, 21 Feb 2012 11:16:51 -0500 Subject: [FieldTrip] CTF to SPM In-Reply-To: References: Message-ID: <4F43C373.9090105@kurage.nimh.nih.gov> You can use AFNI to convert v2 .mri files to .nii files. Not v3 though, use CTF's MRIViewer to convert v3 format to v2 format and then use AFNI. I assume SPM can read .nii files. Davide Rivolta wrote: > Dear all, > > I wish to ask whether there is a way to import anatomical CTF files > (.V2) into SPM. >
Dr. Tom
--
How long have I investigated this one thing, the brain of the leech, so that here the slippery truth might no longer slip from me! Here is my domain! Thus spoke Zarathustra. From jan.schoffelen at donders.ru.nl Tue Feb 21 18:05:06 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 21 Feb 2012 18:05:06 +0100 Subject: [FieldTrip] CTF to SPM In-Reply-To: References: Message-ID: <3672CA8D-132F-4664-8251-56DF2F97FA73@donders.ru.nl> Hi Davide, If you use ft_read_mri to read in your *.mri you can use ft_volumewrite to save the volumetric data as nifti. You can look into the documentation of ft_volumewrite to see how this works. Best, Jan-Mathijs On Feb 21, 2012, at 11:17 AM, Davide Rivolta wrote: > Dear all, > > I wish to ask whether there is a way to import anatomical CTF files (.V2) into SPM. > > Thanks, > Davide > > > -- > Davide Rivolta, PhD > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From kd889 at nyu.edu Tue Feb 21 18:48:10 2012 From: kd889 at nyu.edu (Keith Doelling) Date: Tue, 21 Feb 2012 12:48:10 -0500 Subject: [FieldTrip] ft_channelrepair replaces channel data with NaNs after running PCA In-Reply-To: References: Message-ID: Hi guys, For those that are interested I figured out the problem. Somewhere in the process of running component analysis and then component rejection, fieldtrip was taking .chanpos and .chanori in my .grad field and replacing all the values with NaNs. I fixed the problem by adding cleandata.grad = data.grad just after component rejection. It would be great though, if some one could look at the ft_componentanalysis and ft_rejectcomponent functions and figure out why the grad information is being lost. Thanks! Keith On Fri, Feb 17, 2012 at 12:08 PM, Keith Doelling wrote: > Hi guys, > > I'm struggling with my attempts to interpolate channel data for some bad > channels. I put in the following code: > > > cfg=[]; > cfg.badchannel = 15; > cfg.missingchannel = []; > cfg.neighbours = neighbours; > cfg.trials = 'all'; > cleanchdata = ft_channelrepair(cfg,cleandata); > > > the function the displays the following: > > "the input is raw data with 157 channels and 80 trials > repairing channel AG015 > using neighbour AG010 > using neighbour AG014 > using neighbour AG062 > using neighbour AG092" > > suggesting that neighbours have been selected successfully. > > but a call to chdata.trial(1){15,:) just returns a bunch of NaNs rather > than interpolated data I need. > > I found another email thread similar to this but that solution doesn't > seem to apply to me as the neighbours seemed to have been selected > successfully. > > The other interesting caveat is that ft_channelrepair seems to work fine > if i run it without having run pca (to reject eyeblink and heartbeat > components) beforehand. > > The code for the component analysis and the subsequent rejection are in > separate loops. The PCA is saved into a .mat file and then loaded again > when i'm ready to reject the bad components. But for simplicity's sake the > important code looks like this. > > > % principle component analysis run with 32 components > cfg = []; > cfg.channel = (1:157); > cfg.runica.pca=32; > pca_data = ft_componentanalysis(cfg,data); > > % view components in order to select bad ones > cfg = []; > cfg.layout = layout; % specify the layout file that should be used > for plotting > cfg.viewmode = 'component'; > ft_databrowser(cfg, pca_data); > waitfor(gcf); > > % type bad components as user input > % for example: if runica002 and runica0003 should be rejected, type > "2,3" into the dialogue box > badcomps = inputdlg({'Bad Components:'}); > badcomps = str2double(csv2cell(badcomps{1})); > > % reject bad components > cfg = []; > cfg.component = badcomps; > cleandata = ft_rejectcomponent(cfg,pca_data); > > > the variable 'cleandata' i get out from this code is the same cleandata i > put in to ft_channelrepair. > > Are there any ideas as to what I've done wrong here? Let me know if I need > to give you guys more information. > > Thanks for your help, > Keith > > -- > Keith Doelling > Lab Manager and Research Assistant > David Poeppel Lab > New York University > > -- Keith Doelling Lab Manager and Research Assistant David Poeppel Lab New York University -------------- next part -------------- An HTML attachment was scrubbed... URL: From akiko.ikkai at gmail.com Tue Feb 21 18:52:27 2012 From: akiko.ikkai at gmail.com (Akiko Ikkai) Date: Tue, 21 Feb 2012 12:52:27 -0500 Subject: [FieldTrip] volume conduction model missing .mat In-Reply-To: References: <2341406D-6422-4FD3-AD3C-73D1BF70B6CF@mac.com> Message-ID: Hi Gio, Thank you for sharing your script. cfg.output = 'tpm' for ft_volumesegment seems to make a big difference, and now I could go all the way to actually running beamformer on my data! Of course, I had to add a few things. For example, in order to clean up segmented images, I added lines as seg2.brain(:,:,1:4)=0; seg2.skull(:,:,1:2)=0; to make sure scalp, skull and brain do not intersept at neck. Also did something like below for each tissue type (otherwise the resulting beamformer was too small on the brain) newsbrain = imdilate(seg2.brain,strel_bol(1)); seg2.brain = newsbrain; Fieldtrip developers, are there documentations for "cfg.output = 'tpm' " for segmentation? ft_segmentation help page simply says it's a default option. Thanks for your help! Akiko On Thu, Feb 16, 2012 at 5:52 AM, Gio Piantoni wrote: > Hi Akiko, > > What do you mean "problematic" exactly? From my understanding, there > are 4 steps to get from the MRI to the forward model. > 1. from MRI to segmentation > 2. from segmentation to mesh (bnd) > 3. from mesh to headmodel > 4. from headmodel to forward model > > Here is the code I use. It seems to work fine, but experts might want > to chip in and improve it. > 1. from MRI to segmentation > > %-----------------% > %-read MRI > mrifile = '/path/to/your/mri.nii.gz'; > mri = ft_read_mri(mrifile); > %-----------------% > > %-----------------% > %-segmenting the volume, Tissue Probability Maps > % It takes time to run 'tpm' > cfg1 = []; > cfg1.threshold = []; > cfg1.output = 'tpm'; > cfg1.coordsys = 'spm'; > tpm = ft_volumesegment(cfg1, mri); > tpm.anatomy = mri.anatomy; > %-----------------% > > %-----------------% > %-segmenting the volume > % this is faster after tpm > cfg1 = []; > cfg1.threshold = 1; % 1 is default, my MRI scalps were noisy, so I had > to make it lower. > cfg1.output = 'scalp'; > cfg1.coordsys = 'spm'; > segscalp = ft_volumesegment(cfg1, tpm); > > cfg1 = []; > cfg1.threshold = []; > cfg1.output = {'skull' 'brain'}; > cfg1.coordsys = 'spm'; > segment = ft_volumesegment(cfg1, tpm); > segment.scalp = segscalp.scalp; > %-----------------% > > Check the output with ft_sourceplot > > 2. from segmentation to mesh (bnd) > > %-----------------% > %-prepare mesh for skull and brain (easy) > cfg2 = []; > cfg2.tissue = {'skull', 'brain'}; > cfg2.numvertices = [1200 1000]; > cfg2.transform = segment.transform; > bnd = ft_prepare_mesh_new(cfg2, segment); > %-----------------% > > %-----------------% > %-prepare mesh for scalp (we need to be more liberal with threshold, > bc of poor quality of MRI) > cfg2 = []; > cfg2.tissue = {'scalp'}; > cfg2.numvertices = 2500; > cfg2.thresholdseg = 0.1; > cfg2.transform = segment.transform; > scalp = ft_prepare_mesh_new(cfg2, segment); > %-----------------% > > %-----------------% > %-combine scalp and bnd > bnd = [scalp bnd]; > ft_plot_mesh(bnd(1), 'facealpha', .5) > hold on > ft_plot_mesh(bnd(2), 'facecolor', 'red') > %-----------------% > > If bnd is good, no intersection between meshes and the outline looks > nice, the following should run without problems. Please, do check your > bnd. > Segmentation and ft_prepare_mesh_new work really well. Another > approach to get nice meshes is to skip step 1 and 2 and use > Freesurfer/MNE. You can read the meshes in fieldtrip > (ft_read_headshape, I think). The meshes are in the "bem" folder of > Freesurfer, but I don't remember off the top of my head which files > you should read ("outer_skull, inner_skull", I think). > These meshes have a very very high resolution, you can scale them down > with "reducepatch" in Matlab. > > 3. from mesh to headmodel > %-----------------% > %-headmodel > cfg3 = []; > cfg3.method = 'bem_dipoli'; > cfg3.conductivity = [0.33 0.0042 0.33]; > vol = ft_prepare_headmodel(cfg3, bnd); > %-----------------% > > You can really pick your favorite here: dipoli, openmeeg, bemcp. This > will take time (the more time, the more points on your meshes). > > 4. from headmodel to forward model > You last problem is to get electrodes and headmodel in the same space. > The template in SPM is already in MNI space, your individual MRIs > probably not. You can realign them to MNI space before step 1 using > SPM or FSL. > > elec = ft_read_sens(sensfile); > elec = ft_convert_units(elec, 'mm'); > > %-------% > %-simple transformation (based on visual realignment) > % elecM is an affine matrix that you can get from ft_electroderealign > % electrodes do not need to match the scalp perfectly, but they should > be pretty close by. > elec.chanpos = warp_apply(elecM, elec.chanpos); > elec.elecpos = warp_apply(elecM, elec.elecpos); > %-------% > > [vol, elec] = ft_prepare_vol_sens(vol, elec); > % now you should check that the electrodes are on the scalp. > %-----------------% > > %-----------------% > %-prepare leadfield > cfg4 = []; > cfg4.elec = elec; > cfg4.vol = vol; > cfg4.grid.xgrid = -70:10:70; > cfg4.grid.ygrid = -110:10:80; > cfg4.grid.zgrid = -60:10:90; > cfg4.inwardshift = 1; % to avoid dipoles on the border of bnd(3), > which are very instable > cfg4.grid.tight = 'no'; > cfg4.feedback = 'none'; > lead = ft_prepare_leadfield(cfg4, []); > % use ft_plot_topo3d and ft_plot_dipole to check whether the > projection of your dipole onto the scalp makes sense. > %-----------------% > > "lead" should be your subject-specific, electrode-specific leadfield. > There are quite a few parameters that you can change, but a clean > segmentation and non-intersecting, smooth and realistic-looking meshes > are a must. > Then, using dipoli, openmeeg or bemcp should not change your forward > model too much. > Sorry if some points are not clear, but you should really look at your > MRI/segmentation/meshes/electrodes/forward model as much as possible. > > Hope this will get you started. I appreciate any feedback on improving > the code, this is just my personal attempt. > > Cheers > > Gio > > On Wed, Feb 15, 2012 at 17:45, Akiko Ikkai wrote: > > Dear Fieldtrip users, > > > > Thank you Patrick, Nathan & Gio for your inputs. My MRI anatomical images > > need extensive cleaning (enhance contrasts, get rid of non-zero voxels > > outside the brain, etc...) before segmentation, as well as adjusting > > cfg.threshold for each tissue type during segmentation and each subject. > At > > least testing with SPM standard MRI, segmentation and forward modeling > works > > OK now. > > > > Individual subject's MRI, though, is still problematic, and I have a > > question for Fieldtrip developers: could you let me know whether "Create > BEM > > headmodel for EEG ( > > http://fieldtrip.fcdonders.nl/example/create_bem_headmodel_for_eeg )" > > routine is what you recommend, or it's integrated into a newer function > with > > newer cfg options? Is there a page I missed on the web? > > > > Thank you so much for your time! > > Akiko > > > > On Fri, Feb 10, 2012 at 4:36 AM, Gio Piantoni > > wrote: > >> > >> Hi Akiki and Patrick, > >> > >> I agree with Nathan about segmentation problems. I had the same > >> problem when two of the three meshes intersected each other. Before > >> you run the forward model, you should check the segmentation (bnd) > >> using ft_plot_mesh. > >> ft_plot_mesh(bnd(1), 'facealpha', .5) > >> hold on > >> ft_plot_mesh(bnd(2), 'facecolor', 'r') > >> You will see that the two meshes intersect with each other. Depending > >> on how you created the meshes, you should fix the parameters in such a > >> way that they don't intersect. For example, ft_volumesegment has a > >> cfg.threshold option (you can check how the segmentation went with > >> ft_sourceplot) and ft_prepare_mesh_new has cfg.thresholdseg and > >> cfg.smoothseg. > >> > >> I think that the meshes in SPM are computed on an (affine-transformed) > >> template and not on the anatomically derived meshes. The template is > >> more robust and that's why the two surfaces do not intersect. > >> > >> In general, the segmentation depends on the quality of your MRIs and > >> you should really visually check the segmentation and meshes. When > >> those look ok, the BEM forward model usually works. Hope this helps. > >> > >> Cheers, > >> > >> Gio > >> > >> On Fri, Feb 10, 2012 at 09:00, Nathan Weisz > wrote: > >> > Hi Akiki, > >> > > >> > I am not a headmodel expert. > >> > but looking at the output message, it seems your segementation did not > >> > go > >> > too well (see the "intersect" message). my intuition is then then the > >> > next > >> > temporary file *.ama is not created and ft_prepare_bemmodel then > simply > >> > says > >> > ciao. > >> > > >> > perhaps you want to check / redo the segmentation? > >> > > >> > good luck, > >> > nathan > >> > > >> > > >> > On 09.02.2012, at 23:04, Akiko Ikkai wrote: > >> > > >> > Hi, > >> > > >> > I'm trying to create a volume conduction model for my EEG study based > on > >> > anatomical MRI, and having trouble with ft_prepare_bemmodel > >> > > >> > when I run > >> > cfg = []; > >> > cfg.tissue = [7 4 1]; % value for brain, skull, and scalp > >> > cfg.conductivity = [1 1/80 1]*.33; % after standard_BEM.zip data > >> > cfg.isolatedsource = true; > >> > cfg.method = 'dipoli'; > >> > cfg.sourceunits = 'mm'; > >> > cfg.mriunits = 'mm'; > >> > vol = ft_prepare_bemmodel(cfg, seg4bem); > >> > > >> > I get the following error message while ft_prepare_bemmodel is > running: > >> > > >> > Fatal error in dipoli: interface > >> > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and > >> > /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect > >> > at vertex 1402 of > >> > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri > >> > > >> > Warning: an error ocurred while running dipoli > >> >> In dipoli at 94 > >> > In ft_prepare_bemmodel at 112 > >> > Error using ==> fread > >> > Invalid file identifier. Use fopen to generate a valid file > identifier. > >> > Warning: File > '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' > >> > not > >> > found. > >> >> In dipoli at 102 > >> > In ft_prepare_bemmodel at 112 > >> > > >> > > >> > and the output vol is missing .mat, which causes an error > >> > during ft_sourceanalysis. > >> >>> vol > >> > vol = > >> > cond: [0.3300 0.0041 0.3300] > >> > bnd: [1x3 struct] > >> > source: 3 > >> > skin_surface: 3 > >> > skin: 1 > >> > type: 'dipoli' > >> > > >> > Does anyone know how to correct for "fatal error" so > >> > that ft_prepare_bemmodel creates the correct volume conduction model? > I > >> > opened .tri file and removed line 1402, but got the same results. > >> > > >> > Thanks in advance! Akiko > >> > > >> > -- > >> > Akiko Ikkai, Ph.D. > >> > Postdoctoral Fellow > >> > Department of Psychological and Brain Sciences > >> > Johns Hopkins University > >> > Ames Hall, 3400 N. Charles St. > >> > Baltimore, MD 21218 > >> > > >> > > >> > _______________________________________________ > >> > fieldtrip mailing list > >> > fieldtrip at donders.ru.nl > >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> > > >> > > >> > > >> > _______________________________________________ > >> > fieldtrip mailing list > >> > fieldtrip at donders.ru.nl > >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > -- > > Akiko Ikkai, Ph.D. > > Postdoctoral Fellow > > Department of Psychological and Brain Sciences > > Johns Hopkins University > > Ames Hall, 3400 N. Charles St. > > Baltimore, MD 21218 > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Akiko Ikkai, Ph.D. Postdoctoral Fellow Department of Psychological and Brain Sciences Johns Hopkins University Ames Hall, 3400 N. Charles St. Baltimore, MD 21218 -------------- next part -------------- An HTML attachment was scrubbed... URL: From drivolta81 at gmail.com Wed Feb 22 10:05:01 2012 From: drivolta81 at gmail.com (Davide Rivolta) Date: Wed, 22 Feb 2012 10:05:01 +0100 Subject: [FieldTrip] CTF to SPM In-Reply-To: <3672CA8D-132F-4664-8251-56DF2F97FA73@donders.ru.nl> References: <3672CA8D-132F-4664-8251-56DF2F97FA73@donders.ru.nl> Message-ID: Thank you for the replies. I am trying with ft_volumewrite. I have a small problem. the configuration wants me to specify the cfg.parameter, that is a "string, describing the functional data to be processed, e.g. 'pow', 'coh' or 'nai' ". I am a bit confused, since I have anatomical data, and I am not sure what to put here. Any ideas? Thanks a lot, Davide On Tue, Feb 21, 2012 at 6:05 PM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Hi Davide, > > If you use ft_read_mri to read in your *.mri you can use ft_volumewrite to > save the volumetric data as nifti. You can look into the documentation of > ft_volumewrite to see how this works. > > Best, > > Jan-Mathijs > > On Feb 21, 2012, at 11:17 AM, Davide Rivolta wrote: > > Dear all, > > > I wish to ask whether there is a way to import anatomical CTF files (.V2) > into SPM. > > > Thanks, > Davide > > > -- > Davide Rivolta, PhD > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Davide Rivolta, PhD -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Feb 22 10:47:02 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 22 Feb 2012 10:47:02 +0100 Subject: [FieldTrip] CTF to SPM In-Reply-To: References: <3672CA8D-132F-4664-8251-56DF2F97FA73@donders.ru.nl> Message-ID: <056A85D1-7E54-44B6-9CFA-DCB2BA88C27B@donders.ru.nl> Dear Davide, Did you try 'anatomy' ? BW, Jan-Mathijs On Feb 22, 2012, at 10:05 AM, Davide Rivolta wrote: > Thank you for the replies. > I am trying with ft_volumewrite. > > I have a small problem. the configuration wants me to specify the cfg.parameter, that is a "string, describing the functional data to be processed, e.g. 'pow', 'coh' or 'nai' ". > I am a bit confused, since I have anatomical data, and I am not sure what to put here. > > Any ideas? > > Thanks a lot, > Davide > > > On Tue, Feb 21, 2012 at 6:05 PM, jan-mathijs schoffelen wrote: > Hi Davide, > > If you use ft_read_mri to read in your *.mri you can use ft_volumewrite to save the volumetric data as nifti. You can look into the documentation of ft_volumewrite to see how this works. > > Best, > > Jan-Mathijs > > On Feb 21, 2012, at 11:17 AM, Davide Rivolta wrote: > >> Dear all, >> >> I wish to ask whether there is a way to import anatomical CTF files (.V2) into SPM. >> >> Thanks, >> Davide >> >> >> -- >> Davide Rivolta, PhD >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Davide Rivolta, PhD > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From drivolta81 at gmail.com Wed Feb 22 11:04:11 2012 From: drivolta81 at gmail.com (Davide Rivolta) Date: Wed, 22 Feb 2012 11:04:11 +0100 Subject: [FieldTrip] CTF to SPM In-Reply-To: <056A85D1-7E54-44B6-9CFA-DCB2BA88C27B@donders.ru.nl> References: <3672CA8D-132F-4664-8251-56DF2F97FA73@donders.ru.nl> <056A85D1-7E54-44B6-9CFA-DCB2BA88C27B@donders.ru.nl> Message-ID: Thanks again for the help. I still get an error regarding the name. Maybe is silly. This is my script: for i = 1:size(mri,1) fullname = strcat(inpath, mri{i,1}, '_V2.mri'); mri_V2 = ft_read_mri(fullname); cfg = []; cfg.parameter = 'anatomy'; cfg.filename = mri_V2; cfg.filetype = 'nifti'; ft_volumewrite(cfg, mri_V2); end; ?? Error using ==> fileparts at 17 Input must be a row vector of characters. Error in ==> ft_volumewrite at 411 [pathstr, name, ext] = fileparts(cfg.filename); Thanks again, Davide On Wed, Feb 22, 2012 at 10:47 AM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Dear Davide, > > Did you try 'anatomy' ? > > BW, > > Jan-Mathijs > > > On Feb 22, 2012, at 10:05 AM, Davide Rivolta wrote: > > Thank you for the replies. > I am trying with ft_volumewrite. > > I have a small problem. the configuration wants me to specify the > cfg.parameter, that is a "string, describing the functional data to be > processed, e.g. 'pow', 'coh' or 'nai' ". > I am a bit confused, since I have anatomical data, and I am not sure what > to put here. > > Any ideas? > > Thanks a lot, > Davide > > > On Tue, Feb 21, 2012 at 6:05 PM, jan-mathijs schoffelen < > jan.schoffelen at donders.ru.nl> wrote: > >> Hi Davide, >> >> If you use ft_read_mri to read in your *.mri you can use ft_volumewrite >> to save the volumetric data as nifti. You can look into the documentation >> of ft_volumewrite to see how this works. >> >> Best, >> >> Jan-Mathijs >> >> On Feb 21, 2012, at 11:17 AM, Davide Rivolta wrote: >> >> Dear all, >> >> >> I wish to ask whether there is a way to import anatomical CTF files (.V2) >> into SPM. >> >> >> Thanks, >> Davide >> >> >> -- >> Davide Rivolta, PhD >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Davide Rivolta, PhD > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Davide Rivolta, PhD -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Feb 22 12:04:45 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 22 Feb 2012 12:04:45 +0100 Subject: [FieldTrip] CTF to SPM In-Reply-To: References: <3672CA8D-132F-4664-8251-56DF2F97FA73@donders.ru.nl> <056A85D1-7E54-44B6-9CFA-DCB2BA88C27B@donders.ru.nl> Message-ID: Hi Davide, Perhaps putting the filename as a 'string' may do the trick. In that case it was indeed silly ;-). BW, JM On Feb 22, 2012, at 11:04 AM, Davide Rivolta wrote: > Thanks again for the help. I still get an error regarding the name. Maybe is silly. > > This is my script: > > > for i = 1:size(mri,1) > fullname = strcat(inpath, mri{i,1}, '_V2.mri'); > mri_V2 = ft_read_mri(fullname); > > cfg = []; > cfg.parameter = 'anatomy'; > cfg.filename = mri_V2; > cfg.filetype = 'nifti'; > ft_volumewrite(cfg, mri_V2); > > end; > > ?? Error using ==> fileparts at 17 > Input must be a row vector of characters. > Error in ==> ft_volumewrite at 411 > [pathstr, name, ext] = fileparts(cfg.filename); > > > > Thanks again, > Davide > > > > > On Wed, Feb 22, 2012 at 10:47 AM, jan-mathijs schoffelen wrote: > Dear Davide, > > Did you try 'anatomy' ? > > BW, > > Jan-Mathijs > > > On Feb 22, 2012, at 10:05 AM, Davide Rivolta wrote: > >> Thank you for the replies. >> I am trying with ft_volumewrite. >> >> I have a small problem. the configuration wants me to specify the cfg.parameter, that is a "string, describing the functional data to be processed, e.g. 'pow', 'coh' or 'nai' ". >> I am a bit confused, since I have anatomical data, and I am not sure what to put here. >> >> Any ideas? >> >> Thanks a lot, >> Davide >> >> >> On Tue, Feb 21, 2012 at 6:05 PM, jan-mathijs schoffelen wrote: >> Hi Davide, >> >> If you use ft_read_mri to read in your *.mri you can use ft_volumewrite to save the volumetric data as nifti. You can look into the documentation of ft_volumewrite to see how this works. >> >> Best, >> >> Jan-Mathijs >> >> On Feb 21, 2012, at 11:17 AM, Davide Rivolta wrote: >> >>> Dear all, >>> >>> I wish to ask whether there is a way to import anatomical CTF files (.V2) into SPM. >>> >>> Thanks, >>> Davide >>> >>> >>> -- >>> Davide Rivolta, PhD >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Davide Rivolta, PhD >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Davide Rivolta, PhD > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From drivolta81 at gmail.com Wed Feb 22 12:07:23 2012 From: drivolta81 at gmail.com (Davide Rivolta) Date: Wed, 22 Feb 2012 12:07:23 +0100 Subject: [FieldTrip] CTF to SPM In-Reply-To: References: <3672CA8D-132F-4664-8251-56DF2F97FA73@donders.ru.nl> <056A85D1-7E54-44B6-9CFA-DCB2BA88C27B@donders.ru.nl> Message-ID: Yep, I realized it after sending the email. It was silly indeed. It works fine now, Thanks, Davide On Wed, Feb 22, 2012 at 12:04 PM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Hi Davide, > > Perhaps putting the filename as a 'string' may do the trick. In that case > it was indeed silly ;-). > > BW, > > JM > > On Feb 22, 2012, at 11:04 AM, Davide Rivolta wrote: > > Thanks again for the help. I still get an error regarding the name. > Maybe is silly. > > This is my script: > > > for i = 1:size(mri,1) > fullname = strcat(inpath, mri{i,1}, '_V2.mri'); > mri_V2 = ft_read_mri(fullname); > > cfg = []; > cfg.parameter = 'anatomy'; > cfg.filename = mri_V2; > cfg.filetype = 'nifti'; > ft_volumewrite(cfg, mri_V2); > > end; > > ?? Error using ==> fileparts at 17 > Input must be a row vector of characters. > Error in ==> ft_volumewrite at 411 > [pathstr, name, ext] = fileparts(cfg.filename); > > > > Thanks again, > Davide > > > > > On Wed, Feb 22, 2012 at 10:47 AM, jan-mathijs schoffelen < > jan.schoffelen at donders.ru.nl> wrote: > >> Dear Davide, >> >> Did you try 'anatomy' ? >> >> BW, >> >> Jan-Mathijs >> >> >> On Feb 22, 2012, at 10:05 AM, Davide Rivolta wrote: >> >> Thank you for the replies. >> I am trying with ft_volumewrite. >> >> I have a small problem. the configuration wants me to specify the >> cfg.parameter, that is a "string, describing the functional data to be >> processed, e.g. 'pow', 'coh' or 'nai' ". >> I am a bit confused, since I have anatomical data, and I am not sure what >> to put here. >> >> Any ideas? >> >> Thanks a lot, >> Davide >> >> >> On Tue, Feb 21, 2012 at 6:05 PM, jan-mathijs schoffelen < >> jan.schoffelen at donders.ru.nl> wrote: >> >>> Hi Davide, >>> >>> If you use ft_read_mri to read in your *.mri you can use ft_volumewrite >>> to save the volumetric data as nifti. You can look into the documentation >>> of ft_volumewrite to see how this works. >>> >>> Best, >>> >>> Jan-Mathijs >>> >>> On Feb 21, 2012, at 11:17 AM, Davide Rivolta wrote: >>> >>> Dear all, >>> >>> >>> I wish to ask whether there is a way to import anatomical CTF files >>> (.V2) into SPM. >>> >>> >>> Thanks, >>> Davide >>> >>> >>> -- >>> Davide Rivolta, PhD >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> Jan-Mathijs Schoffelen, MD PhD >>> >>> Donders Institute for Brain, Cognition and Behaviour, >>> Centre for Cognitive Neuroimaging, >>> Radboud University Nijmegen, The Netherlands >>> >>> Max Planck Institute for Psycholinguistics, >>> Nijmegen, The Netherlands >>> >>> J.Schoffelen at donders.ru.nl >>> Telephone: +31-24-3614793 >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> Davide Rivolta, PhD >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Davide Rivolta, PhD > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Davide Rivolta, PhD -------------- next part -------------- An HTML attachment was scrubbed... URL: From jnortonf at uci.edu Thu Feb 23 04:28:24 2012 From: jnortonf at uci.edu (Jessamy Norton-Ford) Date: Wed, 22 Feb 2012 19:28:24 -0800 Subject: [FieldTrip] Fieldtrip tutorial error: trialfun Message-ID: Hello, I am new to Fieldtrip, and have run into the following problems running through the tutorial cfg = []; % empty configuration cfg.dataset = 'Subject01.ds'; % name of CTF dataset cfg.trialdef.eventtype = 'backpanel trigger'; cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 2; cfg.trialdef.eventvalue = 3; % event value of FIC cfg = ft_definetrial(cfg); Warning: no trialfun was specified, using trialfun_general > In ft_definetrial at 123 evaluating trialfunction 'trialfun_general' Warning: adding /Users/jessamynorton-ford/Documents/MATLAB/fieldtrip-20120222/external/ctf toolbox to your Matlab path readCTFds: Data set error : size of meg4 file(s) 0 bytes (from dir command) 179071200 bytes (from res4 file) reading the events from 'Subject01.ds/Subject01.res4' readCTFds: Data set error : size of meg4 file(s) 0 bytes (from dir command) 179071200 bytes (from res4 file) ??? Attempt to reference field of non-structure array. Error in ==> trialfun_general at 118 sel = ismember({event.type}, cfg.trialdef.eventtype); Error in ==> ft_definetrial at 166 [trl, event] = feval(cfg.trialfun, cfg); I found a somewhat similar issue on the boards from May 2011 ( http://mailman.science.ru.nl/pipermail/fieldtrip/2011-May/003827.html), and have since tried several instantiations of FieldTrip (though the version I was running when I first got the error was actually very new). So far I have tried: fieldtrip-20111004 fieldtrip-20111101 fieldtrip-20120220 fieldtrip-20120222 here is my ver info in case it is helpful: MATLAB Version 7.11.0.584 (R2010b) Operating System: Mac OS X Version: 10.6.2 Build: 10C540 Java VM Version: Java 1.6.0_15-b03-219 with Apple Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode ------------------------------------------------------------------------------------- Any suggestions of likely incompatibilities/mistakes on my part would be most helpful. Thank you, -- Jessamy Norton-Ford Doctoral Student, Department of Cognitive Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Feb 23 09:25:58 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 23 Feb 2012 09:25:58 +0100 Subject: [FieldTrip] Fieldtrip tutorial error: trialfun In-Reply-To: References: Message-ID: Dear Jessamy, This looks like you are calling the function from the wrong directory. I can reproduce your error when I call ft_redefinetrial from the following location: XXXXXX/Subject01.ds instead, you should call the function from: XXXXXX, i.e. one directory up (so type 'cd ../' to get there), or use an absolute path in cfg.dataset (i.e. cfg.dataset = '/XXXXXX/Subject01.ds') Best wishes, Jan-Mathijs On Feb 23, 2012, at 4:28 AM, Jessamy Norton-Ford wrote: > Hello, > > I am new to Fieldtrip, and have run into the following problems running through the tutorial > > cfg = []; % empty configuration > cfg.dataset = 'Subject01.ds'; % name of CTF dataset > cfg.trialdef.eventtype = 'backpanel trigger'; > cfg.trialdef.prestim = 1; > cfg.trialdef.poststim = 2; > cfg.trialdef.eventvalue = 3; % event value of FIC > cfg = ft_definetrial(cfg); > > Warning: no trialfun was specified, using trialfun_general > > > In ft_definetrial at 123 > evaluating trialfunction 'trialfun_general' > > Warning: adding > /Users/jessamynorton-ford/Documents/MATLAB/fieldtrip-20120222/external/ctf > toolbox to your Matlab path > > readCTFds: Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file) > > reading the events from 'Subject01.ds/Subject01.res4' > > readCTFds: Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file) > > ??? Attempt to reference field of non-structure array. > > Error in ==> trialfun_general at 118 > sel = ismember({event.type}, cfg.trialdef.eventtype); > > Error in ==> ft_definetrial at 166 > [trl, event] = feval(cfg.trialfun, cfg); > > I found a somewhat similar issue on the boards from May 2011 (http://mailman.science.ru.nl/pipermail/fieldtrip/2011-May/003827.html), and have since tried several instantiations of FieldTrip (though the version I was running when I first got the error was actually very new). So far I have tried: > > fieldtrip-20111004 > fieldtrip-20111101 > fieldtrip-20120220 > fieldtrip-20120222 > > here is my ver info in case it is helpful: > > MATLAB Version 7.11.0.584 (R2010b) > > Operating System: Mac OS X Version: 10.6.2 Build: 10C540 > Java VM Version: Java 1.6.0_15-b03-219 with Apple Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode > ------------------------------------------------------------------------------------- > > Any suggestions of likely incompatibilities/mistakes on my part would be most helpful. > > Thank you, > > -- > Jessamy Norton-Ford > Doctoral Student, Department of Cognitive Sciences > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Feb 23 10:11:29 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 23 Feb 2012 10:11:29 +0100 Subject: [FieldTrip] Fwd: ft_megplanar problem for planar gradient calculation References: Message-ID: Begin forwarded message: > > ---------- Forwarded message ---------- > From: Ion Lavado > Date: 2012/2/21 > Subject: ft_megplanar problem for planar gradient calculation > To: fieldtrip-request at donders.ru.nl > > > Hello, i'm doing the cluster based permutations tests on time-frequency data tutorial. I'm using an Elekta neuromag with 306 channels. My problem comes when i try to calculate the planar gradient. This is what i do: > > %************ READ WORD EVENT ************ > cfg = []; > cfg.dataset = '21_muti.fif'; > cfg.trialdef.eventtype = 'STI101'; > cfg.trialdef.prestim = 1; > cfg.trialdef.poststim = 1; > cfg.trialdef.eventvalue = 1; > cfg = ft_definetrial(cfg); > cfg.channel = {'MEG'}; > cfg.demean = 'yes'; > cfg.baselinewindow = [-0.5 0]; > dataMuti21_words = ft_preprocessing(cfg); > %************ READ PICTURES EVENT ************ > cfg = []; > cfg.dataset = '21_muti.fif'; > cfg.trialdef.eventtype = 'STI101'; > cfg.trialdef.prestim = 1; > cfg.trialdef.poststim = 1; > cfg.trialdef.eventvalue = 6; > cfg = ft_definetrial(cfg); > cfg.channel = {'MEG'}; > cfg.demean = 'yes'; > cfg.baselinewindow = [-0.5 0]; > dataMuti21_pictures = ft_preprocessing(cfg); > > > > %******* CALCULATE PLANAR GRADIENT ****** > cfg = []; > cfg.planarmethod = 'sincos'; > cfg_neighb.method = 'distance'; > cfg.grad = avg_words.grad; > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataMuti21_pictures); > avg_words_planar = ft_megplanar(cfg, dataMuti21_words); > avg_pictures_planar = ft_megplanar(cfg, dataMuti21_pictures); > > > HERE IS WHERE I GET THE ERROR: > ??? Error using ==> ft_checkdata at 359 > This function requires ctf151, ctf275, bti148, bti248, itab153, yokogawa160 or yokogawa64 data as input, but you are giving > neuromag306 data. > > Error in ==> ft_megplanar at 107 > data = ft_checkdata(data, 'datatype', {'raw' 'freq'}, 'feedback', 'yes', 'hassampleinfo', 'yes', 'ismeg', 'yes', 'senstype', > {'ctf151', 'ctf275', 'bti148', 'bti248', 'itab153', 'yokogawa160', 'yokoga > > > Can't i use neuromag306 data type sens for this function? any solution? THANKS IN ADVANCE > > Ion -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu Feb 23 10:19:25 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 23 Feb 2012 10:19:25 +0100 Subject: [FieldTrip] Fwd: ft_megplanar problem for planar gradient calculation In-Reply-To: References: Message-ID: Dear Ion, ft_megplanar is designed to estimate planar gradient information from axial gradiometer data. The Neuromag 306 system is equipped with planar gradiometers, so the data you have is already reflecting the planar magnetic gradient. In other words: there is no need to use ft_megplanar, in your case. Best, Eelke On 23 February 2012 10:11, jan-mathijs schoffelen wrote: > > > Begin forwarded message: > > > ---------- Forwarded message ---------- > From: Ion Lavado > Date: 2012/2/21 > Subject: ft_megplanar problem for planar gradient calculation > To: fieldtrip-request at donders.ru.nl > > > Hello, i'm doing the cluster based permutations tests on time-frequency data > tutorial. I'm using an Elekta neuromag with 306 channels. My problem comes > when i try to calculate the planar gradient. This is what i do: > > %************ READ WORD EVENT ************ > cfg = []; > cfg.dataset                 = '21_muti.fif'; > cfg.trialdef.eventtype      = 'STI101'; > cfg.trialdef.prestim        = 1; > cfg.trialdef.poststim       = 1; > cfg.trialdef.eventvalue     = 1; > cfg = ft_definetrial(cfg); > cfg.channel   = {'MEG'}; > cfg.demean        = 'yes'; > cfg.baselinewindow = [-0.5 0]; > dataMuti21_words = ft_preprocessing(cfg); > %************ READ PICTURES EVENT ************ > cfg = []; > cfg.dataset                 = '21_muti.fif'; > cfg.trialdef.eventtype      = 'STI101'; > cfg.trialdef.prestim        = 1; > cfg.trialdef.poststim       = 1; > cfg.trialdef.eventvalue     = 6; > cfg = ft_definetrial(cfg); > cfg.channel   = {'MEG'}; > cfg.demean        = 'yes'; > cfg.baselinewindow = [-0.5 0]; > dataMuti21_pictures = ft_preprocessing(cfg); > > > > %******* CALCULATE PLANAR GRADIENT ****** > cfg = []; > cfg.planarmethod = 'sincos'; > cfg_neighb.method    = 'distance'; > cfg.grad            = avg_words.grad; > cfg.neighbours       = ft_prepare_neighbours(cfg_neighb, > dataMuti21_pictures); > avg_words_planar = ft_megplanar(cfg, dataMuti21_words); > avg_pictures_planar = ft_megplanar(cfg, dataMuti21_pictures); > > > HERE IS WHERE I GET THE ERROR: > ??? Error using ==> ft_checkdata at 359 > This function requires ctf151, ctf275, bti148, bti248, itab153, yokogawa160 > or yokogawa64 data as input, but you are giving > neuromag306 data. > > Error in ==> ft_megplanar at 107 > data = ft_checkdata(data, 'datatype', {'raw' 'freq'}, 'feedback', 'yes', > 'hassampleinfo', 'yes', 'ismeg', 'yes', 'senstype', > {'ctf151', 'ctf275', 'bti148', 'bti248', 'itab153', 'yokogawa160', 'yokoga > > > Can't i use neuromag306 data type sens for this function? any solution? > THANKS IN ADVANCE > > Ion > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Thu Feb 23 10:20:29 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 23 Feb 2012 10:20:29 +0100 Subject: [FieldTrip] Fwd: ft_megplanar problem for planar gradient calculation In-Reply-To: References: Message-ID: <9F11307A-F697-4D9B-BBC4-694C00760EAC@donders.ru.nl> Dear Ion, In principle, you could do a synthetic planar grdient computation on the 102 magnetometer channels in your data. I don't think that this is supported by FieldTrip though. Obviously, you cannot do the planar gradient computation on the other 204 channels, because they already represent the magnetic field gradient. Best, Jan-Mathijs On Feb 23, 2012, at 10:11 AM, jan-mathijs schoffelen wrote: > > > Begin forwarded message: >> >> ---------- Forwarded message ---------- >> From: Ion Lavado >> Date: 2012/2/21 >> Subject: ft_megplanar problem for planar gradient calculation >> To: fieldtrip-request at donders.ru.nl >> >> >> Hello, i'm doing the cluster based permutations tests on time-frequency data tutorial. I'm using an Elekta neuromag with 306 channels. My problem comes when i try to calculate the planar gradient. This is what i do: >> >> %************ READ WORD EVENT ************ >> cfg = []; >> cfg.dataset = '21_muti.fif'; >> cfg.trialdef.eventtype = 'STI101'; >> cfg.trialdef.prestim = 1; >> cfg.trialdef.poststim = 1; >> cfg.trialdef.eventvalue = 1; >> cfg = ft_definetrial(cfg); >> cfg.channel = {'MEG'}; >> cfg.demean = 'yes'; >> cfg.baselinewindow = [-0.5 0]; >> dataMuti21_words = ft_preprocessing(cfg); >> %************ READ PICTURES EVENT ************ >> cfg = []; >> cfg.dataset = '21_muti.fif'; >> cfg.trialdef.eventtype = 'STI101'; >> cfg.trialdef.prestim = 1; >> cfg.trialdef.poststim = 1; >> cfg.trialdef.eventvalue = 6; >> cfg = ft_definetrial(cfg); >> cfg.channel = {'MEG'}; >> cfg.demean = 'yes'; >> cfg.baselinewindow = [-0.5 0]; >> dataMuti21_pictures = ft_preprocessing(cfg); >> >> >> >> %******* CALCULATE PLANAR GRADIENT ****** >> cfg = []; >> cfg.planarmethod = 'sincos'; >> cfg_neighb.method = 'distance'; >> cfg.grad = avg_words.grad; >> cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataMuti21_pictures); >> avg_words_planar = ft_megplanar(cfg, dataMuti21_words); >> avg_pictures_planar = ft_megplanar(cfg, dataMuti21_pictures); >> >> >> HERE IS WHERE I GET THE ERROR: >> ??? Error using ==> ft_checkdata at 359 >> This function requires ctf151, ctf275, bti148, bti248, itab153, yokogawa160 or yokogawa64 data as input, but you are giving >> neuromag306 data. >> >> Error in ==> ft_megplanar at 107 >> data = ft_checkdata(data, 'datatype', {'raw' 'freq'}, 'feedback', 'yes', 'hassampleinfo', 'yes', 'ismeg', 'yes', 'senstype', >> {'ctf151', 'ctf275', 'bti148', 'bti248', 'itab153', 'yokogawa160', 'yokoga >> >> >> Can't i use neuromag306 data type sens for this function? any solution? THANKS IN ADVANCE >> >> Ion > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Thu Feb 23 10:26:21 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 23 Feb 2012 10:26:21 +0100 Subject: [FieldTrip] Fwd: ft_megplanar problem for planar gradient calculation In-Reply-To: References: Message-ID: <4F46063D.9090501@donders.ru.nl> Hi, I might be mistaken since I am not using a neuromag system, but as far as I know a Neuromag system already has planar gradiometers? If so, then there would be no need to apply ft_megplanar (and actually, it would be an meaningless operation) Best, Jörn On 2/23/2012 10:11 AM, jan-mathijs schoffelen wrote: > > > Begin forwarded message: >> >> ---------- Forwarded message ---------- >> From: *Ion Lavado* > >> Date: 2012/2/21 >> Subject: ft_megplanar problem for planar gradient calculation >> To: fieldtrip-request at donders.ru.nl >> >> >> >> Hello, i'm doing the cluster based permutations tests on >> time-frequency data tutorial. I'm using an Elekta neuromag with 306 >> channels. My problem comes when i try to calculate the planar >> gradient. This is what i do: >> >> %************ READ WORD EVENT ************ >> cfg = []; >> cfg.dataset = '21_muti.fif'; >> cfg.trialdef.eventtype = 'STI101'; >> cfg.trialdef.prestim = 1; >> cfg.trialdef.poststim = 1; >> cfg.trialdef.eventvalue = 1; >> cfg = ft_definetrial(cfg); >> cfg.channel = {'MEG'}; >> cfg.demean = 'yes'; >> cfg.baselinewindow = [-0.5 0]; >> dataMuti21_words = ft_preprocessing(cfg); >> %************ READ PICTURES EVENT ************ >> cfg = []; >> cfg.dataset = '21_muti.fif'; >> cfg.trialdef.eventtype = 'STI101'; >> cfg.trialdef.prestim = 1; >> cfg.trialdef.poststim = 1; >> cfg.trialdef.eventvalue = 6; >> cfg = ft_definetrial(cfg); >> cfg.channel = {'MEG'}; >> cfg.demean = 'yes'; >> cfg.baselinewindow = [-0.5 0]; >> dataMuti21_pictures = ft_preprocessing(cfg); >> >> >> >> %******* CALCULATE PLANAR GRADIENT ****** >> cfg = []; >> cfg.planarmethod = 'sincos'; >> cfg_neighb.method = 'distance'; >> cfg.grad = avg_words.grad; >> cfg.neighbours = ft_prepare_neighbours(cfg_neighb, >> dataMuti21_pictures); >> avg_words_planar = ft_megplanar(cfg, dataMuti21_words); >> avg_pictures_planar = ft_megplanar(cfg, dataMuti21_pictures); >> >> >> HERE IS WHERE I GET THE ERROR: >> ??? Error using ==> ft_checkdata at 359 >> This function requires ctf151, ctf275, bti148, bti248, itab153, >> yokogawa160 or yokogawa64 data as input, but you are giving >> neuromag306 data. >> >> Error in ==> ft_megplanar at 107 >> data = ft_checkdata(data, 'datatype', {'raw' 'freq'}, 'feedback', >> 'yes', 'hassampleinfo', 'yes', 'ismeg', 'yes', 'senstype', >> {'ctf151', 'ctf275', 'bti148', 'bti248', 'itab153', 'yokogawa160', >> 'yokoga >> >> >> Can't i use neuromag306 data type sens for this function? any >> solution? THANKS IN ADVANCE >> >> Ion > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From Hanneke.vanDijk at med.uni-duesseldorf.de Thu Feb 23 10:51:00 2012 From: Hanneke.vanDijk at med.uni-duesseldorf.de (Hanneke.vanDijk at med.uni-duesseldorf.de) Date: Thu, 23 Feb 2012 10:51:00 +0100 Subject: [FieldTrip] [Fieldtrip] ft_megplanar problem for planar gradient calculation Message-ID: <72E993C35FB11743B79FF9286E5B6D8B029F8C31@Mail2-UKD.VMED.UKD> Dear Ion, If your ultimate goal is to combine the horizontal and vertical gradients you can do that later (after ft_timelockanalysis or ft_freqanalysis) using ft_combineplanar. You can skip the ft_megplanar step because the neuromag system already has planar gradiometers. I have done this numerous times and it works perfectly! Hope this helps, Hanneke __________________________________________ Dr. Hanneke van Dijk http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html Institute for Clinical Neuroscience, Heinrich Heine Universität Düsseldorf, Germany Hanneke.vanDijk at med.uni-duesseldorf.de Tel. +49 (0) 211 81 13074 __________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.reuderink at donders.ru.nl Thu Feb 23 13:27:35 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Thu, 23 Feb 2012 13:27:35 +0100 Subject: [FieldTrip] A question In-Reply-To: References: Message-ID: Further, it seems that the data is also scaled automatically, see http://code.google.com/p/fieldtrip/source/browse/trunk/ft_componentanalysis.m?spec=svn5313&r=5313#271 . Best, Boris On Thu, Feb 16, 2012 at 12:39 PM, Stephen Whitmarsh wrote: > Dear All, > > All true, except that ICA implemented by FT does demean the data > before unmixing by default. Use cfg.demean = 'no' if you don't want > to. > > cheers, > stephen > > On 16 February 2012 12:35, Stephen Politzer-Ahles > wrote: >> Hi Shayda, >> >> FieldTrip does not apply a filter by default, and I am not aware of any >> other 'hidden' transformations that happen. You can specify a filter when >> importing the data with ft_preprocessing(), and there are several different >> kinds of filters available, which will affect your data in different ways-- >> see http://fieldtrip.fcdonders.nl/reference/ft_preprocessing. The best thing >> to do is to import your data without using a filter and, if possible, use >> whatever tool comes with your MEG software to import that raw data into >> MATLAB as well (for example, for CTF this would be ds2txt), then you can >> plot them together to make sure there are no differences--when I have tried >> this with EEG data, fieldtrip hasn't changed them. Of course, if you want to >> use a filter, you can also try several filters (you can either filter within >> your system's software and then import straight to Fieldtrip, or use one of >> Fieldtrip's filters during import) and plot them to see how they affect your >> data. >> >> Best, >> Steve Politzer-Ahles >> >> >>> >>> >>> Message: 2 >>> Date: Wed, 15 Feb 2012 14:19:50 -0600 >>> From: Shayda Malekpour >>> To: fieldtrip at donders.ru.nl >>> Subject: [FieldTrip] A question >>> Message-ID: >>> >>>   >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> >>> Dear All, >>> >>> I am using fieldtrip on MEG data set. >>> I want to know if I do not remove any ICA component,  will the data be >>>  the >>> same as the original data, or is there is a filter somewhere in the >>> software that changes the data? If so how much does it change it (What is >>> their relative difference?) >>> >>> Thanks, >>> >>> Sheida >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: >>> >>> >>> ------------------------------ >>> >>> Message: 3 >>> Date: Thu, 16 Feb 2012 09:28:43 +0100 >>> From: Eelke Spaak >>> To: Email discussion list for the FieldTrip project >>>         >>> Subject: Re: [FieldTrip] A question >>> Message-ID: >>> >>>   >>> Content-Type: text/plain; charset=ISO-8859-1 >>> >>> >>> Dear Sheida, >>> >>> You probably need to provide a bit more information before anyone is >>> able to help you. In general, if you perform ICA, you get out >>> component timecourses and mixing/unmixing matrices. If you keep all >>> your components, and multiply them with the mixing matrix, you should >>> get all your original channel timecourses out again. So: if you don't >>> change the data, the data will not be changed :) >>> >>> Best, >>> Eelke >>> >>> On 15 February 2012 21:19, Shayda Malekpour >>> wrote: >>> > Dear All, >>> > >>> > I am using fieldtrip on MEG data set. >>> > I want to know if I do not remove any ICA component,? will the data be? >>> > the >>> >>> > same as the original data, or is there is a filter somewhere in the >>> > software >>> > that changes the data? If so how much does it change it (What is their >>> > relative difference?) >>> > >>> > Thanks, >>> > >>> > Sheida >>> > _______________________________________________ >>> > fieldtrip mailing list >>> > fieldtrip at donders.ru.nl >>> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> ------------------------------ >>> >>> Message: 4 >>> Date: Thu, 16 Feb 2012 10:36:05 +0100 >>> From: "J?rn M. Horschig" >>> To: Email discussion list for the FieldTrip project >>>         >>> Subject: Re: [FieldTrip] A problem in real-time processing of MEG >>>        signal using field trip buffer >>> Message-ID: <4F3CCE05.4050109 at donders.ru.nl> >>> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" >>> >>> Dear Soheila, >>> >>> we were facing the same problem here. Presumably, there is some problem >>> in the shared memory module that the buffer is using. Right now, >>> however, we could not find out where the error precisely comes from, so >>> our best work around is to restart the computer prior recording and >>> optimize settings, such as channels and sampling/decimation rate of >>> acq2ft. In our lab, we managed to find near-optimal settings, so that >>> the buffer crashes only rarely (actually, I never saw it crashing when >>> the acquisition computer was freshly restarted). Note that a lower >>> number of channels or higher decimation does not mean that it runs more >>> stable.  It seems to be literally a trial-and-error approach :/ >>> >>> In order to track this down further, we need some more information, e.g. >>> what MEG system are you using? What's your sampling rate, how many >>> channels do you put into the buffer, and what's your decimation rate? It >>> would be great if you could send me that information so that we can >>> maybe try to track this down. >>> >>> Best regards, >>> J?rn >>> >>> On 2/14/2012 5:42 PM, Soheila Samiee wrote: >>> > Dear group, >>> > >>> > I use FieldTrip for real-time processing of MEG signals using shared >>> > memory and field trip buffer in a machine other than acquisition >>> > system. I use matlab for reading the buffer and processing the data. >>> > During my data acquisition and sending it to other computer with >>> > /acq2ft/ in linux, I face a problem. After sending some blocks of >>> > data, this message: "/Internal Converter thread does not keep up with >>> > load/" is shown in the terminal of /acq2ft/ and in my matlab session I >>> > see an error : "ERROR: the buffer returned an error (517)". It does >>> > not depend on sampling rate of data in acquisition system. The problem >>> > often solve when I restart the computer which receives the data, but >>> > after some minutes of transferring the data I see the message again. >>> > >>> > Would you please help me in solving this problem? >>> > Best Wishes, >>> > Soheila >>> >>> > >>> > >>> > _______________________________________________ >>> > fieldtrip mailing list >>> > fieldtrip at donders.ru.nl >>> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> -- >>> J?rn M. Horschig >>> PhD Student >>> Donders Institute for Brain, Cognition and Behaviour >>> Centre for Cognitive Neuroimaging >>> Radboud University Nijmegen >>> Neuronal Oscillations Group >>> >>> P.O. Box 9101 >>> NL-6500 HB Nijmegen >>> The Netherlands >>> >>> Contact: >>> E-Mail: jm.horschig at donders.ru.nl >>> Tel:    +31-(0)24-36-68493 >>> Web: http://www.ru.nl/donders >>> >>> Visiting address: >>> Trigon, room 2.30 >>> Kapittelweg 29 >>> NL-6525 EN Nijmegen >>> The Netherlands >>> >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: >>> >>> >>> ------------------------------ >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> End of fieldtrip Digest, Vol 15, Issue 17 >>> ***************************************** >> >> >> >> >> -- >> Stephen Politzer-Ahles >> University of Kansas >> Linguistics Department >> http://www.linguistics.ku.edu/ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl From chrysa.lithari at gmail.com Fri Feb 24 11:08:40 2012 From: chrysa.lithari at gmail.com (Chrysa Lithari) Date: Fri, 24 Feb 2012 12:08:40 +0200 Subject: [FieldTrip] coregistration neuromag Message-ID: Hi to all, I just started using fieldtrip and I have the following question. I have the MRI and the polhemus data for each subject. The MRI is in dicom and I can also transform it to 'analyze' format using SPM. The polhemus data are in fif format, together with the functional data. How can I coregister these two types of data in fieldtrip? I searched in the tutorial and it is mentioned that normally MEG systems come with a software allowing to align MRI with the helmet, e.g. CTF. However, I have worked on Neuromag system and I have not done anything like this. How can I do it in Fieltrip? A step by step (AC-PC points, normalization, segmentation etc) guidance would be very helpful stating the functions I have to use and any precautions I have to consider during this process. Best regards and thanks in advance, Chrysa Lithari -- Chrysa Lithari - PhD candidate in Lab of Medical Informatics, Aristotle University of Thessaloniki, Greece - M.Sc. NeuroInformatics, Unversity of Patras, Greece - B.Sc. Computer Science, Aristotle University of Thessaloniki, Greece -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Fri Feb 24 11:24:26 2012 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Fri, 24 Feb 2012 10:24:26 +0000 Subject: [FieldTrip] coregistration neuromag In-Reply-To: References: Message-ID: Dear Chrysa, If you are using SPM already you could also generate a head model and do coregistration with SPM8 and then use it with Fieldtrip. See SPM manual for details. There are some example functions in the Beamforming toolbox in SPM where you can see how the SPM-Fieldtrip interfacing can be done. Best, Vladimir On Fri, Feb 24, 2012 at 10:08 AM, Chrysa Lithari wrote: > Hi to all, > > I just started using fieldtrip and I have the following question. > > I have the MRI and the polhemus data for each subject. > The MRI is in dicom and I can also transform it to 'analyze' format using > SPM. > The polhemus data are in fif format, together with the functional data. > How can I coregister these two types of data in fieldtrip? > I searched in the tutorial and it is mentioned that normally MEG systems > come with a software allowing to align MRI with the helmet, e.g. CTF. > However, I have worked on Neuromag system and I have not done anything like > this. How can I do it in Fieltrip? > A step by step (AC-PC points, normalization, segmentation etc) guidance > would be very helpful stating the functions I have to use and any > precautions I have to consider during this process. > > Best regards and thanks in advance, > Chrysa Lithari > > -- > Chrysa Lithari > - PhD candidate in Lab of Medical Informatics, Aristotle University of > Thessaloniki, Greece > - M.Sc. NeuroInformatics, Unversity of Patras, Greece > - B.Sc. Computer Science, Aristotle University of Thessaloniki, Greece > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From ole.jensen at donders.ru.nl Sun Feb 26 15:41:36 2012 From: ole.jensen at donders.ru.nl (Ole Jensen) Date: Sun, 26 Feb 2012 15:41:36 +0100 Subject: [FieldTrip] senior researcher position at the Donders Institute Message-ID: <4F4A44A0.4010201@donders.ru.nl> Dear colleagues, I would like to bring your attention to the position below. Alt the best, Ole Jensen http://www.neuosc.com ------------------------ *Senior Researcher for 'Neuronal Oscillations and Networks' (1,0 fte) * *Donders Institute, Centre for Cognitive Neuroimaging* *Vacancy number: 30.01.12* *Closing date: 15 April 2012* *Responsibilities* The Neuronal Oscillation group at the Donders Institute for Brain, Cognition and Behaviour has funding available for a senior researcher position. The position has a strong research component, but also includes additional management and teaching responsibilities. The management tasks involve active participation in structuring the research group, including supervision of MSc and PhD students (who will receive senior authorship where applicable). Further, you will contribute to grant writing. The research responsibilities focus on investigating the role of oscillatory neuronal activity involved in shaping the functional architecture of the working brain. This will be done in the context of advanced cognitive paradigms on attention, perception and memory. There will be a strong focus on the role of phase, network interactions and subcortical structures. You will have the following state-of-the-art equipment to your disposal: MEG, (f)MRI, EEG combined with TMS, and EEG combined with fMRI. A further aim is to link structural (e.g. DTI) and functional measurements. You will also participate in conceptually developing the framework for understanding the functional role of brain oscillations. *Work environment* The Donders Institute for Brain, Cognition and Behaviour consists of the Centre for Cognition, the Centre for Cognitive Neuroimaging and the Centre for Neuroscience. The mission of the Centre for Cognitive Neuroimaging is to conduct cutting-edge fundamental research in cognitive neuroscience. Much of the rapid progress in this field is being driven by the development of complex neuro-imaging techniques for measuring activity in the human working brain - an area in which the Centre plays a leading role. The research themes cover central cognitive functions such as perception, action, control, decision making, attention, memory, language, learning and plasticity. The internationally renowned centre currently hosts more than 100 PhD students and postdoctoral researchers from more than 20 countries, offering a stimulating and multidisciplinary research environment. The centre is equipped with three MRI scanners (7T, 3T, 1.5T), a 275-channel MEG system, an EEG-TMS laboratory, several (MR-compatible) EEG systems, and high-performance computational facilities. English is the lingua franca at the centre. You will work within the Neuronal Oscillations group. *What we expect from you* As a candidate for the position, you should have a PhD degree and several years of experience as postdoctoral researcher in a field related to cognitive neuroscience. Selection criteria will consider the record of published research, familiarity with neuroimaging techniques (fMRI, EEG, MEG, and/or TMS) and supervision experience. Proficiency in oral and written English is a prerequisite. You are expected to work in a team, sharing technical know-how and ideas. *What we have to offer* We offer you: - employment: 1,0 fte; - in addition to the salary: an 8% holiday allowance and an 8.3% end-of-year bonus; - the gross salary will be between EUR3,195 and EUR4,970 (scale 12), depending on experience; - salary scale 11 will apply during the first year; - duration of the contract: 6 years maximum. Are you interested in our excellentemployment conditions ? *Would you like to know more?* Further information on:DCCN Further information on:Neuronal Oscillations group Dr. Ole Jensen Telephone: +31 24 3610884 E-mail:ole.jensen at donders.ru.nl *Applications* Are you interested? It is Radboud University Nijmegen's policy to only accept applications by e-mail. Please send your application,/stating vacancy number 30.01.12/, tovacatures at dpo.ru.nl , for the attention of Dr. Ole Jensen, before 15 April 2012. For more information on the application procedure: +31 24 3611173 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tessa.vanleeuwen at fcdonders.ru.nl Mon Feb 27 10:33:50 2012 From: tessa.vanleeuwen at fcdonders.ru.nl (Tessa van Leeuwen) Date: Mon, 27 Feb 2012 10:33:50 +0100 (CET) Subject: [FieldTrip] adapting leadfields after PCA/ICA Message-ID: <1030785558.11966.1330335230620.JavaMail.root@draco.zimbra.ru.nl> Dear FieldTrip users, To save trials I plan on using ICA to remove eog artifacts from my MEG dataset. Because of the large number of channels (271) and limited trial-time (about 300 trials of 1.1 s in each run), we will most likely limit the number of possible components using PCA. The combined PCA/ICA data-cleaning step will have consequences for source reconstruction approaches that we would like to apply to the data later on, e.g. beamforming. When ICA components representing eyeblink artifacts have been removed from the data, how can the leadfield for source reconstruction be adapted to account for the alterations to the data? If anyone has more information about how to do this or can refer me to papers implementing such a pipeline, that would be highly appreciated. Thank you very much in advance for any tips. Best wishes, Tessa van Leeuwen From jan.schoffelen at donders.ru.nl Mon Feb 27 11:14:48 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 27 Feb 2012 11:14:48 +0100 Subject: [FieldTrip] adapting leadfields after PCA/ICA In-Reply-To: <1030785558.11966.1330335230620.JavaMail.root@draco.zimbra.ru.nl> References: <1030785558.11966.1330335230620.JavaMail.root@draco.zimbra.ru.nl> Message-ID: <9E6F733E-B395-486E-907F-C60674592371@donders.ru.nl> Hi Tessa, I imagine that you use ft_componentanalysis and ft_rejectcomponent sequentially in order to remove the eye blink topographies. If you use the data.grad in the output to ft_rejectcomponent for the computation of the leadfields you should be fine. The balancing matrix grad.tra will contain the information that will be used for the correction of the leadfields. Best wishes, Jan-Mathijs On Feb 27, 2012, at 10:33 AM, Tessa van Leeuwen wrote: > Dear FieldTrip users, > > To save trials I plan on using ICA to remove eog artifacts from my MEG dataset. Because of the large number of channels (271) and limited trial-time (about 300 trials of 1.1 s in each run), we will most likely limit the number of possible components using PCA. > > The combined PCA/ICA data-cleaning step will have consequences for source reconstruction approaches that we would like to apply to the data later on, e.g. beamforming. When ICA components representing eyeblink artifacts have been removed from the data, how can the leadfield for source reconstruction be adapted to account for the alterations to the data? > If anyone has more information about how to do this or can refer me to papers implementing such a pipeline, that would be highly appreciated. > > Thank you very much in advance for any tips. > > Best wishes, > Tessa van Leeuwen > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tessa.vanleeuwen at fcdonders.ru.nl Mon Feb 27 12:20:49 2012 From: tessa.vanleeuwen at fcdonders.ru.nl (Tessa van Leeuwen) Date: Mon, 27 Feb 2012 12:20:49 +0100 (CET) Subject: [FieldTrip] adapting leadfields after PCA/ICA In-Reply-To: <9E6F733E-B395-486E-907F-C60674592371@donders.ru.nl> Message-ID: <1972515496.15972.1330341648951.JavaMail.root@draco.zimbra.ru.nl> Hi Jan-Mathijs, Thank you for this quick and informative reply; we indeed use ft_componentanalysis and ft_rejectcomponent sequentially. I will make sure to save the grad structures for the later source analysis. Great! Thank you again, best, Tessa ----- "jan-mathijs schoffelen" wrote: > From: "jan-mathijs schoffelen" > To: "Email discussion list for the FieldTrip project" > Sent: Monday, February 27, 2012 11:14:48 AM > Subject: Re: [FieldTrip] adapting leadfields after PCA/ICA > > Hi Tessa, > I imagine that you use ft_componentanalysis and ft_rejectcomponent sequentially in order to remove the eye blink topographies. If you use the data.grad in the output to ft_rejectcomponent for the computation of the leadfields you should be fine. The balancing matrix grad.tra will contain the information that will be used for the correction of the leadfields. > Best wishes, > Jan-Mathijs > > On Feb 27, 2012, at 10:33 AM, Tessa van Leeuwen wrote: Dear FieldTrip users, > > To save trials I plan on using ICA to remove eog artifacts from my MEG dataset. Because of the large number of channels (271) and limited trial-time (about 300 trials of 1.1 s in each run), we will most likely limit the number of possible components using PCA. > > The combined PCA/ICA data-cleaning step will have consequences for source reconstruction approaches that we would like to apply to the data later on, e.g. beamforming. When ICA components representing eyeblink artifacts have been removed from the data, how can the leadfield for source reconstruction be adapted to account for the alterations to the data? > If anyone has more information about how to do this or can refer me to papers implementing such a pipeline, that would be highly appreciated. > > Thank you very much in advance for any tips. > > Best wishes, > Tessa van Leeuwen > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > Jan-Mathijs Schoffelen, MD PhD > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From max-philipp.stenner at med.ovgu.de Mon Feb 27 17:02:32 2012 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Mon, 27 Feb 2012 16:02:32 +0000 Subject: [FieldTrip] spm_eeg_ft2spm Message-ID: Dear fieldtrippers, I am trying to convert preprocessed/epoched fieldtrip data to spm8 using spm_eeg_ft2spm (for VB-ECD source analysis). I derived volume conduction models for my participants using spm_eeg_convert on data (that was not preprocessed/epoched) a while ago without encountering major problems. spm_eeg_ft2spm, however, requires an input argument "filename", for which I have tried various definitions (a result-filename, the original ft-datafile and filenames both with and without .dat of the same session of the spm_eeg_convert output). As I am not familiar with file_arrays and find little help within the function scripts, I was wondering whether anyone could tell me the (probably simple) solution to overcome the error 'mat2file' Cant open file. What does spm_eeg_ft2spm require as "filename" input? I am using fieldtrip-20111130 on a Windows7 PC. Thanks a lot, best Max From litvak.vladimir at gmail.com Mon Feb 27 17:18:37 2012 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Mon, 27 Feb 2012 16:18:37 +0000 Subject: [FieldTrip] spm_eeg_ft2spm In-Reply-To: References: Message-ID: <712F7AE2-5CF6-46D1-BEF3-AB699031DCD7@gmail.com> Hi Max, filename is the name for the new SPM dataset that you are generating. Not sure how volume conduction models are relevant here. Perhaps since we sit in the same building it'd be easier if you come to talk to me directly. Fieldtrip mailing list is not quite relevant for these issues as they are more SPM-related. Best, Vladimir On 27 Feb 2012, at 16:02, "Stenner, Max-Philipp" wrote: > Dear fieldtrippers, > > > > I am trying to convert preprocessed/epoched fieldtrip data to spm8 using spm_eeg_ft2spm (for VB-ECD source analysis). > > > > I derived volume conduction models for my participants using spm_eeg_convert on data (that was not preprocessed/epoched) a while ago without encountering major problems. spm_eeg_ft2spm, however, requires an input argument "filename", for which I have tried various definitions (a result-filename, the original ft-datafile and filenames both with and without .dat of the same session of the spm_eeg_convert output). As I am not familiar with file_arrays and find little help within the function scripts, I was wondering whether anyone could tell me the (probably simple) solution to overcome the error > > > > 'mat2file' Cant open file. > > > > What does spm_eeg_ft2spm require as "filename" input? > > > > I am using fieldtrip-20111130 on a Windows7 PC. > > > > Thanks a lot, > > best > > Max > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From s.bogels at psy.gla.ac.uk Tue Feb 28 13:12:47 2012 From: s.bogels at psy.gla.ac.uk (=?ISO-8859-1?Q?Sara_B=F6gels?=) Date: Tue, 28 Feb 2012 12:12:47 +0000 Subject: [FieldTrip] MNE: sourcespace and volume aligned? Message-ID: <4F4CC4BF.9030003@psy.gla.ac.uk> Hi all, I am working my way through the MNE tutorial and plotted the mesh and vol on top of each other at the end of the Freesurfer and MNE suite steps to check whether they are aligned. The volume seems to fit quite well into the mesh but is a bit smaller (see attached figures), but definitely not a factor 10. However, from the figure (5) in the tutorial, it seems as if the mesh has to be exactly on top of the volume. Does my plot show that the two are misaligned? If so, what might be the problem? I tried to use ft_determine_coordsys on the vol, but that gives me the error message: 'unknown units (dm)'. If I use it on the sourcespace I get the output that the units are 'cm'. Any help is appreciated. Thank you, Sara Bögels -------------- next part -------------- A non-text attachment was scrubbed... Name: mesh_vol_plot2.jpg Type: image/jpeg Size: 135822 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mesh_vol_plot.jpg Type: image/jpeg Size: 104188 bytes Desc: not available URL: From Lilla.Magyari at mpi.nl Tue Feb 28 14:52:55 2012 From: Lilla.Magyari at mpi.nl (Magyari, Lilla) Date: Tue, 28 Feb 2012 14:52:55 +0100 Subject: [FieldTrip] MNE: sourcespace and volume aligned? In-Reply-To: <4F4CC4BF.9030003@psy.gla.ac.uk> References: <4F4CC4BF.9030003@psy.gla.ac.uk> Message-ID: <4F4CDC37.6000504@mpi.nl> hi Sara, I think the alignment looks just good. The volume conductor is made from the (inside) skull surface, so it is a bit bigger indeed than the sourcespace. For me, it seems that there is also space between the vol and the sourcespace on the picture in the tutorial, but it is more difficult to see because it is colored. Probably, it wasn't plot with exactly the same piece of code than what is indicate above it. About the error message. I am wondering which version of Fieldtrip are you using? Because I had similar problems with my units when I used an earlier version of FieldTrip where the ft_convert_unit function worked a bit differently than now. In any case, we are simplifying this anatomical preprocessing pipeline (all things that you do in FieldTrip before using FreeSurfer) right now, so you can see the new version of the tutorial in a few days. Best, Lilla Sara Bögels wrote: > Hi all, > > I am working my way through the MNE tutorial and plotted the mesh and > vol on top of each other at the end of the Freesurfer and MNE suite > steps to check whether they are aligned. The volume seems to fit quite > well into the mesh but is a bit smaller (see attached figures), but > definitely not a factor 10. However, from the figure (5) in the > tutorial, it seems as if the mesh has to be exactly on top of the > volume. Does my plot show that the two are misaligned? If so, what might > be the problem? > > I tried to use ft_determine_coordsys on the vol, but that gives me the > error message: 'unknown units (dm)'. If I use it on the sourcespace I > get the output that the units are 'cm'. > > Any help is appreciated. > > Thank you, > Sara Bögels > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Andrew.Dykstra at med.uni-heidelberg.de Tue Feb 28 17:34:59 2012 From: Andrew.Dykstra at med.uni-heidelberg.de (Andrew R. Dykstra) Date: Tue, 28 Feb 2012 17:34:59 +0100 Subject: [FieldTrip] getting started with Neuromag 122 data Message-ID: Hi everyone, I'm new to Fieldtrip and would like to use it to process data collected on a Neuromag 122 system. However, I'm running into some fairly simple issues with regard to reading header information and events. Regarding header information, it seems that fieldtrip can read the fif file's header and raw data, but some fields in the header are not assigned correctly. For example, hdr.chantype returns 'unknown' for all channels in the data set (whereas they should be either 'meg_planar ' or trigger lines). Also, hdr.grad returns empty arrays. Regarding reading events, I read Yang Zhang's solution of using mne_make_combined_ event_file.m from the MNE stream and manually creating the event structure (from this list on Jan 8, 2010: http://mailman.science.ru.nl/pipermail/fieldtrip/2010-January/002551.html). This will should also work for me, but I was wondering if there is now a more streamlined way of accomplishing this in Fieldtrip, especially for fif files either containing or associated with an event list based on a text file with sample numbers, latencies, and event types. I did not see an option in ft_read_event to do this. Any suggestions would be much appreciated. Andy Andrew R. Dykstra, PhD Auditory Cognition Lab Neurologie und Poliklinik Universitätsklinikum Heidelberg Im Neuenheimer Feld 400 69120 Heidelberg "How small the cosmos. How paltry and puny compared to human consciousness . . . to a single individual recollection." - Vladimir Nabokov -------------- next part -------------- An HTML attachment was scrubbed... URL: From ali at cs.ru.nl Wed Feb 29 21:10:54 2012 From: ali at cs.ru.nl (Ali Bahramisharif) Date: Wed, 29 Feb 2012 21:10:54 +0100 Subject: [FieldTrip] question about MNI alignment Message-ID: Dear Fieldtrip users, I want to create MNI-aligned grids in individual head-space, and I follow the guidelines in : http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space?s[]=template&s[]=grid I do not know how old this page is, but I noticed that for example in the current version "cfg.coordinates" should be "cfg.coordsys". I have the following problems: 1- When I run "ft_plot_mesh(template_grid);", I get a cubic grid which is apparently different from the one shown in the page. 2- When I run, ft_plot_vol(hdm), it does not seem to be aligned to "ft_plot_sens(ft_read_sens(dataset{i}));" I checked my segmented volumes, and they seem to be fine, and I did not need to run flipdim. I am wondering whether my segmented data is correct or it should be flipped somewhere. Please let me know if anybody knows how to resolve this problem. Cheers, Ali From mcoskun at mail.uh.edu Wed Feb 1 13:55:15 2012 From: mcoskun at mail.uh.edu (Mehmet-Akif Coskun) Date: Wed, 01 Feb 2012 06:55:15 -0600 Subject: [FieldTrip] Error -> ft_databrowser Message-ID: <7220b947bb8f3.4f28e1d3@mail.uh.edu> Dear Fieldtrippers, I am encountering a strange error while i try to use ft_databrowser. The error code is as below. I have never seen this error earlier. I used ft_databrowser many times and its only last 2 days that i am getting the error. I downloaded a newer version of fieldtrip (fieldtrip-20120130) and used the newer version but still the same error. Strangely, i dont get this error when i tried with other computers (same matlab version (R2010a), same operating system (windows 7) on both computers. Has anyone got this error before? what may cause this error? fieldtrip version 20120130, matlab version R2010a, operating system windows 7. Thanks in advance for any suggestions. ??? Error using ==> ft_fetch_data at 57 data does not contain a consistent trial definition, fetching data is not possible Error in ==> ft_databrowser>redraw_cb at 1159 art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', endsample); Error in ==> ft_databrowser at 535 redraw_cb(h); -------------- next part -------------- An HTML attachment was scrubbed... URL: From Ulrich.Pomper at charite.de Wed Feb 1 14:44:44 2012 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Wed, 1 Feb 2012 14:44:44 +0100 Subject: [FieldTrip] Defining cfg.neighbourdist at source level In-Reply-To: References: <4F22C422.4080906@charite.de> <4F26B91E.2050200@donders.ru.nl> <4F26BE42.5030204@charite.de> Message-ID: <4F2941CC.6030609@charite.de> Dear Robert and Stephan, Thank you for your replies. I guess I use what Robert called the 'regular' 3D grid, but I'm not quite sure. The structures of my headmodel and leadfield matrix are the following (based on data from a BEM standard file): vol = bnd: [1x3 struct] cond: [0.3300 0.0041 0.3300] mat: [3000x3000 double] type: 'dipoli' ldf = xgrid: [-65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68] ygrid: [-107 -100 -93 -86 -79 -72 -65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68 75] zgrid: [-52 -45 -38 -31 -24 -17 -10 -3 4 11 18 25 32 39 46 53 60 67 74 81] dim: [20 27 20] pos: [10800x3 double] inside: [1x5739 double] outside: [1x5061 double] leadfield: {1x10800 cell} cfg: [1x1 struct] In any case, I still don't quite understand how to calculate the neighbours to each voxel. By saying that the "neighbours are trivial to find and you do not have to specify a structure", do you mean that I don't need to define the cfg.neighbours property at all (given that I do use a regular 3D grid)? Thanks again for your help, cheers, Ulrich On 31.01.2012 21:48, smoratti at psi.ucm.es wrote: Dear Robert, To do clustering on a 3D source surface I always had to "trick" field trip and squeezed the 3D source surface data into a ERF structure treating the 3D surface points as sensors. Then by triangulation I found the neighbors. However, if there is a more elegant method implemented in ft_sourcestatistc, I would be very interested to know how to do it. Where can I find some hints on that? Best, Stephan ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 28223 Pozuelo de Alarcón (Madrid) Spain and Center for Biomedical Technology Laboratory for Cognitive and Computational Neuroscience Parque Científico y Tecnológico de la Universidad Politecnica de Madrid Campus Montegancedo 28223 Pozuelo de Alarcón (Madrid) Spain email: smoratti at psi.ucm.es Tel.: +34 679219982 El 31/01/2012, a las 15:37, Robert Oostenveld escribió: Dear Ulrich If your source locations are defined on a regular 3D grid that can be represented as volume, then the neighbours are trivial to find and you do not have to specify a structure for the neighbours. If you have done source reconstruction on a 3D folded cortical sheet that is defined by a triangulated surface, then it is also possible to cluster along the surface. I don't know the details for the cortical sheet clustering from the top of my head, if you are interested please let me know and I'll look them up. best Robert On 30 Jan 2012, at 16:58, Pomper, Ulrich wrote: Dear Jörn, Thanks for you reply. I did mean source-level, so like you said, I am trying to define the neighbouring voxels for each voxel. As far as I understand, leaving cfg.neighbours blank means that the clustering is done over the time and frequency dimensions only, not over space. The FT help reads: %If you specify an empty neighbourhood structure, clustering will only be done in frequency and time (if available) and not over neighbouring channels. Has anybody done clustering in source space using all three dimensions and could explain how this works? Cheers, Ulrich _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus -------------- next part -------------- An HTML attachment was scrubbed... URL: From MEpstein at NKI.RFMH.ORG Wed Feb 1 20:44:47 2012 From: MEpstein at NKI.RFMH.ORG (Epstein, Michael) Date: Wed, 1 Feb 2012 14:44:47 -0500 Subject: [FieldTrip] rereferencing after preproc Message-ID: <2586A1048152BE4D861E64A98700AD420A601176@nki-mail.NKI.rfmh.org> Hi all, I'm trying to analyze a dataset using multiple reference points - is there a way to re-reference the data after the whole preprocessing step? I'm using ft_rejectvisual to clean the data, so I want to reference after that, in order to preserve as much consistency between the two sets as is possible. I was trying to use ft_preproc_rereference to achieve this goal, but that only takes in channel x time data, not trial data or freq data. Is there a different way to rereference? Thanks, -Michael Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Wed Feb 1 21:00:33 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Wed, 1 Feb 2012 21:00:33 +0100 Subject: [FieldTrip] rereferencing after preproc In-Reply-To: <2586A1048152BE4D861E64A98700AD420A601176@nki-mail.NKI.rfmh.org> References: <2586A1048152BE4D861E64A98700AD420A601176@nki-mail.NKI.rfmh.org> Message-ID: Hi Michael, Probably ft_preprocessing with the options cfg.reref = 'yes' and cfg.refchannel = '' is what you are looking for. ft_preproc_rereference is a lower-level FieldTrip function, which indeed operates directly on a channel x time matrix. ft_preprocessing contains all the necessary bookkeeping wrappers around ft_preproc_* so that you can conveniently apply the preprocessing functions on FieldTrip-style data structures. Hope this helps. Eelke On 1 February 2012 20:44, Epstein, Michael wrote: > Hi all, > > > > I’m trying to analyze a dataset using multiple reference points – is there a > way to re-reference the data after the whole preprocessing step? I’m using > ft_rejectvisual to clean the data, so I want to reference after that, in > order to preserve as much consistency between the two sets as is possible. > > > > I was trying to use ft_preproc_rereference to achieve this goal, but that > only takes in channel x time data, not trial data or freq data. Is there a > different way to rereference? > > > > Thanks, > > > > -Michael > > > > ________________________________ > Conserve Resources. Print only when necessary. > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended > recipient. It may contain confidential information which is legally > privilegedor otherwise protected by law. If you received this e-mail in > error or from someone who is not authorized to send it to you, you are > strictly prohibited from reviewing, using, disseminating, distributing or > copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN > E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your > cooperation. > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From MEpstein at NKI.RFMH.ORG Wed Feb 1 21:05:49 2012 From: MEpstein at NKI.RFMH.ORG (Epstein, Michael) Date: Wed, 1 Feb 2012 15:05:49 -0500 Subject: [FieldTrip] rereferencing after preproc In-Reply-To: References: <2586A1048152BE4D861E64A98700AD420A601176@nki-mail.NKI.rfmh.org> Message-ID: <2586A1048152BE4D861E64A98700AD420A601194@nki-mail.NKI.rfmh.org> Oh I see - I didn't realize you could use that function on data you had already preprocessed once. Thank you, that's useful. -Michael -----Original Message----- From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Eelke Spaak Sent: Wednesday, February 01, 2012 3:01 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] rereferencing after preproc Hi Michael, Probably ft_preprocessing with the options cfg.reref = 'yes' and cfg.refchannel = '' is what you are looking for. ft_preproc_rereference is a lower-level FieldTrip function, which indeed operates directly on a channel x time matrix. ft_preprocessing contains all the necessary bookkeeping wrappers around ft_preproc_* so that you can conveniently apply the preprocessing functions on FieldTrip-style data structures. Hope this helps. Eelke On 1 February 2012 20:44, Epstein, Michael wrote: > Hi all, > > > > I'm trying to analyze a dataset using multiple reference points - is there a > way to re-reference the data after the whole preprocessing step? I'm using > ft_rejectvisual to clean the data, so I want to reference after that, in > order to preserve as much consistency between the two sets as is possible. > > > > I was trying to use ft_preproc_rereference to achieve this goal, but that > only takes in channel x time data, not trial data or freq data. Is there a > different way to rereference? > > > > Thanks, > > > > -Michael > > > > ________________________________ > Conserve Resources. Print only when necessary. > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended > recipient. It may contain confidential information which is legally > privilegedor otherwise protected by law. If you received this e-mail in > error or from someone who is not authorized to send it to you, you are > strictly prohibited from reviewing, using, disseminating, distributing or > copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN > E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your > cooperation. > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. From inieuwenhuis at berkeley.edu Wed Feb 1 21:20:20 2012 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Wed, 01 Feb 2012 12:20:20 -0800 Subject: [FieldTrip] rereferencing after preproc In-Reply-To: <2586A1048152BE4D861E64A98700AD420A601194@nki-mail.NKI.rfmh.org> References: <2586A1048152BE4D861E64A98700AD420A601176@nki-mail.NKI.rfmh.org> <2586A1048152BE4D861E64A98700AD420A601194@nki-mail.NKI.rfmh.org> Message-ID: <4F299E84.7040804@berkeley.edu> Hi, just a little addition. You mention freq data, but you can't re-reference after freq analysis. Has to take place before. (Just in case you meant that) Good luck, Ingrid -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 On 2/1/2012 12:05 PM, Epstein, Michael wrote: > Oh I see - I didn't realize you could use that function on data you had > already preprocessed once. > > Thank you, that's useful. > > -Michael > > -----Original Message----- > From: fieldtrip-bounces at donders.ru.nl > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Eelke Spaak > Sent: Wednesday, February 01, 2012 3:01 PM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] rereferencing after preproc > > Hi Michael, > > Probably ft_preprocessing with the options cfg.reref = 'yes' and > cfg.refchannel = '' is what you are looking for. > > ft_preproc_rereference is a lower-level FieldTrip function, which > indeed operates directly on a channel x time matrix. ft_preprocessing > contains all the necessary bookkeeping wrappers around ft_preproc_* so > that you can conveniently apply the preprocessing functions on > FieldTrip-style data structures. > > Hope this helps. > > Eelke > > On 1 February 2012 20:44, Epstein, Michael > wrote: >> Hi all, >> >> >> >> I'm trying to analyze a dataset using multiple reference points - is > there a >> way to re-reference the data after the whole preprocessing step? I'm > using >> ft_rejectvisual to clean the data, so I want to reference after that, > in >> order to preserve as much consistency between the two sets as is > possible. >> >> >> I was trying to use ft_preproc_rereference to achieve this goal, but > that >> only takes in channel x time data, not trial data or freq data. Is > there a >> different way to rereference? >> >> >> >> Thanks, >> >> >> >> -Michael >> >> >> >> ________________________________ >> Conserve Resources. Print only when necessary. >> >> IMPORTANT NOTICE: This e-mail is meant only for the use of the > intended >> recipient. It may contain confidential information which is legally >> privilegedor otherwise protected by law. If you received this e-mail > in >> error or from someone who is not authorized to send it to you, you are >> strictly prohibited from reviewing, using, disseminating, distributing > or >> copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY > RETURN >> E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your >> cooperation. >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Conserve Resources. Print only when necessary. > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 From jm.horschig at donders.ru.nl Thu Feb 2 09:30:37 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 02 Feb 2012 09:30:37 +0100 Subject: [FieldTrip] rereferencing after preproc In-Reply-To: <4F299E84.7040804@berkeley.edu> References: <2586A1048152BE4D861E64A98700AD420A601176@nki-mail.NKI.rfmh.org> <2586A1048152BE4D861E64A98700AD420A601194@nki-mail.NKI.rfmh.org> <4F299E84.7040804@berkeley.edu> Message-ID: <4F2A49AD.1050303@donders.ru.nl> Hi, another addition: ft_apply_montage is doing the same (ft_preprocessing also calls this function), but it also changes the labels. This is useful when, for example, wanting to construct bipolar channels like hEOG and vEOG. Best, Jörn On 2/1/2012 9:20 PM, Ingrid Nieuwenhuis wrote: > Hi, just a little addition. You mention freq data, but you can't > re-reference after freq analysis. Has to take place before. (Just in > case you meant that) > Good luck, > Ingrid > -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From sysoevao at psychiatry.wustl.edu Thu Feb 2 23:49:41 2012 From: sysoevao at psychiatry.wustl.edu (Sysoeva, Olga Vladimirovna) Date: Thu, 2 Feb 2012 16:49:41 -0600 Subject: [FieldTrip] channels interpolation Message-ID: <76DC57362137854CB9592B496182D5FA09D909A83B@wusmexmbx2.medpriv.wucon.wustl.edu> Dear group, Am I doing something wrong or is it a bug? I needed to do some bad channel interpolation for my dataset (epoched data). So I found out that there is a ft_channel_repair function. And I tried to use it in the following way. cfg = []; cfg.method = 'distance'%, 'triangulation' or 'template' (default = 'distance') cfg.neighbourdist = 4; % number, maximum distance between neighbouring sensors (only for 'distance') cfg.layout = 'C:\Matlab_programs\Fieldtrip\My_Fieldtrip\EEG1010_modified32.lay'; [neighbours] = ft_prepare_neighbours(cfg, data) cfg = []; cfg.badchannel = {'F4'};%cell-array, see FT_CHANNELSELECTION for details cfg.neighbours = neighbours; [interp] = ft_channelrepair(cfg, data) But I'm getting the error ??? Reference to non-existent field 'pnt'. It seems to me that I'm not preparing the sensor(electrode) structure correctly, but I couldn't find mistake. I do follow the tutorial. There are a link that I need to prepare the electrode structure as in ft_fetch_sens function, but I my version of Fieldtrip I do not have this function. I'll appreciate any help, Best Regards, Olga. __________________________________________________________ Olga Sysoeva, Research Associate, PhD Psychiatry Department, Washington University School of Medicine Campus Box 8134 660 South Euclid Ave Saint Louis, MO 63110-9909 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Fri Feb 3 09:50:26 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Fri, 03 Feb 2012 09:50:26 +0100 Subject: [FieldTrip] channels interpolation In-Reply-To: <76DC57362137854CB9592B496182D5FA09D909A83B@wusmexmbx2.medpriv.wucon.wustl.edu> References: <76DC57362137854CB9592B496182D5FA09D909A83B@wusmexmbx2.medpriv.wucon.wustl.edu> Message-ID: <4F2B9FD2.7070003@donders.ru.nl> Dear Olga, indeed that there is a problem with the sensor definition. In addition to specifying neighbours, the channelrepair function needs to know the distance between channels. Therefore, you need to provide a definition of the sensor position additionally. However, the error message you get is not the one you should see - there should be one that is more elaborate and intuitively understandable ;) Could you send me (outside the mailinglist) the whole error message, including the lines where this goes wrong? I will then fix the problem asap. Btw, the ft_fetch_sens function has recently been moved to the FieldTrip/private folder, that means Matlab prevents you from seeing or calling the function directly, but if you just cd to that directory, you can access the file. Also, I just changed the error message that you should have seen to be more elaborate (will be available from tomorrow on). Best, Jörn On 2/2/2012 11:49 PM, Sysoeva, Olga Vladimirovna wrote: > > Dear group, > > Am I doing something wrong or is it a bug? > > I needed to do some bad channel interpolation for my dataset (epoched > data). > > So I found out that there is a ft_channel_repair function. And I tried > to use it in the following way. > > cfg = []; > > cfg.method = 'distance'%, 'triangulation' or 'template' > (default = 'distance') > > cfg.neighbourdist = 4; % number, maximum distance between neighbouring > sensors (only for 'distance') > > cfg.layout = > 'C:\Matlab_programs\Fieldtrip\My_Fieldtrip\EEG1010_modified32.lay'; > > [neighbours] = ft_prepare_neighbours(cfg, data) > > cfg = []; > > cfg.badchannel = {'F4'};%cell-array, see FT_CHANNELSELECTION for > details > > cfg.neighbours = neighbours; > > [interp] = ft_channelrepair(cfg, data) > > But I'm getting the error ??? Reference to non-existent field 'pnt'. > > It seems to me that I'm not preparing the sensor(electrode) structure > correctly, but I couldn't find mistake. I do follow the tutorial. > There are a link that I need to prepare the electrode structure as in > ft_fetch_sens function, but I my version of Fieldtrip I do not have > this function. > > I'll appreciate any help, > > Best Regards, > > Olga. > > __________________________________________________________ > > Olga Sysoeva, > > Research Associate, PhD > > Psychiatry Department, > > Washington University School of Medicine > > Campus Box 8134 > > 660 South Euclid Ave > > Saint Louis, MO 63110-9909 > > > ------------------------------------------------------------------------ > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying or the taking of any action in reliance on > the contents of this information is strictly prohibited. If you have > received this email in error, please immediately notify the sender via > telephone or return mail. > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From chadbircher at yahoo.com Fri Feb 3 17:06:45 2012 From: chadbircher at yahoo.com (Chad Bircher) Date: Fri, 3 Feb 2012 08:06:45 -0800 (PST) Subject: [FieldTrip] Pthread install Message-ID: <1328285205.47747.YahooMailNeo@web162006.mail.bf1.yahoo.com> I am trying to install the peer directories, but cannot run peercompile('VC') on my Windows7 64bit machine using Microsoft Visual C++ express 2012.  I am getting an error that it cannot find pthread.h  I am not a systems developer, and do not know how to install this correctly.  Every attempt I have made still does not allow peercompile to run. How do I install pthread on this sort of a system? Thank you Chad -------------- next part -------------- An HTML attachment was scrubbed... URL: From Ulrich.Pomper at charite.de Mon Feb 6 14:05:38 2012 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Mon, 6 Feb 2012 14:05:38 +0100 Subject: [FieldTrip] Fwd: Re: Defining cfg.neighbourdist at source level In-Reply-To: <2594dc0d96864f1a8d49694602e55bce@EXCCAHT-2.mail.uke.ads> References: <2594dc0d96864f1a8d49694602e55bce@EXCCAHT-2.mail.uke.ads> Message-ID: <4F2FD022.3000407@charite.de> Dear fieldtrippers, I'm still in need of an advise on the issue below. Any help would be greatly appreciated!! Dear Robert and Stephan, Thank you for your replies. I guess I use what Robert called the 'regular' 3D grid, but I'm not quite sure. The structures of my headmodel and leadfield matrix are the following (based on data from a BEM standard file): vol = bnd: [1x3 struct] cond: [0.3300 0.0041 0.3300] mat: [3000x3000 double] type: 'dipoli' ldf = xgrid: [-65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68] ygrid: [-107 -100 -93 -86 -79 -72 -65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68 75] zgrid: [-52 -45 -38 -31 -24 -17 -10 -3 4 11 18 25 32 39 46 53 60 67 74 81] dim: [20 27 20] pos: [10800x3 double] inside: [1x5739 double] outside: [1x5061 double] leadfield: {1x10800 cell} cfg: [1x1 struct] In any case, I still don't quite understand how to calculate the neighbours to each voxel. By saying that the "neighbours are trivial to find and you do not have to specify a structure", do you mean that I don't need to define the cfg.neighbours property at all (given that I do use a regular 3D grid)? Thanks again for your help, cheers, Ulrich On 31.01.2012 21:48, smoratti at psi.ucm.es wrote: Dear Robert, To do clustering on a 3D source surface I always had to "trick" field trip and squeezed the 3D source surface data into a ERF structure treating the 3D surface points as sensors. Then by triangulation I found the neighbors. However, if there is a more elegant method implemented in ft_sourcestatistc, I would be very interested to know how to do it. Where can I find some hints on that? Best, Stephan ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 28223 Pozuelo de Alarcón (Madrid) Spain and Center for Biomedical Technology Laboratory for Cognitive and Computational Neuroscience Parque Científico y Tecnológico de la Universidad Politecnica de Madrid Campus Montegancedo 28223 Pozuelo de Alarcón (Madrid) Spain email: smoratti at psi.ucm.es Tel.: +34 679219982 El 31/01/2012, a las 15:37, Robert Oostenveld escribió: Dear Ulrich If your source locations are defined on a regular 3D grid that can be represented as volume, then the neighbours are trivial to find and you do not have to specify a structure for the neighbours. If you have done source reconstruction on a 3D folded cortical sheet that is defined by a triangulated surface, then it is also possible to cluster along the surface. I don't know the details for the cortical sheet clustering from the top of my head, if you are interested please let me know and I'll look them up. best Robert On 30 Jan 2012, at 16:58, Pomper, Ulrich wrote: Dear Jörn, Thanks for you reply. I did mean source-level, so like you said, I am trying to define the neighbouring voxels for each voxel. As far as I understand, leaving cfg.neighbours blank means that the clustering is done over the time and frequency dimensions only, not over space. The FT help reads: %If you specify an empty neighbourhood structure, clustering will only be done in frequency and time (if available) and not over neighbouring channels. Has anybody done clustering in source space using all three dimensions and could explain how this works? Cheers, Ulrich _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus -------------- next part -------------- An HTML attachment was scrubbed... URL: From phc5 at georgetown.edu Tue Feb 7 05:56:09 2012 From: phc5 at georgetown.edu (patrick cox) Date: Mon, 6 Feb 2012 23:56:09 -0500 Subject: [FieldTrip] Computing the system matrix in a the forward model? Message-ID: Hi, I have just started using feildtrip, and I am trying to do some source localization using beamforming. I am working with EEG data and would like to anatomically constrain the forward model, so I am trying out the various BEM methods in fieldtrip. As a first pass I have been using the SPM T1 template, but I also have anatomical scans of my subjects. My problem is that when I try to calculate the model for the volume conductor using most of the methods (openmeeg, dipoli), my vol structure does not contain a vol.mat field (which I believe is the system matrix). The one BEM method that actully returns a vol with a system matrix is the BEMCP method, but the vol.mat file is all NaNs! I have tracked the problem to the calculation of the Cij's, particularly C12 and C21, in the ft_headmodel_bemcp.m which contain a large number of NaN entries. Does anyone have a fix for this, or a advice on how to producing vol structures with system matrices/vol.mat fields using the other BEM methods? Thanks! Patrick Cox -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue Feb 7 11:26:24 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 7 Feb 2012 10:26:24 +0000 Subject: [FieldTrip] Pthread install In-Reply-To: <1328285205.47747.YahooMailNeo@web162006.mail.bf1.yahoo.com> References: <1328285205.47747.YahooMailNeo@web162006.mail.bf1.yahoo.com> Message-ID: Dear Chad All peer functions rely on a single mex file. That mex file implements a TCP server and client in a seperate thread, which allows MATLAB to receive data while at the same time busy with computations. The TCP networking details are slightly different between operating systems. The computers we work with most are unix-bases (linux, os x), therefore those are the ones that we primarily target with out code. Stefan, a former colleague at the Donders has compiled it once on windows32 and 64, but that mex file has not been kept up to date since then. The peer TCP server and client are derived from the FieldTrip buffer (see http://fieldtrip.fcdonders.nl/development/realtime) which is the result of a project to allow MATLAB to do efficient and easy computations on real-time streamed EEG and MEG data. The fieldtrip realtime buffer works well on all operating systems, so as such there is no reason to assume that peer would also not work. The TCP server and the other peer threads (i.e. announce, discover, expire) are all implemented with posix threads, which is the default on unix-like operating systems (linux, os x). On MS Windows there is another threading system, but there is a port of pthreads for windows (see http://sourceware.org/pthreads-win32/). At the time we implemented this stuff, there was only a version available for 32-bit windows, whereas nowadays most Windows computers are 64 bit. Stefan made a 64-bit version of the "ptherads-win32" library himself, that is the one we also use for the fieldtrip buffer. That library and header files can be found in fieldtrip/realtime/buffer/pthreads-win64. It might also be that there is an official release of the pthreads library for win64, if there is, I suggest you use that instead of the fieldtrip version. An alternative might be to use mingw as a compiler: if I recall correctly it also includes pthreads. But then, I don't know how easy or hard it is to use the mingw compiler in combination with MATLAB. hope this helps, Robert PS yet another aspect is the peerslave.exe command line application that allows to start a slave prior to starting MATLAB. Although also for that one Stefan managed to get a version compiled, but I know that that version is buggy. Even the linux version is not 100% stable. At the time Stefan worked with us, it was decided not to spend time on resolving the windows bugs in command-line version. Therefore I suggest that you first focus on getting the mex file to work, and only then start thinking on whether you need the peerslave.exe command-line version. On 3 Feb 2012, at 16:06, Chad Bircher wrote: > I am trying to install the peer directories, but cannot run peercompile('VC') on my Windows7 64bit machine using Microsoft Visual C++ express 2012. I am getting an error that it cannot find pthread.h > I am not a systems developer, and do not know how to install this correctly. Every attempt I have made still does not allow peercompile to run. > How do I install pthread on this sort of a system? > Thank you > Chad > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue Feb 7 11:34:20 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 7 Feb 2012 10:34:20 +0000 Subject: [FieldTrip] Defining cfg.neighbourdist at source level In-Reply-To: <4F2941CC.6030609@charite.de> References: <4F22C422.4080906@charite.de> <4F26B91E.2050200@donders.ru.nl> <4F26BE42.5030204@charite.de> <4F2941CC.6030609@charite.de> Message-ID: <93BEC2B0-B372-4EA9-BE41-1D0606B217FF@donders.ru.nl> Dear Ulrich On 1 Feb 2012, at 13:44, Pomper, Ulrich wrote: > Dear Robert and Stephan, > Thank you for your replies. > I guess I use what Robert called the 'regular' 3D grid, but I'm not quite sure. ... > ldf = > > xgrid: [-65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68] > ygrid: [-107 -100 -93 -86 -79 -72 -65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68 75] > zgrid: [-52 -45 -38 -31 -24 -17 -10 -3 4 11 18 25 32 39 46 53 60 67 74 81] > dim: [20 27 20] > pos: [10800x3 double] ... > > In any case, I still don't quite understand how to calculate the neighbours to each voxel. Yes, you are using a regular 3D grid with dipole positions that are placed at the center of a large number of voxels which jointly fill a cube that spans the head. Just like an MRI. If you look in ldf.pos you will see all positions. Those positions form a 20x27x20 regular grid, with the x-, y, and z-values according to xgrid/ygrid/zgrid. You have a grid spacing of 7mm in each direction. The first positions is [-65 -107 -52] and its neighbours are the grid points that are 7mm to the right, top and front. Just think of it as functional_data = rand(20, 27, 20) i.e. a cube. It is clear for each voxel what the neighbours are. FieldTrip makes use of vectorization, i.e. the 3d matrix with the functional data can also be represented by MATLAB as a vector. functional_data = functional_data(:) What you then get is a vector of length 10800, i.e. matching all the [x y z] positions as they are specified in ldf.pos. > By saying that the "neighbours are trivial to find and you do not have to specify a structure", do you mean that I don't need to define the cfg.neighbours property at all (given that I do use a regular 3D grid)? correct. Robert From Ulrich.Pomper at charite.de Tue Feb 7 11:40:27 2012 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Tue, 7 Feb 2012 11:40:27 +0100 Subject: [FieldTrip] Defining cfg.neighbourdist at source level In-Reply-To: <93BEC2B0-B372-4EA9-BE41-1D0606B217FF@donders.ru.nl> References: <4F22C422.4080906@charite.de> <4F26B91E.2050200@donders.ru.nl> <4F26BE42.5030204@charite.de> <4F2941CC.6030609@charite.de> <93BEC2B0-B372-4EA9-BE41-1D0606B217FF@donders.ru.nl> Message-ID: <4F30FF9B.8080300@charite.de> Thanks a lot Robert, now I get it! Best, Ulrich On 07.02.2012 11:34, Robert Oostenveld wrote: Dear Ulrich On 1 Feb 2012, at 13:44, Pomper, Ulrich wrote: > Dear Robert and Stephan, > Thank you for your replies. > I guess I use what Robert called the 'regular' 3D grid, but I'm not quite sure. ... > ldf = > > xgrid: [-65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68] > ygrid: [-107 -100 -93 -86 -79 -72 -65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68 75] > zgrid: [-52 -45 -38 -31 -24 -17 -10 -3 4 11 18 25 32 39 46 53 60 67 74 81] > dim: [20 27 20] > pos: [10800x3 double] ... > > In any case, I still don't quite understand how to calculate the neighbours to each voxel. Yes, you are using a regular 3D grid with dipole positions that are placed at the center of a large number of voxels which jointly fill a cube that spans the head. Just like an MRI. If you look in ldf.pos you will see all positions. Those positions form a 20x27x20 regular grid, with the x-, y, and z-values according to xgrid/ygrid/zgrid. You have a grid spacing of 7mm in each direction. The first positions is [-65 -107 -52] and its neighbours are the grid points that are 7mm to the right, top and front. Just think of it as functional_data = rand(20, 27, 20) i.e. a cube. It is clear for each voxel what the neighbours are. FieldTrip makes use of vectorization, i.e. the 3d matrix with the functional data can also be represented by MATLAB as a vector. functional_data = functional_data(:) What you then get is a vector of length 10800, i.e. matching all the [x y z] positions as they are specified in ldf.pos. > By saying that the "neighbours are trivial to find and you do not have to specify a structure", do you mean that I don't need to define the cfg.neighbours property at all (given that I do use a regular 3D grid)? correct. Robert _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue Feb 7 11:42:57 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 7 Feb 2012 10:42:57 +0000 Subject: [FieldTrip] Defining cfg.neighbourdist at source level In-Reply-To: <61FDD8CB-F79B-48A6-BC19-015F778A4945@psi.ucm.es> References: <4F22C422.4080906@charite.de> <4F26B91E.2050200@donders.ru.nl> <4F26BE42.5030204@charite.de> <61FDD8CB-F79B-48A6-BC19-015F778A4945@psi.ucm.es> Message-ID: <8AD16232-88F0-4C2E-87FA-03D22928B940@donders.ru.nl> Dear Stephan In fieldtrip/rpivate/clusterstat around line 194 you can see posclusobs = findcluster(reshape(postailobs, [cfg.dim,1]),channeighbstructmat,cfg.minnbchan); that is the section that should get used (the present code still thinks that source is always a 3d regular grid, which is not the case for a surface grid) Furthermore, in ft_prepare_neighbours there is the subfunction "compneighbstructfromtri" that is of relevance. This is a section of the code that needs to be cleaned up and the clustering along the sheet should become a standard feature instead of something that can be managed by a hack. Concrete code suggestions (evt. through bugzilla.fcdonders.nl) are welcome. best Robert On 31 Jan 2012, at 20:48, smoratti at psi.ucm.es wrote: > Dear Robert, > > To do clustering on a 3D source surface I always had to "trick" field trip and squeezed the 3D source surface data into a ERF structure treating the 3D surface points as sensors. Then by triangulation I found the neighbors. However, if there is a more elegant method implemented in ft_sourcestatistc, I would be very interested to know how to do it. Where can I find some hints on that? > > Best, > > Stephan > > ________________________________________________________ > Stephan Moratti, PhD > > see also: http://web.me.com/smoratti/ > > Universidad Complutense de Madrid > Facultad de Psicología > Departamento de Psicología Básica I > Campus de Somosaguas > 28223 Pozuelo de Alarcón (Madrid) > Spain > > and > > Center for Biomedical Technology > Laboratory for Cognitive and Computational Neuroscience > Parque Científico y Tecnológico de la Universidad Politecnica de Madrid > Campus Montegancedo > 28223 Pozuelo de Alarcón (Madrid) > Spain > > > email: smoratti at psi.ucm.es > Tel.: +34 679219982 > > El 31/01/2012, a las 15:37, Robert Oostenveld escribió: > >> Dear Ulrich >> >> If your source locations are defined on a regular 3D grid that can be represented as volume, then the neighbours are trivial to find and you do not have to specify a structure for the neighbours. >> >> If you have done source reconstruction on a 3D folded cortical sheet that is defined by a triangulated surface, then it is also possible to cluster along the surface. I don't know the details for the cortical sheet clustering from the top of my head, if you are interested please let me know and I'll look them up. >> >> best >> Robert >> >> >> >> >> On 30 Jan 2012, at 16:58, Pomper, Ulrich wrote: >> >>> Dear Jörn, >>> Thanks for you reply. I did mean source-level, so like you said, I am trying to define the neighbouring voxels for each voxel. >>> As far as I understand, leaving cfg.neighbours blank means that the clustering is done over the time and frequency dimensions only, not over space. >>> The FT help reads: >>> %If you specify an empty neighbourhood structure, clustering will only be done in frequency and time (if available) and not over neighbouring channels. >>> >>> Has anybody done clustering in source space using all three dimensions and could explain how this works? >>> Cheers, >>> Ulrich >>> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Wed Feb 8 17:14:17 2012 From: lihqih at gmail.com (qi li) Date: Wed, 8 Feb 2012 11:14:17 -0500 Subject: [FieldTrip] coordinate transform Message-ID: Hi, I want to do a coordinate transformation of the sensor positions by knowing the fiducial point(na,lpa,rpa). Is there any function can do this? More specifically I want to know the 3 translational and 3 rotational degree changes between the original coordinate and the changed one. Thanks a lot! Qi From adama.sophie at gmail.com Wed Feb 8 18:03:12 2012 From: adama.sophie at gmail.com (Sophie ADAMA) Date: Wed, 8 Feb 2012 18:03:12 +0100 Subject: [FieldTrip] signal acquisition with Biosemi Message-ID: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> Hi, I am trying to use the acquisition program acquire.m with Biosemi but I get the following error. ??? Undefined function or method 'gdfdatatype' for input arguments of type 'char'. Error in ==> acquire at 51 [datatyp,limits,datatypes,HDR.Bits,HDR.GDFTYP]=gdfdatatype('int32'); There is no gdfdatatype function in the toolbox. What should I do? Can somebody help me, please ? Sophie -------------- next part -------------- An HTML attachment was scrubbed... URL: From tomh at kurage.nimh.nih.gov Wed Feb 8 18:17:53 2012 From: tomh at kurage.nimh.nih.gov (Tom Holroyd (NIH/NIMH) [E]) Date: Wed, 08 Feb 2012 12:17:53 -0500 Subject: [FieldTrip] coordinate transform In-Reply-To: References: Message-ID: <4F32AE41.1030907@kurage.nimh.nih.gov> Here is a function that creates the fiducial basis. You can use it to transform the sensor coordinates into head coordinates. There are lots of comments. Oh, it's written in Python. qi li wrote: > Hi, > > I want to do a coordinate transformation of the sensor positions by > knowing the fiducial point(na,lpa,rpa). Is there any function can do > this? More specifically I want to know the 3 translational and 3 > rotational degree changes between the original coordinate and the > changed one. > > Thanks a lot! > > Qi > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- "The test of a first-rate intelligence is the ability to hold two opposed ideas in the mind at the same time, and still retain the ability to function." — F. Scott Fitzgerald -------------- next part -------------- A non-text attachment was scrubbed... Name: fid.py Type: application/x-python Size: 1651 bytes Desc: not available URL: From gonzalo.rojas.costa at gmail.com Wed Feb 8 20:13:13 2012 From: gonzalo.rojas.costa at gmail.com (Gonzalo Rojas Costa) Date: Wed, 8 Feb 2012 16:13:13 -0300 Subject: [FieldTrip] Cadwell EASY 3 (.ez3) format Message-ID: Hi: How can I read some Cadwell Easy 3 (.ez3) format files that I have ?... Any converter ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Clinica Las Condes Santiago Chile From hamzaf at sabanciuniv.edu Thu Feb 9 06:16:26 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Thu, 9 Feb 2012 07:16:26 +0200 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> Message-ID: Yes, I faced that problem before. I searched for the function and found it in https://sccn.ucsd.edu/svn/software/tags/EEGLAB7_0_1_5beta/external/fieldtrip-20090727/external/biosig/gdfdatatype.m But also I did face another problem after that as I remember. Could you check and tell us the result? Best, Hamza On Wed, Feb 8, 2012 at 7:03 PM, Sophie ADAMA wrote: > Hi,**** > > ** ** > > I am trying to use the acquisition program *acquire.m* with Biosemi but I > get the following error.**** > > ** ** > > ** ** > > *??? Undefined function or method 'gdfdatatype' for input arguments of > type 'char'.* > > * * > > *Error in ==> acquire at 51* > > *[datatyp,limits,datatypes,HDR.Bits,HDR.GDFTYP]=gdfdatatype('int32');* > > ** ** > > There is no *gdfdatatype* function in the toolbox.**** > > **** > > What should I do? Can somebody help me, please ?**** > > ** ** > > Sophie**** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Feb 9 09:23:45 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 9 Feb 2012 09:23:45 +0100 Subject: [FieldTrip] coordinate transform In-Reply-To: References: Message-ID: <83467D5B-606E-40AF-B407-D8CD0F3F2AC1@donders.ru.nl> Hi Qi, Could you be a bit more specific? In what coordinate system are the fiducials defined? MRI-voxel space? MEG-dewar space? Something else? There is a headcoordinates function in fieldtrip/private, which is computing a 4x4 affine transformation matrix for you (from which the rotation and translation can be determined). The high level fieldtrip functions you may want to look into are ft_electroderealign, or ft_volumerealign. Best, Jan-Mathijs On Feb 8, 2012, at 5:14 PM, qi li wrote: > Hi, > > I want to do a coordinate transformation of the sensor positions by > knowing the fiducial point(na,lpa,rpa). Is there any function can do > this? More specifically I want to know the 3 translational and 3 > rotational degree changes between the original coordinate and the > changed one. > > Thanks a lot! > > Qi > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Feb 9 15:41:23 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 9 Feb 2012 14:41:23 +0000 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> Message-ID: Dear Sophie and Hamza the acquire script that is present in the fieldtrip/realtime/acquisition/biosemi directory is only an example script that was written for initial testing. It acquires data in MATLAB, processes it and writes to a file. I believe that the normal way of acquiring data for biosemi is to run the biosemi2ft.exe application, i.e. not in MATLAB. Philip (CC) should be able to tell what the the normal use is, they do this in their lab every day. best Robert On 9 Feb 2012, at 5:16, Hamza Fawzi Altakroury (Student) wrote: > Yes, I faced that problem before. > > I searched for the function and found it in > > https://sccn.ucsd.edu/svn/software/tags/EEGLAB7_0_1_5beta/external/fieldtrip-20090727/external/biosig/gdfdatatype.m > > But also I did face another problem after that as I remember. Could you check and tell us the result? > > Best, > > Hamza > > On Wed, Feb 8, 2012 at 7:03 PM, Sophie ADAMA wrote: > Hi, > > > > I am trying to use the acquisition program acquire.m with Biosemi but I get the following error. > > > > > > ??? Undefined function or method 'gdfdatatype' for input arguments of type 'char'. > > > > Error in ==> acquire at 51 > > [datatyp,limits,datatypes,HDR.Bits,HDR.GDFTYP]=gdfdatatype('int32'); > > > > There is no gdfdatatype function in the toolbox. > > > What should I do? Can somebody help me, please ? > > > > Sophie > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Feb 9 17:56:06 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 9 Feb 2012 16:56:06 +0000 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> <09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl> Message-ID: <8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl> On behalf of Philip... On 9 Feb 2012, at 15:31, Philip van den Broek wrote: > Dear Sophie and Hamza, > > The connection between the Biosemi Active2 system and the FieldTrip buffer is handled by interfacing software biosemi2ft (part of fieldtrip), and should be started from the terminal (mac) or command prompt (windows). > > The interfacing software is located in the FieldTrip folder: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > > The BioSemi system needs a configuration (.cfg) file in which some acquisition-related settings are specified. Configuration files for the BioSemi system specify for example from how many channels data should be streamed and/or recorded, and whether the data should be downsampled. For more information about configuration files for different acquisition systems, see the Fieldtrip website. > > To start the buffer that connects to the Biosemi Active2, open the terminal (Mac) or command prompt (PC) and in the folder where you would like to save your data execute (change path according to your system and location of fieldtrip toolbox): > > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > > : configuration file > : base name of the gdf file. The suffix .gdf and session counters will be added automatically. > : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) > : optional, default is 1972 > an example: > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 > Note that the manually specified name of the file will overwrite any existing file, so make sure myfile.gdf doesn't exist. > > Once this is running, you get access to the data through the fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip fileio functions give you access to the data: > ft_read_header('buffer://localhost:1972'), or > ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100,........ > For further information, see fieldtrip website. > (more info on how we use the system at our department can be found here: http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) > > Hope this helps you to get things running in your place. If you have any further questions, just let me know. > > Best regards, > > > Philip van den Broek > Radboud University Nijmegen > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > > P.O. Box 9104, 6500 HE Nijmegen > Montessorilaan 3, 6525 HR Nijmegen > The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From adama.sophie at gmail.com Thu Feb 9 20:37:09 2012 From: adama.sophie at gmail.com (Sophie ADAMA) Date: Thu, 09 Feb 2012 20:37:09 +0100 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> <09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl> <8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl> Message-ID: <4F342065.8050707@gmail.com> Hi, Thanks for your response. I tried that but I get this: *command not found*. I am using Mac OS Lion. Any suggestions? Thanks Sophie Le 09.02.12 17:56, Robert Oostenveld a écrit : > On behalf of Philip... > > > On 9 Feb 2012, at 15:31, Philip van den Broek wrote: > >> Dear Sophie and Hamza, >> >> The connection between the Biosemi Active2 system and the FieldTrip >> buffer is handled by interfacing software biosemi2ft (part of >> fieldtrip), and should be started from the terminal (mac) or command >> prompt (windows). >> >> The interfacing software is located in the FieldTrip folder: >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft >> >> The BioSemi system needs a configuration (.cfg) file in which some >> acquisition-related settings are specified. Configuration files for >> the BioSemi system specify for example from how many channels data >> should be streamed and/or recorded, and whether the data should be >> downsampled. For more information about configuration files for >> different acquisition systems, see the Fieldtrip website >> . >> >> To start the buffer that connects to the Biosemi Active2, open the >> terminal (Mac) or command prompt (PC) and in the folder where you >> would like to save your data execute (change path according to your >> system and location of fieldtrip toolbox): >> >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft >> >> : configuration file >> : base name of the gdf file. The suffix .gdf and session counters will be added automatically. >> : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) >> : optional, default is 1972 >> an example: >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 >> >> Note that the manually specified name of the file will overwrite any >> existing file, so make sure myfile.gdf doesn't exist. >> >> Once this is running, you get access to the data through the >> fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip >> fileio functions give you access to the data: >> ft_read_header('buffer://localhost:1972' >> ), or >> ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100 >> ,........ >> For further information, see fieldtrip website. >> >> (more info on how we use the system at our department can be found >> here: >> http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) >> >> Hope this helps you to get things running in your place. If you have >> any further questions, just let me know. >> >> Best regards, >> >> >> Philip van den Broek >> Radboud University Nijmegen >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognition >> >> P.O. Box 9104, 6500 HE Nijmegen >> Montessorilaan 3, 6525 HR Nijmegen >> The Netherlands > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From akiko.ikkai at gmail.com Thu Feb 9 23:04:30 2012 From: akiko.ikkai at gmail.com (Akiko Ikkai) Date: Thu, 9 Feb 2012 17:04:30 -0500 Subject: [FieldTrip] volume conduction model missing .mat Message-ID: Hi, I'm trying to create a volume conduction model for my EEG study based on anatomical MRI, and having trouble with ft_prepare_bemmodel when I run cfg = []; cfg.tissue = [7 4 1]; % value for brain, skull, and scalp cfg.conductivity = [1 1/80 1]*.33; % after standard_BEM.zip data cfg.isolatedsource = true; cfg.method = 'dipoli'; cfg.sourceunits = 'mm'; cfg.mriunits = 'mm'; vol = ft_prepare_bemmodel(cfg, seg4bem); I get the following error message while ft_prepare_bemmodel is running: Fatal error in dipoli: interface /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect at vertex 1402 of /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri Warning: an error ocurred while running dipoli > In dipoli at 94 In ft_prepare_bemmodel at 112 Error using ==> fread Invalid file identifier. Use fopen to generate a valid file identifier. Warning: File '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' not found. > In dipoli at 102 In ft_prepare_bemmodel at 112 and the output vol is missing .mat, which causes an error during ft_sourceanalysis. >> vol vol = cond: [0.3300 0.0041 0.3300] bnd: [1x3 struct] source: 3 skin_surface: 3 skin: 1 type: 'dipoli' Does anyone know how to correct for "fatal error" so that ft_prepare_bemmodel creates the correct volume conduction model? I opened .tri file and removed line 1402, but got the same results. Thanks in advance! Akiko -- Akiko Ikkai, Ph.D. Postdoctoral Fellow Department of Psychological and Brain Sciences Johns Hopkins University Ames Hall, 3400 N. Charles St. Baltimore, MD 21218 -------------- next part -------------- An HTML attachment was scrubbed... URL: From phc5 at georgetown.edu Thu Feb 9 23:15:30 2012 From: phc5 at georgetown.edu (patrick cox) Date: Thu, 9 Feb 2012 17:15:30 -0500 Subject: [FieldTrip] volume conduction model missing .mat In-Reply-To: References: Message-ID: Hi Akiko, I had that same problem and also tried using the 'bemcp' which gave me a vol.mat file that was all NaNs. I did not figure out how to solve the problem in FT directly, but have been having some success creating the head model in SPM and loading that into FeildTrip. The SPM manual helped me. Hope that is somewhat helpful, Pat Patrick Cox Prethesis Student Lab For Computational Cognitive Science Georgetown University Medical Center 3970 Reservoir Rd. NW Washington, DC 20007 On Thu, Feb 9, 2012 at 5:04 PM, Akiko Ikkai wrote: > Hi, > > I'm trying to create a volume conduction model for my EEG study based on > anatomical MRI, and having trouble with ft_prepare_bemmodel > > when I run > cfg = []; > cfg.tissue = [7 4 1]; % value for brain, skull, and scalp > cfg.conductivity = [1 1/80 1]*.33; % after standard_BEM.zip data > cfg.isolatedsource = true; > cfg.method = 'dipoli'; > cfg.sourceunits = 'mm'; > cfg.mriunits = 'mm'; > vol = ft_prepare_bemmodel(cfg, seg4bem); > > I get the following error message while ft_prepare_bemmodel is running: > > Fatal error in dipoli: interface > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and > /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect > at vertex 1402 of /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri > > Warning: an error ocurred while running dipoli > > In dipoli at 94 > In ft_prepare_bemmodel at 112 > Error using ==> fread > Invalid file identifier. Use fopen to generate a valid file identifier. > Warning: File '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' not > found. > > In dipoli at 102 > In ft_prepare_bemmodel at 112 > > > and the output vol is missing .mat, which causes an error > during ft_sourceanalysis. > >> vol > vol = > cond: [0.3300 0.0041 0.3300] > bnd: [1x3 struct] > source: 3 > skin_surface: 3 > skin: 1 > type: 'dipoli' > > Does anyone know how to correct for "fatal error" so > that ft_prepare_bemmodel creates the correct volume conduction model? I > opened .tri file and removed line 1402, but got the same results. > > Thanks in advance! Akiko > > -- > Akiko Ikkai, Ph.D. > Postdoctoral Fellow > Department of Psychological and Brain Sciences > Johns Hopkins University > Ames Hall, 3400 N. Charles St. > Baltimore, MD 21218 > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Fri Feb 10 06:26:22 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Fri, 10 Feb 2012 07:26:22 +0200 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <4F342065.8050707@gmail.com> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> <09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl> <8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl> <4F342065.8050707@gmail.com> Message-ID: Hello, I tried the biosemi2tf.exe command it works well on Windows. But, unfortunately I don't know about the Mac OS. Best, Hamza On Thu, Feb 9, 2012 at 9:37 PM, Sophie ADAMA wrote: > Hi, > > Thanks for your response. > > I tried that but I get this: *command not found*. I am using Mac OS Lion. > > Any suggestions? > > Thanks > > Sophie > > Le 09.02.12 17:56, Robert Oostenveld a écrit : > > On behalf of Philip... > > > On 9 Feb 2012, at 15:31, Philip van den Broek wrote: > > Dear Sophie and Hamza, > > The connection between the Biosemi Active2 system and the FieldTrip buffer > is handled by interfacing software biosemi2ft (part of fieldtrip), and > should be started from the terminal (mac) or command prompt (windows). > > The interfacing software is located in the FieldTrip folder: > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > > The BioSemi system needs a configuration (.cfg) file in which some > acquisition-related settings are specified. Configuration files for the > BioSemi system specify for example from how many channels data should be > streamed and/or recorded, and whether the data should be downsampled. For > more information about configuration files for different acquisition > systems, see the Fieldtrip website > . > > To start the buffer that connects to the Biosemi Active2, open the > terminal (Mac) or command prompt (PC) and in the folder where you would > like to save your data execute (change path according to your system and > location of fieldtrip toolbox): > > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > > : configuration file > : base name of the gdf file. The suffix .gdf and session counters will be added automatically. > : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) > : optional, default is 1972 > > an example: > > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 > > Note that the manually specified name of the file will overwrite any > existing file, so make sure myfile.gdf doesn't exist. > Once this is running, you get access to the data through the fieldtrip > buffer filled with data by biosemi2ft, i.e., fieldtrip fileio functions > give you access to the data: > ft_read_header('buffer://localhost:1972'), or > ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100 > ,........ > For further information, see fieldtrip website. > > (more info on how we use the system at our department can be found here: > http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation > ) > > Hope this helps you to get things running in your place. If you have any > further questions, just let me know. > > Best regards, > > Philip van den Broek > Radboud University Nijmegen > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > > P.O. Box 9104, 6500 HE Nijmegen > Montessorilaan 3, 6525 HR Nijmegen > The Netherlands > > > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at mac.com Fri Feb 10 09:00:44 2012 From: nathanweisz at mac.com (Nathan Weisz) Date: Fri, 10 Feb 2012 09:00:44 +0100 Subject: [FieldTrip] volume conduction model missing .mat In-Reply-To: References: Message-ID: <2341406D-6422-4FD3-AD3C-73D1BF70B6CF@mac.com> Hi Akiki, I am not a headmodel expert. but looking at the output message, it seems your segementation did not go too well (see the "intersect" message). my intuition is then then the next temporary file *.ama is not created and ft_prepare_bemmodel then simply says ciao. perhaps you want to check / redo the segmentation? good luck, nathan On 09.02.2012, at 23:04, Akiko Ikkai wrote: > Hi, > > I'm trying to create a volume conduction model for my EEG study based on anatomical MRI, and having trouble with ft_prepare_bemmodel > > when I run > cfg = []; > cfg.tissue = [7 4 1]; % value for brain, skull, and scalp > cfg.conductivity = [1 1/80 1]*.33; % after standard_BEM.zip data > cfg.isolatedsource = true; > cfg.method = 'dipoli'; > cfg.sourceunits = 'mm'; > cfg.mriunits = 'mm'; > vol = ft_prepare_bemmodel(cfg, seg4bem); > > I get the following error message while ft_prepare_bemmodel is running: > > Fatal error in dipoli: interface /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect > at vertex 1402 of /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri > > Warning: an error ocurred while running dipoli > > In dipoli at 94 > In ft_prepare_bemmodel at 112 > Error using ==> fread > Invalid file identifier. Use fopen to generate a valid file identifier. > Warning: File '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' not > found. > > In dipoli at 102 > In ft_prepare_bemmodel at 112 > > > and the output vol is missing .mat, which causes an error during ft_sourceanalysis. > >> vol > vol = > cond: [0.3300 0.0041 0.3300] > bnd: [1x3 struct] > source: 3 > skin_surface: 3 > skin: 1 > type: 'dipoli' > > Does anyone know how to correct for "fatal error" so that ft_prepare_bemmodel creates the correct volume conduction model? I opened .tri file and removed line 1402, but got the same results. > > Thanks in advance! Akiko > > -- > Akiko Ikkai, Ph.D. > Postdoctoral Fellow > Department of Psychological and Brain Sciences > Johns Hopkins University > Ames Hall, 3400 N. Charles St. > Baltimore, MD 21218 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.piantoni at nin.knaw.nl Fri Feb 10 10:36:20 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Fri, 10 Feb 2012 10:36:20 +0100 Subject: [FieldTrip] volume conduction model missing .mat In-Reply-To: <2341406D-6422-4FD3-AD3C-73D1BF70B6CF@mac.com> References: <2341406D-6422-4FD3-AD3C-73D1BF70B6CF@mac.com> Message-ID: Hi Akiki and Patrick, I agree with Nathan about segmentation problems. I had the same problem when two of the three meshes intersected each other. Before you run the forward model, you should check the segmentation (bnd) using ft_plot_mesh. ft_plot_mesh(bnd(1), 'facealpha', .5) hold on ft_plot_mesh(bnd(2), 'facecolor', 'r') You will see that the two meshes intersect with each other. Depending on how you created the meshes, you should fix the parameters in such a way that they don't intersect. For example, ft_volumesegment has a cfg.threshold option (you can check how the segmentation went with ft_sourceplot) and ft_prepare_mesh_new has cfg.thresholdseg and cfg.smoothseg. I think that the meshes in SPM are computed on an (affine-transformed) template and not on the anatomically derived meshes. The template is more robust and that's why the two surfaces do not intersect. In general, the segmentation depends on the quality of your MRIs and you should really visually check the segmentation and meshes. When those look ok, the BEM forward model usually works. Hope this helps. Cheers, Gio On Fri, Feb 10, 2012 at 09:00, Nathan Weisz wrote: > Hi Akiki, > > I am not a headmodel expert. > but looking at the output message, it seems your segementation did not go > too well (see the "intersect" message). my intuition is then then the next > temporary file *.ama is not created and ft_prepare_bemmodel then simply says > ciao. > > perhaps you want to check / redo the segmentation? > > good luck, > nathan > > > On 09.02.2012, at 23:04, Akiko Ikkai wrote: > > Hi, > > I'm trying to create a volume conduction model for my EEG study based on > anatomical MRI, and having trouble with ft_prepare_bemmodel > > when I run > cfg                = []; > cfg.tissue         = [7 4 1]; % value for brain, skull, and scalp > cfg.conductivity   = [1 1/80 1]*.33; % after standard_BEM.zip data > cfg.isolatedsource = true; > cfg.method         = 'dipoli'; > cfg.sourceunits = 'mm'; > cfg.mriunits = 'mm'; > vol = ft_prepare_bemmodel(cfg, seg4bem); > > I get the following error message while ft_prepare_bemmodel is running: > > Fatal error in dipoli:  interface > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and > /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect >  at vertex 1402 of /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri > > Warning: an error ocurred while running dipoli >> In dipoli at 94 >   In ft_prepare_bemmodel at 112 > Error using ==> fread > Invalid file identifier.  Use fopen to generate a valid file identifier. > Warning: File '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' not > found. >> In dipoli at 102 >   In ft_prepare_bemmodel at 112 > > > and the output vol is missing .mat, which causes an error > during ft_sourceanalysis. >>> vol > vol = >             cond: [0.3300 0.0041 0.3300] >              bnd: [1x3 struct] >           source: 3 >     skin_surface: 3 >             skin: 1 >             type: 'dipoli' > > Does anyone know how to correct for "fatal error" so > that ft_prepare_bemmodel creates the correct volume conduction model? I > opened .tri file and removed line 1402, but got the same results. > > Thanks in advance! Akiko > > -- > Akiko Ikkai, Ph.D. > Postdoctoral Fellow > Department of Psychological and Brain Sciences > Johns Hopkins University > Ames Hall, 3400 N. Charles St. > Baltimore, MD 21218 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From adama.sophie at gmail.com Fri Feb 10 14:53:48 2012 From: adama.sophie at gmail.com (Sophie ADAMA) Date: Fri, 10 Feb 2012 14:53:48 +0100 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> <09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl> <8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl> <4F342065.8050707@gmail.com> Message-ID: <016201cce7fb$6a4b9e90$3ee2dbb0$@gmail.com> Hi, I tried it on Windows too, and it works perfectly. But I’m a Mac girl J and I will be happy if someone could help me. Thank you From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) Sent: vendredi 10 février 2012 06:26 To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] signal acquisition with Biosemi Hello, I tried the biosemi2tf.exe command it works well on Windows. But, unfortunately I don't know about the Mac OS. Best, Hamza On Thu, Feb 9, 2012 at 9:37 PM, Sophie ADAMA wrote: Hi, Thanks for your response. I tried that but I get this: command not found. I am using Mac OS Lion. Any suggestions? Thanks Sophie Le 09.02.12 17:56, Robert Oostenveld a écrit : On behalf of Philip... On 9 Feb 2012, at 15:31, Philip van den Broek wrote: Dear Sophie and Hamza, The connection between the Biosemi Active2 system and the FieldTrip buffer is handled by interfacing software biosemi2ft (part of fieldtrip), and should be started from the terminal (mac) or command prompt (windows). The interfacing software is located in the FieldTrip folder: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft The BioSemi system needs a configuration (.cfg) file in which some acquisition-related settings are specified. Configuration files for the BioSemi system specify for example from how many channels data should be streamed and/or recorded, and whether the data should be downsampled. For more information about configuration files for different acquisition systems, see the Fieldtrip website . To start the buffer that connects to the Biosemi Active2, open the terminal (Mac) or command prompt (PC) and in the folder where you would like to save your data execute (change path according to your system and location of fieldtrip toolbox): ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft : configuration file : base name of the gdf file. The suffix .gdf and session counters will be added automatically. : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) : optional, default is 1972 an example: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 Note that the manually specified name of the file will overwrite any existing file, so make sure myfile.gdf doesn't exist. Once this is running, you get access to the data through the fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip fileio functions give you access to the data: ft_read_header('buffer://localhost:1972'), or ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100,........ For further information, see fieldtrip website. (more info on how we use the system at our department can be found here: http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) Hope this helps you to get things running in your place. If you have any further questions, just let me know. Best regards, Philip van den Broek Radboud University Nijmegen Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104, 6500 HE Nijmegen Montessorilaan 3, 6525 HR Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From elilife at gmail.com Fri Feb 10 15:34:45 2012 From: elilife at gmail.com (Eliana Garcia) Date: Fri, 10 Feb 2012 15:34:45 +0100 Subject: [FieldTrip] elilife@gmail.com Message-ID: -- Eliana García Cossio Applied Neurotechnology Lab. Graduate School of Neural and Behavioral Science - Max Planck Research School Institute of Medical Psychology and Behavioral Neurobiology Universität Tübingen (+0049) 01 577-8587604 Otfried-Müller-Str. 47, 72076 Tübingen- Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.severens at maartenskliniek.nl Fri Feb 10 15:46:07 2012 From: m.severens at maartenskliniek.nl (Severens, Marianne) Date: Fri, 10 Feb 2012 15:46:07 +0100 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <016201cce7fb$6a4b9e90$3ee2dbb0$@gmail.com> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com><09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl><8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl><4F342065.8050707@gmail.com> <016201cce7fb$6a4b9e90$3ee2dbb0$@gmail.com> Message-ID: <70FC3ACFFB46314EBEAF9101EA45F50E06D8EC7A0C@smkexch02.maartenskliniek.nl> Hi Sophie Are you sure that the correct version of the biosemi2ft (so the one for the mac) is in the folder that you are specifying? Maybe you can try it first without the optional parameters, so just ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft Best, Marianne From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Sophie ADAMA Sent: vrijdag 10 februari 2012 14:54 To: 'Email discussion list for the FieldTrip project' Subject: Re: [FieldTrip] signal acquisition with Biosemi Hi, I tried it on Windows too, and it works perfectly. But I’m a Mac girl ☺ and I will be happy if someone could help me. Thank you From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) Sent: vendredi 10 février 2012 06:26 To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] signal acquisition with Biosemi Hello, I tried the biosemi2tf.exe command it works well on Windows. But, unfortunately I don't know about the Mac OS. Best, Hamza On Thu, Feb 9, 2012 at 9:37 PM, Sophie ADAMA > wrote: Hi, Thanks for your response. I tried that but I get this: command not found. I am using Mac OS Lion. Any suggestions? Thanks Sophie Le 09.02.12 17:56, Robert Oostenveld a écrit : On behalf of Philip... On 9 Feb 2012, at 15:31, Philip van den Broek wrote: Dear Sophie and Hamza, The connection between the Biosemi Active2 system and the FieldTrip buffer is handled by interfacing software biosemi2ft (part of fieldtrip), and should be started from the terminal (mac) or command prompt (windows). The interfacing software is located in the FieldTrip folder: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft The BioSemi system needs a configuration (.cfg) file in which some acquisition-related settings are specified. Configuration files for the BioSemi system specify for example from how many channels data should be streamed and/or recorded, and whether the data should be downsampled. For more information about configuration files for different acquisition systems, see the Fieldtrip website. To start the buffer that connects to the Biosemi Active2, open the terminal (Mac) or command prompt (PC) and in the folder where you would like to save your data execute (change path according to your system and location of fieldtrip toolbox): ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft : configuration file : base name of the gdf file. The suffix .gdf and session counters will be added automatically. : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) : optional, default is 1972 an example: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 Note that the manually specified name of the file will overwrite any existing file, so make sure myfile.gdf doesn't exist. Once this is running, you get access to the data through the fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip fileio functions give you access to the data: ft_read_header('buffer://localhost:1972'), or ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100,........ For further information, see fieldtrip website. (more info on how we use the system at our department can be found here: http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) Hope this helps you to get things running in your place. If you have any further questions, just let me know. Best regards, Philip van den Broek Radboud University Nijmegen Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104, 6500 HE Nijmegen Montessorilaan 3, 6525 HR Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University ________________________________ Disclaimer Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. Sint Maartenskliniek Hengstdal 3, 6574 NA Ubbergen (bij Nijmegen) Telefoon 024-3659 911 Telefax 024-3659 204 KvK nummer 41055111 -------------- next part -------------- An HTML attachment was scrubbed... URL: From isabella.premoli at gmail.com Fri Feb 10 15:48:24 2012 From: isabella.premoli at gmail.com (isabella premoli) Date: Fri, 10 Feb 2012 15:48:24 +0100 Subject: [FieldTrip] TMS-EEG data analysis Message-ID: Dear FieldTrip community, My name is Isabella and I have just started using FieldTrip to analyze TMS-EEG data. I was wondering whether the Donders Institute will provide courses on FieldTrip regarding this specific analysis. In case the answer is positive, I would be very happy to join. Cheers, Isabella -- Isabella Premoli, PhD student Motor Cortex Laboratory Schleusenweg 2-16 D-60528 Frankfurt am Main Tel: +49-69-6301-83826 -------------- next part -------------- An HTML attachment was scrubbed... URL: From elilife at gmail.com Fri Feb 10 16:26:46 2012 From: elilife at gmail.com (Eliana Garcia) Date: Fri, 10 Feb 2012 16:26:46 +0100 Subject: [FieldTrip] wPLI and analysis of band frequencies Message-ID: Hello! I am currently trying to analyze my data using the wPLI. However I would like to do a band frequency analysis i.e calculate a wPLI value for example for the beta band, but this is not possible since the wPLI is calculated for a time window (according to the time-frequency transformation resolution) and for a certain specific frequency across trials. Guggisberg et al ('Mapping functional connectivity in Patients with Brain lesions') solved this problem in the case of coherence, calculating the sum of autospectra and sum of cross-spectra of the corresponding frequency bins. However, I think that this approach will influence a lot false negatives in the case of the wPLI, since the shifts of phases for the components of the certain band can somehow cancel to each other. Another idea could be to calculate the wPLI for each frequency bin and then average across the band frequency, but I am not sure if this will be really representative of functional connectivity for this band. I still have no clue and what could be the best approach. Thank you so much, -- Eliana García Cossio Applied Neurotechnology Lab. Graduate School of Neural and Behavioral Science - Max Planck Research School Institute of Medical Psychology and Behavioral Neurobiology Universität Tübingen -------------- next part -------------- An HTML attachment was scrubbed... URL: From adama.sophie at gmail.com Sat Feb 11 18:29:33 2012 From: adama.sophie at gmail.com (Sophie ADAMA) Date: Sat, 11 Feb 2012 18:29:33 +0100 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <70FC3ACFFB46314EBEAF9101EA45F50E06D8EC7A0C@smkexch02.maartenskliniek.nl> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com><09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl><8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl><4F342065.8050707@gmail.com> <016201cce7fb$6a4b9e90$3ee2dbb0$@gmail.com> <70FC3ACFFB46314EBEAF9101EA45F50E06D8EC7A0C@smkexch02.maartenskliniek.nl> Message-ID: <002101cce8e2$bb478060$31d68120$@gmail.com> Hi Marianne, There are 3 biosemi2ft in that folder : biosemi2ft.cc, biosemi2ft.exe and biosemi2ft.maci; but when I type ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft in the command line, it says No such file or directory. Sophie From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Severens, Marianne Sent: vendredi 10 février 2012 15:46 To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] signal acquisition with Biosemi Hi Sophie Are you sure that the correct version of the biosemi2ft (so the one for the mac) is in the folder that you are specifying? Maybe you can try it first without the optional parameters, so just ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft Best, Marianne From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Sophie ADAMA Sent: vrijdag 10 februari 2012 14:54 To: 'Email discussion list for the FieldTrip project' Subject: Re: [FieldTrip] signal acquisition with Biosemi Hi, I tried it on Windows too, and it works perfectly. But I’m a Mac girl J and I will be happy if someone could help me. Thank you From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) Sent: vendredi 10 février 2012 06:26 To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] signal acquisition with Biosemi Hello, I tried the biosemi2tf.exe command it works well on Windows. But, unfortunately I don't know about the Mac OS. Best, Hamza On Thu, Feb 9, 2012 at 9:37 PM, Sophie ADAMA wrote: Hi, Thanks for your response. I tried that but I get this: command not found. I am using Mac OS Lion. Any suggestions? Thanks Sophie Le 09.02.12 17:56, Robert Oostenveld a écrit : On behalf of Philip... On 9 Feb 2012, at 15:31, Philip van den Broek wrote: Dear Sophie and Hamza, The connection between the Biosemi Active2 system and the FieldTrip buffer is handled by interfacing software biosemi2ft (part of fieldtrip), and should be started from the terminal (mac) or command prompt (windows). The interfacing software is located in the FieldTrip folder: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft The BioSemi system needs a configuration (.cfg) file in which some acquisition-related settings are specified. Configuration files for the BioSemi system specify for example from how many channels data should be streamed and/or recorded, and whether the data should be downsampled. For more information about configuration files for different acquisition systems, see the Fieldtrip website . To start the buffer that connects to the Biosemi Active2, open the terminal (Mac) or command prompt (PC) and in the folder where you would like to save your data execute (change path according to your system and location of fieldtrip toolbox): ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft : configuration file : base name of the gdf file. The suffix .gdf and session counters will be added automatically. : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) : optional, default is 1972 an example: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 Note that the manually specified name of the file will overwrite any existing file, so make sure myfile.gdf doesn't exist. Once this is running, you get access to the data through the fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip fileio functions give you access to the data: ft_read_header('buffer://localhost:1972'), or ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100,........ For further information, see fieldtrip website. (more info on how we use the system at our department can be found here: http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) Hope this helps you to get things running in your place. If you have any further questions, just let me know. Best regards, Philip van den Broek Radboud University Nijmegen Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104, 6500 HE Nijmegen Montessorilaan 3, 6525 HR Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University _____ Disclaimer Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. Sint Maartenskliniek Hengstdal 3, 6574 NA Ubbergen (bij Nijmegen) Telefoon 024-3659 911 Telefax 024-3659 204 KvK nummer 41055111 -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.severens at maartenskliniek.nl Mon Feb 13 15:52:29 2012 From: m.severens at maartenskliniek.nl (Severens, Marianne) Date: Mon, 13 Feb 2012 15:52:29 +0100 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <002101cce8e2$bb478060$31d68120$@gmail.com> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com><09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl><8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl><4F342065.8050707@gmail.com><016201cce7fb$6a4b9e90$3ee2dbb0$@gmail.com><70FC3ACFFB46314EBEAF9101EA45F50E06D8EC7A0C@smkexch02.maartenskliniek.nl>, <002101cce8e2$bb478060$31d68120$@gmail.com> Message-ID: <70FC3ACFFB46314EBEAF9101EA45F50E06D145F312@smkexch02.maartenskliniek.nl> Hi Sophie I've checked the script that we use to startup the buffer in our lab. Apparently you need to type ./ before the command. This is what our script looks like: cd to the /fieldtrip/realtime/acquisition/biosemi/ folder. Then run the biosemi2ft: ./biosemi2ft (with optional parameters) I think you can also put a path in the gdf filename, so it does not save it in the fieldtrip folder, but you will have to check that. I hope this works for you! Best, Marianne ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Sophie ADAMA [adama.sophie at gmail.com] Sent: Saturday, February 11, 2012 6:29 PM To: 'Email discussion list for the FieldTrip project' Subject: Re: [FieldTrip] signal acquisition with Biosemi Hi Marianne, There are 3 biosemi2ft in that folder : biosemi2ft.cc, biosemi2ft.exe and biosemi2ft.maci; but when I type ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft in the command line, it says No such file or directory. Sophie From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Severens, Marianne Sent: vendredi 10 février 2012 15:46 To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] signal acquisition with Biosemi Hi Sophie Are you sure that the correct version of the biosemi2ft (so the one for the mac) is in the folder that you are specifying? Maybe you can try it first without the optional parameters, so just ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft Best, Marianne From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Sophie ADAMA Sent: vrijdag 10 februari 2012 14:54 To: 'Email discussion list for the FieldTrip project' Subject: Re: [FieldTrip] signal acquisition with Biosemi Hi, I tried it on Windows too, and it works perfectly. But I’m a Mac girl ☺ and I will be happy if someone could help me. Thank you From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) Sent: vendredi 10 février 2012 06:26 To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] signal acquisition with Biosemi Hello, I tried the biosemi2tf.exe command it works well on Windows. But, unfortunately I don't know about the Mac OS. Best, Hamza On Thu, Feb 9, 2012 at 9:37 PM, Sophie ADAMA > wrote: Hi, Thanks for your response. I tried that but I get this: command not found. I am using Mac OS Lion. Any suggestions? Thanks Sophie Le 09.02.12 17:56, Robert Oostenveld a écrit : On behalf of Philip... On 9 Feb 2012, at 15:31, Philip van den Broek wrote: Dear Sophie and Hamza, The connection between the Biosemi Active2 system and the FieldTrip buffer is handled by interfacing software biosemi2ft (part of fieldtrip), and should be started from the terminal (mac) or command prompt (windows). The interfacing software is located in the FieldTrip folder: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft The BioSemi system needs a configuration (.cfg) file in which some acquisition-related settings are specified. Configuration files for the BioSemi system specify for example from how many channels data should be streamed and/or recorded, and whether the data should be downsampled. For more information about configuration files for different acquisition systems, see the Fieldtrip website. To start the buffer that connects to the Biosemi Active2, open the terminal (Mac) or command prompt (PC) and in the folder where you would like to save your data execute (change path according to your system and location of fieldtrip toolbox): ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft : configuration file : base name of the gdf file. The suffix .gdf and session counters will be added automatically. : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) : optional, default is 1972 an example: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 Note that the manually specified name of the file will overwrite any existing file, so make sure myfile.gdf doesn't exist. Once this is running, you get access to the data through the fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip fileio functions give you access to the data: ft_read_header('buffer://localhost:1972'), or ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100,........ For further information, see fieldtrip website. (more info on how we use the system at our department can be found here: http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) Hope this helps you to get things running in your place. If you have any further questions, just let me know. Best regards, Philip van den Broek Radboud University Nijmegen Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104, 6500 HE Nijmegen Montessorilaan 3, 6525 HR Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University ________________________________ Disclaimer Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. Sint Maartenskliniek Hengstdal 3, 6574 NA Ubbergen (bij Nijmegen) Telefoon 024-3659 911 Telefax 024-3659 204 KvK nummer 41055111 Disclaimer Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. Sint Maartenskliniek Hengstdal 3, 6574 NA Ubbergen (bij Nijmegen) Telefoon 024-3659 911 Telefax 024-3659 204 KvK nummer 41055111 From p.vandenbroek at donders.ru.nl Mon Feb 13 19:08:15 2012 From: p.vandenbroek at donders.ru.nl (Philip van den Broek) Date: Mon, 13 Feb 2012 19:08:15 +0100 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <70FC3ACFFB46314EBEAF9101EA45F50E06D145F312@smkexch02.maartenskliniek.nl> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> <09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl> <8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl> <4F342065.8050707@gmail.com> <016201cce7fb$6a4b9e90$3ee2dbb0$@gmail.com> <70FC3ACFFB46314EBEAF9101EA45F50E06D8EC7A0C@smkexch02.maartenskliniek.nl> <002101cce8e2$bb478060$31d68120$@gmail.com> <70FC3ACFFB46314EBEAF9101EA45F50E06D145F312@smkexch02.maartenskliniek.nl> Message-ID: Hi Sophie, If you specify a file and path, you don't need ./ in front of it, only when you try to execute a file in the current folder. In our local fieldtrip distribution for biosemi2ft, contrary to yours, apparently the extension .maci is missing so you need to specify the extension as well: If you are in the folder: ./biosemi2ft.maci (with optional parameters) or from anywhere else: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft.maci (with optional parameters) Gr. Philip On Feb 13, 2012, at 3:52 PM, Severens, Marianne wrote: > Hi Sophie > > I've checked the script that we use to startup the buffer in our lab. Apparently you need to type ./ before the command. This is what our script looks like: > cd to the /fieldtrip/realtime/acquisition/biosemi/ folder. > Then run the biosemi2ft: ./biosemi2ft (with optional parameters) > > I think you can also put a path in the gdf filename, so it does not save it in the fieldtrip folder, but you will have to check that. > > I hope this works for you! > Best, Marianne > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Sophie ADAMA [adama.sophie at gmail.com] > Sent: Saturday, February 11, 2012 6:29 PM > To: 'Email discussion list for the FieldTrip project' > Subject: Re: [FieldTrip] signal acquisition with Biosemi > > Hi Marianne, > > There are 3 biosemi2ft in that folder : biosemi2ft.cc, biosemi2ft.exe and biosemi2ft.maci; but when I type ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > in the command line, it says No such file or directory. > > Sophie > > From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Severens, Marianne > Sent: vendredi 10 février 2012 15:46 > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] signal acquisition with Biosemi > > Hi Sophie > > Are you sure that the correct version of the biosemi2ft (so the one for the mac) is in the folder that you are specifying? Maybe you can try it first without the optional parameters, so just > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > > Best, Marianne > > From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Sophie ADAMA > Sent: vrijdag 10 februari 2012 14:54 > To: 'Email discussion list for the FieldTrip project' > Subject: Re: [FieldTrip] signal acquisition with Biosemi > > Hi, > > I tried it on Windows too, and it works perfectly. > > But I’m a Mac girl ☺ and I will be happy if someone could help me. > > Thank you > > > From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) > Sent: vendredi 10 février 2012 06:26 > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] signal acquisition with Biosemi > > Hello, > > I tried the biosemi2tf.exe command it works well on Windows. > > But, unfortunately I don't know about the Mac OS. > > Best, > > Hamza > On Thu, Feb 9, 2012 at 9:37 PM, Sophie ADAMA > wrote: > Hi, > > Thanks for your response. > > I tried that but I get this: command not found. I am using Mac OS Lion. > > Any suggestions? > > Thanks > > Sophie > Le 09.02.12 17:56, Robert Oostenveld a écrit : > On behalf of Philip... > > > On 9 Feb 2012, at 15:31, Philip van den Broek wrote: > > > Dear Sophie and Hamza, > > The connection between the Biosemi Active2 system and the FieldTrip buffer is handled by interfacing software biosemi2ft (part of fieldtrip), and should be started from the terminal (mac) or command prompt (windows). > > The interfacing software is located in the FieldTrip folder: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > > The BioSemi system needs a configuration (.cfg) file in which some acquisition-related settings are specified. Configuration files for the BioSemi system specify for example from how many channels data should be streamed and/or recorded, and whether the data should be downsampled. For more information about configuration files for different acquisition systems, see the Fieldtrip website. > > To start the buffer that connects to the Biosemi Active2, open the terminal (Mac) or command prompt (PC) and in the folder where you would like to save your data execute (change path according to your system and location of fieldtrip toolbox): > > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > > > > : configuration file > > : base name of the gdf file. The suffix .gdf and session counters will be added automatically. > > : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) > > : optional, default is 1972 > > an example: > > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 > > Note that the manually specified name of the file will overwrite any existing file, so make sure myfile.gdf doesn't exist. > Once this is running, you get access to the data through the fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip fileio functions give you access to the data: > ft_read_header('buffer://localhost:1972'), or > ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100,........ > For further information, see fieldtrip website. > > (more info on how we use the system at our department can be found here: http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) > > Hope this helps you to get things running in your place. If you have any further questions, just let me know. > > Best regards, > > Philip van den Broek > Radboud University Nijmegen > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > > P.O. Box 9104, 6500 HE Nijmegen > Montessorilaan 3, 6525 HR Nijmegen > The Netherlands > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > ________________________________ > Disclaimer > Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. > > Sint Maartenskliniek > Hengstdal 3, > 6574 NA Ubbergen (bij Nijmegen) > Telefoon 024-3659 911 > Telefax 024-3659 204 > KvK nummer 41055111 > > Disclaimer > Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. > > Sint Maartenskliniek > Hengstdal 3, > 6574 NA Ubbergen (bij Nijmegen) > Telefoon 024-3659 911 > Telefax 024-3659 204 > KvK nummer 41055111 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From sysoevao at psychiatry.wustl.edu Mon Feb 13 21:49:17 2012 From: sysoevao at psychiatry.wustl.edu (Sysoeva, Olga Vladimirovna) Date: Mon, 13 Feb 2012 14:49:17 -0600 Subject: [FieldTrip] one/two-tails analysis Message-ID: <76DC57362137854CB9592B496182D5FA09D91CC315@wusmexmbx2.medpriv.wucon.wustl.edu> Dear group, I do face some weird results during my analysis. Usually I do t-test analysis to compare 2 condions/groups and use 2-tails, as far as I do not have any preliminary hypothesis about the direction of the effect. So my script looks something like Script 1 (see below). Important here is that I do keep the default parameters, cfg.tail = 0; cfg.clustertail = 0; To my understanding of statistic, if you have the two-tail effect, and group 1 has bigger mean than gr2, you should have the effect with one-tail as well and even more significant. But what I discovered just today that if I change this parameter to 1, cfg.tail = 1; cfg.clustertail = 1; in order to look spesifically for the one-tail effect (gr1 is bigger than gr2), my very significant 2 tail effect just disappeared completely. Is it a bug? Your comments are appreciated. Best reGards, Olga. Script 1 cfg = []; cfg.method = 'montecarlo'; % use the Monte Carlo Method to calculate the significance probability cfg.statistic = 'indepsamplesT'; % use the independent samples T-statistic as a measure to evaluate % the effect at the sample level % cfg.statistic = 'indepsamplesF'; % use the independent samples T-statistic as a measure to evaluate % cfg.computecritval = 'yes' % the effect at the sample level cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; % alpha level of the sample-specific test statistic that will be used for thresholding cfg.clusterstatistic = 'maxsum'; % test statistic that will be evaluated under the permutation distribution. cfg.minnbchan = 1; % minimum number of neighborhood channels that is required for a selected % sample to be included in the clustering algorithm (default=0). cfg.tail = 0; % -1, 1 or 0 (default = 0); one-sided or two-sided test cfg.clustertail = 0; cfg.alpha = 0.05; % alpha level of the permutation test cfg.numrandomization = 1000; % number of draws from the permutation distribution cfg.neighbourdist = 0.2; %cfg.neighbours = cfg_n; cfg.channel = {'all', '-HEOG', '-VEOG', '-EKG'}; cfg.latency = [0. 0.5]; cfg.layout = 'C:\Matlab_programs\Fieldtrip\My_Fieldtrip\EEG1010_modified32.lay'; subj1 = length(GROUP {nGroup1,1}); subj2 = length(GROUP {nGroup2,1}); design = zeros(1,subj1+subj2); design(1,1:subj1) = 1; design(1,subj1+1:subj1+subj2) = 2; cfg.design = design; cfg.ivar = 1; [stat] = ft_timelockstatistics(cfg, peak1_gr1 , peak1_gr2 ); ____________________________________________________________________________ Olga Sysoeva, Research Associate, PhD Psychiatry Department, Washington University School of Medicine Campus Box 8134 660 South Euclid Ave Saint Louis, MO 63110-9909 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From adama.sophie at gmail.com Tue Feb 14 15:06:21 2012 From: adama.sophie at gmail.com (Sophie ADAMA) Date: Tue, 14 Feb 2012 15:06:21 +0100 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> <09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl> <8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl> <4F342065.8050707@gmail.com> <016201cce7fb$6a4b9e90$3ee2dbb0$@gmail.com> <70FC3ACFFB46314EBEAF9101EA45F50E06D8EC7A0C@smkexch02.maartenskliniek.nl> <002101cce8e2$bb478060$31d68120$@gmail.com> <70FC3ACFFB46314EBEAF9101EA45F50E06D145F312@smkexch02.maartenskliniek.nl> Message-ID: <4F3A6A5D.1050101@gmail.com> Hi everybody, I tried all this but it still doesn't work. The latest error I got was: *Access denied* Sincerly, Sophie Le 13.02.12 19:08, Philip van den Broek a écrit : > Hi Sophie, > > If you specify a file and path, you don't need ./ in front of it, only > when you try to execute a file in the current folder. In our local > fieldtrip distribution for biosemi2ft, contrary to yours, apparently > the extension .maci is missing so you need to specify the extension as > well: > If you are in the folder: > ./biosemi2ft.maci (with optional parameters) > > or from anywhere else: > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft.maci (with > optional parameters) > > Gr. Philip > > On Feb 13, 2012, at 3:52 PM, Severens, Marianne wrote: > >> Hi Sophie >> >> I've checked the script that we use to startup the buffer in our lab. >> Apparently you need to type ./ before the command. This is what our >> script looks like: >> cd to the /fieldtrip/realtime/acquisition/biosemi/ folder. >> Then run the biosemi2ft: ./biosemi2ft (with optional parameters) >> >> I think you can also put a path in the gdf filename, so it does not >> save it in the fieldtrip folder, but you will have to check that. >> >> I hope this works for you! >> Best, Marianne >> ________________________________________ >> From: fieldtrip-bounces at donders.ru.nl >> >> [fieldtrip-bounces at donders.ru.nl >> ] On Behalf Of Sophie ADAMA >> [adama.sophie at gmail.com ] >> Sent: Saturday, February 11, 2012 6:29 PM >> To: 'Email discussion list for the FieldTrip project' >> Subject: Re: [FieldTrip] signal acquisition with Biosemi >> >> Hi Marianne, >> >> There are 3 biosemi2ft in that folder : biosemi2ft.cc, biosemi2ft.exe >> and biosemi2ft.maci; but when I type >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft >> in the command line, it says No such file or directory. >> >> Sophie >> >> From: fieldtrip-bounces at donders.ru.nl >> >> [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Severens, Marianne >> Sent: vendredi 10 février 2012 15:46 >> To: Email discussion list for the FieldTrip project >> Subject: Re: [FieldTrip] signal acquisition with Biosemi >> >> Hi Sophie >> >> Are you sure that the correct version of the biosemi2ft (so the one >> for the mac) is in the folder that you are specifying? Maybe you can >> try it first without the optional parameters, so just >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft >> >> Best, Marianne >> >> From: fieldtrip-bounces at donders.ru.nl >> >> [mailto:fieldtrip-bounces at donders.ru.nl] >> On Behalf Of Sophie ADAMA >> Sent: vrijdag 10 februari 2012 14:54 >> To: 'Email discussion list for the FieldTrip project' >> Subject: Re: [FieldTrip] signal acquisition with Biosemi >> >> Hi, >> >> I tried it on Windows too, and it works perfectly. >> >> But I'm a Mac girl ? and I will be happy if someone could help me. >> >> Thank you >> >> >> From: fieldtrip-bounces at donders.ru.nl >> >> [mailto:fieldtrip-bounces at donders.ru.nl] >> On Behalf Of Hamza Fawzi Altakroury (Student) >> Sent: vendredi 10 février 2012 06:26 >> To: Email discussion list for the FieldTrip project >> Subject: Re: [FieldTrip] signal acquisition with Biosemi >> >> Hello, >> >> I tried the biosemi2tf.exe command it works well on Windows. >> >> But, unfortunately I don't know about the Mac OS. >> >> Best, >> >> Hamza >> On Thu, Feb 9, 2012 at 9:37 PM, Sophie ADAMA > > wrote: >> Hi, >> >> Thanks for your response. >> >> I tried that but I get this: command not found. I am using Mac OS Lion. >> >> Any suggestions? >> >> Thanks >> >> Sophie >> Le 09.02.12 17:56, Robert Oostenveld a écrit : >> On behalf of Philip... >> >> >> On 9 Feb 2012, at 15:31, Philip van den Broek wrote: >> >> >> Dear Sophie and Hamza, >> >> The connection between the Biosemi Active2 system and the FieldTrip >> buffer is handled by interfacing software biosemi2ft (part of >> fieldtrip), and should be started from the terminal (mac) or command >> prompt (windows). >> >> The interfacing software is located in the FieldTrip folder: >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft >> >> The BioSemi system needs a configuration (.cfg) file in which some >> acquisition-related settings are specified. Configuration files for >> the BioSemi system specify for example from how many channels data >> should be streamed and/or recorded, and whether the data should be >> downsampled. For more information about configuration files for >> different acquisition systems, see the Fieldtrip >> website. >> >> To start the buffer that connects to the Biosemi Active2, open the >> terminal (Mac) or command prompt (PC) and in the folder where you >> would like to save your data execute (change path according to your >> system and location of fieldtrip toolbox): >> >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft >> >> >> >> >> : configuration file >> >> : base name of the gdf file. The suffix .gdf and session >> counters will be added automatically. >> >> : optional, default is 'localhost', specify '-' to spawn a >> local buffer (recommended) >> >> : optional, default is 1972 >> >> an example: >> >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg >> myfile - 1972 >> >> Note that the manually specified name of the file will overwrite any >> existing file, so make sure myfile.gdf doesn't exist. >> Once this is running, you get access to the data through the >> fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip >> fileio functions give you access to the data: >> ft_read_header('buffer://localhost:1972' >> ), or >> ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100 >> ,........ >> For further information, see fieldtrip website. >> >> (more info on how we use the system at our department can be found >> here: >> http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) >> >> Hope this helps you to get things running in your place. If you have >> any further questions, just let me know. >> >> Best regards, >> >> Philip van den Broek >> Radboud University Nijmegen >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognition >> >> P.O. Box 9104, 6500 HE Nijmegen >> Montessorilaan 3, 6525 HR Nijmegen >> The Netherlands >> >> >> >> _______________________________________________ >> >> fieldtrip mailing list >> >> fieldtrip at donders.ru.nl >> >> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Hamza Fawzi Altakroury >> Graduate student - MA >> Faculty of Engineering and Natural Sciences >> Sabanc? University >> >> ________________________________ >> Disclaimer >> Vrijgave van de informatie verzonden met dit e-mail bericht is >> geaccordeerd door de ontvanger en/of zijn behandelend arts. >> Verstrekking van deze informatie is conform het Privacy reglement van >> de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de >> geadresseerde. Gebruik van deze informatie door anderen dan de >> geadresseerde is, zonder voorafgaande schriftelijke toestemming van >> de rechthebbende , verboden. De Sint Maartenskliniek staat niet in >> voor de juiste en volledige overbrenging van de inhoud van een >> gezonden e-mail, noch voor de ontvangst daarvan. >> >> Sint Maartenskliniek >> Hengstdal 3, >> 6574 NA Ubbergen (bij Nijmegen) >> Telefoon 024-3659 911 >> Telefax 024-3659 204 >> KvK nummer 41055111 >> >> Disclaimer >> Vrijgave van de informatie verzonden met dit e-mail bericht is >> geaccordeerd door de ontvanger en/of zijn behandelend arts. >> Verstrekking van deze informatie is conform het Privacy reglement van >> de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de >> geadresseerde. Gebruik van deze informatie door anderen dan de >> geadresseerde is, zonder voorafgaande schriftelijke toestemming van >> de rechthebbende , verboden. De Sint Maartenskliniek staat niet in >> voor de juiste en volledige overbrenging van de inhoud van een >> gezonden e-mail, noch voor de ontvangst daarvan. >> >> Sint Maartenskliniek >> Hengstdal 3, >> 6574 NA Ubbergen (bij Nijmegen) >> Telefoon 024-3659 911 >> Telefax 024-3659 204 >> KvK nummer 41055111 >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From sla.samiee at gmail.com Tue Feb 14 17:42:50 2012 From: sla.samiee at gmail.com (Soheila Samiee) Date: Tue, 14 Feb 2012 11:42:50 -0500 Subject: [FieldTrip] A problem in real-time processing of MEG signal using field trip buffer Message-ID: Dear group, I use FieldTrip for real-time processing of MEG signals using shared memory and field trip buffer in a machine other than acquisition system. I use matlab for reading the buffer and processing the data. During my data acquisition and sending it to other computer with *acq2ft*in linux, I face a problem. After sending some blocks of data, this message: "*Internal Converter thread does not keep up with load*" is shown in the terminal of *acq2ft* and in my matlab session I see an error : "ERROR: the buffer returned an error (517)". It does not depend on sampling rate of data in acquisition system. The problem often solve when I restart the computer which receives the data, but after some minutes of transferring the data I see the message again. Would you please help me in solving this problem? Best Wishes, Soheila -------------- next part -------------- An HTML attachment was scrubbed... URL: From akiko.ikkai at gmail.com Wed Feb 15 17:45:37 2012 From: akiko.ikkai at gmail.com (Akiko Ikkai) Date: Wed, 15 Feb 2012 11:45:37 -0500 Subject: [FieldTrip] volume conduction model missing .mat In-Reply-To: References: <2341406D-6422-4FD3-AD3C-73D1BF70B6CF@mac.com> Message-ID: Dear Fieldtrip users, Thank you Patrick, Nathan & Gio for your inputs. My MRI anatomical images need extensive cleaning (enhance contrasts, get rid of non-zero voxels outside the brain, etc...) before segmentation, as well as adjusting cfg.threshold for each tissue type during segmentation and each subject. At least testing with SPM standard MRI, segmentation and forward modeling works OK now. Individual subject's MRI, though, is still problematic, and I have a question for Fieldtrip developers: could you let me know whether "Create BEM headmodel for EEG ( http://fieldtrip.fcdonders.nl/example/create_bem_headmodel_for_eeg )" routine is what you recommend, or it's integrated into a newer function with newer cfg options? Is there a page I missed on the web? Thank you so much for your time! Akiko On Fri, Feb 10, 2012 at 4:36 AM, Gio Piantoni wrote: > Hi Akiki and Patrick, > > I agree with Nathan about segmentation problems. I had the same > problem when two of the three meshes intersected each other. Before > you run the forward model, you should check the segmentation (bnd) > using ft_plot_mesh. > ft_plot_mesh(bnd(1), 'facealpha', .5) > hold on > ft_plot_mesh(bnd(2), 'facecolor', 'r') > You will see that the two meshes intersect with each other. Depending > on how you created the meshes, you should fix the parameters in such a > way that they don't intersect. For example, ft_volumesegment has a > cfg.threshold option (you can check how the segmentation went with > ft_sourceplot) and ft_prepare_mesh_new has cfg.thresholdseg and > cfg.smoothseg. > > I think that the meshes in SPM are computed on an (affine-transformed) > template and not on the anatomically derived meshes. The template is > more robust and that's why the two surfaces do not intersect. > > In general, the segmentation depends on the quality of your MRIs and > you should really visually check the segmentation and meshes. When > those look ok, the BEM forward model usually works. Hope this helps. > > Cheers, > > Gio > > On Fri, Feb 10, 2012 at 09:00, Nathan Weisz wrote: > > Hi Akiki, > > > > I am not a headmodel expert. > > but looking at the output message, it seems your segementation did not go > > too well (see the "intersect" message). my intuition is then then the > next > > temporary file *.ama is not created and ft_prepare_bemmodel then simply > says > > ciao. > > > > perhaps you want to check / redo the segmentation? > > > > good luck, > > nathan > > > > > > On 09.02.2012, at 23:04, Akiko Ikkai wrote: > > > > Hi, > > > > I'm trying to create a volume conduction model for my EEG study based on > > anatomical MRI, and having trouble with ft_prepare_bemmodel > > > > when I run > > cfg = []; > > cfg.tissue = [7 4 1]; % value for brain, skull, and scalp > > cfg.conductivity = [1 1/80 1]*.33; % after standard_BEM.zip data > > cfg.isolatedsource = true; > > cfg.method = 'dipoli'; > > cfg.sourceunits = 'mm'; > > cfg.mriunits = 'mm'; > > vol = ft_prepare_bemmodel(cfg, seg4bem); > > > > I get the following error message while ft_prepare_bemmodel is running: > > > > Fatal error in dipoli: interface > > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and > > /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect > > at vertex 1402 of > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri > > > > Warning: an error ocurred while running dipoli > >> In dipoli at 94 > > In ft_prepare_bemmodel at 112 > > Error using ==> fread > > Invalid file identifier. Use fopen to generate a valid file identifier. > > Warning: File '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' > not > > found. > >> In dipoli at 102 > > In ft_prepare_bemmodel at 112 > > > > > > and the output vol is missing .mat, which causes an error > > during ft_sourceanalysis. > >>> vol > > vol = > > cond: [0.3300 0.0041 0.3300] > > bnd: [1x3 struct] > > source: 3 > > skin_surface: 3 > > skin: 1 > > type: 'dipoli' > > > > Does anyone know how to correct for "fatal error" so > > that ft_prepare_bemmodel creates the correct volume conduction model? I > > opened .tri file and removed line 1402, but got the same results. > > > > Thanks in advance! Akiko > > > > -- > > Akiko Ikkai, Ph.D. > > Postdoctoral Fellow > > Department of Psychological and Brain Sciences > > Johns Hopkins University > > Ames Hall, 3400 N. Charles St. > > Baltimore, MD 21218 > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Akiko Ikkai, Ph.D. Postdoctoral Fellow Department of Psychological and Brain Sciences Johns Hopkins University Ames Hall, 3400 N. Charles St. Baltimore, MD 21218 -------------- next part -------------- An HTML attachment was scrubbed... URL: From shayda.malekpour at gmail.com Wed Feb 15 21:19:50 2012 From: shayda.malekpour at gmail.com (Shayda Malekpour) Date: Wed, 15 Feb 2012 14:19:50 -0600 Subject: [FieldTrip] A question Message-ID: Dear All, I am using fieldtrip on MEG data set. I want to know if I do not remove any ICA component, will the data be the same as the original data, or is there is a filter somewhere in the software that changes the data? If so how much does it change it (What is their relative difference?) Thanks, Sheida -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu Feb 16 09:28:43 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 16 Feb 2012 09:28:43 +0100 Subject: [FieldTrip] A question In-Reply-To: References: Message-ID: Dear Sheida, You probably need to provide a bit more information before anyone is able to help you. In general, if you perform ICA, you get out component timecourses and mixing/unmixing matrices. If you keep all your components, and multiply them with the mixing matrix, you should get all your original channel timecourses out again. So: if you don't change the data, the data will not be changed :) Best, Eelke On 15 February 2012 21:19, Shayda Malekpour wrote: > Dear All, > > I am using fieldtrip on MEG data set. > I want to know if I do not remove any ICA component,  will the data be  the > same as the original data, or is there is a filter somewhere in the software > that changes the data? If so how much does it change it (What is their > relative difference?) > > Thanks, > > Sheida > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Thu Feb 16 10:36:05 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 16 Feb 2012 10:36:05 +0100 Subject: [FieldTrip] A problem in real-time processing of MEG signal using field trip buffer In-Reply-To: References: Message-ID: <4F3CCE05.4050109@donders.ru.nl> Dear Soheila, we were facing the same problem here. Presumably, there is some problem in the shared memory module that the buffer is using. Right now, however, we could not find out where the error precisely comes from, so our best work around is to restart the computer prior recording and optimize settings, such as channels and sampling/decimation rate of acq2ft. In our lab, we managed to find near-optimal settings, so that the buffer crashes only rarely (actually, I never saw it crashing when the acquisition computer was freshly restarted). Note that a lower number of channels or higher decimation does not mean that it runs more stable. It seems to be literally a trial-and-error approach :/ In order to track this down further, we need some more information, e.g. what MEG system are you using? What's your sampling rate, how many channels do you put into the buffer, and what's your decimation rate? It would be great if you could send me that information so that we can maybe try to track this down. Best regards, Jörn On 2/14/2012 5:42 PM, Soheila Samiee wrote: > Dear group, > > I use FieldTrip for real-time processing of MEG signals using shared > memory and field trip buffer in a machine other than acquisition > system. I use matlab for reading the buffer and processing the data. > During my data acquisition and sending it to other computer with > /acq2ft/ in linux, I face a problem. After sending some blocks of > data, this message: "/Internal Converter thread does not keep up with > load/" is shown in the terminal of /acq2ft/ and in my matlab session I > see an error : "ERROR: the buffer returned an error (517)". It does > not depend on sampling rate of data in acquisition system. The problem > often solve when I restart the computer which receives the data, but > after some minutes of transferring the data I see the message again. > > Would you please help me in solving this problem? > Best Wishes, > Soheila > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.piantoni at nin.knaw.nl Thu Feb 16 11:52:45 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Thu, 16 Feb 2012 11:52:45 +0100 Subject: [FieldTrip] volume conduction model missing .mat In-Reply-To: References: <2341406D-6422-4FD3-AD3C-73D1BF70B6CF@mac.com> Message-ID: Hi Akiko, What do you mean "problematic" exactly? From my understanding, there are 4 steps to get from the MRI to the forward model. 1. from MRI to segmentation 2. from segmentation to mesh (bnd) 3. from mesh to headmodel 4. from headmodel to forward model Here is the code I use. It seems to work fine, but experts might want to chip in and improve it. 1. from MRI to segmentation %-----------------% %-read MRI mrifile = '/path/to/your/mri.nii.gz'; mri = ft_read_mri(mrifile); %-----------------% %-----------------% %-segmenting the volume, Tissue Probability Maps % It takes time to run 'tpm' cfg1 = []; cfg1.threshold = []; cfg1.output = 'tpm'; cfg1.coordsys = 'spm'; tpm = ft_volumesegment(cfg1, mri); tpm.anatomy = mri.anatomy; %-----------------% %-----------------% %-segmenting the volume % this is faster after tpm cfg1 = []; cfg1.threshold = 1; % 1 is default, my MRI scalps were noisy, so I had to make it lower. cfg1.output = 'scalp'; cfg1.coordsys = 'spm'; segscalp = ft_volumesegment(cfg1, tpm); cfg1 = []; cfg1.threshold = []; cfg1.output = {'skull' 'brain'}; cfg1.coordsys = 'spm'; segment = ft_volumesegment(cfg1, tpm); segment.scalp = segscalp.scalp; %-----------------% Check the output with ft_sourceplot 2. from segmentation to mesh (bnd) %-----------------% %-prepare mesh for skull and brain (easy) cfg2 = []; cfg2.tissue = {'skull', 'brain'}; cfg2.numvertices = [1200 1000]; cfg2.transform = segment.transform; bnd = ft_prepare_mesh_new(cfg2, segment); %-----------------% %-----------------% %-prepare mesh for scalp (we need to be more liberal with threshold, bc of poor quality of MRI) cfg2 = []; cfg2.tissue = {'scalp'}; cfg2.numvertices = 2500; cfg2.thresholdseg = 0.1; cfg2.transform = segment.transform; scalp = ft_prepare_mesh_new(cfg2, segment); %-----------------% %-----------------% %-combine scalp and bnd bnd = [scalp bnd]; ft_plot_mesh(bnd(1), 'facealpha', .5) hold on ft_plot_mesh(bnd(2), 'facecolor', 'red') %-----------------% If bnd is good, no intersection between meshes and the outline looks nice, the following should run without problems. Please, do check your bnd. Segmentation and ft_prepare_mesh_new work really well. Another approach to get nice meshes is to skip step 1 and 2 and use Freesurfer/MNE. You can read the meshes in fieldtrip (ft_read_headshape, I think). The meshes are in the "bem" folder of Freesurfer, but I don't remember off the top of my head which files you should read ("outer_skull, inner_skull", I think). These meshes have a very very high resolution, you can scale them down with "reducepatch" in Matlab. 3. from mesh to headmodel %-----------------% %-headmodel cfg3 = []; cfg3.method = 'bem_dipoli'; cfg3.conductivity = [0.33 0.0042 0.33]; vol = ft_prepare_headmodel(cfg3, bnd); %-----------------% You can really pick your favorite here: dipoli, openmeeg, bemcp. This will take time (the more time, the more points on your meshes). 4. from headmodel to forward model You last problem is to get electrodes and headmodel in the same space. The template in SPM is already in MNI space, your individual MRIs probably not. You can realign them to MNI space before step 1 using SPM or FSL. elec = ft_read_sens(sensfile); elec = ft_convert_units(elec, 'mm'); %-------% %-simple transformation (based on visual realignment) % elecM is an affine matrix that you can get from ft_electroderealign % electrodes do not need to match the scalp perfectly, but they should be pretty close by. elec.chanpos = warp_apply(elecM, elec.chanpos); elec.elecpos = warp_apply(elecM, elec.elecpos); %-------% [vol, elec] = ft_prepare_vol_sens(vol, elec); % now you should check that the electrodes are on the scalp. %-----------------% %-----------------% %-prepare leadfield cfg4 = []; cfg4.elec = elec; cfg4.vol = vol; cfg4.grid.xgrid = -70:10:70; cfg4.grid.ygrid = -110:10:80; cfg4.grid.zgrid = -60:10:90; cfg4.inwardshift = 1; % to avoid dipoles on the border of bnd(3), which are very instable cfg4.grid.tight = 'no'; cfg4.feedback = 'none'; lead = ft_prepare_leadfield(cfg4, []); % use ft_plot_topo3d and ft_plot_dipole to check whether the projection of your dipole onto the scalp makes sense. %-----------------% "lead" should be your subject-specific, electrode-specific leadfield. There are quite a few parameters that you can change, but a clean segmentation and non-intersecting, smooth and realistic-looking meshes are a must. Then, using dipoli, openmeeg or bemcp should not change your forward model too much. Sorry if some points are not clear, but you should really look at your MRI/segmentation/meshes/electrodes/forward model as much as possible. Hope this will get you started. I appreciate any feedback on improving the code, this is just my personal attempt. Cheers Gio On Wed, Feb 15, 2012 at 17:45, Akiko Ikkai wrote: > Dear Fieldtrip users, > > Thank you Patrick, Nathan & Gio for your inputs. My MRI anatomical images > need extensive cleaning (enhance contrasts, get rid of non-zero voxels > outside the brain, etc...) before segmentation, as well as adjusting > cfg.threshold for each tissue type during segmentation and each subject. At > least testing with SPM standard MRI, segmentation and forward modeling works > OK now. > > Individual subject's MRI, though, is still problematic, and I have a > question for Fieldtrip developers: could you let me know whether "Create BEM > headmodel for EEG ( >  http://fieldtrip.fcdonders.nl/example/create_bem_headmodel_for_eeg )" > routine is what you recommend, or it's integrated into a newer function with > newer cfg options? Is there a page I missed on the web? > > Thank you so much for your time! > Akiko > > On Fri, Feb 10, 2012 at 4:36 AM, Gio Piantoni > wrote: >> >> Hi Akiki and Patrick, >> >> I agree with Nathan about segmentation problems. I had the same >> problem when two of the three meshes intersected each other. Before >> you run the forward model, you should check the segmentation (bnd) >> using ft_plot_mesh. >> ft_plot_mesh(bnd(1), 'facealpha', .5) >> hold on >> ft_plot_mesh(bnd(2), 'facecolor', 'r') >> You will see that the two meshes intersect with each other. Depending >> on how you created the meshes, you should fix the parameters in such a >> way that they don't intersect. For example, ft_volumesegment has a >> cfg.threshold option (you can check how the segmentation went with >> ft_sourceplot) and ft_prepare_mesh_new has cfg.thresholdseg and >> cfg.smoothseg. >> >> I think that the meshes in SPM are computed on an (affine-transformed) >> template and not on the anatomically derived meshes. The template is >> more robust and that's why the two surfaces do not intersect. >> >> In general, the segmentation depends on the quality of your MRIs and >> you should really visually check the segmentation and meshes. When >> those look ok, the BEM forward model usually works. Hope this helps. >> >> Cheers, >> >> Gio >> >> On Fri, Feb 10, 2012 at 09:00, Nathan Weisz wrote: >> > Hi Akiki, >> > >> > I am not a headmodel expert. >> > but looking at the output message, it seems your segementation did not >> > go >> > too well (see the "intersect" message). my intuition is then then the >> > next >> > temporary file *.ama is not created and ft_prepare_bemmodel then simply >> > says >> > ciao. >> > >> > perhaps you want to check / redo the segmentation? >> > >> > good luck, >> > nathan >> > >> > >> > On 09.02.2012, at 23:04, Akiko Ikkai wrote: >> > >> > Hi, >> > >> > I'm trying to create a volume conduction model for my EEG study based on >> > anatomical MRI, and having trouble with ft_prepare_bemmodel >> > >> > when I run >> > cfg                = []; >> > cfg.tissue         = [7 4 1]; % value for brain, skull, and scalp >> > cfg.conductivity   = [1 1/80 1]*.33; % after standard_BEM.zip data >> > cfg.isolatedsource = true; >> > cfg.method         = 'dipoli'; >> > cfg.sourceunits = 'mm'; >> > cfg.mriunits = 'mm'; >> > vol = ft_prepare_bemmodel(cfg, seg4bem); >> > >> > I get the following error message while ft_prepare_bemmodel is running: >> > >> > Fatal error in dipoli:  interface >> > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and >> > /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect >> >  at vertex 1402 of >> > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri >> > >> > Warning: an error ocurred while running dipoli >> >> In dipoli at 94 >> >   In ft_prepare_bemmodel at 112 >> > Error using ==> fread >> > Invalid file identifier.  Use fopen to generate a valid file identifier. >> > Warning: File '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' >> > not >> > found. >> >> In dipoli at 102 >> >   In ft_prepare_bemmodel at 112 >> > >> > >> > and the output vol is missing .mat, which causes an error >> > during ft_sourceanalysis. >> >>> vol >> > vol = >> >             cond: [0.3300 0.0041 0.3300] >> >              bnd: [1x3 struct] >> >           source: 3 >> >     skin_surface: 3 >> >             skin: 1 >> >             type: 'dipoli' >> > >> > Does anyone know how to correct for "fatal error" so >> > that ft_prepare_bemmodel creates the correct volume conduction model? I >> > opened .tri file and removed line 1402, but got the same results. >> > >> > Thanks in advance! Akiko >> > >> > -- >> > Akiko Ikkai, Ph.D. >> > Postdoctoral Fellow >> > Department of Psychological and Brain Sciences >> > Johns Hopkins University >> > Ames Hall, 3400 N. Charles St. >> > Baltimore, MD 21218 >> > >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > >> > >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Akiko Ikkai, Ph.D. > Postdoctoral Fellow > Department of Psychological and Brain Sciences > Johns Hopkins University > Ames Hall, 3400 N. Charles St. > Baltimore, MD 21218 > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From politzerahless at gmail.com Thu Feb 16 12:35:13 2012 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Thu, 16 Feb 2012 05:35:13 -0600 Subject: [FieldTrip] A question Message-ID: Hi Shayda, FieldTrip does not apply a filter by default, and I am not aware of any other 'hidden' transformations that happen. You can specify a filter when importing the data with ft_preprocessing(), and there are several different kinds of filters available, which will affect your data in different ways-- see http://fieldtrip.fcdonders.nl/reference/ft_preprocessing. The best thing to do is to import your data without using a filter and, if possible, use whatever tool comes with your MEG software to import that raw data into MATLAB as well (for example, for CTF this would be ds2txt), then you can plot them together to make sure there are no differences--when I have tried this with EEG data, fieldtrip hasn't changed them. Of course, if you want to use a filter, you can also try several filters (you can either filter within your system's software and then import straight to Fieldtrip, or use one of Fieldtrip's filters during import) and plot them to see how they affect your data. Best, Steve Politzer-Ahles > > Message: 2 > Date: Wed, 15 Feb 2012 14:19:50 -0600 > From: Shayda Malekpour > To: fieldtrip at donders.ru.nl > Subject: [FieldTrip] A question > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > Dear All, > > I am using fieldtrip on MEG data set. > I want to know if I do not remove any ICA component, will the data be the > same as the original data, or is there is a filter somewhere in the > software that changes the data? If so how much does it change it (What is > their relative difference?) > > Thanks, > > Sheida > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120215/ba4458d8/attachment-0001.html > > > > ------------------------------ > > Message: 3 > Date: Thu, 16 Feb 2012 09:28:43 +0100 > From: Eelke Spaak > To: Email discussion list for the FieldTrip project > > Subject: Re: [FieldTrip] A question > Message-ID: > > > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Sheida, > > You probably need to provide a bit more information before anyone is > able to help you. In general, if you perform ICA, you get out > component timecourses and mixing/unmixing matrices. If you keep all > your components, and multiply them with the mixing matrix, you should > get all your original channel timecourses out again. So: if you don't > change the data, the data will not be changed :) > > Best, > Eelke > > On 15 February 2012 21:19, Shayda Malekpour > wrote: > > Dear All, > > > > I am using fieldtrip on MEG data set. > > I want to know if I do not remove any ICA component,? will the data be? > the > > same as the original data, or is there is a filter somewhere in the > software > > that changes the data? If so how much does it change it (What is their > > relative difference?) > > > > Thanks, > > > > Sheida > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > ------------------------------ > > Message: 4 > Date: Thu, 16 Feb 2012 10:36:05 +0100 > From: "J?rn M. Horschig" > To: Email discussion list for the FieldTrip project > > Subject: Re: [FieldTrip] A problem in real-time processing of MEG > signal using field trip buffer > Message-ID: <4F3CCE05.4050109 at donders.ru.nl> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Dear Soheila, > > we were facing the same problem here. Presumably, there is some problem > in the shared memory module that the buffer is using. Right now, > however, we could not find out where the error precisely comes from, so > our best work around is to restart the computer prior recording and > optimize settings, such as channels and sampling/decimation rate of > acq2ft. In our lab, we managed to find near-optimal settings, so that > the buffer crashes only rarely (actually, I never saw it crashing when > the acquisition computer was freshly restarted). Note that a lower > number of channels or higher decimation does not mean that it runs more > stable. It seems to be literally a trial-and-error approach :/ > > In order to track this down further, we need some more information, e.g. > what MEG system are you using? What's your sampling rate, how many > channels do you put into the buffer, and what's your decimation rate? It > would be great if you could send me that information so that we can > maybe try to track this down. > > Best regards, > J?rn > > On 2/14/2012 5:42 PM, Soheila Samiee wrote: > > Dear group, > > > > I use FieldTrip for real-time processing of MEG signals using shared > > memory and field trip buffer in a machine other than acquisition > > system. I use matlab for reading the buffer and processing the data. > > During my data acquisition and sending it to other computer with > > /acq2ft/ in linux, I face a problem. After sending some blocks of > > data, this message: "/Internal Converter thread does not keep up with > > load/" is shown in the terminal of /acq2ft/ and in my matlab session I > > see an error : "ERROR: the buffer returned an error (517)". It does > > not depend on sampling rate of data in acquisition system. The problem > > often solve when I restart the computer which receives the data, but > > after some minutes of transferring the data I see the message again. > > > > Would you please help me in solving this problem? > > Best Wishes, > > Soheila > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > J?rn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120216/c01be767/attachment.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 15, Issue 17 > ***************************************** > -- Stephen Politzer-Ahles University of Kansas Linguistics Department http://www.linguistics.ku.edu/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Feb 16 12:39:25 2012 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 16 Feb 2012 12:39:25 +0100 Subject: [FieldTrip] A question In-Reply-To: References: Message-ID: Dear All, All true, except that ICA implemented by FT does demean the data before unmixing by default. Use cfg.demean = 'no' if you don't want to. cheers, stephen On 16 February 2012 12:35, Stephen Politzer-Ahles wrote: > Hi Shayda, > > FieldTrip does not apply a filter by default, and I am not aware of any > other 'hidden' transformations that happen. You can specify a filter when > importing the data with ft_preprocessing(), and there are several different > kinds of filters available, which will affect your data in different ways-- > see http://fieldtrip.fcdonders.nl/reference/ft_preprocessing. The best thing > to do is to import your data without using a filter and, if possible, use > whatever tool comes with your MEG software to import that raw data into > MATLAB as well (for example, for CTF this would be ds2txt), then you can > plot them together to make sure there are no differences--when I have tried > this with EEG data, fieldtrip hasn't changed them. Of course, if you want to > use a filter, you can also try several filters (you can either filter within > your system's software and then import straight to Fieldtrip, or use one of > Fieldtrip's filters during import) and plot them to see how they affect your > data. > > Best, > Steve Politzer-Ahles > > >> >> >> Message: 2 >> Date: Wed, 15 Feb 2012 14:19:50 -0600 >> From: Shayda Malekpour >> To: fieldtrip at donders.ru.nl >> Subject: [FieldTrip] A question >> Message-ID: >> >>   >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Dear All, >> >> I am using fieldtrip on MEG data set. >> I want to know if I do not remove any ICA component,  will the data be >>  the >> same as the original data, or is there is a filter somewhere in the >> software that changes the data? If so how much does it change it (What is >> their relative difference?) >> >> Thanks, >> >> Sheida >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> >> >> ------------------------------ >> >> Message: 3 >> Date: Thu, 16 Feb 2012 09:28:43 +0100 >> From: Eelke Spaak >> To: Email discussion list for the FieldTrip project >>         >> Subject: Re: [FieldTrip] A question >> Message-ID: >> >>   >> Content-Type: text/plain; charset=ISO-8859-1 >> >> >> Dear Sheida, >> >> You probably need to provide a bit more information before anyone is >> able to help you. In general, if you perform ICA, you get out >> component timecourses and mixing/unmixing matrices. If you keep all >> your components, and multiply them with the mixing matrix, you should >> get all your original channel timecourses out again. So: if you don't >> change the data, the data will not be changed :) >> >> Best, >> Eelke >> >> On 15 February 2012 21:19, Shayda Malekpour >> wrote: >> > Dear All, >> > >> > I am using fieldtrip on MEG data set. >> > I want to know if I do not remove any ICA component,? will the data be? >> > the >> >> > same as the original data, or is there is a filter somewhere in the >> > software >> > that changes the data? If so how much does it change it (What is their >> > relative difference?) >> > >> > Thanks, >> > >> > Sheida >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> ------------------------------ >> >> Message: 4 >> Date: Thu, 16 Feb 2012 10:36:05 +0100 >> From: "J?rn M. Horschig" >> To: Email discussion list for the FieldTrip project >>         >> Subject: Re: [FieldTrip] A problem in real-time processing of MEG >>        signal using field trip buffer >> Message-ID: <4F3CCE05.4050109 at donders.ru.nl> >> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" >> >> Dear Soheila, >> >> we were facing the same problem here. Presumably, there is some problem >> in the shared memory module that the buffer is using. Right now, >> however, we could not find out where the error precisely comes from, so >> our best work around is to restart the computer prior recording and >> optimize settings, such as channels and sampling/decimation rate of >> acq2ft. In our lab, we managed to find near-optimal settings, so that >> the buffer crashes only rarely (actually, I never saw it crashing when >> the acquisition computer was freshly restarted). Note that a lower >> number of channels or higher decimation does not mean that it runs more >> stable.  It seems to be literally a trial-and-error approach :/ >> >> In order to track this down further, we need some more information, e.g. >> what MEG system are you using? What's your sampling rate, how many >> channels do you put into the buffer, and what's your decimation rate? It >> would be great if you could send me that information so that we can >> maybe try to track this down. >> >> Best regards, >> J?rn >> >> On 2/14/2012 5:42 PM, Soheila Samiee wrote: >> > Dear group, >> > >> > I use FieldTrip for real-time processing of MEG signals using shared >> > memory and field trip buffer in a machine other than acquisition >> > system. I use matlab for reading the buffer and processing the data. >> > During my data acquisition and sending it to other computer with >> > /acq2ft/ in linux, I face a problem. After sending some blocks of >> > data, this message: "/Internal Converter thread does not keep up with >> > load/" is shown in the terminal of /acq2ft/ and in my matlab session I >> > see an error : "ERROR: the buffer returned an error (517)". It does >> > not depend on sampling rate of data in acquisition system. The problem >> > often solve when I restart the computer which receives the data, but >> > after some minutes of transferring the data I see the message again. >> > >> > Would you please help me in solving this problem? >> > Best Wishes, >> > Soheila >> >> > >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -- >> J?rn M. Horschig >> PhD Student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> Neuronal Oscillations Group >> >> P.O. Box 9101 >> NL-6500 HB Nijmegen >> The Netherlands >> >> Contact: >> E-Mail: jm.horschig at donders.ru.nl >> Tel:    +31-(0)24-36-68493 >> Web: http://www.ru.nl/donders >> >> Visiting address: >> Trigon, room 2.30 >> Kapittelweg 29 >> NL-6525 EN Nijmegen >> The Netherlands >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> >> >> ------------------------------ >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> End of fieldtrip Digest, Vol 15, Issue 17 >> ***************************************** > > > > > -- > Stephen Politzer-Ahles > University of Kansas > Linguistics Department > http://www.linguistics.ku.edu/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From carsten.wolters at uni-muenster.de Thu Feb 16 14:01:36 2012 From: carsten.wolters at uni-muenster.de (Dr. Carsten Wolters) Date: Thu, 16 Feb 2012 14:01:36 +0100 Subject: [FieldTrip] =?iso-8859-1?q?Postdoctoral_research_associate_positi?= =?iso-8859-1?q?on_available__at_the_University_of_M=FCnster?= Message-ID: <4F3CFE30.4050502@uni-muenster.de> Neuroscientist with focus on MR image analysis The Medical Faculty of the University of Münster is searching for a postdoctoral research associate at the 'Translational Research Imaging Center' (TRIC), where a new 3T MR-system for neuroimaging research will be put into operation soon. This position is focused on image processing and optimization to support the interdisciplinary working groups from the faculties of Medicine and Psychology. The position (TVL13) is initially limited to 3 years with possibility of extension. The area of responsibility includes the analysis of structural and functional MR data and the post-processing of fMRI- and DTI- measurements as well as the implementation of new post-processing methods for imaging and spectroscopy. Furthermore, the applicant should be interested in integration of different neuroimaging methods (multimodal integration). Besides an interdisciplinary and team-oriented working style, a high degree of mathematical and statistical knowledge is required. The applicant should possess a master degree (or equivalent) in natural or engineering sciences and a PhD and should be qualified by his scientific work and his own research that will also be pursued at the University of Münster. Applications of women and disabled applicants are explicitly welcome and will be preferred at same qualification, merits and achievements. For further questions please consult Dr. rer. nat. H. Kugel, the responsible senior physicist at the TRIC (Email: kugel at uni-muenster.de, Phone:+49/( 0)251 / 83-56145). The position will be open until filled. Applications should contain a personal statement of research background and interests, CV, list of publications and grants as well as the names of three referees and preprints of the three most important publications. Applications should be send to: *Dekan der Medizinischen Fakultät der Westfälischen Wilhelms-Universität Münster, Albert-Schweitzer-Campus 1, Gebäude D3, 48149 Münster * -- PD.Dr.rer.nat. Carsten Wolters Institute for Biomagnetism and Biosignalanalysis University of Muenster, 48149 Muenster, Germany Tel.: +49/(0)251-83-56904 Fax: +49/(0)251-83-56874 http://biomag.uni-muenster.de -------------- next part -------------- A non-text attachment was scrubbed... Name: MRTPostprocessing_Englisch.pdf Type: application/x-pdf Size: 166979 bytes Desc: not available URL: From jpnv2006 at gmail.com Thu Feb 16 17:35:28 2012 From: jpnv2006 at gmail.com (Juan Pablo Neira) Date: Thu, 16 Feb 2012 17:35:28 +0100 Subject: [FieldTrip] Align EEG electrode positions to BEM headmodel Question Message-ID: Hello, I am trying to align EEG electrodes to an individual MRI and a BEM model.  I am using the example: "Align EEG electrode positions to BEM headmodel" http://fieldtrip.fcdonders.nl/example/align_eeg_electrode_positions_to_bem_headmodel But I am having the next problem in "% align using fiducials" part: * Template structure (label, chanpos and elecpos) - sens_t structure (label, chanpos and elecpos) elec_mni.label = {'Nz', 'LPA', 'RPA'}; elec_mni.chanpos = [   head_Nas   head_Lpa   head_Rpa   ]; elec_mni.elecpos = [   head_Nas   head_Lpa   head_Rpa   ]; elec_mni.unit = 'mm'; % align using fiducials cfg = []; cfg.method = 'fiducial'; cfg.template= elec_mni; cfg.elec     = sens_t; cfg.casesensitive  = 'no';%'yes' or 'no' sens_aligned = ft_electroderealign(cfg); %Error message: %----------------------------------------------------- ??? Subscripted assignment between dissimilar structures. Error in ==> ft_electroderealign at 183     tmp(i) = ft_datatype_sens(template(i)); % ensure up-to-date sensor     descriptions (Oct 2011) %------------------------------------------------------- I have some questions that maybe can help to find the error: -  According to the example in the webpage, there are 2 functions from the private directory used:  electrodenormalize.m & warp_apply.m, but electrodenormalize.m never was used. Also in "% align using fiducials" the method used was 'realignfiducial', but that method is not available in electroderealign function. Is it possible the example is using the wrong function? - How should be the structure of the fiducials in the main sensor structure (sens_t). As 3 more electrodes (label+fid, chanpos+fid and elecpos+fid) or in a different place, for example sens_t.fid.pnt and sens_t.fid.label? By the way I am using Matlab 2011 and fieldtrip version 20120208 Best regards and thanks for the help. Jua Pablo Neira Vesga Christian Albrechts Universität Clinic Kiel, Germany From kd889 at nyu.edu Fri Feb 17 18:08:53 2012 From: kd889 at nyu.edu (Keith Doelling) Date: Fri, 17 Feb 2012 12:08:53 -0500 Subject: [FieldTrip] ft_channelrepair replaces channel data with NaNs after running PCA Message-ID: Hi guys, I'm struggling with my attempts to interpolate channel data for some bad channels. I put in the following code: cfg=[]; cfg.badchannel = 15; cfg.missingchannel = []; cfg.neighbours = neighbours; cfg.trials = 'all'; cleanchdata = ft_channelrepair(cfg,cleandata); the function the displays the following: "the input is raw data with 157 channels and 80 trials repairing channel AG015 using neighbour AG010 using neighbour AG014 using neighbour AG062 using neighbour AG092" suggesting that neighbours have been selected successfully. but a call to chdata.trial(1){15,:) just returns a bunch of NaNs rather than interpolated data I need. I found another email thread similar to this but that solution doesn't seem to apply to me as the neighbours seemed to have been selected successfully. The other interesting caveat is that ft_channelrepair seems to work fine if i run it without having run pca (to reject eyeblink and heartbeat components) beforehand. The code for the component analysis and the subsequent rejection are in separate loops. The PCA is saved into a .mat file and then loaded again when i'm ready to reject the bad components. But for simplicity's sake the important code looks like this. % principle component analysis run with 32 components cfg = []; cfg.channel = (1:157); cfg.runica.pca=32; pca_data = ft_componentanalysis(cfg,data); % view components in order to select bad ones cfg = []; cfg.layout = layout; % specify the layout file that should be used for plotting cfg.viewmode = 'component'; ft_databrowser(cfg, pca_data); waitfor(gcf); % type bad components as user input % for example: if runica002 and runica0003 should be rejected, type "2,3" into the dialogue box badcomps = inputdlg({'Bad Components:'}); badcomps = str2double(csv2cell(badcomps{1})); % reject bad components cfg = []; cfg.component = badcomps; cleandata = ft_rejectcomponent(cfg,pca_data); the variable 'cleandata' i get out from this code is the same cleandata i put in to ft_channelrepair. Are there any ideas as to what I've done wrong here? Let me know if I need to give you guys more information. Thanks for your help, Keith -- Keith Doelling Lab Manager and Research Assistant David Poeppel Lab New York University -------------- next part -------------- An HTML attachment was scrubbed... URL: From karl.doron at gmail.com Sat Feb 18 02:16:50 2012 From: karl.doron at gmail.com (Karl Doron) Date: Fri, 17 Feb 2012 17:16:50 -0800 Subject: [FieldTrip] help with channel combination In-Reply-To: References: Message-ID: Hello, I'm trying to run ft_connectivityanalysis on a reduced set of MEG channels, i.e., left and right posterior channels. Because neighboring channels are highly correlated, I'd like to exclude them and look only at "inter-hemispheric" connections. I'm having some troubling getting ft_channelcombination to produce this set of channels. I have 43 channels per hemisphere giving n(n-1)/2 connections. I made an NX2 matrix using repmat.m and passed it as cfg.channelcmb; however the output of ft_connectivityanalysis gave a vector for 'cohspctrm' rather than a chan_chan_freq matrix. Thanks for any suggestions. Karl Doron UC Santa Barbara -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Sat Feb 18 10:24:02 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Sat, 18 Feb 2012 10:24:02 +0100 Subject: [FieldTrip] help with channel combination In-Reply-To: References: Message-ID: Hi Karl, This is perfectly fine behavior. ft_connectivityanalysis either outputs a 'chan_chan_freq' matrix, or a 'chancmb_freq' matrix. The former will be the output when the input freq-structure contains fourier-spectra, and the cfg lacks a channelcmb field. Ft_connectivityanalysis then computes connectivity between all channel pairs, which can conveniently be stored in a square matrix 'chan_chan' for each frequency. If the freq-structure contains cross-spectra (and power-spectra), or if you specify a cfg.channelcmb in combination with fourierspectra in the input, you will get the connectivity data to be 'chancmb_freq', i.e. each row in the matrix contains a spectrum. The reason for this is that it is a priori unlikely that the channelcmb-array defines a set of channel pairs that can be represented in a square all-to-all matrix. If it is your intention to end up with a square matrix, you may want to consider first doing a subselection of channels, i.e. computing your fourierspectra only on the subset of channels you want to use in a later step, and then call ft_connectivityanalysis without a channelcmb field in the cfg. See for some additional information about the different representation of frequency domain data: http://fieldtrip.fcdonders.nl/faq/in_what_way_can_frequency_domain_data_be_represented_in_fieldtrip Cheers, Jan-Mathijs On Feb 18, 2012, at 2:16 AM, Karl Doron wrote: > Hello, > > I'm trying to run ft_connectivityanalysis on a reduced set of MEG channels, i.e., left and right posterior channels. Because neighboring channels are highly correlated, I'd like to exclude them and look only at "inter-hemispheric" connections. > > I'm having some troubling getting ft_channelcombination to produce this set of channels. I have 43 channels per hemisphere giving n(n-1)/2 connections. I made an NX2 matrix using repmat.m and passed it as cfg.channelcmb; however the output of ft_connectivityanalysis gave a vector for 'cohspctrm' rather than a chan_chan_freq matrix. > > Thanks for any suggestions. > > Karl Doron > UC Santa Barbara > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhaoyizhe at gmail.com Mon Feb 20 11:51:07 2012 From: zhaoyizhe at gmail.com (zhaoyizhe) Date: Mon, 20 Feb 2012 18:51:07 +0800 Subject: [FieldTrip] question about ft_sourceinterpolate Message-ID: <52DE5EF7-93B4-4261-AAC9-A1550A37C986@gmail.com> Dear all, I have a problem in function of 'ft_sourceinterpolate'. I run the scrips below, and data from the ftp sever as the test data. the result is below: ??? Error using ==> ft_checkconfig at 162 The field cfg.parameter is required cfg.parameter='all' has been tried. the result is below: ??? Reference to non-existent field 'all'. Would you mind tell me how to deal with it? Thanks a lot in advance. -------------------------------------- close clc clear load source mri = ft_read_mri('Subject01.mri'); cfg = []; cfg.downsample = 2; sourcePostInt = ft_sourceinterpolate(cfg, sourcePost , mri); -------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From mark.noordenbos at gmail.com Mon Feb 20 12:25:46 2012 From: mark.noordenbos at gmail.com (Mark Noordenbos) Date: Mon, 20 Feb 2012 12:25:46 +0100 Subject: [FieldTrip] clusterstatistics Message-ID: Dear Fieldtrippers, I have a question about how to report the findings using clusterstatistics. I used the cluster method to determine at which channels activity is significant different from zero. The cluster method revealed a significant cluster ranging from about 258-370 ms (using ft_clusterplot). If I only look at a certain channel (e.g., Fz) the activity is only significant during 272-322 ms. The time interval of the cluster is determined by the first and the last sample where the activity is significant, regardless if a certain channel shows significant activity during the complete time interval. For instance, if a certain channel shows significant activity only at sample X and another channel only at sample X+100, the cluster ranges from sample X to X+100. My problem is how to report the finding of the significant cluster. If I report that a significant cluster was found from 258-370 ms and show a plot of the activity at Fz (272-322 ms). Then the time intervals and p-values do not correspond. The stat structure contains only the p-value for the time interval of the cluster and not of the individual channels. Any suggestions or examples of how to report clusterstatistics. Regards, Mark -- Mark Noordenbos, MSc Radboud University Nijmegen Behavioural Science Institute P.O. Box 9104, Room A05.36 6500 HE Nijmegen The Netherlands Email: m.noordenbos at bsi.ru.nl Telephone: +31 24 3612070 Fax: +31 24 3616211 http://www.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From Lilla.Magyari at mpi.nl Mon Feb 20 14:44:57 2012 From: Lilla.Magyari at mpi.nl (Magyari, Lilla) Date: Mon, 20 Feb 2012 14:44:57 +0100 Subject: [FieldTrip] question about ft_sourceinterpolate In-Reply-To: <52DE5EF7-93B4-4261-AAC9-A1550A37C986@gmail.com> References: <52DE5EF7-93B4-4261-AAC9-A1550A37C986@gmail.com> Message-ID: <4F424E59.9030609@mpi.nl> Hi, ft_sourceinterpolate is probably requires the specific field of your functional data that should be interpolated. I do not know what kind of source-reconstruction you did on your data, and what kind of fields your data has (sourcePost), but it will be probably the "avg.pow" field. So, I suggest to try this: cfg.parameter = 'avg.pow'; Best, Lilla zhaoyizhe wrote: > Dear all, > > I have a problem in function of 'ft_sourceinterpolate'. > > I run the scrips below, and data from the ftp sever as the test data. > > the result is below: > ??? Error using ==> ft_checkconfig at 162 > The field cfg.parameter is required > > > cfg.parameter='all' has been tried. > the result is below: > ??? Reference to non-existent field 'all'. > > Would you mind tell me how to deal with it? Thanks a lot in advance. > > > -------------------------------------- > close > clc > clear > > > load source > mri = ft_read_mri('Subject01.mri'); > > cfg = []; > cfg.downsample = 2; > sourcePostInt = ft_sourceinterpolate(cfg, sourcePost , mri); > > -------------------------------------- > > > ------------------------------------------------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- PhD student Language and Cognition Group research assistant Neurobiology of Language Group Max Planck Institute for Psycholinguistics Nijmegen, P.O. Box 310, 6500AH, the Netherlands Phone: 0031 24 3521561 From zhaoyizhe at gmail.com Mon Feb 20 15:22:41 2012 From: zhaoyizhe at gmail.com (zhaoyizhe) Date: Mon, 20 Feb 2012 22:22:41 +0800 Subject: [FieldTrip] question about ft_sourceinterpolate In-Reply-To: <4F424E59.9030609@mpi.nl> References: <52DE5EF7-93B4-4261-AAC9-A1550A37C986@gmail.com> <4F424E59.9030609@mpi.nl> Message-ID: <64945130-6612-4591-B986-69C2A3904F69@gmail.com> Hi, Lilla, Thank you for your timely help! The problem has been solved! Cheers, Yizhe From sla.samiee at gmail.com Mon Feb 20 17:21:58 2012 From: sla.samiee at gmail.com (Soheila Samiee) Date: Mon, 20 Feb 2012 11:21:58 -0500 Subject: [FieldTrip] A problem in real-time processing of MEG signal using field trip buffer In-Reply-To: <4F3CCE05.4050109@donders.ru.nl> References: <4F3CCE05.4050109@donders.ru.nl> Message-ID: Dear Jörn, Thanks for your answer. I use CTF/VSM MedTech System. I use 364 channels and the sampling rate is 1200. The decimation rate is 1. As I saw in my recording there are two reasons for crashing in matlab session one of them is about transferring data which rarely occurs when the system is freshly restarted and the second one is related to reading data from buffer. When the number of samples of data which should be read is high we may see such problem. I wanted to check the timing of MEG System data stream and I used a m-file similar to what is published in fieldtrip website ( http://fieldtrip.fcdonders.nl/example/measuring_the_timing_delay_and_jitter_for_a_real-time_application), I attach the mfile to this email. When I run it step by step there is no problem, but when I run the whole file the problem of crashing matlab is occurred exactly when "i=2" and we are on the line of reading the data (*dat = buffer('get_dat', [s(i-1),s(i)],host,port); *). The problem occurs even if I restarted the computer just before running this file. On the other hand, although when the computer is freshly restarted we won't see any crash in matlab session during transferring data, but sometimes we see the message of "*Internal Converter thread does not keep up with load*" in the *acq2ft *terminal in acquisition system. This problem is depend on the rate of sending the data which is related to number of the channels and sampling rate, when we have more sampling rate or more number of channels we will see this message more times and when this message show on the screen, no data transfer to field trip buffer and we can't read data on the other computer. I appreciate it if you help me solve both of these problems about matlab crash and error in data transferring. All the best, Soheila On Thu, Feb 16, 2012 at 4:36 AM, "Jörn M. Horschig" < jm.horschig at donders.ru.nl> wrote: > Dear Soheila, > > we were facing the same problem here. Presumably, there is some problem in > the shared memory module that the buffer is using. Right now, however, we > could not find out where the error precisely comes from, so our best work > around is to restart the computer prior recording and optimize settings, > such as channels and sampling/decimation rate of acq2ft. In our lab, we > managed to find near-optimal settings, so that the buffer crashes only > rarely (actually, I never saw it crashing when the acquisition computer was > freshly restarted). Note that a lower number of channels or higher > decimation does not mean that it runs more stable. It seems to be > literally a trial-and-error approach :/ > > In order to track this down further, we need some more information, e.g. > what MEG system are you using? What's your sampling rate, how many channels > do you put into the buffer, and what's your decimation rate? It would be > great if you could send me that information so that we can maybe try to > track this down. > > Best regards, > Jörn > > > On 2/14/2012 5:42 PM, Soheila Samiee wrote: > > Dear group, > > I use FieldTrip for real-time processing of MEG signals using shared > memory and field trip buffer in a machine other than acquisition system. I > use matlab for reading the buffer and processing the data. > During my data acquisition and sending it to other computer with *acq2ft*in linux, I face a problem. After sending some blocks of data, this > message: "*Internal Converter thread does not keep up with load*" is > shown in the terminal of *acq2ft* and in my matlab session I see an error > : "ERROR: the buffer returned an error (517)". It does not depend on > sampling rate of data in acquisition system. The problem often solve when I > restart the computer which receives the data, but after some minutes of > transferring the data I see the message again. > > Would you please help me in solving this problem? > Best Wishes, > Soheila > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: DataStreamTiming.m Type: text/x-objcsrc Size: 1005 bytes Desc: not available URL: From g.piantoni at nin.knaw.nl Mon Feb 20 18:41:22 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Mon, 20 Feb 2012 18:41:22 +0100 Subject: [FieldTrip] clusterstatistics In-Reply-To: References: Message-ID: Hi Mark, It seems to me that clusterstatistics is giving the appropriate answer. Indeed it takes advantage of the information which can be sparse over multiple channels/frequency/time bins. The only criterion is that this activity is contiguous. I don't follow your example about significant activity at X and X+100 on two different channels. There should be some continuity between the two. As you mentioned, the cluster can span one channels between 0 and 100 and in another neighboring channel between 50 and 150. The cluster will correctly include both channels and the time window between 0 and 150. This is because there is some overlap in time between the two channels. If you think in terms of activity, you can report that activity is significantly different from baseline between 258 and 370 ms, over your channels. The p-value only belongs to the cluster, not to the single time point or channel. If you use bonferroni correction, you can attach single p-values to each timepoint/channel. If you have a priori hypothesis that you expect activity in Fz, you can specify a single channel in timelockstatistics. Depending your data, you might see more power (because you're testing fewer channels at the same time). Hope this helps, Gio -- 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.giovannipiantoni.com On Mon, Feb 20, 2012 at 12:25, Mark Noordenbos wrote: > Dear Fieldtrippers, > > > I have a question about how to report the findings using clusterstatistics. > I used the cluster method to determine at which channels activity is > significant different from zero. > > The cluster method revealed a significant cluster ranging from about 258-370 > ms (using ft_clusterplot). If I only look at a certain channel (e.g., Fz) > the activity is only significant during 272-322 ms. > > > The time interval of the cluster is determined by the first and the last > sample where the activity is significant, regardless if a certain channel > shows significant activity during the complete time interval. For instance, > if a certain channel shows significant activity only at sample X and another > channel only at sample X+100, the cluster ranges from sample X to X+100. > > > My problem is how to report the finding of the significant cluster. If I > report that a significant cluster was found from 258-370 ms and show a plot > of the activity at Fz (272-322 ms). Then the time intervals and p-values do > not correspond. The stat structure contains only the p-value for the time > interval of the cluster and not of the individual channels. > > > Any suggestions or examples of how to report clusterstatistics. > > > Regards, > Mark > > -- > Mark Noordenbos, MSc > > Radboud University Nijmegen > Behavioural Science Institute > > P.O. Box 9104, Room A05.36 > 6500 HE Nijmegen > The Netherlands > > Email: m.noordenbos at bsi.ru.nl > Telephone: +31 24 3612070 > Fax:          +31 24 3616211 > > http://www.ru.nl > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From drivolta81 at gmail.com Tue Feb 21 11:17:00 2012 From: drivolta81 at gmail.com (Davide Rivolta) Date: Tue, 21 Feb 2012 11:17:00 +0100 Subject: [FieldTrip] CTF to SPM Message-ID: Dear all, I wish to ask whether there is a way to import anatomical CTF files (.V2) into SPM. Thanks, Davide -- Davide Rivolta, PhD -------------- next part -------------- An HTML attachment was scrubbed... URL: From tomh at kurage.nimh.nih.gov Tue Feb 21 17:16:51 2012 From: tomh at kurage.nimh.nih.gov (Tom Holroyd (NIH/NIMH) [E]) Date: Tue, 21 Feb 2012 11:16:51 -0500 Subject: [FieldTrip] CTF to SPM In-Reply-To: References: Message-ID: <4F43C373.9090105@kurage.nimh.nih.gov> You can use AFNI to convert v2 .mri files to .nii files. Not v3 though, use CTF's MRIViewer to convert v3 format to v2 format and then use AFNI. I assume SPM can read .nii files. Davide Rivolta wrote: > Dear all, > > I wish to ask whether there is a way to import anatomical CTF files > (.V2) into SPM. >
Dr. Tom
--
How long have I investigated this one thing, the brain of the leech, so that here the slippery truth might no longer slip from me! Here is my domain! Thus spoke Zarathustra. From jan.schoffelen at donders.ru.nl Tue Feb 21 18:05:06 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 21 Feb 2012 18:05:06 +0100 Subject: [FieldTrip] CTF to SPM In-Reply-To: References: Message-ID: <3672CA8D-132F-4664-8251-56DF2F97FA73@donders.ru.nl> Hi Davide, If you use ft_read_mri to read in your *.mri you can use ft_volumewrite to save the volumetric data as nifti. You can look into the documentation of ft_volumewrite to see how this works. Best, Jan-Mathijs On Feb 21, 2012, at 11:17 AM, Davide Rivolta wrote: > Dear all, > > I wish to ask whether there is a way to import anatomical CTF files (.V2) into SPM. > > Thanks, > Davide > > > -- > Davide Rivolta, PhD > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From kd889 at nyu.edu Tue Feb 21 18:48:10 2012 From: kd889 at nyu.edu (Keith Doelling) Date: Tue, 21 Feb 2012 12:48:10 -0500 Subject: [FieldTrip] ft_channelrepair replaces channel data with NaNs after running PCA In-Reply-To: References: Message-ID: Hi guys, For those that are interested I figured out the problem. Somewhere in the process of running component analysis and then component rejection, fieldtrip was taking .chanpos and .chanori in my .grad field and replacing all the values with NaNs. I fixed the problem by adding cleandata.grad = data.grad just after component rejection. It would be great though, if some one could look at the ft_componentanalysis and ft_rejectcomponent functions and figure out why the grad information is being lost. Thanks! Keith On Fri, Feb 17, 2012 at 12:08 PM, Keith Doelling wrote: > Hi guys, > > I'm struggling with my attempts to interpolate channel data for some bad > channels. I put in the following code: > > > cfg=[]; > cfg.badchannel = 15; > cfg.missingchannel = []; > cfg.neighbours = neighbours; > cfg.trials = 'all'; > cleanchdata = ft_channelrepair(cfg,cleandata); > > > the function the displays the following: > > "the input is raw data with 157 channels and 80 trials > repairing channel AG015 > using neighbour AG010 > using neighbour AG014 > using neighbour AG062 > using neighbour AG092" > > suggesting that neighbours have been selected successfully. > > but a call to chdata.trial(1){15,:) just returns a bunch of NaNs rather > than interpolated data I need. > > I found another email thread similar to this but that solution doesn't > seem to apply to me as the neighbours seemed to have been selected > successfully. > > The other interesting caveat is that ft_channelrepair seems to work fine > if i run it without having run pca (to reject eyeblink and heartbeat > components) beforehand. > > The code for the component analysis and the subsequent rejection are in > separate loops. The PCA is saved into a .mat file and then loaded again > when i'm ready to reject the bad components. But for simplicity's sake the > important code looks like this. > > > % principle component analysis run with 32 components > cfg = []; > cfg.channel = (1:157); > cfg.runica.pca=32; > pca_data = ft_componentanalysis(cfg,data); > > % view components in order to select bad ones > cfg = []; > cfg.layout = layout; % specify the layout file that should be used > for plotting > cfg.viewmode = 'component'; > ft_databrowser(cfg, pca_data); > waitfor(gcf); > > % type bad components as user input > % for example: if runica002 and runica0003 should be rejected, type > "2,3" into the dialogue box > badcomps = inputdlg({'Bad Components:'}); > badcomps = str2double(csv2cell(badcomps{1})); > > % reject bad components > cfg = []; > cfg.component = badcomps; > cleandata = ft_rejectcomponent(cfg,pca_data); > > > the variable 'cleandata' i get out from this code is the same cleandata i > put in to ft_channelrepair. > > Are there any ideas as to what I've done wrong here? Let me know if I need > to give you guys more information. > > Thanks for your help, > Keith > > -- > Keith Doelling > Lab Manager and Research Assistant > David Poeppel Lab > New York University > > -- Keith Doelling Lab Manager and Research Assistant David Poeppel Lab New York University -------------- next part -------------- An HTML attachment was scrubbed... URL: From akiko.ikkai at gmail.com Tue Feb 21 18:52:27 2012 From: akiko.ikkai at gmail.com (Akiko Ikkai) Date: Tue, 21 Feb 2012 12:52:27 -0500 Subject: [FieldTrip] volume conduction model missing .mat In-Reply-To: References: <2341406D-6422-4FD3-AD3C-73D1BF70B6CF@mac.com> Message-ID: Hi Gio, Thank you for sharing your script. cfg.output = 'tpm' for ft_volumesegment seems to make a big difference, and now I could go all the way to actually running beamformer on my data! Of course, I had to add a few things. For example, in order to clean up segmented images, I added lines as seg2.brain(:,:,1:4)=0; seg2.skull(:,:,1:2)=0; to make sure scalp, skull and brain do not intersept at neck. Also did something like below for each tissue type (otherwise the resulting beamformer was too small on the brain) newsbrain = imdilate(seg2.brain,strel_bol(1)); seg2.brain = newsbrain; Fieldtrip developers, are there documentations for "cfg.output = 'tpm' " for segmentation? ft_segmentation help page simply says it's a default option. Thanks for your help! Akiko On Thu, Feb 16, 2012 at 5:52 AM, Gio Piantoni wrote: > Hi Akiko, > > What do you mean "problematic" exactly? From my understanding, there > are 4 steps to get from the MRI to the forward model. > 1. from MRI to segmentation > 2. from segmentation to mesh (bnd) > 3. from mesh to headmodel > 4. from headmodel to forward model > > Here is the code I use. It seems to work fine, but experts might want > to chip in and improve it. > 1. from MRI to segmentation > > %-----------------% > %-read MRI > mrifile = '/path/to/your/mri.nii.gz'; > mri = ft_read_mri(mrifile); > %-----------------% > > %-----------------% > %-segmenting the volume, Tissue Probability Maps > % It takes time to run 'tpm' > cfg1 = []; > cfg1.threshold = []; > cfg1.output = 'tpm'; > cfg1.coordsys = 'spm'; > tpm = ft_volumesegment(cfg1, mri); > tpm.anatomy = mri.anatomy; > %-----------------% > > %-----------------% > %-segmenting the volume > % this is faster after tpm > cfg1 = []; > cfg1.threshold = 1; % 1 is default, my MRI scalps were noisy, so I had > to make it lower. > cfg1.output = 'scalp'; > cfg1.coordsys = 'spm'; > segscalp = ft_volumesegment(cfg1, tpm); > > cfg1 = []; > cfg1.threshold = []; > cfg1.output = {'skull' 'brain'}; > cfg1.coordsys = 'spm'; > segment = ft_volumesegment(cfg1, tpm); > segment.scalp = segscalp.scalp; > %-----------------% > > Check the output with ft_sourceplot > > 2. from segmentation to mesh (bnd) > > %-----------------% > %-prepare mesh for skull and brain (easy) > cfg2 = []; > cfg2.tissue = {'skull', 'brain'}; > cfg2.numvertices = [1200 1000]; > cfg2.transform = segment.transform; > bnd = ft_prepare_mesh_new(cfg2, segment); > %-----------------% > > %-----------------% > %-prepare mesh for scalp (we need to be more liberal with threshold, > bc of poor quality of MRI) > cfg2 = []; > cfg2.tissue = {'scalp'}; > cfg2.numvertices = 2500; > cfg2.thresholdseg = 0.1; > cfg2.transform = segment.transform; > scalp = ft_prepare_mesh_new(cfg2, segment); > %-----------------% > > %-----------------% > %-combine scalp and bnd > bnd = [scalp bnd]; > ft_plot_mesh(bnd(1), 'facealpha', .5) > hold on > ft_plot_mesh(bnd(2), 'facecolor', 'red') > %-----------------% > > If bnd is good, no intersection between meshes and the outline looks > nice, the following should run without problems. Please, do check your > bnd. > Segmentation and ft_prepare_mesh_new work really well. Another > approach to get nice meshes is to skip step 1 and 2 and use > Freesurfer/MNE. You can read the meshes in fieldtrip > (ft_read_headshape, I think). The meshes are in the "bem" folder of > Freesurfer, but I don't remember off the top of my head which files > you should read ("outer_skull, inner_skull", I think). > These meshes have a very very high resolution, you can scale them down > with "reducepatch" in Matlab. > > 3. from mesh to headmodel > %-----------------% > %-headmodel > cfg3 = []; > cfg3.method = 'bem_dipoli'; > cfg3.conductivity = [0.33 0.0042 0.33]; > vol = ft_prepare_headmodel(cfg3, bnd); > %-----------------% > > You can really pick your favorite here: dipoli, openmeeg, bemcp. This > will take time (the more time, the more points on your meshes). > > 4. from headmodel to forward model > You last problem is to get electrodes and headmodel in the same space. > The template in SPM is already in MNI space, your individual MRIs > probably not. You can realign them to MNI space before step 1 using > SPM or FSL. > > elec = ft_read_sens(sensfile); > elec = ft_convert_units(elec, 'mm'); > > %-------% > %-simple transformation (based on visual realignment) > % elecM is an affine matrix that you can get from ft_electroderealign > % electrodes do not need to match the scalp perfectly, but they should > be pretty close by. > elec.chanpos = warp_apply(elecM, elec.chanpos); > elec.elecpos = warp_apply(elecM, elec.elecpos); > %-------% > > [vol, elec] = ft_prepare_vol_sens(vol, elec); > % now you should check that the electrodes are on the scalp. > %-----------------% > > %-----------------% > %-prepare leadfield > cfg4 = []; > cfg4.elec = elec; > cfg4.vol = vol; > cfg4.grid.xgrid = -70:10:70; > cfg4.grid.ygrid = -110:10:80; > cfg4.grid.zgrid = -60:10:90; > cfg4.inwardshift = 1; % to avoid dipoles on the border of bnd(3), > which are very instable > cfg4.grid.tight = 'no'; > cfg4.feedback = 'none'; > lead = ft_prepare_leadfield(cfg4, []); > % use ft_plot_topo3d and ft_plot_dipole to check whether the > projection of your dipole onto the scalp makes sense. > %-----------------% > > "lead" should be your subject-specific, electrode-specific leadfield. > There are quite a few parameters that you can change, but a clean > segmentation and non-intersecting, smooth and realistic-looking meshes > are a must. > Then, using dipoli, openmeeg or bemcp should not change your forward > model too much. > Sorry if some points are not clear, but you should really look at your > MRI/segmentation/meshes/electrodes/forward model as much as possible. > > Hope this will get you started. I appreciate any feedback on improving > the code, this is just my personal attempt. > > Cheers > > Gio > > On Wed, Feb 15, 2012 at 17:45, Akiko Ikkai wrote: > > Dear Fieldtrip users, > > > > Thank you Patrick, Nathan & Gio for your inputs. My MRI anatomical images > > need extensive cleaning (enhance contrasts, get rid of non-zero voxels > > outside the brain, etc...) before segmentation, as well as adjusting > > cfg.threshold for each tissue type during segmentation and each subject. > At > > least testing with SPM standard MRI, segmentation and forward modeling > works > > OK now. > > > > Individual subject's MRI, though, is still problematic, and I have a > > question for Fieldtrip developers: could you let me know whether "Create > BEM > > headmodel for EEG ( > > http://fieldtrip.fcdonders.nl/example/create_bem_headmodel_for_eeg )" > > routine is what you recommend, or it's integrated into a newer function > with > > newer cfg options? Is there a page I missed on the web? > > > > Thank you so much for your time! > > Akiko > > > > On Fri, Feb 10, 2012 at 4:36 AM, Gio Piantoni > > wrote: > >> > >> Hi Akiki and Patrick, > >> > >> I agree with Nathan about segmentation problems. I had the same > >> problem when two of the three meshes intersected each other. Before > >> you run the forward model, you should check the segmentation (bnd) > >> using ft_plot_mesh. > >> ft_plot_mesh(bnd(1), 'facealpha', .5) > >> hold on > >> ft_plot_mesh(bnd(2), 'facecolor', 'r') > >> You will see that the two meshes intersect with each other. Depending > >> on how you created the meshes, you should fix the parameters in such a > >> way that they don't intersect. For example, ft_volumesegment has a > >> cfg.threshold option (you can check how the segmentation went with > >> ft_sourceplot) and ft_prepare_mesh_new has cfg.thresholdseg and > >> cfg.smoothseg. > >> > >> I think that the meshes in SPM are computed on an (affine-transformed) > >> template and not on the anatomically derived meshes. The template is > >> more robust and that's why the two surfaces do not intersect. > >> > >> In general, the segmentation depends on the quality of your MRIs and > >> you should really visually check the segmentation and meshes. When > >> those look ok, the BEM forward model usually works. Hope this helps. > >> > >> Cheers, > >> > >> Gio > >> > >> On Fri, Feb 10, 2012 at 09:00, Nathan Weisz > wrote: > >> > Hi Akiki, > >> > > >> > I am not a headmodel expert. > >> > but looking at the output message, it seems your segementation did not > >> > go > >> > too well (see the "intersect" message). my intuition is then then the > >> > next > >> > temporary file *.ama is not created and ft_prepare_bemmodel then > simply > >> > says > >> > ciao. > >> > > >> > perhaps you want to check / redo the segmentation? > >> > > >> > good luck, > >> > nathan > >> > > >> > > >> > On 09.02.2012, at 23:04, Akiko Ikkai wrote: > >> > > >> > Hi, > >> > > >> > I'm trying to create a volume conduction model for my EEG study based > on > >> > anatomical MRI, and having trouble with ft_prepare_bemmodel > >> > > >> > when I run > >> > cfg = []; > >> > cfg.tissue = [7 4 1]; % value for brain, skull, and scalp > >> > cfg.conductivity = [1 1/80 1]*.33; % after standard_BEM.zip data > >> > cfg.isolatedsource = true; > >> > cfg.method = 'dipoli'; > >> > cfg.sourceunits = 'mm'; > >> > cfg.mriunits = 'mm'; > >> > vol = ft_prepare_bemmodel(cfg, seg4bem); > >> > > >> > I get the following error message while ft_prepare_bemmodel is > running: > >> > > >> > Fatal error in dipoli: interface > >> > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and > >> > /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect > >> > at vertex 1402 of > >> > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri > >> > > >> > Warning: an error ocurred while running dipoli > >> >> In dipoli at 94 > >> > In ft_prepare_bemmodel at 112 > >> > Error using ==> fread > >> > Invalid file identifier. Use fopen to generate a valid file > identifier. > >> > Warning: File > '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' > >> > not > >> > found. > >> >> In dipoli at 102 > >> > In ft_prepare_bemmodel at 112 > >> > > >> > > >> > and the output vol is missing .mat, which causes an error > >> > during ft_sourceanalysis. > >> >>> vol > >> > vol = > >> > cond: [0.3300 0.0041 0.3300] > >> > bnd: [1x3 struct] > >> > source: 3 > >> > skin_surface: 3 > >> > skin: 1 > >> > type: 'dipoli' > >> > > >> > Does anyone know how to correct for "fatal error" so > >> > that ft_prepare_bemmodel creates the correct volume conduction model? > I > >> > opened .tri file and removed line 1402, but got the same results. > >> > > >> > Thanks in advance! Akiko > >> > > >> > -- > >> > Akiko Ikkai, Ph.D. > >> > Postdoctoral Fellow > >> > Department of Psychological and Brain Sciences > >> > Johns Hopkins University > >> > Ames Hall, 3400 N. Charles St. > >> > Baltimore, MD 21218 > >> > > >> > > >> > _______________________________________________ > >> > fieldtrip mailing list > >> > fieldtrip at donders.ru.nl > >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> > > >> > > >> > > >> > _______________________________________________ > >> > fieldtrip mailing list > >> > fieldtrip at donders.ru.nl > >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > -- > > Akiko Ikkai, Ph.D. > > Postdoctoral Fellow > > Department of Psychological and Brain Sciences > > Johns Hopkins University > > Ames Hall, 3400 N. Charles St. > > Baltimore, MD 21218 > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Akiko Ikkai, Ph.D. Postdoctoral Fellow Department of Psychological and Brain Sciences Johns Hopkins University Ames Hall, 3400 N. Charles St. Baltimore, MD 21218 -------------- next part -------------- An HTML attachment was scrubbed... URL: From drivolta81 at gmail.com Wed Feb 22 10:05:01 2012 From: drivolta81 at gmail.com (Davide Rivolta) Date: Wed, 22 Feb 2012 10:05:01 +0100 Subject: [FieldTrip] CTF to SPM In-Reply-To: <3672CA8D-132F-4664-8251-56DF2F97FA73@donders.ru.nl> References: <3672CA8D-132F-4664-8251-56DF2F97FA73@donders.ru.nl> Message-ID: Thank you for the replies. I am trying with ft_volumewrite. I have a small problem. the configuration wants me to specify the cfg.parameter, that is a "string, describing the functional data to be processed, e.g. 'pow', 'coh' or 'nai' ". I am a bit confused, since I have anatomical data, and I am not sure what to put here. Any ideas? Thanks a lot, Davide On Tue, Feb 21, 2012 at 6:05 PM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Hi Davide, > > If you use ft_read_mri to read in your *.mri you can use ft_volumewrite to > save the volumetric data as nifti. You can look into the documentation of > ft_volumewrite to see how this works. > > Best, > > Jan-Mathijs > > On Feb 21, 2012, at 11:17 AM, Davide Rivolta wrote: > > Dear all, > > > I wish to ask whether there is a way to import anatomical CTF files (.V2) > into SPM. > > > Thanks, > Davide > > > -- > Davide Rivolta, PhD > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Davide Rivolta, PhD -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Feb 22 10:47:02 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 22 Feb 2012 10:47:02 +0100 Subject: [FieldTrip] CTF to SPM In-Reply-To: References: <3672CA8D-132F-4664-8251-56DF2F97FA73@donders.ru.nl> Message-ID: <056A85D1-7E54-44B6-9CFA-DCB2BA88C27B@donders.ru.nl> Dear Davide, Did you try 'anatomy' ? BW, Jan-Mathijs On Feb 22, 2012, at 10:05 AM, Davide Rivolta wrote: > Thank you for the replies. > I am trying with ft_volumewrite. > > I have a small problem. the configuration wants me to specify the cfg.parameter, that is a "string, describing the functional data to be processed, e.g. 'pow', 'coh' or 'nai' ". > I am a bit confused, since I have anatomical data, and I am not sure what to put here. > > Any ideas? > > Thanks a lot, > Davide > > > On Tue, Feb 21, 2012 at 6:05 PM, jan-mathijs schoffelen wrote: > Hi Davide, > > If you use ft_read_mri to read in your *.mri you can use ft_volumewrite to save the volumetric data as nifti. You can look into the documentation of ft_volumewrite to see how this works. > > Best, > > Jan-Mathijs > > On Feb 21, 2012, at 11:17 AM, Davide Rivolta wrote: > >> Dear all, >> >> I wish to ask whether there is a way to import anatomical CTF files (.V2) into SPM. >> >> Thanks, >> Davide >> >> >> -- >> Davide Rivolta, PhD >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Davide Rivolta, PhD > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From drivolta81 at gmail.com Wed Feb 22 11:04:11 2012 From: drivolta81 at gmail.com (Davide Rivolta) Date: Wed, 22 Feb 2012 11:04:11 +0100 Subject: [FieldTrip] CTF to SPM In-Reply-To: <056A85D1-7E54-44B6-9CFA-DCB2BA88C27B@donders.ru.nl> References: <3672CA8D-132F-4664-8251-56DF2F97FA73@donders.ru.nl> <056A85D1-7E54-44B6-9CFA-DCB2BA88C27B@donders.ru.nl> Message-ID: Thanks again for the help. I still get an error regarding the name. Maybe is silly. This is my script: for i = 1:size(mri,1) fullname = strcat(inpath, mri{i,1}, '_V2.mri'); mri_V2 = ft_read_mri(fullname); cfg = []; cfg.parameter = 'anatomy'; cfg.filename = mri_V2; cfg.filetype = 'nifti'; ft_volumewrite(cfg, mri_V2); end; ?? Error using ==> fileparts at 17 Input must be a row vector of characters. Error in ==> ft_volumewrite at 411 [pathstr, name, ext] = fileparts(cfg.filename); Thanks again, Davide On Wed, Feb 22, 2012 at 10:47 AM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Dear Davide, > > Did you try 'anatomy' ? > > BW, > > Jan-Mathijs > > > On Feb 22, 2012, at 10:05 AM, Davide Rivolta wrote: > > Thank you for the replies. > I am trying with ft_volumewrite. > > I have a small problem. the configuration wants me to specify the > cfg.parameter, that is a "string, describing the functional data to be > processed, e.g. 'pow', 'coh' or 'nai' ". > I am a bit confused, since I have anatomical data, and I am not sure what > to put here. > > Any ideas? > > Thanks a lot, > Davide > > > On Tue, Feb 21, 2012 at 6:05 PM, jan-mathijs schoffelen < > jan.schoffelen at donders.ru.nl> wrote: > >> Hi Davide, >> >> If you use ft_read_mri to read in your *.mri you can use ft_volumewrite >> to save the volumetric data as nifti. You can look into the documentation >> of ft_volumewrite to see how this works. >> >> Best, >> >> Jan-Mathijs >> >> On Feb 21, 2012, at 11:17 AM, Davide Rivolta wrote: >> >> Dear all, >> >> >> I wish to ask whether there is a way to import anatomical CTF files (.V2) >> into SPM. >> >> >> Thanks, >> Davide >> >> >> -- >> Davide Rivolta, PhD >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Davide Rivolta, PhD > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Davide Rivolta, PhD -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Feb 22 12:04:45 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 22 Feb 2012 12:04:45 +0100 Subject: [FieldTrip] CTF to SPM In-Reply-To: References: <3672CA8D-132F-4664-8251-56DF2F97FA73@donders.ru.nl> <056A85D1-7E54-44B6-9CFA-DCB2BA88C27B@donders.ru.nl> Message-ID: Hi Davide, Perhaps putting the filename as a 'string' may do the trick. In that case it was indeed silly ;-). BW, JM On Feb 22, 2012, at 11:04 AM, Davide Rivolta wrote: > Thanks again for the help. I still get an error regarding the name. Maybe is silly. > > This is my script: > > > for i = 1:size(mri,1) > fullname = strcat(inpath, mri{i,1}, '_V2.mri'); > mri_V2 = ft_read_mri(fullname); > > cfg = []; > cfg.parameter = 'anatomy'; > cfg.filename = mri_V2; > cfg.filetype = 'nifti'; > ft_volumewrite(cfg, mri_V2); > > end; > > ?? Error using ==> fileparts at 17 > Input must be a row vector of characters. > Error in ==> ft_volumewrite at 411 > [pathstr, name, ext] = fileparts(cfg.filename); > > > > Thanks again, > Davide > > > > > On Wed, Feb 22, 2012 at 10:47 AM, jan-mathijs schoffelen wrote: > Dear Davide, > > Did you try 'anatomy' ? > > BW, > > Jan-Mathijs > > > On Feb 22, 2012, at 10:05 AM, Davide Rivolta wrote: > >> Thank you for the replies. >> I am trying with ft_volumewrite. >> >> I have a small problem. the configuration wants me to specify the cfg.parameter, that is a "string, describing the functional data to be processed, e.g. 'pow', 'coh' or 'nai' ". >> I am a bit confused, since I have anatomical data, and I am not sure what to put here. >> >> Any ideas? >> >> Thanks a lot, >> Davide >> >> >> On Tue, Feb 21, 2012 at 6:05 PM, jan-mathijs schoffelen wrote: >> Hi Davide, >> >> If you use ft_read_mri to read in your *.mri you can use ft_volumewrite to save the volumetric data as nifti. You can look into the documentation of ft_volumewrite to see how this works. >> >> Best, >> >> Jan-Mathijs >> >> On Feb 21, 2012, at 11:17 AM, Davide Rivolta wrote: >> >>> Dear all, >>> >>> I wish to ask whether there is a way to import anatomical CTF files (.V2) into SPM. >>> >>> Thanks, >>> Davide >>> >>> >>> -- >>> Davide Rivolta, PhD >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Davide Rivolta, PhD >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Davide Rivolta, PhD > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From drivolta81 at gmail.com Wed Feb 22 12:07:23 2012 From: drivolta81 at gmail.com (Davide Rivolta) Date: Wed, 22 Feb 2012 12:07:23 +0100 Subject: [FieldTrip] CTF to SPM In-Reply-To: References: <3672CA8D-132F-4664-8251-56DF2F97FA73@donders.ru.nl> <056A85D1-7E54-44B6-9CFA-DCB2BA88C27B@donders.ru.nl> Message-ID: Yep, I realized it after sending the email. It was silly indeed. It works fine now, Thanks, Davide On Wed, Feb 22, 2012 at 12:04 PM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Hi Davide, > > Perhaps putting the filename as a 'string' may do the trick. In that case > it was indeed silly ;-). > > BW, > > JM > > On Feb 22, 2012, at 11:04 AM, Davide Rivolta wrote: > > Thanks again for the help. I still get an error regarding the name. > Maybe is silly. > > This is my script: > > > for i = 1:size(mri,1) > fullname = strcat(inpath, mri{i,1}, '_V2.mri'); > mri_V2 = ft_read_mri(fullname); > > cfg = []; > cfg.parameter = 'anatomy'; > cfg.filename = mri_V2; > cfg.filetype = 'nifti'; > ft_volumewrite(cfg, mri_V2); > > end; > > ?? Error using ==> fileparts at 17 > Input must be a row vector of characters. > Error in ==> ft_volumewrite at 411 > [pathstr, name, ext] = fileparts(cfg.filename); > > > > Thanks again, > Davide > > > > > On Wed, Feb 22, 2012 at 10:47 AM, jan-mathijs schoffelen < > jan.schoffelen at donders.ru.nl> wrote: > >> Dear Davide, >> >> Did you try 'anatomy' ? >> >> BW, >> >> Jan-Mathijs >> >> >> On Feb 22, 2012, at 10:05 AM, Davide Rivolta wrote: >> >> Thank you for the replies. >> I am trying with ft_volumewrite. >> >> I have a small problem. the configuration wants me to specify the >> cfg.parameter, that is a "string, describing the functional data to be >> processed, e.g. 'pow', 'coh' or 'nai' ". >> I am a bit confused, since I have anatomical data, and I am not sure what >> to put here. >> >> Any ideas? >> >> Thanks a lot, >> Davide >> >> >> On Tue, Feb 21, 2012 at 6:05 PM, jan-mathijs schoffelen < >> jan.schoffelen at donders.ru.nl> wrote: >> >>> Hi Davide, >>> >>> If you use ft_read_mri to read in your *.mri you can use ft_volumewrite >>> to save the volumetric data as nifti. You can look into the documentation >>> of ft_volumewrite to see how this works. >>> >>> Best, >>> >>> Jan-Mathijs >>> >>> On Feb 21, 2012, at 11:17 AM, Davide Rivolta wrote: >>> >>> Dear all, >>> >>> >>> I wish to ask whether there is a way to import anatomical CTF files >>> (.V2) into SPM. >>> >>> >>> Thanks, >>> Davide >>> >>> >>> -- >>> Davide Rivolta, PhD >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> Jan-Mathijs Schoffelen, MD PhD >>> >>> Donders Institute for Brain, Cognition and Behaviour, >>> Centre for Cognitive Neuroimaging, >>> Radboud University Nijmegen, The Netherlands >>> >>> Max Planck Institute for Psycholinguistics, >>> Nijmegen, The Netherlands >>> >>> J.Schoffelen at donders.ru.nl >>> Telephone: +31-24-3614793 >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> Davide Rivolta, PhD >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Davide Rivolta, PhD > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Davide Rivolta, PhD -------------- next part -------------- An HTML attachment was scrubbed... URL: From jnortonf at uci.edu Thu Feb 23 04:28:24 2012 From: jnortonf at uci.edu (Jessamy Norton-Ford) Date: Wed, 22 Feb 2012 19:28:24 -0800 Subject: [FieldTrip] Fieldtrip tutorial error: trialfun Message-ID: Hello, I am new to Fieldtrip, and have run into the following problems running through the tutorial cfg = []; % empty configuration cfg.dataset = 'Subject01.ds'; % name of CTF dataset cfg.trialdef.eventtype = 'backpanel trigger'; cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 2; cfg.trialdef.eventvalue = 3; % event value of FIC cfg = ft_definetrial(cfg); Warning: no trialfun was specified, using trialfun_general > In ft_definetrial at 123 evaluating trialfunction 'trialfun_general' Warning: adding /Users/jessamynorton-ford/Documents/MATLAB/fieldtrip-20120222/external/ctf toolbox to your Matlab path readCTFds: Data set error : size of meg4 file(s) 0 bytes (from dir command) 179071200 bytes (from res4 file) reading the events from 'Subject01.ds/Subject01.res4' readCTFds: Data set error : size of meg4 file(s) 0 bytes (from dir command) 179071200 bytes (from res4 file) ??? Attempt to reference field of non-structure array. Error in ==> trialfun_general at 118 sel = ismember({event.type}, cfg.trialdef.eventtype); Error in ==> ft_definetrial at 166 [trl, event] = feval(cfg.trialfun, cfg); I found a somewhat similar issue on the boards from May 2011 ( http://mailman.science.ru.nl/pipermail/fieldtrip/2011-May/003827.html), and have since tried several instantiations of FieldTrip (though the version I was running when I first got the error was actually very new). So far I have tried: fieldtrip-20111004 fieldtrip-20111101 fieldtrip-20120220 fieldtrip-20120222 here is my ver info in case it is helpful: MATLAB Version 7.11.0.584 (R2010b) Operating System: Mac OS X Version: 10.6.2 Build: 10C540 Java VM Version: Java 1.6.0_15-b03-219 with Apple Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode ------------------------------------------------------------------------------------- Any suggestions of likely incompatibilities/mistakes on my part would be most helpful. Thank you, -- Jessamy Norton-Ford Doctoral Student, Department of Cognitive Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Feb 23 09:25:58 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 23 Feb 2012 09:25:58 +0100 Subject: [FieldTrip] Fieldtrip tutorial error: trialfun In-Reply-To: References: Message-ID: Dear Jessamy, This looks like you are calling the function from the wrong directory. I can reproduce your error when I call ft_redefinetrial from the following location: XXXXXX/Subject01.ds instead, you should call the function from: XXXXXX, i.e. one directory up (so type 'cd ../' to get there), or use an absolute path in cfg.dataset (i.e. cfg.dataset = '/XXXXXX/Subject01.ds') Best wishes, Jan-Mathijs On Feb 23, 2012, at 4:28 AM, Jessamy Norton-Ford wrote: > Hello, > > I am new to Fieldtrip, and have run into the following problems running through the tutorial > > cfg = []; % empty configuration > cfg.dataset = 'Subject01.ds'; % name of CTF dataset > cfg.trialdef.eventtype = 'backpanel trigger'; > cfg.trialdef.prestim = 1; > cfg.trialdef.poststim = 2; > cfg.trialdef.eventvalue = 3; % event value of FIC > cfg = ft_definetrial(cfg); > > Warning: no trialfun was specified, using trialfun_general > > > In ft_definetrial at 123 > evaluating trialfunction 'trialfun_general' > > Warning: adding > /Users/jessamynorton-ford/Documents/MATLAB/fieldtrip-20120222/external/ctf > toolbox to your Matlab path > > readCTFds: Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file) > > reading the events from 'Subject01.ds/Subject01.res4' > > readCTFds: Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file) > > ??? Attempt to reference field of non-structure array. > > Error in ==> trialfun_general at 118 > sel = ismember({event.type}, cfg.trialdef.eventtype); > > Error in ==> ft_definetrial at 166 > [trl, event] = feval(cfg.trialfun, cfg); > > I found a somewhat similar issue on the boards from May 2011 (http://mailman.science.ru.nl/pipermail/fieldtrip/2011-May/003827.html), and have since tried several instantiations of FieldTrip (though the version I was running when I first got the error was actually very new). So far I have tried: > > fieldtrip-20111004 > fieldtrip-20111101 > fieldtrip-20120220 > fieldtrip-20120222 > > here is my ver info in case it is helpful: > > MATLAB Version 7.11.0.584 (R2010b) > > Operating System: Mac OS X Version: 10.6.2 Build: 10C540 > Java VM Version: Java 1.6.0_15-b03-219 with Apple Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode > ------------------------------------------------------------------------------------- > > Any suggestions of likely incompatibilities/mistakes on my part would be most helpful. > > Thank you, > > -- > Jessamy Norton-Ford > Doctoral Student, Department of Cognitive Sciences > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Feb 23 10:11:29 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 23 Feb 2012 10:11:29 +0100 Subject: [FieldTrip] Fwd: ft_megplanar problem for planar gradient calculation References: Message-ID: Begin forwarded message: > > ---------- Forwarded message ---------- > From: Ion Lavado > Date: 2012/2/21 > Subject: ft_megplanar problem for planar gradient calculation > To: fieldtrip-request at donders.ru.nl > > > Hello, i'm doing the cluster based permutations tests on time-frequency data tutorial. I'm using an Elekta neuromag with 306 channels. My problem comes when i try to calculate the planar gradient. This is what i do: > > %************ READ WORD EVENT ************ > cfg = []; > cfg.dataset = '21_muti.fif'; > cfg.trialdef.eventtype = 'STI101'; > cfg.trialdef.prestim = 1; > cfg.trialdef.poststim = 1; > cfg.trialdef.eventvalue = 1; > cfg = ft_definetrial(cfg); > cfg.channel = {'MEG'}; > cfg.demean = 'yes'; > cfg.baselinewindow = [-0.5 0]; > dataMuti21_words = ft_preprocessing(cfg); > %************ READ PICTURES EVENT ************ > cfg = []; > cfg.dataset = '21_muti.fif'; > cfg.trialdef.eventtype = 'STI101'; > cfg.trialdef.prestim = 1; > cfg.trialdef.poststim = 1; > cfg.trialdef.eventvalue = 6; > cfg = ft_definetrial(cfg); > cfg.channel = {'MEG'}; > cfg.demean = 'yes'; > cfg.baselinewindow = [-0.5 0]; > dataMuti21_pictures = ft_preprocessing(cfg); > > > > %******* CALCULATE PLANAR GRADIENT ****** > cfg = []; > cfg.planarmethod = 'sincos'; > cfg_neighb.method = 'distance'; > cfg.grad = avg_words.grad; > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataMuti21_pictures); > avg_words_planar = ft_megplanar(cfg, dataMuti21_words); > avg_pictures_planar = ft_megplanar(cfg, dataMuti21_pictures); > > > HERE IS WHERE I GET THE ERROR: > ??? Error using ==> ft_checkdata at 359 > This function requires ctf151, ctf275, bti148, bti248, itab153, yokogawa160 or yokogawa64 data as input, but you are giving > neuromag306 data. > > Error in ==> ft_megplanar at 107 > data = ft_checkdata(data, 'datatype', {'raw' 'freq'}, 'feedback', 'yes', 'hassampleinfo', 'yes', 'ismeg', 'yes', 'senstype', > {'ctf151', 'ctf275', 'bti148', 'bti248', 'itab153', 'yokogawa160', 'yokoga > > > Can't i use neuromag306 data type sens for this function? any solution? THANKS IN ADVANCE > > Ion -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu Feb 23 10:19:25 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 23 Feb 2012 10:19:25 +0100 Subject: [FieldTrip] Fwd: ft_megplanar problem for planar gradient calculation In-Reply-To: References: Message-ID: Dear Ion, ft_megplanar is designed to estimate planar gradient information from axial gradiometer data. The Neuromag 306 system is equipped with planar gradiometers, so the data you have is already reflecting the planar magnetic gradient. In other words: there is no need to use ft_megplanar, in your case. Best, Eelke On 23 February 2012 10:11, jan-mathijs schoffelen wrote: > > > Begin forwarded message: > > > ---------- Forwarded message ---------- > From: Ion Lavado > Date: 2012/2/21 > Subject: ft_megplanar problem for planar gradient calculation > To: fieldtrip-request at donders.ru.nl > > > Hello, i'm doing the cluster based permutations tests on time-frequency data > tutorial. I'm using an Elekta neuromag with 306 channels. My problem comes > when i try to calculate the planar gradient. This is what i do: > > %************ READ WORD EVENT ************ > cfg = []; > cfg.dataset                 = '21_muti.fif'; > cfg.trialdef.eventtype      = 'STI101'; > cfg.trialdef.prestim        = 1; > cfg.trialdef.poststim       = 1; > cfg.trialdef.eventvalue     = 1; > cfg = ft_definetrial(cfg); > cfg.channel   = {'MEG'}; > cfg.demean        = 'yes'; > cfg.baselinewindow = [-0.5 0]; > dataMuti21_words = ft_preprocessing(cfg); > %************ READ PICTURES EVENT ************ > cfg = []; > cfg.dataset                 = '21_muti.fif'; > cfg.trialdef.eventtype      = 'STI101'; > cfg.trialdef.prestim        = 1; > cfg.trialdef.poststim       = 1; > cfg.trialdef.eventvalue     = 6; > cfg = ft_definetrial(cfg); > cfg.channel   = {'MEG'}; > cfg.demean        = 'yes'; > cfg.baselinewindow = [-0.5 0]; > dataMuti21_pictures = ft_preprocessing(cfg); > > > > %******* CALCULATE PLANAR GRADIENT ****** > cfg = []; > cfg.planarmethod = 'sincos'; > cfg_neighb.method    = 'distance'; > cfg.grad            = avg_words.grad; > cfg.neighbours       = ft_prepare_neighbours(cfg_neighb, > dataMuti21_pictures); > avg_words_planar = ft_megplanar(cfg, dataMuti21_words); > avg_pictures_planar = ft_megplanar(cfg, dataMuti21_pictures); > > > HERE IS WHERE I GET THE ERROR: > ??? Error using ==> ft_checkdata at 359 > This function requires ctf151, ctf275, bti148, bti248, itab153, yokogawa160 > or yokogawa64 data as input, but you are giving > neuromag306 data. > > Error in ==> ft_megplanar at 107 > data = ft_checkdata(data, 'datatype', {'raw' 'freq'}, 'feedback', 'yes', > 'hassampleinfo', 'yes', 'ismeg', 'yes', 'senstype', > {'ctf151', 'ctf275', 'bti148', 'bti248', 'itab153', 'yokogawa160', 'yokoga > > > Can't i use neuromag306 data type sens for this function? any solution? > THANKS IN ADVANCE > > Ion > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Thu Feb 23 10:20:29 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 23 Feb 2012 10:20:29 +0100 Subject: [FieldTrip] Fwd: ft_megplanar problem for planar gradient calculation In-Reply-To: References: Message-ID: <9F11307A-F697-4D9B-BBC4-694C00760EAC@donders.ru.nl> Dear Ion, In principle, you could do a synthetic planar grdient computation on the 102 magnetometer channels in your data. I don't think that this is supported by FieldTrip though. Obviously, you cannot do the planar gradient computation on the other 204 channels, because they already represent the magnetic field gradient. Best, Jan-Mathijs On Feb 23, 2012, at 10:11 AM, jan-mathijs schoffelen wrote: > > > Begin forwarded message: >> >> ---------- Forwarded message ---------- >> From: Ion Lavado >> Date: 2012/2/21 >> Subject: ft_megplanar problem for planar gradient calculation >> To: fieldtrip-request at donders.ru.nl >> >> >> Hello, i'm doing the cluster based permutations tests on time-frequency data tutorial. I'm using an Elekta neuromag with 306 channels. My problem comes when i try to calculate the planar gradient. This is what i do: >> >> %************ READ WORD EVENT ************ >> cfg = []; >> cfg.dataset = '21_muti.fif'; >> cfg.trialdef.eventtype = 'STI101'; >> cfg.trialdef.prestim = 1; >> cfg.trialdef.poststim = 1; >> cfg.trialdef.eventvalue = 1; >> cfg = ft_definetrial(cfg); >> cfg.channel = {'MEG'}; >> cfg.demean = 'yes'; >> cfg.baselinewindow = [-0.5 0]; >> dataMuti21_words = ft_preprocessing(cfg); >> %************ READ PICTURES EVENT ************ >> cfg = []; >> cfg.dataset = '21_muti.fif'; >> cfg.trialdef.eventtype = 'STI101'; >> cfg.trialdef.prestim = 1; >> cfg.trialdef.poststim = 1; >> cfg.trialdef.eventvalue = 6; >> cfg = ft_definetrial(cfg); >> cfg.channel = {'MEG'}; >> cfg.demean = 'yes'; >> cfg.baselinewindow = [-0.5 0]; >> dataMuti21_pictures = ft_preprocessing(cfg); >> >> >> >> %******* CALCULATE PLANAR GRADIENT ****** >> cfg = []; >> cfg.planarmethod = 'sincos'; >> cfg_neighb.method = 'distance'; >> cfg.grad = avg_words.grad; >> cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataMuti21_pictures); >> avg_words_planar = ft_megplanar(cfg, dataMuti21_words); >> avg_pictures_planar = ft_megplanar(cfg, dataMuti21_pictures); >> >> >> HERE IS WHERE I GET THE ERROR: >> ??? Error using ==> ft_checkdata at 359 >> This function requires ctf151, ctf275, bti148, bti248, itab153, yokogawa160 or yokogawa64 data as input, but you are giving >> neuromag306 data. >> >> Error in ==> ft_megplanar at 107 >> data = ft_checkdata(data, 'datatype', {'raw' 'freq'}, 'feedback', 'yes', 'hassampleinfo', 'yes', 'ismeg', 'yes', 'senstype', >> {'ctf151', 'ctf275', 'bti148', 'bti248', 'itab153', 'yokogawa160', 'yokoga >> >> >> Can't i use neuromag306 data type sens for this function? any solution? THANKS IN ADVANCE >> >> Ion > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Thu Feb 23 10:26:21 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 23 Feb 2012 10:26:21 +0100 Subject: [FieldTrip] Fwd: ft_megplanar problem for planar gradient calculation In-Reply-To: References: Message-ID: <4F46063D.9090501@donders.ru.nl> Hi, I might be mistaken since I am not using a neuromag system, but as far as I know a Neuromag system already has planar gradiometers? If so, then there would be no need to apply ft_megplanar (and actually, it would be an meaningless operation) Best, Jörn On 2/23/2012 10:11 AM, jan-mathijs schoffelen wrote: > > > Begin forwarded message: >> >> ---------- Forwarded message ---------- >> From: *Ion Lavado* > >> Date: 2012/2/21 >> Subject: ft_megplanar problem for planar gradient calculation >> To: fieldtrip-request at donders.ru.nl >> >> >> >> Hello, i'm doing the cluster based permutations tests on >> time-frequency data tutorial. I'm using an Elekta neuromag with 306 >> channels. My problem comes when i try to calculate the planar >> gradient. This is what i do: >> >> %************ READ WORD EVENT ************ >> cfg = []; >> cfg.dataset = '21_muti.fif'; >> cfg.trialdef.eventtype = 'STI101'; >> cfg.trialdef.prestim = 1; >> cfg.trialdef.poststim = 1; >> cfg.trialdef.eventvalue = 1; >> cfg = ft_definetrial(cfg); >> cfg.channel = {'MEG'}; >> cfg.demean = 'yes'; >> cfg.baselinewindow = [-0.5 0]; >> dataMuti21_words = ft_preprocessing(cfg); >> %************ READ PICTURES EVENT ************ >> cfg = []; >> cfg.dataset = '21_muti.fif'; >> cfg.trialdef.eventtype = 'STI101'; >> cfg.trialdef.prestim = 1; >> cfg.trialdef.poststim = 1; >> cfg.trialdef.eventvalue = 6; >> cfg = ft_definetrial(cfg); >> cfg.channel = {'MEG'}; >> cfg.demean = 'yes'; >> cfg.baselinewindow = [-0.5 0]; >> dataMuti21_pictures = ft_preprocessing(cfg); >> >> >> >> %******* CALCULATE PLANAR GRADIENT ****** >> cfg = []; >> cfg.planarmethod = 'sincos'; >> cfg_neighb.method = 'distance'; >> cfg.grad = avg_words.grad; >> cfg.neighbours = ft_prepare_neighbours(cfg_neighb, >> dataMuti21_pictures); >> avg_words_planar = ft_megplanar(cfg, dataMuti21_words); >> avg_pictures_planar = ft_megplanar(cfg, dataMuti21_pictures); >> >> >> HERE IS WHERE I GET THE ERROR: >> ??? Error using ==> ft_checkdata at 359 >> This function requires ctf151, ctf275, bti148, bti248, itab153, >> yokogawa160 or yokogawa64 data as input, but you are giving >> neuromag306 data. >> >> Error in ==> ft_megplanar at 107 >> data = ft_checkdata(data, 'datatype', {'raw' 'freq'}, 'feedback', >> 'yes', 'hassampleinfo', 'yes', 'ismeg', 'yes', 'senstype', >> {'ctf151', 'ctf275', 'bti148', 'bti248', 'itab153', 'yokogawa160', >> 'yokoga >> >> >> Can't i use neuromag306 data type sens for this function? any >> solution? THANKS IN ADVANCE >> >> Ion > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From Hanneke.vanDijk at med.uni-duesseldorf.de Thu Feb 23 10:51:00 2012 From: Hanneke.vanDijk at med.uni-duesseldorf.de (Hanneke.vanDijk at med.uni-duesseldorf.de) Date: Thu, 23 Feb 2012 10:51:00 +0100 Subject: [FieldTrip] [Fieldtrip] ft_megplanar problem for planar gradient calculation Message-ID: <72E993C35FB11743B79FF9286E5B6D8B029F8C31@Mail2-UKD.VMED.UKD> Dear Ion, If your ultimate goal is to combine the horizontal and vertical gradients you can do that later (after ft_timelockanalysis or ft_freqanalysis) using ft_combineplanar. You can skip the ft_megplanar step because the neuromag system already has planar gradiometers. I have done this numerous times and it works perfectly! Hope this helps, Hanneke __________________________________________ Dr. Hanneke van Dijk http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html Institute for Clinical Neuroscience, Heinrich Heine Universität Düsseldorf, Germany Hanneke.vanDijk at med.uni-duesseldorf.de Tel. +49 (0) 211 81 13074 __________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.reuderink at donders.ru.nl Thu Feb 23 13:27:35 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Thu, 23 Feb 2012 13:27:35 +0100 Subject: [FieldTrip] A question In-Reply-To: References: Message-ID: Further, it seems that the data is also scaled automatically, see http://code.google.com/p/fieldtrip/source/browse/trunk/ft_componentanalysis.m?spec=svn5313&r=5313#271 . Best, Boris On Thu, Feb 16, 2012 at 12:39 PM, Stephen Whitmarsh wrote: > Dear All, > > All true, except that ICA implemented by FT does demean the data > before unmixing by default. Use cfg.demean = 'no' if you don't want > to. > > cheers, > stephen > > On 16 February 2012 12:35, Stephen Politzer-Ahles > wrote: >> Hi Shayda, >> >> FieldTrip does not apply a filter by default, and I am not aware of any >> other 'hidden' transformations that happen. You can specify a filter when >> importing the data with ft_preprocessing(), and there are several different >> kinds of filters available, which will affect your data in different ways-- >> see http://fieldtrip.fcdonders.nl/reference/ft_preprocessing. The best thing >> to do is to import your data without using a filter and, if possible, use >> whatever tool comes with your MEG software to import that raw data into >> MATLAB as well (for example, for CTF this would be ds2txt), then you can >> plot them together to make sure there are no differences--when I have tried >> this with EEG data, fieldtrip hasn't changed them. Of course, if you want to >> use a filter, you can also try several filters (you can either filter within >> your system's software and then import straight to Fieldtrip, or use one of >> Fieldtrip's filters during import) and plot them to see how they affect your >> data. >> >> Best, >> Steve Politzer-Ahles >> >> >>> >>> >>> Message: 2 >>> Date: Wed, 15 Feb 2012 14:19:50 -0600 >>> From: Shayda Malekpour >>> To: fieldtrip at donders.ru.nl >>> Subject: [FieldTrip] A question >>> Message-ID: >>> >>>   >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> >>> Dear All, >>> >>> I am using fieldtrip on MEG data set. >>> I want to know if I do not remove any ICA component,  will the data be >>>  the >>> same as the original data, or is there is a filter somewhere in the >>> software that changes the data? If so how much does it change it (What is >>> their relative difference?) >>> >>> Thanks, >>> >>> Sheida >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: >>> >>> >>> ------------------------------ >>> >>> Message: 3 >>> Date: Thu, 16 Feb 2012 09:28:43 +0100 >>> From: Eelke Spaak >>> To: Email discussion list for the FieldTrip project >>>         >>> Subject: Re: [FieldTrip] A question >>> Message-ID: >>> >>>   >>> Content-Type: text/plain; charset=ISO-8859-1 >>> >>> >>> Dear Sheida, >>> >>> You probably need to provide a bit more information before anyone is >>> able to help you. In general, if you perform ICA, you get out >>> component timecourses and mixing/unmixing matrices. If you keep all >>> your components, and multiply them with the mixing matrix, you should >>> get all your original channel timecourses out again. So: if you don't >>> change the data, the data will not be changed :) >>> >>> Best, >>> Eelke >>> >>> On 15 February 2012 21:19, Shayda Malekpour >>> wrote: >>> > Dear All, >>> > >>> > I am using fieldtrip on MEG data set. >>> > I want to know if I do not remove any ICA component,? will the data be? >>> > the >>> >>> > same as the original data, or is there is a filter somewhere in the >>> > software >>> > that changes the data? If so how much does it change it (What is their >>> > relative difference?) >>> > >>> > Thanks, >>> > >>> > Sheida >>> > _______________________________________________ >>> > fieldtrip mailing list >>> > fieldtrip at donders.ru.nl >>> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> ------------------------------ >>> >>> Message: 4 >>> Date: Thu, 16 Feb 2012 10:36:05 +0100 >>> From: "J?rn M. Horschig" >>> To: Email discussion list for the FieldTrip project >>>         >>> Subject: Re: [FieldTrip] A problem in real-time processing of MEG >>>        signal using field trip buffer >>> Message-ID: <4F3CCE05.4050109 at donders.ru.nl> >>> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" >>> >>> Dear Soheila, >>> >>> we were facing the same problem here. Presumably, there is some problem >>> in the shared memory module that the buffer is using. Right now, >>> however, we could not find out where the error precisely comes from, so >>> our best work around is to restart the computer prior recording and >>> optimize settings, such as channels and sampling/decimation rate of >>> acq2ft. In our lab, we managed to find near-optimal settings, so that >>> the buffer crashes only rarely (actually, I never saw it crashing when >>> the acquisition computer was freshly restarted). Note that a lower >>> number of channels or higher decimation does not mean that it runs more >>> stable.  It seems to be literally a trial-and-error approach :/ >>> >>> In order to track this down further, we need some more information, e.g. >>> what MEG system are you using? What's your sampling rate, how many >>> channels do you put into the buffer, and what's your decimation rate? It >>> would be great if you could send me that information so that we can >>> maybe try to track this down. >>> >>> Best regards, >>> J?rn >>> >>> On 2/14/2012 5:42 PM, Soheila Samiee wrote: >>> > Dear group, >>> > >>> > I use FieldTrip for real-time processing of MEG signals using shared >>> > memory and field trip buffer in a machine other than acquisition >>> > system. I use matlab for reading the buffer and processing the data. >>> > During my data acquisition and sending it to other computer with >>> > /acq2ft/ in linux, I face a problem. After sending some blocks of >>> > data, this message: "/Internal Converter thread does not keep up with >>> > load/" is shown in the terminal of /acq2ft/ and in my matlab session I >>> > see an error : "ERROR: the buffer returned an error (517)". It does >>> > not depend on sampling rate of data in acquisition system. The problem >>> > often solve when I restart the computer which receives the data, but >>> > after some minutes of transferring the data I see the message again. >>> > >>> > Would you please help me in solving this problem? >>> > Best Wishes, >>> > Soheila >>> >>> > >>> > >>> > _______________________________________________ >>> > fieldtrip mailing list >>> > fieldtrip at donders.ru.nl >>> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> -- >>> J?rn M. Horschig >>> PhD Student >>> Donders Institute for Brain, Cognition and Behaviour >>> Centre for Cognitive Neuroimaging >>> Radboud University Nijmegen >>> Neuronal Oscillations Group >>> >>> P.O. Box 9101 >>> NL-6500 HB Nijmegen >>> The Netherlands >>> >>> Contact: >>> E-Mail: jm.horschig at donders.ru.nl >>> Tel:    +31-(0)24-36-68493 >>> Web: http://www.ru.nl/donders >>> >>> Visiting address: >>> Trigon, room 2.30 >>> Kapittelweg 29 >>> NL-6525 EN Nijmegen >>> The Netherlands >>> >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: >>> >>> >>> ------------------------------ >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> End of fieldtrip Digest, Vol 15, Issue 17 >>> ***************************************** >> >> >> >> >> -- >> Stephen Politzer-Ahles >> University of Kansas >> Linguistics Department >> http://www.linguistics.ku.edu/ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl From chrysa.lithari at gmail.com Fri Feb 24 11:08:40 2012 From: chrysa.lithari at gmail.com (Chrysa Lithari) Date: Fri, 24 Feb 2012 12:08:40 +0200 Subject: [FieldTrip] coregistration neuromag Message-ID: Hi to all, I just started using fieldtrip and I have the following question. I have the MRI and the polhemus data for each subject. The MRI is in dicom and I can also transform it to 'analyze' format using SPM. The polhemus data are in fif format, together with the functional data. How can I coregister these two types of data in fieldtrip? I searched in the tutorial and it is mentioned that normally MEG systems come with a software allowing to align MRI with the helmet, e.g. CTF. However, I have worked on Neuromag system and I have not done anything like this. How can I do it in Fieltrip? A step by step (AC-PC points, normalization, segmentation etc) guidance would be very helpful stating the functions I have to use and any precautions I have to consider during this process. Best regards and thanks in advance, Chrysa Lithari -- Chrysa Lithari - PhD candidate in Lab of Medical Informatics, Aristotle University of Thessaloniki, Greece - M.Sc. NeuroInformatics, Unversity of Patras, Greece - B.Sc. Computer Science, Aristotle University of Thessaloniki, Greece -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Fri Feb 24 11:24:26 2012 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Fri, 24 Feb 2012 10:24:26 +0000 Subject: [FieldTrip] coregistration neuromag In-Reply-To: References: Message-ID: Dear Chrysa, If you are using SPM already you could also generate a head model and do coregistration with SPM8 and then use it with Fieldtrip. See SPM manual for details. There are some example functions in the Beamforming toolbox in SPM where you can see how the SPM-Fieldtrip interfacing can be done. Best, Vladimir On Fri, Feb 24, 2012 at 10:08 AM, Chrysa Lithari wrote: > Hi to all, > > I just started using fieldtrip and I have the following question. > > I have the MRI and the polhemus data for each subject. > The MRI is in dicom and I can also transform it to 'analyze' format using > SPM. > The polhemus data are in fif format, together with the functional data. > How can I coregister these two types of data in fieldtrip? > I searched in the tutorial and it is mentioned that normally MEG systems > come with a software allowing to align MRI with the helmet, e.g. CTF. > However, I have worked on Neuromag system and I have not done anything like > this. How can I do it in Fieltrip? > A step by step (AC-PC points, normalization, segmentation etc) guidance > would be very helpful stating the functions I have to use and any > precautions I have to consider during this process. > > Best regards and thanks in advance, > Chrysa Lithari > > -- > Chrysa Lithari > - PhD candidate in Lab of Medical Informatics, Aristotle University of > Thessaloniki, Greece > - M.Sc. NeuroInformatics, Unversity of Patras, Greece > - B.Sc. Computer Science, Aristotle University of Thessaloniki, Greece > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From ole.jensen at donders.ru.nl Sun Feb 26 15:41:36 2012 From: ole.jensen at donders.ru.nl (Ole Jensen) Date: Sun, 26 Feb 2012 15:41:36 +0100 Subject: [FieldTrip] senior researcher position at the Donders Institute Message-ID: <4F4A44A0.4010201@donders.ru.nl> Dear colleagues, I would like to bring your attention to the position below. Alt the best, Ole Jensen http://www.neuosc.com ------------------------ *Senior Researcher for 'Neuronal Oscillations and Networks' (1,0 fte) * *Donders Institute, Centre for Cognitive Neuroimaging* *Vacancy number: 30.01.12* *Closing date: 15 April 2012* *Responsibilities* The Neuronal Oscillation group at the Donders Institute for Brain, Cognition and Behaviour has funding available for a senior researcher position. The position has a strong research component, but also includes additional management and teaching responsibilities. The management tasks involve active participation in structuring the research group, including supervision of MSc and PhD students (who will receive senior authorship where applicable). Further, you will contribute to grant writing. The research responsibilities focus on investigating the role of oscillatory neuronal activity involved in shaping the functional architecture of the working brain. This will be done in the context of advanced cognitive paradigms on attention, perception and memory. There will be a strong focus on the role of phase, network interactions and subcortical structures. You will have the following state-of-the-art equipment to your disposal: MEG, (f)MRI, EEG combined with TMS, and EEG combined with fMRI. A further aim is to link structural (e.g. DTI) and functional measurements. You will also participate in conceptually developing the framework for understanding the functional role of brain oscillations. *Work environment* The Donders Institute for Brain, Cognition and Behaviour consists of the Centre for Cognition, the Centre for Cognitive Neuroimaging and the Centre for Neuroscience. The mission of the Centre for Cognitive Neuroimaging is to conduct cutting-edge fundamental research in cognitive neuroscience. Much of the rapid progress in this field is being driven by the development of complex neuro-imaging techniques for measuring activity in the human working brain - an area in which the Centre plays a leading role. The research themes cover central cognitive functions such as perception, action, control, decision making, attention, memory, language, learning and plasticity. The internationally renowned centre currently hosts more than 100 PhD students and postdoctoral researchers from more than 20 countries, offering a stimulating and multidisciplinary research environment. The centre is equipped with three MRI scanners (7T, 3T, 1.5T), a 275-channel MEG system, an EEG-TMS laboratory, several (MR-compatible) EEG systems, and high-performance computational facilities. English is the lingua franca at the centre. You will work within the Neuronal Oscillations group. *What we expect from you* As a candidate for the position, you should have a PhD degree and several years of experience as postdoctoral researcher in a field related to cognitive neuroscience. Selection criteria will consider the record of published research, familiarity with neuroimaging techniques (fMRI, EEG, MEG, and/or TMS) and supervision experience. Proficiency in oral and written English is a prerequisite. You are expected to work in a team, sharing technical know-how and ideas. *What we have to offer* We offer you: - employment: 1,0 fte; - in addition to the salary: an 8% holiday allowance and an 8.3% end-of-year bonus; - the gross salary will be between EUR3,195 and EUR4,970 (scale 12), depending on experience; - salary scale 11 will apply during the first year; - duration of the contract: 6 years maximum. Are you interested in our excellentemployment conditions ? *Would you like to know more?* Further information on:DCCN Further information on:Neuronal Oscillations group Dr. Ole Jensen Telephone: +31 24 3610884 E-mail:ole.jensen at donders.ru.nl *Applications* Are you interested? It is Radboud University Nijmegen's policy to only accept applications by e-mail. Please send your application,/stating vacancy number 30.01.12/, tovacatures at dpo.ru.nl , for the attention of Dr. Ole Jensen, before 15 April 2012. For more information on the application procedure: +31 24 3611173 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tessa.vanleeuwen at fcdonders.ru.nl Mon Feb 27 10:33:50 2012 From: tessa.vanleeuwen at fcdonders.ru.nl (Tessa van Leeuwen) Date: Mon, 27 Feb 2012 10:33:50 +0100 (CET) Subject: [FieldTrip] adapting leadfields after PCA/ICA Message-ID: <1030785558.11966.1330335230620.JavaMail.root@draco.zimbra.ru.nl> Dear FieldTrip users, To save trials I plan on using ICA to remove eog artifacts from my MEG dataset. Because of the large number of channels (271) and limited trial-time (about 300 trials of 1.1 s in each run), we will most likely limit the number of possible components using PCA. The combined PCA/ICA data-cleaning step will have consequences for source reconstruction approaches that we would like to apply to the data later on, e.g. beamforming. When ICA components representing eyeblink artifacts have been removed from the data, how can the leadfield for source reconstruction be adapted to account for the alterations to the data? If anyone has more information about how to do this or can refer me to papers implementing such a pipeline, that would be highly appreciated. Thank you very much in advance for any tips. Best wishes, Tessa van Leeuwen From jan.schoffelen at donders.ru.nl Mon Feb 27 11:14:48 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 27 Feb 2012 11:14:48 +0100 Subject: [FieldTrip] adapting leadfields after PCA/ICA In-Reply-To: <1030785558.11966.1330335230620.JavaMail.root@draco.zimbra.ru.nl> References: <1030785558.11966.1330335230620.JavaMail.root@draco.zimbra.ru.nl> Message-ID: <9E6F733E-B395-486E-907F-C60674592371@donders.ru.nl> Hi Tessa, I imagine that you use ft_componentanalysis and ft_rejectcomponent sequentially in order to remove the eye blink topographies. If you use the data.grad in the output to ft_rejectcomponent for the computation of the leadfields you should be fine. The balancing matrix grad.tra will contain the information that will be used for the correction of the leadfields. Best wishes, Jan-Mathijs On Feb 27, 2012, at 10:33 AM, Tessa van Leeuwen wrote: > Dear FieldTrip users, > > To save trials I plan on using ICA to remove eog artifacts from my MEG dataset. Because of the large number of channels (271) and limited trial-time (about 300 trials of 1.1 s in each run), we will most likely limit the number of possible components using PCA. > > The combined PCA/ICA data-cleaning step will have consequences for source reconstruction approaches that we would like to apply to the data later on, e.g. beamforming. When ICA components representing eyeblink artifacts have been removed from the data, how can the leadfield for source reconstruction be adapted to account for the alterations to the data? > If anyone has more information about how to do this or can refer me to papers implementing such a pipeline, that would be highly appreciated. > > Thank you very much in advance for any tips. > > Best wishes, > Tessa van Leeuwen > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tessa.vanleeuwen at fcdonders.ru.nl Mon Feb 27 12:20:49 2012 From: tessa.vanleeuwen at fcdonders.ru.nl (Tessa van Leeuwen) Date: Mon, 27 Feb 2012 12:20:49 +0100 (CET) Subject: [FieldTrip] adapting leadfields after PCA/ICA In-Reply-To: <9E6F733E-B395-486E-907F-C60674592371@donders.ru.nl> Message-ID: <1972515496.15972.1330341648951.JavaMail.root@draco.zimbra.ru.nl> Hi Jan-Mathijs, Thank you for this quick and informative reply; we indeed use ft_componentanalysis and ft_rejectcomponent sequentially. I will make sure to save the grad structures for the later source analysis. Great! Thank you again, best, Tessa ----- "jan-mathijs schoffelen" wrote: > From: "jan-mathijs schoffelen" > To: "Email discussion list for the FieldTrip project" > Sent: Monday, February 27, 2012 11:14:48 AM > Subject: Re: [FieldTrip] adapting leadfields after PCA/ICA > > Hi Tessa, > I imagine that you use ft_componentanalysis and ft_rejectcomponent sequentially in order to remove the eye blink topographies. If you use the data.grad in the output to ft_rejectcomponent for the computation of the leadfields you should be fine. The balancing matrix grad.tra will contain the information that will be used for the correction of the leadfields. > Best wishes, > Jan-Mathijs > > On Feb 27, 2012, at 10:33 AM, Tessa van Leeuwen wrote: Dear FieldTrip users, > > To save trials I plan on using ICA to remove eog artifacts from my MEG dataset. Because of the large number of channels (271) and limited trial-time (about 300 trials of 1.1 s in each run), we will most likely limit the number of possible components using PCA. > > The combined PCA/ICA data-cleaning step will have consequences for source reconstruction approaches that we would like to apply to the data later on, e.g. beamforming. When ICA components representing eyeblink artifacts have been removed from the data, how can the leadfield for source reconstruction be adapted to account for the alterations to the data? > If anyone has more information about how to do this or can refer me to papers implementing such a pipeline, that would be highly appreciated. > > Thank you very much in advance for any tips. > > Best wishes, > Tessa van Leeuwen > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > Jan-Mathijs Schoffelen, MD PhD > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From max-philipp.stenner at med.ovgu.de Mon Feb 27 17:02:32 2012 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Mon, 27 Feb 2012 16:02:32 +0000 Subject: [FieldTrip] spm_eeg_ft2spm Message-ID: Dear fieldtrippers, I am trying to convert preprocessed/epoched fieldtrip data to spm8 using spm_eeg_ft2spm (for VB-ECD source analysis). I derived volume conduction models for my participants using spm_eeg_convert on data (that was not preprocessed/epoched) a while ago without encountering major problems. spm_eeg_ft2spm, however, requires an input argument "filename", for which I have tried various definitions (a result-filename, the original ft-datafile and filenames both with and without .dat of the same session of the spm_eeg_convert output). As I am not familiar with file_arrays and find little help within the function scripts, I was wondering whether anyone could tell me the (probably simple) solution to overcome the error 'mat2file' Cant open file. What does spm_eeg_ft2spm require as "filename" input? I am using fieldtrip-20111130 on a Windows7 PC. Thanks a lot, best Max From litvak.vladimir at gmail.com Mon Feb 27 17:18:37 2012 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Mon, 27 Feb 2012 16:18:37 +0000 Subject: [FieldTrip] spm_eeg_ft2spm In-Reply-To: References: Message-ID: <712F7AE2-5CF6-46D1-BEF3-AB699031DCD7@gmail.com> Hi Max, filename is the name for the new SPM dataset that you are generating. Not sure how volume conduction models are relevant here. Perhaps since we sit in the same building it'd be easier if you come to talk to me directly. Fieldtrip mailing list is not quite relevant for these issues as they are more SPM-related. Best, Vladimir On 27 Feb 2012, at 16:02, "Stenner, Max-Philipp" wrote: > Dear fieldtrippers, > > > > I am trying to convert preprocessed/epoched fieldtrip data to spm8 using spm_eeg_ft2spm (for VB-ECD source analysis). > > > > I derived volume conduction models for my participants using spm_eeg_convert on data (that was not preprocessed/epoched) a while ago without encountering major problems. spm_eeg_ft2spm, however, requires an input argument "filename", for which I have tried various definitions (a result-filename, the original ft-datafile and filenames both with and without .dat of the same session of the spm_eeg_convert output). As I am not familiar with file_arrays and find little help within the function scripts, I was wondering whether anyone could tell me the (probably simple) solution to overcome the error > > > > 'mat2file' Cant open file. > > > > What does spm_eeg_ft2spm require as "filename" input? > > > > I am using fieldtrip-20111130 on a Windows7 PC. > > > > Thanks a lot, > > best > > Max > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From s.bogels at psy.gla.ac.uk Tue Feb 28 13:12:47 2012 From: s.bogels at psy.gla.ac.uk (=?ISO-8859-1?Q?Sara_B=F6gels?=) Date: Tue, 28 Feb 2012 12:12:47 +0000 Subject: [FieldTrip] MNE: sourcespace and volume aligned? Message-ID: <4F4CC4BF.9030003@psy.gla.ac.uk> Hi all, I am working my way through the MNE tutorial and plotted the mesh and vol on top of each other at the end of the Freesurfer and MNE suite steps to check whether they are aligned. The volume seems to fit quite well into the mesh but is a bit smaller (see attached figures), but definitely not a factor 10. However, from the figure (5) in the tutorial, it seems as if the mesh has to be exactly on top of the volume. Does my plot show that the two are misaligned? If so, what might be the problem? I tried to use ft_determine_coordsys on the vol, but that gives me the error message: 'unknown units (dm)'. If I use it on the sourcespace I get the output that the units are 'cm'. Any help is appreciated. Thank you, Sara Bögels -------------- next part -------------- A non-text attachment was scrubbed... Name: mesh_vol_plot2.jpg Type: image/jpeg Size: 135822 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mesh_vol_plot.jpg Type: image/jpeg Size: 104188 bytes Desc: not available URL: From Lilla.Magyari at mpi.nl Tue Feb 28 14:52:55 2012 From: Lilla.Magyari at mpi.nl (Magyari, Lilla) Date: Tue, 28 Feb 2012 14:52:55 +0100 Subject: [FieldTrip] MNE: sourcespace and volume aligned? In-Reply-To: <4F4CC4BF.9030003@psy.gla.ac.uk> References: <4F4CC4BF.9030003@psy.gla.ac.uk> Message-ID: <4F4CDC37.6000504@mpi.nl> hi Sara, I think the alignment looks just good. The volume conductor is made from the (inside) skull surface, so it is a bit bigger indeed than the sourcespace. For me, it seems that there is also space between the vol and the sourcespace on the picture in the tutorial, but it is more difficult to see because it is colored. Probably, it wasn't plot with exactly the same piece of code than what is indicate above it. About the error message. I am wondering which version of Fieldtrip are you using? Because I had similar problems with my units when I used an earlier version of FieldTrip where the ft_convert_unit function worked a bit differently than now. In any case, we are simplifying this anatomical preprocessing pipeline (all things that you do in FieldTrip before using FreeSurfer) right now, so you can see the new version of the tutorial in a few days. Best, Lilla Sara Bögels wrote: > Hi all, > > I am working my way through the MNE tutorial and plotted the mesh and > vol on top of each other at the end of the Freesurfer and MNE suite > steps to check whether they are aligned. The volume seems to fit quite > well into the mesh but is a bit smaller (see attached figures), but > definitely not a factor 10. However, from the figure (5) in the > tutorial, it seems as if the mesh has to be exactly on top of the > volume. Does my plot show that the two are misaligned? If so, what might > be the problem? > > I tried to use ft_determine_coordsys on the vol, but that gives me the > error message: 'unknown units (dm)'. If I use it on the sourcespace I > get the output that the units are 'cm'. > > Any help is appreciated. > > Thank you, > Sara Bögels > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Andrew.Dykstra at med.uni-heidelberg.de Tue Feb 28 17:34:59 2012 From: Andrew.Dykstra at med.uni-heidelberg.de (Andrew R. Dykstra) Date: Tue, 28 Feb 2012 17:34:59 +0100 Subject: [FieldTrip] getting started with Neuromag 122 data Message-ID: Hi everyone, I'm new to Fieldtrip and would like to use it to process data collected on a Neuromag 122 system. However, I'm running into some fairly simple issues with regard to reading header information and events. Regarding header information, it seems that fieldtrip can read the fif file's header and raw data, but some fields in the header are not assigned correctly. For example, hdr.chantype returns 'unknown' for all channels in the data set (whereas they should be either 'meg_planar ' or trigger lines). Also, hdr.grad returns empty arrays. Regarding reading events, I read Yang Zhang's solution of using mne_make_combined_ event_file.m from the MNE stream and manually creating the event structure (from this list on Jan 8, 2010: http://mailman.science.ru.nl/pipermail/fieldtrip/2010-January/002551.html). This will should also work for me, but I was wondering if there is now a more streamlined way of accomplishing this in Fieldtrip, especially for fif files either containing or associated with an event list based on a text file with sample numbers, latencies, and event types. I did not see an option in ft_read_event to do this. Any suggestions would be much appreciated. Andy Andrew R. Dykstra, PhD Auditory Cognition Lab Neurologie und Poliklinik Universitätsklinikum Heidelberg Im Neuenheimer Feld 400 69120 Heidelberg "How small the cosmos. How paltry and puny compared to human consciousness . . . to a single individual recollection." - Vladimir Nabokov -------------- next part -------------- An HTML attachment was scrubbed... URL: From ali at cs.ru.nl Wed Feb 29 21:10:54 2012 From: ali at cs.ru.nl (Ali Bahramisharif) Date: Wed, 29 Feb 2012 21:10:54 +0100 Subject: [FieldTrip] question about MNI alignment Message-ID: Dear Fieldtrip users, I want to create MNI-aligned grids in individual head-space, and I follow the guidelines in : http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space?s[]=template&s[]=grid I do not know how old this page is, but I noticed that for example in the current version "cfg.coordinates" should be "cfg.coordsys". I have the following problems: 1- When I run "ft_plot_mesh(template_grid);", I get a cubic grid which is apparently different from the one shown in the page. 2- When I run, ft_plot_vol(hdm), it does not seem to be aligned to "ft_plot_sens(ft_read_sens(dataset{i}));" I checked my segmented volumes, and they seem to be fine, and I did not need to run flipdim. I am wondering whether my segmented data is correct or it should be flipped somewhere. Please let me know if anybody knows how to resolve this problem. Cheers, Ali From mcoskun at mail.uh.edu Wed Feb 1 13:55:15 2012 From: mcoskun at mail.uh.edu (Mehmet-Akif Coskun) Date: Wed, 01 Feb 2012 06:55:15 -0600 Subject: [FieldTrip] Error -> ft_databrowser Message-ID: <7220b947bb8f3.4f28e1d3@mail.uh.edu> Dear Fieldtrippers, I am encountering a strange error while i try to use ft_databrowser. The error code is as below. I have never seen this error earlier. I used ft_databrowser many times and its only last 2 days that i am getting the error. I downloaded a newer version of fieldtrip (fieldtrip-20120130) and used the newer version but still the same error. Strangely, i dont get this error when i tried with other computers (same matlab version (R2010a), same operating system (windows 7) on both computers. Has anyone got this error before? what may cause this error? fieldtrip version 20120130, matlab version R2010a, operating system windows 7. Thanks in advance for any suggestions. ??? Error using ==> ft_fetch_data at 57 data does not contain a consistent trial definition, fetching data is not possible Error in ==> ft_databrowser>redraw_cb at 1159 art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', endsample); Error in ==> ft_databrowser at 535 redraw_cb(h); -------------- next part -------------- An HTML attachment was scrubbed... URL: From Ulrich.Pomper at charite.de Wed Feb 1 14:44:44 2012 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Wed, 1 Feb 2012 14:44:44 +0100 Subject: [FieldTrip] Defining cfg.neighbourdist at source level In-Reply-To: References: <4F22C422.4080906@charite.de> <4F26B91E.2050200@donders.ru.nl> <4F26BE42.5030204@charite.de> Message-ID: <4F2941CC.6030609@charite.de> Dear Robert and Stephan, Thank you for your replies. I guess I use what Robert called the 'regular' 3D grid, but I'm not quite sure. The structures of my headmodel and leadfield matrix are the following (based on data from a BEM standard file): vol = bnd: [1x3 struct] cond: [0.3300 0.0041 0.3300] mat: [3000x3000 double] type: 'dipoli' ldf = xgrid: [-65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68] ygrid: [-107 -100 -93 -86 -79 -72 -65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68 75] zgrid: [-52 -45 -38 -31 -24 -17 -10 -3 4 11 18 25 32 39 46 53 60 67 74 81] dim: [20 27 20] pos: [10800x3 double] inside: [1x5739 double] outside: [1x5061 double] leadfield: {1x10800 cell} cfg: [1x1 struct] In any case, I still don't quite understand how to calculate the neighbours to each voxel. By saying that the "neighbours are trivial to find and you do not have to specify a structure", do you mean that I don't need to define the cfg.neighbours property at all (given that I do use a regular 3D grid)? Thanks again for your help, cheers, Ulrich On 31.01.2012 21:48, smoratti at psi.ucm.es wrote: Dear Robert, To do clustering on a 3D source surface I always had to "trick" field trip and squeezed the 3D source surface data into a ERF structure treating the 3D surface points as sensors. Then by triangulation I found the neighbors. However, if there is a more elegant method implemented in ft_sourcestatistc, I would be very interested to know how to do it. Where can I find some hints on that? Best, Stephan ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 28223 Pozuelo de Alarcón (Madrid) Spain and Center for Biomedical Technology Laboratory for Cognitive and Computational Neuroscience Parque Científico y Tecnológico de la Universidad Politecnica de Madrid Campus Montegancedo 28223 Pozuelo de Alarcón (Madrid) Spain email: smoratti at psi.ucm.es Tel.: +34 679219982 El 31/01/2012, a las 15:37, Robert Oostenveld escribió: Dear Ulrich If your source locations are defined on a regular 3D grid that can be represented as volume, then the neighbours are trivial to find and you do not have to specify a structure for the neighbours. If you have done source reconstruction on a 3D folded cortical sheet that is defined by a triangulated surface, then it is also possible to cluster along the surface. I don't know the details for the cortical sheet clustering from the top of my head, if you are interested please let me know and I'll look them up. best Robert On 30 Jan 2012, at 16:58, Pomper, Ulrich wrote: Dear Jörn, Thanks for you reply. I did mean source-level, so like you said, I am trying to define the neighbouring voxels for each voxel. As far as I understand, leaving cfg.neighbours blank means that the clustering is done over the time and frequency dimensions only, not over space. The FT help reads: %If you specify an empty neighbourhood structure, clustering will only be done in frequency and time (if available) and not over neighbouring channels. Has anybody done clustering in source space using all three dimensions and could explain how this works? Cheers, Ulrich _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus -------------- next part -------------- An HTML attachment was scrubbed... URL: From MEpstein at NKI.RFMH.ORG Wed Feb 1 20:44:47 2012 From: MEpstein at NKI.RFMH.ORG (Epstein, Michael) Date: Wed, 1 Feb 2012 14:44:47 -0500 Subject: [FieldTrip] rereferencing after preproc Message-ID: <2586A1048152BE4D861E64A98700AD420A601176@nki-mail.NKI.rfmh.org> Hi all, I'm trying to analyze a dataset using multiple reference points - is there a way to re-reference the data after the whole preprocessing step? I'm using ft_rejectvisual to clean the data, so I want to reference after that, in order to preserve as much consistency between the two sets as is possible. I was trying to use ft_preproc_rereference to achieve this goal, but that only takes in channel x time data, not trial data or freq data. Is there a different way to rereference? Thanks, -Michael Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Wed Feb 1 21:00:33 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Wed, 1 Feb 2012 21:00:33 +0100 Subject: [FieldTrip] rereferencing after preproc In-Reply-To: <2586A1048152BE4D861E64A98700AD420A601176@nki-mail.NKI.rfmh.org> References: <2586A1048152BE4D861E64A98700AD420A601176@nki-mail.NKI.rfmh.org> Message-ID: Hi Michael, Probably ft_preprocessing with the options cfg.reref = 'yes' and cfg.refchannel = '' is what you are looking for. ft_preproc_rereference is a lower-level FieldTrip function, which indeed operates directly on a channel x time matrix. ft_preprocessing contains all the necessary bookkeeping wrappers around ft_preproc_* so that you can conveniently apply the preprocessing functions on FieldTrip-style data structures. Hope this helps. Eelke On 1 February 2012 20:44, Epstein, Michael wrote: > Hi all, > > > > I’m trying to analyze a dataset using multiple reference points – is there a > way to re-reference the data after the whole preprocessing step? I’m using > ft_rejectvisual to clean the data, so I want to reference after that, in > order to preserve as much consistency between the two sets as is possible. > > > > I was trying to use ft_preproc_rereference to achieve this goal, but that > only takes in channel x time data, not trial data or freq data. Is there a > different way to rereference? > > > > Thanks, > > > > -Michael > > > > ________________________________ > Conserve Resources. Print only when necessary. > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended > recipient. It may contain confidential information which is legally > privilegedor otherwise protected by law. If you received this e-mail in > error or from someone who is not authorized to send it to you, you are > strictly prohibited from reviewing, using, disseminating, distributing or > copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN > E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your > cooperation. > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From MEpstein at NKI.RFMH.ORG Wed Feb 1 21:05:49 2012 From: MEpstein at NKI.RFMH.ORG (Epstein, Michael) Date: Wed, 1 Feb 2012 15:05:49 -0500 Subject: [FieldTrip] rereferencing after preproc In-Reply-To: References: <2586A1048152BE4D861E64A98700AD420A601176@nki-mail.NKI.rfmh.org> Message-ID: <2586A1048152BE4D861E64A98700AD420A601194@nki-mail.NKI.rfmh.org> Oh I see - I didn't realize you could use that function on data you had already preprocessed once. Thank you, that's useful. -Michael -----Original Message----- From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Eelke Spaak Sent: Wednesday, February 01, 2012 3:01 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] rereferencing after preproc Hi Michael, Probably ft_preprocessing with the options cfg.reref = 'yes' and cfg.refchannel = '' is what you are looking for. ft_preproc_rereference is a lower-level FieldTrip function, which indeed operates directly on a channel x time matrix. ft_preprocessing contains all the necessary bookkeeping wrappers around ft_preproc_* so that you can conveniently apply the preprocessing functions on FieldTrip-style data structures. Hope this helps. Eelke On 1 February 2012 20:44, Epstein, Michael wrote: > Hi all, > > > > I'm trying to analyze a dataset using multiple reference points - is there a > way to re-reference the data after the whole preprocessing step? I'm using > ft_rejectvisual to clean the data, so I want to reference after that, in > order to preserve as much consistency between the two sets as is possible. > > > > I was trying to use ft_preproc_rereference to achieve this goal, but that > only takes in channel x time data, not trial data or freq data. Is there a > different way to rereference? > > > > Thanks, > > > > -Michael > > > > ________________________________ > Conserve Resources. Print only when necessary. > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended > recipient. It may contain confidential information which is legally > privilegedor otherwise protected by law. If you received this e-mail in > error or from someone who is not authorized to send it to you, you are > strictly prohibited from reviewing, using, disseminating, distributing or > copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN > E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your > cooperation. > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. From inieuwenhuis at berkeley.edu Wed Feb 1 21:20:20 2012 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Wed, 01 Feb 2012 12:20:20 -0800 Subject: [FieldTrip] rereferencing after preproc In-Reply-To: <2586A1048152BE4D861E64A98700AD420A601194@nki-mail.NKI.rfmh.org> References: <2586A1048152BE4D861E64A98700AD420A601176@nki-mail.NKI.rfmh.org> <2586A1048152BE4D861E64A98700AD420A601194@nki-mail.NKI.rfmh.org> Message-ID: <4F299E84.7040804@berkeley.edu> Hi, just a little addition. You mention freq data, but you can't re-reference after freq analysis. Has to take place before. (Just in case you meant that) Good luck, Ingrid -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 On 2/1/2012 12:05 PM, Epstein, Michael wrote: > Oh I see - I didn't realize you could use that function on data you had > already preprocessed once. > > Thank you, that's useful. > > -Michael > > -----Original Message----- > From: fieldtrip-bounces at donders.ru.nl > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Eelke Spaak > Sent: Wednesday, February 01, 2012 3:01 PM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] rereferencing after preproc > > Hi Michael, > > Probably ft_preprocessing with the options cfg.reref = 'yes' and > cfg.refchannel = '' is what you are looking for. > > ft_preproc_rereference is a lower-level FieldTrip function, which > indeed operates directly on a channel x time matrix. ft_preprocessing > contains all the necessary bookkeeping wrappers around ft_preproc_* so > that you can conveniently apply the preprocessing functions on > FieldTrip-style data structures. > > Hope this helps. > > Eelke > > On 1 February 2012 20:44, Epstein, Michael > wrote: >> Hi all, >> >> >> >> I'm trying to analyze a dataset using multiple reference points - is > there a >> way to re-reference the data after the whole preprocessing step? I'm > using >> ft_rejectvisual to clean the data, so I want to reference after that, > in >> order to preserve as much consistency between the two sets as is > possible. >> >> >> I was trying to use ft_preproc_rereference to achieve this goal, but > that >> only takes in channel x time data, not trial data or freq data. Is > there a >> different way to rereference? >> >> >> >> Thanks, >> >> >> >> -Michael >> >> >> >> ________________________________ >> Conserve Resources. Print only when necessary. >> >> IMPORTANT NOTICE: This e-mail is meant only for the use of the > intended >> recipient. It may contain confidential information which is legally >> privilegedor otherwise protected by law. If you received this e-mail > in >> error or from someone who is not authorized to send it to you, you are >> strictly prohibited from reviewing, using, disseminating, distributing > or >> copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY > RETURN >> E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your >> cooperation. >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Conserve Resources. Print only when necessary. > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 From jm.horschig at donders.ru.nl Thu Feb 2 09:30:37 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 02 Feb 2012 09:30:37 +0100 Subject: [FieldTrip] rereferencing after preproc In-Reply-To: <4F299E84.7040804@berkeley.edu> References: <2586A1048152BE4D861E64A98700AD420A601176@nki-mail.NKI.rfmh.org> <2586A1048152BE4D861E64A98700AD420A601194@nki-mail.NKI.rfmh.org> <4F299E84.7040804@berkeley.edu> Message-ID: <4F2A49AD.1050303@donders.ru.nl> Hi, another addition: ft_apply_montage is doing the same (ft_preprocessing also calls this function), but it also changes the labels. This is useful when, for example, wanting to construct bipolar channels like hEOG and vEOG. Best, Jörn On 2/1/2012 9:20 PM, Ingrid Nieuwenhuis wrote: > Hi, just a little addition. You mention freq data, but you can't > re-reference after freq analysis. Has to take place before. (Just in > case you meant that) > Good luck, > Ingrid > -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From sysoevao at psychiatry.wustl.edu Thu Feb 2 23:49:41 2012 From: sysoevao at psychiatry.wustl.edu (Sysoeva, Olga Vladimirovna) Date: Thu, 2 Feb 2012 16:49:41 -0600 Subject: [FieldTrip] channels interpolation Message-ID: <76DC57362137854CB9592B496182D5FA09D909A83B@wusmexmbx2.medpriv.wucon.wustl.edu> Dear group, Am I doing something wrong or is it a bug? I needed to do some bad channel interpolation for my dataset (epoched data). So I found out that there is a ft_channel_repair function. And I tried to use it in the following way. cfg = []; cfg.method = 'distance'%, 'triangulation' or 'template' (default = 'distance') cfg.neighbourdist = 4; % number, maximum distance between neighbouring sensors (only for 'distance') cfg.layout = 'C:\Matlab_programs\Fieldtrip\My_Fieldtrip\EEG1010_modified32.lay'; [neighbours] = ft_prepare_neighbours(cfg, data) cfg = []; cfg.badchannel = {'F4'};%cell-array, see FT_CHANNELSELECTION for details cfg.neighbours = neighbours; [interp] = ft_channelrepair(cfg, data) But I'm getting the error ??? Reference to non-existent field 'pnt'. It seems to me that I'm not preparing the sensor(electrode) structure correctly, but I couldn't find mistake. I do follow the tutorial. There are a link that I need to prepare the electrode structure as in ft_fetch_sens function, but I my version of Fieldtrip I do not have this function. I'll appreciate any help, Best Regards, Olga. __________________________________________________________ Olga Sysoeva, Research Associate, PhD Psychiatry Department, Washington University School of Medicine Campus Box 8134 660 South Euclid Ave Saint Louis, MO 63110-9909 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Fri Feb 3 09:50:26 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Fri, 03 Feb 2012 09:50:26 +0100 Subject: [FieldTrip] channels interpolation In-Reply-To: <76DC57362137854CB9592B496182D5FA09D909A83B@wusmexmbx2.medpriv.wucon.wustl.edu> References: <76DC57362137854CB9592B496182D5FA09D909A83B@wusmexmbx2.medpriv.wucon.wustl.edu> Message-ID: <4F2B9FD2.7070003@donders.ru.nl> Dear Olga, indeed that there is a problem with the sensor definition. In addition to specifying neighbours, the channelrepair function needs to know the distance between channels. Therefore, you need to provide a definition of the sensor position additionally. However, the error message you get is not the one you should see - there should be one that is more elaborate and intuitively understandable ;) Could you send me (outside the mailinglist) the whole error message, including the lines where this goes wrong? I will then fix the problem asap. Btw, the ft_fetch_sens function has recently been moved to the FieldTrip/private folder, that means Matlab prevents you from seeing or calling the function directly, but if you just cd to that directory, you can access the file. Also, I just changed the error message that you should have seen to be more elaborate (will be available from tomorrow on). Best, Jörn On 2/2/2012 11:49 PM, Sysoeva, Olga Vladimirovna wrote: > > Dear group, > > Am I doing something wrong or is it a bug? > > I needed to do some bad channel interpolation for my dataset (epoched > data). > > So I found out that there is a ft_channel_repair function. And I tried > to use it in the following way. > > cfg = []; > > cfg.method = 'distance'%, 'triangulation' or 'template' > (default = 'distance') > > cfg.neighbourdist = 4; % number, maximum distance between neighbouring > sensors (only for 'distance') > > cfg.layout = > 'C:\Matlab_programs\Fieldtrip\My_Fieldtrip\EEG1010_modified32.lay'; > > [neighbours] = ft_prepare_neighbours(cfg, data) > > cfg = []; > > cfg.badchannel = {'F4'};%cell-array, see FT_CHANNELSELECTION for > details > > cfg.neighbours = neighbours; > > [interp] = ft_channelrepair(cfg, data) > > But I'm getting the error ??? Reference to non-existent field 'pnt'. > > It seems to me that I'm not preparing the sensor(electrode) structure > correctly, but I couldn't find mistake. I do follow the tutorial. > There are a link that I need to prepare the electrode structure as in > ft_fetch_sens function, but I my version of Fieldtrip I do not have > this function. > > I'll appreciate any help, > > Best Regards, > > Olga. > > __________________________________________________________ > > Olga Sysoeva, > > Research Associate, PhD > > Psychiatry Department, > > Washington University School of Medicine > > Campus Box 8134 > > 660 South Euclid Ave > > Saint Louis, MO 63110-9909 > > > ------------------------------------------------------------------------ > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying or the taking of any action in reliance on > the contents of this information is strictly prohibited. If you have > received this email in error, please immediately notify the sender via > telephone or return mail. > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From chadbircher at yahoo.com Fri Feb 3 17:06:45 2012 From: chadbircher at yahoo.com (Chad Bircher) Date: Fri, 3 Feb 2012 08:06:45 -0800 (PST) Subject: [FieldTrip] Pthread install Message-ID: <1328285205.47747.YahooMailNeo@web162006.mail.bf1.yahoo.com> I am trying to install the peer directories, but cannot run peercompile('VC') on my Windows7 64bit machine using Microsoft Visual C++ express 2012.  I am getting an error that it cannot find pthread.h  I am not a systems developer, and do not know how to install this correctly.  Every attempt I have made still does not allow peercompile to run. How do I install pthread on this sort of a system? Thank you Chad -------------- next part -------------- An HTML attachment was scrubbed... URL: From Ulrich.Pomper at charite.de Mon Feb 6 14:05:38 2012 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Mon, 6 Feb 2012 14:05:38 +0100 Subject: [FieldTrip] Fwd: Re: Defining cfg.neighbourdist at source level In-Reply-To: <2594dc0d96864f1a8d49694602e55bce@EXCCAHT-2.mail.uke.ads> References: <2594dc0d96864f1a8d49694602e55bce@EXCCAHT-2.mail.uke.ads> Message-ID: <4F2FD022.3000407@charite.de> Dear fieldtrippers, I'm still in need of an advise on the issue below. Any help would be greatly appreciated!! Dear Robert and Stephan, Thank you for your replies. I guess I use what Robert called the 'regular' 3D grid, but I'm not quite sure. The structures of my headmodel and leadfield matrix are the following (based on data from a BEM standard file): vol = bnd: [1x3 struct] cond: [0.3300 0.0041 0.3300] mat: [3000x3000 double] type: 'dipoli' ldf = xgrid: [-65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68] ygrid: [-107 -100 -93 -86 -79 -72 -65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68 75] zgrid: [-52 -45 -38 -31 -24 -17 -10 -3 4 11 18 25 32 39 46 53 60 67 74 81] dim: [20 27 20] pos: [10800x3 double] inside: [1x5739 double] outside: [1x5061 double] leadfield: {1x10800 cell} cfg: [1x1 struct] In any case, I still don't quite understand how to calculate the neighbours to each voxel. By saying that the "neighbours are trivial to find and you do not have to specify a structure", do you mean that I don't need to define the cfg.neighbours property at all (given that I do use a regular 3D grid)? Thanks again for your help, cheers, Ulrich On 31.01.2012 21:48, smoratti at psi.ucm.es wrote: Dear Robert, To do clustering on a 3D source surface I always had to "trick" field trip and squeezed the 3D source surface data into a ERF structure treating the 3D surface points as sensors. Then by triangulation I found the neighbors. However, if there is a more elegant method implemented in ft_sourcestatistc, I would be very interested to know how to do it. Where can I find some hints on that? Best, Stephan ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 28223 Pozuelo de Alarcón (Madrid) Spain and Center for Biomedical Technology Laboratory for Cognitive and Computational Neuroscience Parque Científico y Tecnológico de la Universidad Politecnica de Madrid Campus Montegancedo 28223 Pozuelo de Alarcón (Madrid) Spain email: smoratti at psi.ucm.es Tel.: +34 679219982 El 31/01/2012, a las 15:37, Robert Oostenveld escribió: Dear Ulrich If your source locations are defined on a regular 3D grid that can be represented as volume, then the neighbours are trivial to find and you do not have to specify a structure for the neighbours. If you have done source reconstruction on a 3D folded cortical sheet that is defined by a triangulated surface, then it is also possible to cluster along the surface. I don't know the details for the cortical sheet clustering from the top of my head, if you are interested please let me know and I'll look them up. best Robert On 30 Jan 2012, at 16:58, Pomper, Ulrich wrote: Dear Jörn, Thanks for you reply. I did mean source-level, so like you said, I am trying to define the neighbouring voxels for each voxel. As far as I understand, leaving cfg.neighbours blank means that the clustering is done over the time and frequency dimensions only, not over space. The FT help reads: %If you specify an empty neighbourhood structure, clustering will only be done in frequency and time (if available) and not over neighbouring channels. Has anybody done clustering in source space using all three dimensions and could explain how this works? Cheers, Ulrich _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus -------------- next part -------------- An HTML attachment was scrubbed... URL: From phc5 at georgetown.edu Tue Feb 7 05:56:09 2012 From: phc5 at georgetown.edu (patrick cox) Date: Mon, 6 Feb 2012 23:56:09 -0500 Subject: [FieldTrip] Computing the system matrix in a the forward model? Message-ID: Hi, I have just started using feildtrip, and I am trying to do some source localization using beamforming. I am working with EEG data and would like to anatomically constrain the forward model, so I am trying out the various BEM methods in fieldtrip. As a first pass I have been using the SPM T1 template, but I also have anatomical scans of my subjects. My problem is that when I try to calculate the model for the volume conductor using most of the methods (openmeeg, dipoli), my vol structure does not contain a vol.mat field (which I believe is the system matrix). The one BEM method that actully returns a vol with a system matrix is the BEMCP method, but the vol.mat file is all NaNs! I have tracked the problem to the calculation of the Cij's, particularly C12 and C21, in the ft_headmodel_bemcp.m which contain a large number of NaN entries. Does anyone have a fix for this, or a advice on how to producing vol structures with system matrices/vol.mat fields using the other BEM methods? Thanks! Patrick Cox -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue Feb 7 11:26:24 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 7 Feb 2012 10:26:24 +0000 Subject: [FieldTrip] Pthread install In-Reply-To: <1328285205.47747.YahooMailNeo@web162006.mail.bf1.yahoo.com> References: <1328285205.47747.YahooMailNeo@web162006.mail.bf1.yahoo.com> Message-ID: Dear Chad All peer functions rely on a single mex file. That mex file implements a TCP server and client in a seperate thread, which allows MATLAB to receive data while at the same time busy with computations. The TCP networking details are slightly different between operating systems. The computers we work with most are unix-bases (linux, os x), therefore those are the ones that we primarily target with out code. Stefan, a former colleague at the Donders has compiled it once on windows32 and 64, but that mex file has not been kept up to date since then. The peer TCP server and client are derived from the FieldTrip buffer (see http://fieldtrip.fcdonders.nl/development/realtime) which is the result of a project to allow MATLAB to do efficient and easy computations on real-time streamed EEG and MEG data. The fieldtrip realtime buffer works well on all operating systems, so as such there is no reason to assume that peer would also not work. The TCP server and the other peer threads (i.e. announce, discover, expire) are all implemented with posix threads, which is the default on unix-like operating systems (linux, os x). On MS Windows there is another threading system, but there is a port of pthreads for windows (see http://sourceware.org/pthreads-win32/). At the time we implemented this stuff, there was only a version available for 32-bit windows, whereas nowadays most Windows computers are 64 bit. Stefan made a 64-bit version of the "ptherads-win32" library himself, that is the one we also use for the fieldtrip buffer. That library and header files can be found in fieldtrip/realtime/buffer/pthreads-win64. It might also be that there is an official release of the pthreads library for win64, if there is, I suggest you use that instead of the fieldtrip version. An alternative might be to use mingw as a compiler: if I recall correctly it also includes pthreads. But then, I don't know how easy or hard it is to use the mingw compiler in combination with MATLAB. hope this helps, Robert PS yet another aspect is the peerslave.exe command line application that allows to start a slave prior to starting MATLAB. Although also for that one Stefan managed to get a version compiled, but I know that that version is buggy. Even the linux version is not 100% stable. At the time Stefan worked with us, it was decided not to spend time on resolving the windows bugs in command-line version. Therefore I suggest that you first focus on getting the mex file to work, and only then start thinking on whether you need the peerslave.exe command-line version. On 3 Feb 2012, at 16:06, Chad Bircher wrote: > I am trying to install the peer directories, but cannot run peercompile('VC') on my Windows7 64bit machine using Microsoft Visual C++ express 2012. I am getting an error that it cannot find pthread.h > I am not a systems developer, and do not know how to install this correctly. Every attempt I have made still does not allow peercompile to run. > How do I install pthread on this sort of a system? > Thank you > Chad > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue Feb 7 11:34:20 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 7 Feb 2012 10:34:20 +0000 Subject: [FieldTrip] Defining cfg.neighbourdist at source level In-Reply-To: <4F2941CC.6030609@charite.de> References: <4F22C422.4080906@charite.de> <4F26B91E.2050200@donders.ru.nl> <4F26BE42.5030204@charite.de> <4F2941CC.6030609@charite.de> Message-ID: <93BEC2B0-B372-4EA9-BE41-1D0606B217FF@donders.ru.nl> Dear Ulrich On 1 Feb 2012, at 13:44, Pomper, Ulrich wrote: > Dear Robert and Stephan, > Thank you for your replies. > I guess I use what Robert called the 'regular' 3D grid, but I'm not quite sure. ... > ldf = > > xgrid: [-65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68] > ygrid: [-107 -100 -93 -86 -79 -72 -65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68 75] > zgrid: [-52 -45 -38 -31 -24 -17 -10 -3 4 11 18 25 32 39 46 53 60 67 74 81] > dim: [20 27 20] > pos: [10800x3 double] ... > > In any case, I still don't quite understand how to calculate the neighbours to each voxel. Yes, you are using a regular 3D grid with dipole positions that are placed at the center of a large number of voxels which jointly fill a cube that spans the head. Just like an MRI. If you look in ldf.pos you will see all positions. Those positions form a 20x27x20 regular grid, with the x-, y, and z-values according to xgrid/ygrid/zgrid. You have a grid spacing of 7mm in each direction. The first positions is [-65 -107 -52] and its neighbours are the grid points that are 7mm to the right, top and front. Just think of it as functional_data = rand(20, 27, 20) i.e. a cube. It is clear for each voxel what the neighbours are. FieldTrip makes use of vectorization, i.e. the 3d matrix with the functional data can also be represented by MATLAB as a vector. functional_data = functional_data(:) What you then get is a vector of length 10800, i.e. matching all the [x y z] positions as they are specified in ldf.pos. > By saying that the "neighbours are trivial to find and you do not have to specify a structure", do you mean that I don't need to define the cfg.neighbours property at all (given that I do use a regular 3D grid)? correct. Robert From Ulrich.Pomper at charite.de Tue Feb 7 11:40:27 2012 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Tue, 7 Feb 2012 11:40:27 +0100 Subject: [FieldTrip] Defining cfg.neighbourdist at source level In-Reply-To: <93BEC2B0-B372-4EA9-BE41-1D0606B217FF@donders.ru.nl> References: <4F22C422.4080906@charite.de> <4F26B91E.2050200@donders.ru.nl> <4F26BE42.5030204@charite.de> <4F2941CC.6030609@charite.de> <93BEC2B0-B372-4EA9-BE41-1D0606B217FF@donders.ru.nl> Message-ID: <4F30FF9B.8080300@charite.de> Thanks a lot Robert, now I get it! Best, Ulrich On 07.02.2012 11:34, Robert Oostenveld wrote: Dear Ulrich On 1 Feb 2012, at 13:44, Pomper, Ulrich wrote: > Dear Robert and Stephan, > Thank you for your replies. > I guess I use what Robert called the 'regular' 3D grid, but I'm not quite sure. ... > ldf = > > xgrid: [-65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68] > ygrid: [-107 -100 -93 -86 -79 -72 -65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68 75] > zgrid: [-52 -45 -38 -31 -24 -17 -10 -3 4 11 18 25 32 39 46 53 60 67 74 81] > dim: [20 27 20] > pos: [10800x3 double] ... > > In any case, I still don't quite understand how to calculate the neighbours to each voxel. Yes, you are using a regular 3D grid with dipole positions that are placed at the center of a large number of voxels which jointly fill a cube that spans the head. Just like an MRI. If you look in ldf.pos you will see all positions. Those positions form a 20x27x20 regular grid, with the x-, y, and z-values according to xgrid/ygrid/zgrid. You have a grid spacing of 7mm in each direction. The first positions is [-65 -107 -52] and its neighbours are the grid points that are 7mm to the right, top and front. Just think of it as functional_data = rand(20, 27, 20) i.e. a cube. It is clear for each voxel what the neighbours are. FieldTrip makes use of vectorization, i.e. the 3d matrix with the functional data can also be represented by MATLAB as a vector. functional_data = functional_data(:) What you then get is a vector of length 10800, i.e. matching all the [x y z] positions as they are specified in ldf.pos. > By saying that the "neighbours are trivial to find and you do not have to specify a structure", do you mean that I don't need to define the cfg.neighbours property at all (given that I do use a regular 3D grid)? correct. Robert _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue Feb 7 11:42:57 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 7 Feb 2012 10:42:57 +0000 Subject: [FieldTrip] Defining cfg.neighbourdist at source level In-Reply-To: <61FDD8CB-F79B-48A6-BC19-015F778A4945@psi.ucm.es> References: <4F22C422.4080906@charite.de> <4F26B91E.2050200@donders.ru.nl> <4F26BE42.5030204@charite.de> <61FDD8CB-F79B-48A6-BC19-015F778A4945@psi.ucm.es> Message-ID: <8AD16232-88F0-4C2E-87FA-03D22928B940@donders.ru.nl> Dear Stephan In fieldtrip/rpivate/clusterstat around line 194 you can see posclusobs = findcluster(reshape(postailobs, [cfg.dim,1]),channeighbstructmat,cfg.minnbchan); that is the section that should get used (the present code still thinks that source is always a 3d regular grid, which is not the case for a surface grid) Furthermore, in ft_prepare_neighbours there is the subfunction "compneighbstructfromtri" that is of relevance. This is a section of the code that needs to be cleaned up and the clustering along the sheet should become a standard feature instead of something that can be managed by a hack. Concrete code suggestions (evt. through bugzilla.fcdonders.nl) are welcome. best Robert On 31 Jan 2012, at 20:48, smoratti at psi.ucm.es wrote: > Dear Robert, > > To do clustering on a 3D source surface I always had to "trick" field trip and squeezed the 3D source surface data into a ERF structure treating the 3D surface points as sensors. Then by triangulation I found the neighbors. However, if there is a more elegant method implemented in ft_sourcestatistc, I would be very interested to know how to do it. Where can I find some hints on that? > > Best, > > Stephan > > ________________________________________________________ > Stephan Moratti, PhD > > see also: http://web.me.com/smoratti/ > > Universidad Complutense de Madrid > Facultad de Psicología > Departamento de Psicología Básica I > Campus de Somosaguas > 28223 Pozuelo de Alarcón (Madrid) > Spain > > and > > Center for Biomedical Technology > Laboratory for Cognitive and Computational Neuroscience > Parque Científico y Tecnológico de la Universidad Politecnica de Madrid > Campus Montegancedo > 28223 Pozuelo de Alarcón (Madrid) > Spain > > > email: smoratti at psi.ucm.es > Tel.: +34 679219982 > > El 31/01/2012, a las 15:37, Robert Oostenveld escribió: > >> Dear Ulrich >> >> If your source locations are defined on a regular 3D grid that can be represented as volume, then the neighbours are trivial to find and you do not have to specify a structure for the neighbours. >> >> If you have done source reconstruction on a 3D folded cortical sheet that is defined by a triangulated surface, then it is also possible to cluster along the surface. I don't know the details for the cortical sheet clustering from the top of my head, if you are interested please let me know and I'll look them up. >> >> best >> Robert >> >> >> >> >> On 30 Jan 2012, at 16:58, Pomper, Ulrich wrote: >> >>> Dear Jörn, >>> Thanks for you reply. I did mean source-level, so like you said, I am trying to define the neighbouring voxels for each voxel. >>> As far as I understand, leaving cfg.neighbours blank means that the clustering is done over the time and frequency dimensions only, not over space. >>> The FT help reads: >>> %If you specify an empty neighbourhood structure, clustering will only be done in frequency and time (if available) and not over neighbouring channels. >>> >>> Has anybody done clustering in source space using all three dimensions and could explain how this works? >>> Cheers, >>> Ulrich >>> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Wed Feb 8 17:14:17 2012 From: lihqih at gmail.com (qi li) Date: Wed, 8 Feb 2012 11:14:17 -0500 Subject: [FieldTrip] coordinate transform Message-ID: Hi, I want to do a coordinate transformation of the sensor positions by knowing the fiducial point(na,lpa,rpa). Is there any function can do this? More specifically I want to know the 3 translational and 3 rotational degree changes between the original coordinate and the changed one. Thanks a lot! Qi From adama.sophie at gmail.com Wed Feb 8 18:03:12 2012 From: adama.sophie at gmail.com (Sophie ADAMA) Date: Wed, 8 Feb 2012 18:03:12 +0100 Subject: [FieldTrip] signal acquisition with Biosemi Message-ID: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> Hi, I am trying to use the acquisition program acquire.m with Biosemi but I get the following error. ??? Undefined function or method 'gdfdatatype' for input arguments of type 'char'. Error in ==> acquire at 51 [datatyp,limits,datatypes,HDR.Bits,HDR.GDFTYP]=gdfdatatype('int32'); There is no gdfdatatype function in the toolbox. What should I do? Can somebody help me, please ? Sophie -------------- next part -------------- An HTML attachment was scrubbed... URL: From tomh at kurage.nimh.nih.gov Wed Feb 8 18:17:53 2012 From: tomh at kurage.nimh.nih.gov (Tom Holroyd (NIH/NIMH) [E]) Date: Wed, 08 Feb 2012 12:17:53 -0500 Subject: [FieldTrip] coordinate transform In-Reply-To: References: Message-ID: <4F32AE41.1030907@kurage.nimh.nih.gov> Here is a function that creates the fiducial basis. You can use it to transform the sensor coordinates into head coordinates. There are lots of comments. Oh, it's written in Python. qi li wrote: > Hi, > > I want to do a coordinate transformation of the sensor positions by > knowing the fiducial point(na,lpa,rpa). Is there any function can do > this? More specifically I want to know the 3 translational and 3 > rotational degree changes between the original coordinate and the > changed one. > > Thanks a lot! > > Qi > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- "The test of a first-rate intelligence is the ability to hold two opposed ideas in the mind at the same time, and still retain the ability to function." — F. Scott Fitzgerald -------------- next part -------------- A non-text attachment was scrubbed... Name: fid.py Type: application/x-python Size: 1651 bytes Desc: not available URL: From gonzalo.rojas.costa at gmail.com Wed Feb 8 20:13:13 2012 From: gonzalo.rojas.costa at gmail.com (Gonzalo Rojas Costa) Date: Wed, 8 Feb 2012 16:13:13 -0300 Subject: [FieldTrip] Cadwell EASY 3 (.ez3) format Message-ID: Hi: How can I read some Cadwell Easy 3 (.ez3) format files that I have ?... Any converter ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Clinica Las Condes Santiago Chile From hamzaf at sabanciuniv.edu Thu Feb 9 06:16:26 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Thu, 9 Feb 2012 07:16:26 +0200 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> Message-ID: Yes, I faced that problem before. I searched for the function and found it in https://sccn.ucsd.edu/svn/software/tags/EEGLAB7_0_1_5beta/external/fieldtrip-20090727/external/biosig/gdfdatatype.m But also I did face another problem after that as I remember. Could you check and tell us the result? Best, Hamza On Wed, Feb 8, 2012 at 7:03 PM, Sophie ADAMA wrote: > Hi,**** > > ** ** > > I am trying to use the acquisition program *acquire.m* with Biosemi but I > get the following error.**** > > ** ** > > ** ** > > *??? Undefined function or method 'gdfdatatype' for input arguments of > type 'char'.* > > * * > > *Error in ==> acquire at 51* > > *[datatyp,limits,datatypes,HDR.Bits,HDR.GDFTYP]=gdfdatatype('int32');* > > ** ** > > There is no *gdfdatatype* function in the toolbox.**** > > **** > > What should I do? Can somebody help me, please ?**** > > ** ** > > Sophie**** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Feb 9 09:23:45 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 9 Feb 2012 09:23:45 +0100 Subject: [FieldTrip] coordinate transform In-Reply-To: References: Message-ID: <83467D5B-606E-40AF-B407-D8CD0F3F2AC1@donders.ru.nl> Hi Qi, Could you be a bit more specific? In what coordinate system are the fiducials defined? MRI-voxel space? MEG-dewar space? Something else? There is a headcoordinates function in fieldtrip/private, which is computing a 4x4 affine transformation matrix for you (from which the rotation and translation can be determined). The high level fieldtrip functions you may want to look into are ft_electroderealign, or ft_volumerealign. Best, Jan-Mathijs On Feb 8, 2012, at 5:14 PM, qi li wrote: > Hi, > > I want to do a coordinate transformation of the sensor positions by > knowing the fiducial point(na,lpa,rpa). Is there any function can do > this? More specifically I want to know the 3 translational and 3 > rotational degree changes between the original coordinate and the > changed one. > > Thanks a lot! > > Qi > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Feb 9 15:41:23 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 9 Feb 2012 14:41:23 +0000 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> Message-ID: Dear Sophie and Hamza the acquire script that is present in the fieldtrip/realtime/acquisition/biosemi directory is only an example script that was written for initial testing. It acquires data in MATLAB, processes it and writes to a file. I believe that the normal way of acquiring data for biosemi is to run the biosemi2ft.exe application, i.e. not in MATLAB. Philip (CC) should be able to tell what the the normal use is, they do this in their lab every day. best Robert On 9 Feb 2012, at 5:16, Hamza Fawzi Altakroury (Student) wrote: > Yes, I faced that problem before. > > I searched for the function and found it in > > https://sccn.ucsd.edu/svn/software/tags/EEGLAB7_0_1_5beta/external/fieldtrip-20090727/external/biosig/gdfdatatype.m > > But also I did face another problem after that as I remember. Could you check and tell us the result? > > Best, > > Hamza > > On Wed, Feb 8, 2012 at 7:03 PM, Sophie ADAMA wrote: > Hi, > > > > I am trying to use the acquisition program acquire.m with Biosemi but I get the following error. > > > > > > ??? Undefined function or method 'gdfdatatype' for input arguments of type 'char'. > > > > Error in ==> acquire at 51 > > [datatyp,limits,datatypes,HDR.Bits,HDR.GDFTYP]=gdfdatatype('int32'); > > > > There is no gdfdatatype function in the toolbox. > > > What should I do? Can somebody help me, please ? > > > > Sophie > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Feb 9 17:56:06 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 9 Feb 2012 16:56:06 +0000 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> <09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl> Message-ID: <8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl> On behalf of Philip... On 9 Feb 2012, at 15:31, Philip van den Broek wrote: > Dear Sophie and Hamza, > > The connection between the Biosemi Active2 system and the FieldTrip buffer is handled by interfacing software biosemi2ft (part of fieldtrip), and should be started from the terminal (mac) or command prompt (windows). > > The interfacing software is located in the FieldTrip folder: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > > The BioSemi system needs a configuration (.cfg) file in which some acquisition-related settings are specified. Configuration files for the BioSemi system specify for example from how many channels data should be streamed and/or recorded, and whether the data should be downsampled. For more information about configuration files for different acquisition systems, see the Fieldtrip website. > > To start the buffer that connects to the Biosemi Active2, open the terminal (Mac) or command prompt (PC) and in the folder where you would like to save your data execute (change path according to your system and location of fieldtrip toolbox): > > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > > : configuration file > : base name of the gdf file. The suffix .gdf and session counters will be added automatically. > : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) > : optional, default is 1972 > an example: > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 > Note that the manually specified name of the file will overwrite any existing file, so make sure myfile.gdf doesn't exist. > > Once this is running, you get access to the data through the fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip fileio functions give you access to the data: > ft_read_header('buffer://localhost:1972'), or > ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100,........ > For further information, see fieldtrip website. > (more info on how we use the system at our department can be found here: http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) > > Hope this helps you to get things running in your place. If you have any further questions, just let me know. > > Best regards, > > > Philip van den Broek > Radboud University Nijmegen > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > > P.O. Box 9104, 6500 HE Nijmegen > Montessorilaan 3, 6525 HR Nijmegen > The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From adama.sophie at gmail.com Thu Feb 9 20:37:09 2012 From: adama.sophie at gmail.com (Sophie ADAMA) Date: Thu, 09 Feb 2012 20:37:09 +0100 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> <09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl> <8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl> Message-ID: <4F342065.8050707@gmail.com> Hi, Thanks for your response. I tried that but I get this: *command not found*. I am using Mac OS Lion. Any suggestions? Thanks Sophie Le 09.02.12 17:56, Robert Oostenveld a écrit : > On behalf of Philip... > > > On 9 Feb 2012, at 15:31, Philip van den Broek wrote: > >> Dear Sophie and Hamza, >> >> The connection between the Biosemi Active2 system and the FieldTrip >> buffer is handled by interfacing software biosemi2ft (part of >> fieldtrip), and should be started from the terminal (mac) or command >> prompt (windows). >> >> The interfacing software is located in the FieldTrip folder: >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft >> >> The BioSemi system needs a configuration (.cfg) file in which some >> acquisition-related settings are specified. Configuration files for >> the BioSemi system specify for example from how many channels data >> should be streamed and/or recorded, and whether the data should be >> downsampled. For more information about configuration files for >> different acquisition systems, see the Fieldtrip website >> . >> >> To start the buffer that connects to the Biosemi Active2, open the >> terminal (Mac) or command prompt (PC) and in the folder where you >> would like to save your data execute (change path according to your >> system and location of fieldtrip toolbox): >> >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft >> >> : configuration file >> : base name of the gdf file. The suffix .gdf and session counters will be added automatically. >> : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) >> : optional, default is 1972 >> an example: >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 >> >> Note that the manually specified name of the file will overwrite any >> existing file, so make sure myfile.gdf doesn't exist. >> >> Once this is running, you get access to the data through the >> fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip >> fileio functions give you access to the data: >> ft_read_header('buffer://localhost:1972' >> ), or >> ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100 >> ,........ >> For further information, see fieldtrip website. >> >> (more info on how we use the system at our department can be found >> here: >> http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) >> >> Hope this helps you to get things running in your place. If you have >> any further questions, just let me know. >> >> Best regards, >> >> >> Philip van den Broek >> Radboud University Nijmegen >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognition >> >> P.O. Box 9104, 6500 HE Nijmegen >> Montessorilaan 3, 6525 HR Nijmegen >> The Netherlands > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From akiko.ikkai at gmail.com Thu Feb 9 23:04:30 2012 From: akiko.ikkai at gmail.com (Akiko Ikkai) Date: Thu, 9 Feb 2012 17:04:30 -0500 Subject: [FieldTrip] volume conduction model missing .mat Message-ID: Hi, I'm trying to create a volume conduction model for my EEG study based on anatomical MRI, and having trouble with ft_prepare_bemmodel when I run cfg = []; cfg.tissue = [7 4 1]; % value for brain, skull, and scalp cfg.conductivity = [1 1/80 1]*.33; % after standard_BEM.zip data cfg.isolatedsource = true; cfg.method = 'dipoli'; cfg.sourceunits = 'mm'; cfg.mriunits = 'mm'; vol = ft_prepare_bemmodel(cfg, seg4bem); I get the following error message while ft_prepare_bemmodel is running: Fatal error in dipoli: interface /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect at vertex 1402 of /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri Warning: an error ocurred while running dipoli > In dipoli at 94 In ft_prepare_bemmodel at 112 Error using ==> fread Invalid file identifier. Use fopen to generate a valid file identifier. Warning: File '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' not found. > In dipoli at 102 In ft_prepare_bemmodel at 112 and the output vol is missing .mat, which causes an error during ft_sourceanalysis. >> vol vol = cond: [0.3300 0.0041 0.3300] bnd: [1x3 struct] source: 3 skin_surface: 3 skin: 1 type: 'dipoli' Does anyone know how to correct for "fatal error" so that ft_prepare_bemmodel creates the correct volume conduction model? I opened .tri file and removed line 1402, but got the same results. Thanks in advance! Akiko -- Akiko Ikkai, Ph.D. Postdoctoral Fellow Department of Psychological and Brain Sciences Johns Hopkins University Ames Hall, 3400 N. Charles St. Baltimore, MD 21218 -------------- next part -------------- An HTML attachment was scrubbed... URL: From phc5 at georgetown.edu Thu Feb 9 23:15:30 2012 From: phc5 at georgetown.edu (patrick cox) Date: Thu, 9 Feb 2012 17:15:30 -0500 Subject: [FieldTrip] volume conduction model missing .mat In-Reply-To: References: Message-ID: Hi Akiko, I had that same problem and also tried using the 'bemcp' which gave me a vol.mat file that was all NaNs. I did not figure out how to solve the problem in FT directly, but have been having some success creating the head model in SPM and loading that into FeildTrip. The SPM manual helped me. Hope that is somewhat helpful, Pat Patrick Cox Prethesis Student Lab For Computational Cognitive Science Georgetown University Medical Center 3970 Reservoir Rd. NW Washington, DC 20007 On Thu, Feb 9, 2012 at 5:04 PM, Akiko Ikkai wrote: > Hi, > > I'm trying to create a volume conduction model for my EEG study based on > anatomical MRI, and having trouble with ft_prepare_bemmodel > > when I run > cfg = []; > cfg.tissue = [7 4 1]; % value for brain, skull, and scalp > cfg.conductivity = [1 1/80 1]*.33; % after standard_BEM.zip data > cfg.isolatedsource = true; > cfg.method = 'dipoli'; > cfg.sourceunits = 'mm'; > cfg.mriunits = 'mm'; > vol = ft_prepare_bemmodel(cfg, seg4bem); > > I get the following error message while ft_prepare_bemmodel is running: > > Fatal error in dipoli: interface > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and > /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect > at vertex 1402 of /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri > > Warning: an error ocurred while running dipoli > > In dipoli at 94 > In ft_prepare_bemmodel at 112 > Error using ==> fread > Invalid file identifier. Use fopen to generate a valid file identifier. > Warning: File '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' not > found. > > In dipoli at 102 > In ft_prepare_bemmodel at 112 > > > and the output vol is missing .mat, which causes an error > during ft_sourceanalysis. > >> vol > vol = > cond: [0.3300 0.0041 0.3300] > bnd: [1x3 struct] > source: 3 > skin_surface: 3 > skin: 1 > type: 'dipoli' > > Does anyone know how to correct for "fatal error" so > that ft_prepare_bemmodel creates the correct volume conduction model? I > opened .tri file and removed line 1402, but got the same results. > > Thanks in advance! Akiko > > -- > Akiko Ikkai, Ph.D. > Postdoctoral Fellow > Department of Psychological and Brain Sciences > Johns Hopkins University > Ames Hall, 3400 N. Charles St. > Baltimore, MD 21218 > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Fri Feb 10 06:26:22 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Fri, 10 Feb 2012 07:26:22 +0200 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <4F342065.8050707@gmail.com> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> <09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl> <8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl> <4F342065.8050707@gmail.com> Message-ID: Hello, I tried the biosemi2tf.exe command it works well on Windows. But, unfortunately I don't know about the Mac OS. Best, Hamza On Thu, Feb 9, 2012 at 9:37 PM, Sophie ADAMA wrote: > Hi, > > Thanks for your response. > > I tried that but I get this: *command not found*. I am using Mac OS Lion. > > Any suggestions? > > Thanks > > Sophie > > Le 09.02.12 17:56, Robert Oostenveld a écrit : > > On behalf of Philip... > > > On 9 Feb 2012, at 15:31, Philip van den Broek wrote: > > Dear Sophie and Hamza, > > The connection between the Biosemi Active2 system and the FieldTrip buffer > is handled by interfacing software biosemi2ft (part of fieldtrip), and > should be started from the terminal (mac) or command prompt (windows). > > The interfacing software is located in the FieldTrip folder: > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > > The BioSemi system needs a configuration (.cfg) file in which some > acquisition-related settings are specified. Configuration files for the > BioSemi system specify for example from how many channels data should be > streamed and/or recorded, and whether the data should be downsampled. For > more information about configuration files for different acquisition > systems, see the Fieldtrip website > . > > To start the buffer that connects to the Biosemi Active2, open the > terminal (Mac) or command prompt (PC) and in the folder where you would > like to save your data execute (change path according to your system and > location of fieldtrip toolbox): > > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > > : configuration file > : base name of the gdf file. The suffix .gdf and session counters will be added automatically. > : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) > : optional, default is 1972 > > an example: > > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 > > Note that the manually specified name of the file will overwrite any > existing file, so make sure myfile.gdf doesn't exist. > Once this is running, you get access to the data through the fieldtrip > buffer filled with data by biosemi2ft, i.e., fieldtrip fileio functions > give you access to the data: > ft_read_header('buffer://localhost:1972'), or > ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100 > ,........ > For further information, see fieldtrip website. > > (more info on how we use the system at our department can be found here: > http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation > ) > > Hope this helps you to get things running in your place. If you have any > further questions, just let me know. > > Best regards, > > Philip van den Broek > Radboud University Nijmegen > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > > P.O. Box 9104, 6500 HE Nijmegen > Montessorilaan 3, 6525 HR Nijmegen > The Netherlands > > > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at mac.com Fri Feb 10 09:00:44 2012 From: nathanweisz at mac.com (Nathan Weisz) Date: Fri, 10 Feb 2012 09:00:44 +0100 Subject: [FieldTrip] volume conduction model missing .mat In-Reply-To: References: Message-ID: <2341406D-6422-4FD3-AD3C-73D1BF70B6CF@mac.com> Hi Akiki, I am not a headmodel expert. but looking at the output message, it seems your segementation did not go too well (see the "intersect" message). my intuition is then then the next temporary file *.ama is not created and ft_prepare_bemmodel then simply says ciao. perhaps you want to check / redo the segmentation? good luck, nathan On 09.02.2012, at 23:04, Akiko Ikkai wrote: > Hi, > > I'm trying to create a volume conduction model for my EEG study based on anatomical MRI, and having trouble with ft_prepare_bemmodel > > when I run > cfg = []; > cfg.tissue = [7 4 1]; % value for brain, skull, and scalp > cfg.conductivity = [1 1/80 1]*.33; % after standard_BEM.zip data > cfg.isolatedsource = true; > cfg.method = 'dipoli'; > cfg.sourceunits = 'mm'; > cfg.mriunits = 'mm'; > vol = ft_prepare_bemmodel(cfg, seg4bem); > > I get the following error message while ft_prepare_bemmodel is running: > > Fatal error in dipoli: interface /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect > at vertex 1402 of /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri > > Warning: an error ocurred while running dipoli > > In dipoli at 94 > In ft_prepare_bemmodel at 112 > Error using ==> fread > Invalid file identifier. Use fopen to generate a valid file identifier. > Warning: File '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' not > found. > > In dipoli at 102 > In ft_prepare_bemmodel at 112 > > > and the output vol is missing .mat, which causes an error during ft_sourceanalysis. > >> vol > vol = > cond: [0.3300 0.0041 0.3300] > bnd: [1x3 struct] > source: 3 > skin_surface: 3 > skin: 1 > type: 'dipoli' > > Does anyone know how to correct for "fatal error" so that ft_prepare_bemmodel creates the correct volume conduction model? I opened .tri file and removed line 1402, but got the same results. > > Thanks in advance! Akiko > > -- > Akiko Ikkai, Ph.D. > Postdoctoral Fellow > Department of Psychological and Brain Sciences > Johns Hopkins University > Ames Hall, 3400 N. Charles St. > Baltimore, MD 21218 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.piantoni at nin.knaw.nl Fri Feb 10 10:36:20 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Fri, 10 Feb 2012 10:36:20 +0100 Subject: [FieldTrip] volume conduction model missing .mat In-Reply-To: <2341406D-6422-4FD3-AD3C-73D1BF70B6CF@mac.com> References: <2341406D-6422-4FD3-AD3C-73D1BF70B6CF@mac.com> Message-ID: Hi Akiki and Patrick, I agree with Nathan about segmentation problems. I had the same problem when two of the three meshes intersected each other. Before you run the forward model, you should check the segmentation (bnd) using ft_plot_mesh. ft_plot_mesh(bnd(1), 'facealpha', .5) hold on ft_plot_mesh(bnd(2), 'facecolor', 'r') You will see that the two meshes intersect with each other. Depending on how you created the meshes, you should fix the parameters in such a way that they don't intersect. For example, ft_volumesegment has a cfg.threshold option (you can check how the segmentation went with ft_sourceplot) and ft_prepare_mesh_new has cfg.thresholdseg and cfg.smoothseg. I think that the meshes in SPM are computed on an (affine-transformed) template and not on the anatomically derived meshes. The template is more robust and that's why the two surfaces do not intersect. In general, the segmentation depends on the quality of your MRIs and you should really visually check the segmentation and meshes. When those look ok, the BEM forward model usually works. Hope this helps. Cheers, Gio On Fri, Feb 10, 2012 at 09:00, Nathan Weisz wrote: > Hi Akiki, > > I am not a headmodel expert. > but looking at the output message, it seems your segementation did not go > too well (see the "intersect" message). my intuition is then then the next > temporary file *.ama is not created and ft_prepare_bemmodel then simply says > ciao. > > perhaps you want to check / redo the segmentation? > > good luck, > nathan > > > On 09.02.2012, at 23:04, Akiko Ikkai wrote: > > Hi, > > I'm trying to create a volume conduction model for my EEG study based on > anatomical MRI, and having trouble with ft_prepare_bemmodel > > when I run > cfg                = []; > cfg.tissue         = [7 4 1]; % value for brain, skull, and scalp > cfg.conductivity   = [1 1/80 1]*.33; % after standard_BEM.zip data > cfg.isolatedsource = true; > cfg.method         = 'dipoli'; > cfg.sourceunits = 'mm'; > cfg.mriunits = 'mm'; > vol = ft_prepare_bemmodel(cfg, seg4bem); > > I get the following error message while ft_prepare_bemmodel is running: > > Fatal error in dipoli:  interface > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and > /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect >  at vertex 1402 of /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri > > Warning: an error ocurred while running dipoli >> In dipoli at 94 >   In ft_prepare_bemmodel at 112 > Error using ==> fread > Invalid file identifier.  Use fopen to generate a valid file identifier. > Warning: File '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' not > found. >> In dipoli at 102 >   In ft_prepare_bemmodel at 112 > > > and the output vol is missing .mat, which causes an error > during ft_sourceanalysis. >>> vol > vol = >             cond: [0.3300 0.0041 0.3300] >              bnd: [1x3 struct] >           source: 3 >     skin_surface: 3 >             skin: 1 >             type: 'dipoli' > > Does anyone know how to correct for "fatal error" so > that ft_prepare_bemmodel creates the correct volume conduction model? I > opened .tri file and removed line 1402, but got the same results. > > Thanks in advance! Akiko > > -- > Akiko Ikkai, Ph.D. > Postdoctoral Fellow > Department of Psychological and Brain Sciences > Johns Hopkins University > Ames Hall, 3400 N. Charles St. > Baltimore, MD 21218 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From adama.sophie at gmail.com Fri Feb 10 14:53:48 2012 From: adama.sophie at gmail.com (Sophie ADAMA) Date: Fri, 10 Feb 2012 14:53:48 +0100 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> <09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl> <8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl> <4F342065.8050707@gmail.com> Message-ID: <016201cce7fb$6a4b9e90$3ee2dbb0$@gmail.com> Hi, I tried it on Windows too, and it works perfectly. But I’m a Mac girl J and I will be happy if someone could help me. Thank you From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) Sent: vendredi 10 février 2012 06:26 To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] signal acquisition with Biosemi Hello, I tried the biosemi2tf.exe command it works well on Windows. But, unfortunately I don't know about the Mac OS. Best, Hamza On Thu, Feb 9, 2012 at 9:37 PM, Sophie ADAMA wrote: Hi, Thanks for your response. I tried that but I get this: command not found. I am using Mac OS Lion. Any suggestions? Thanks Sophie Le 09.02.12 17:56, Robert Oostenveld a écrit : On behalf of Philip... On 9 Feb 2012, at 15:31, Philip van den Broek wrote: Dear Sophie and Hamza, The connection between the Biosemi Active2 system and the FieldTrip buffer is handled by interfacing software biosemi2ft (part of fieldtrip), and should be started from the terminal (mac) or command prompt (windows). The interfacing software is located in the FieldTrip folder: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft The BioSemi system needs a configuration (.cfg) file in which some acquisition-related settings are specified. Configuration files for the BioSemi system specify for example from how many channels data should be streamed and/or recorded, and whether the data should be downsampled. For more information about configuration files for different acquisition systems, see the Fieldtrip website . To start the buffer that connects to the Biosemi Active2, open the terminal (Mac) or command prompt (PC) and in the folder where you would like to save your data execute (change path according to your system and location of fieldtrip toolbox): ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft : configuration file : base name of the gdf file. The suffix .gdf and session counters will be added automatically. : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) : optional, default is 1972 an example: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 Note that the manually specified name of the file will overwrite any existing file, so make sure myfile.gdf doesn't exist. Once this is running, you get access to the data through the fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip fileio functions give you access to the data: ft_read_header('buffer://localhost:1972'), or ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100,........ For further information, see fieldtrip website. (more info on how we use the system at our department can be found here: http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) Hope this helps you to get things running in your place. If you have any further questions, just let me know. Best regards, Philip van den Broek Radboud University Nijmegen Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104, 6500 HE Nijmegen Montessorilaan 3, 6525 HR Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From elilife at gmail.com Fri Feb 10 15:34:45 2012 From: elilife at gmail.com (Eliana Garcia) Date: Fri, 10 Feb 2012 15:34:45 +0100 Subject: [FieldTrip] elilife@gmail.com Message-ID: -- Eliana García Cossio Applied Neurotechnology Lab. Graduate School of Neural and Behavioral Science - Max Planck Research School Institute of Medical Psychology and Behavioral Neurobiology Universität Tübingen (+0049) 01 577-8587604 Otfried-Müller-Str. 47, 72076 Tübingen- Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.severens at maartenskliniek.nl Fri Feb 10 15:46:07 2012 From: m.severens at maartenskliniek.nl (Severens, Marianne) Date: Fri, 10 Feb 2012 15:46:07 +0100 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <016201cce7fb$6a4b9e90$3ee2dbb0$@gmail.com> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com><09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl><8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl><4F342065.8050707@gmail.com> <016201cce7fb$6a4b9e90$3ee2dbb0$@gmail.com> Message-ID: <70FC3ACFFB46314EBEAF9101EA45F50E06D8EC7A0C@smkexch02.maartenskliniek.nl> Hi Sophie Are you sure that the correct version of the biosemi2ft (so the one for the mac) is in the folder that you are specifying? Maybe you can try it first without the optional parameters, so just ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft Best, Marianne From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Sophie ADAMA Sent: vrijdag 10 februari 2012 14:54 To: 'Email discussion list for the FieldTrip project' Subject: Re: [FieldTrip] signal acquisition with Biosemi Hi, I tried it on Windows too, and it works perfectly. But I’m a Mac girl ☺ and I will be happy if someone could help me. Thank you From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) Sent: vendredi 10 février 2012 06:26 To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] signal acquisition with Biosemi Hello, I tried the biosemi2tf.exe command it works well on Windows. But, unfortunately I don't know about the Mac OS. Best, Hamza On Thu, Feb 9, 2012 at 9:37 PM, Sophie ADAMA > wrote: Hi, Thanks for your response. I tried that but I get this: command not found. I am using Mac OS Lion. Any suggestions? Thanks Sophie Le 09.02.12 17:56, Robert Oostenveld a écrit : On behalf of Philip... On 9 Feb 2012, at 15:31, Philip van den Broek wrote: Dear Sophie and Hamza, The connection between the Biosemi Active2 system and the FieldTrip buffer is handled by interfacing software biosemi2ft (part of fieldtrip), and should be started from the terminal (mac) or command prompt (windows). The interfacing software is located in the FieldTrip folder: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft The BioSemi system needs a configuration (.cfg) file in which some acquisition-related settings are specified. Configuration files for the BioSemi system specify for example from how many channels data should be streamed and/or recorded, and whether the data should be downsampled. For more information about configuration files for different acquisition systems, see the Fieldtrip website. To start the buffer that connects to the Biosemi Active2, open the terminal (Mac) or command prompt (PC) and in the folder where you would like to save your data execute (change path according to your system and location of fieldtrip toolbox): ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft : configuration file : base name of the gdf file. The suffix .gdf and session counters will be added automatically. : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) : optional, default is 1972 an example: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 Note that the manually specified name of the file will overwrite any existing file, so make sure myfile.gdf doesn't exist. Once this is running, you get access to the data through the fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip fileio functions give you access to the data: ft_read_header('buffer://localhost:1972'), or ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100,........ For further information, see fieldtrip website. (more info on how we use the system at our department can be found here: http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) Hope this helps you to get things running in your place. If you have any further questions, just let me know. Best regards, Philip van den Broek Radboud University Nijmegen Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104, 6500 HE Nijmegen Montessorilaan 3, 6525 HR Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University ________________________________ Disclaimer Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. Sint Maartenskliniek Hengstdal 3, 6574 NA Ubbergen (bij Nijmegen) Telefoon 024-3659 911 Telefax 024-3659 204 KvK nummer 41055111 -------------- next part -------------- An HTML attachment was scrubbed... URL: From isabella.premoli at gmail.com Fri Feb 10 15:48:24 2012 From: isabella.premoli at gmail.com (isabella premoli) Date: Fri, 10 Feb 2012 15:48:24 +0100 Subject: [FieldTrip] TMS-EEG data analysis Message-ID: Dear FieldTrip community, My name is Isabella and I have just started using FieldTrip to analyze TMS-EEG data. I was wondering whether the Donders Institute will provide courses on FieldTrip regarding this specific analysis. In case the answer is positive, I would be very happy to join. Cheers, Isabella -- Isabella Premoli, PhD student Motor Cortex Laboratory Schleusenweg 2-16 D-60528 Frankfurt am Main Tel: +49-69-6301-83826 -------------- next part -------------- An HTML attachment was scrubbed... URL: From elilife at gmail.com Fri Feb 10 16:26:46 2012 From: elilife at gmail.com (Eliana Garcia) Date: Fri, 10 Feb 2012 16:26:46 +0100 Subject: [FieldTrip] wPLI and analysis of band frequencies Message-ID: Hello! I am currently trying to analyze my data using the wPLI. However I would like to do a band frequency analysis i.e calculate a wPLI value for example for the beta band, but this is not possible since the wPLI is calculated for a time window (according to the time-frequency transformation resolution) and for a certain specific frequency across trials. Guggisberg et al ('Mapping functional connectivity in Patients with Brain lesions') solved this problem in the case of coherence, calculating the sum of autospectra and sum of cross-spectra of the corresponding frequency bins. However, I think that this approach will influence a lot false negatives in the case of the wPLI, since the shifts of phases for the components of the certain band can somehow cancel to each other. Another idea could be to calculate the wPLI for each frequency bin and then average across the band frequency, but I am not sure if this will be really representative of functional connectivity for this band. I still have no clue and what could be the best approach. Thank you so much, -- Eliana García Cossio Applied Neurotechnology Lab. Graduate School of Neural and Behavioral Science - Max Planck Research School Institute of Medical Psychology and Behavioral Neurobiology Universität Tübingen -------------- next part -------------- An HTML attachment was scrubbed... URL: From adama.sophie at gmail.com Sat Feb 11 18:29:33 2012 From: adama.sophie at gmail.com (Sophie ADAMA) Date: Sat, 11 Feb 2012 18:29:33 +0100 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <70FC3ACFFB46314EBEAF9101EA45F50E06D8EC7A0C@smkexch02.maartenskliniek.nl> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com><09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl><8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl><4F342065.8050707@gmail.com> <016201cce7fb$6a4b9e90$3ee2dbb0$@gmail.com> <70FC3ACFFB46314EBEAF9101EA45F50E06D8EC7A0C@smkexch02.maartenskliniek.nl> Message-ID: <002101cce8e2$bb478060$31d68120$@gmail.com> Hi Marianne, There are 3 biosemi2ft in that folder : biosemi2ft.cc, biosemi2ft.exe and biosemi2ft.maci; but when I type ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft in the command line, it says No such file or directory. Sophie From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Severens, Marianne Sent: vendredi 10 février 2012 15:46 To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] signal acquisition with Biosemi Hi Sophie Are you sure that the correct version of the biosemi2ft (so the one for the mac) is in the folder that you are specifying? Maybe you can try it first without the optional parameters, so just ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft Best, Marianne From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Sophie ADAMA Sent: vrijdag 10 februari 2012 14:54 To: 'Email discussion list for the FieldTrip project' Subject: Re: [FieldTrip] signal acquisition with Biosemi Hi, I tried it on Windows too, and it works perfectly. But I’m a Mac girl J and I will be happy if someone could help me. Thank you From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) Sent: vendredi 10 février 2012 06:26 To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] signal acquisition with Biosemi Hello, I tried the biosemi2tf.exe command it works well on Windows. But, unfortunately I don't know about the Mac OS. Best, Hamza On Thu, Feb 9, 2012 at 9:37 PM, Sophie ADAMA wrote: Hi, Thanks for your response. I tried that but I get this: command not found. I am using Mac OS Lion. Any suggestions? Thanks Sophie Le 09.02.12 17:56, Robert Oostenveld a écrit : On behalf of Philip... On 9 Feb 2012, at 15:31, Philip van den Broek wrote: Dear Sophie and Hamza, The connection between the Biosemi Active2 system and the FieldTrip buffer is handled by interfacing software biosemi2ft (part of fieldtrip), and should be started from the terminal (mac) or command prompt (windows). The interfacing software is located in the FieldTrip folder: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft The BioSemi system needs a configuration (.cfg) file in which some acquisition-related settings are specified. Configuration files for the BioSemi system specify for example from how many channels data should be streamed and/or recorded, and whether the data should be downsampled. For more information about configuration files for different acquisition systems, see the Fieldtrip website . To start the buffer that connects to the Biosemi Active2, open the terminal (Mac) or command prompt (PC) and in the folder where you would like to save your data execute (change path according to your system and location of fieldtrip toolbox): ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft : configuration file : base name of the gdf file. The suffix .gdf and session counters will be added automatically. : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) : optional, default is 1972 an example: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 Note that the manually specified name of the file will overwrite any existing file, so make sure myfile.gdf doesn't exist. Once this is running, you get access to the data through the fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip fileio functions give you access to the data: ft_read_header('buffer://localhost:1972'), or ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100,........ For further information, see fieldtrip website. (more info on how we use the system at our department can be found here: http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) Hope this helps you to get things running in your place. If you have any further questions, just let me know. Best regards, Philip van den Broek Radboud University Nijmegen Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104, 6500 HE Nijmegen Montessorilaan 3, 6525 HR Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University _____ Disclaimer Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. Sint Maartenskliniek Hengstdal 3, 6574 NA Ubbergen (bij Nijmegen) Telefoon 024-3659 911 Telefax 024-3659 204 KvK nummer 41055111 -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.severens at maartenskliniek.nl Mon Feb 13 15:52:29 2012 From: m.severens at maartenskliniek.nl (Severens, Marianne) Date: Mon, 13 Feb 2012 15:52:29 +0100 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <002101cce8e2$bb478060$31d68120$@gmail.com> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com><09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl><8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl><4F342065.8050707@gmail.com><016201cce7fb$6a4b9e90$3ee2dbb0$@gmail.com><70FC3ACFFB46314EBEAF9101EA45F50E06D8EC7A0C@smkexch02.maartenskliniek.nl>, <002101cce8e2$bb478060$31d68120$@gmail.com> Message-ID: <70FC3ACFFB46314EBEAF9101EA45F50E06D145F312@smkexch02.maartenskliniek.nl> Hi Sophie I've checked the script that we use to startup the buffer in our lab. Apparently you need to type ./ before the command. This is what our script looks like: cd to the /fieldtrip/realtime/acquisition/biosemi/ folder. Then run the biosemi2ft: ./biosemi2ft (with optional parameters) I think you can also put a path in the gdf filename, so it does not save it in the fieldtrip folder, but you will have to check that. I hope this works for you! Best, Marianne ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Sophie ADAMA [adama.sophie at gmail.com] Sent: Saturday, February 11, 2012 6:29 PM To: 'Email discussion list for the FieldTrip project' Subject: Re: [FieldTrip] signal acquisition with Biosemi Hi Marianne, There are 3 biosemi2ft in that folder : biosemi2ft.cc, biosemi2ft.exe and biosemi2ft.maci; but when I type ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft in the command line, it says No such file or directory. Sophie From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Severens, Marianne Sent: vendredi 10 février 2012 15:46 To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] signal acquisition with Biosemi Hi Sophie Are you sure that the correct version of the biosemi2ft (so the one for the mac) is in the folder that you are specifying? Maybe you can try it first without the optional parameters, so just ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft Best, Marianne From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Sophie ADAMA Sent: vrijdag 10 februari 2012 14:54 To: 'Email discussion list for the FieldTrip project' Subject: Re: [FieldTrip] signal acquisition with Biosemi Hi, I tried it on Windows too, and it works perfectly. But I’m a Mac girl ☺ and I will be happy if someone could help me. Thank you From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) Sent: vendredi 10 février 2012 06:26 To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] signal acquisition with Biosemi Hello, I tried the biosemi2tf.exe command it works well on Windows. But, unfortunately I don't know about the Mac OS. Best, Hamza On Thu, Feb 9, 2012 at 9:37 PM, Sophie ADAMA > wrote: Hi, Thanks for your response. I tried that but I get this: command not found. I am using Mac OS Lion. Any suggestions? Thanks Sophie Le 09.02.12 17:56, Robert Oostenveld a écrit : On behalf of Philip... On 9 Feb 2012, at 15:31, Philip van den Broek wrote: Dear Sophie and Hamza, The connection between the Biosemi Active2 system and the FieldTrip buffer is handled by interfacing software biosemi2ft (part of fieldtrip), and should be started from the terminal (mac) or command prompt (windows). The interfacing software is located in the FieldTrip folder: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft The BioSemi system needs a configuration (.cfg) file in which some acquisition-related settings are specified. Configuration files for the BioSemi system specify for example from how many channels data should be streamed and/or recorded, and whether the data should be downsampled. For more information about configuration files for different acquisition systems, see the Fieldtrip website. To start the buffer that connects to the Biosemi Active2, open the terminal (Mac) or command prompt (PC) and in the folder where you would like to save your data execute (change path according to your system and location of fieldtrip toolbox): ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft : configuration file : base name of the gdf file. The suffix .gdf and session counters will be added automatically. : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) : optional, default is 1972 an example: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 Note that the manually specified name of the file will overwrite any existing file, so make sure myfile.gdf doesn't exist. Once this is running, you get access to the data through the fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip fileio functions give you access to the data: ft_read_header('buffer://localhost:1972'), or ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100,........ For further information, see fieldtrip website. (more info on how we use the system at our department can be found here: http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) Hope this helps you to get things running in your place. If you have any further questions, just let me know. Best regards, Philip van den Broek Radboud University Nijmegen Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104, 6500 HE Nijmegen Montessorilaan 3, 6525 HR Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University ________________________________ Disclaimer Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. Sint Maartenskliniek Hengstdal 3, 6574 NA Ubbergen (bij Nijmegen) Telefoon 024-3659 911 Telefax 024-3659 204 KvK nummer 41055111 Disclaimer Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. Sint Maartenskliniek Hengstdal 3, 6574 NA Ubbergen (bij Nijmegen) Telefoon 024-3659 911 Telefax 024-3659 204 KvK nummer 41055111 From p.vandenbroek at donders.ru.nl Mon Feb 13 19:08:15 2012 From: p.vandenbroek at donders.ru.nl (Philip van den Broek) Date: Mon, 13 Feb 2012 19:08:15 +0100 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: <70FC3ACFFB46314EBEAF9101EA45F50E06D145F312@smkexch02.maartenskliniek.nl> References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> <09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl> <8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl> <4F342065.8050707@gmail.com> <016201cce7fb$6a4b9e90$3ee2dbb0$@gmail.com> <70FC3ACFFB46314EBEAF9101EA45F50E06D8EC7A0C@smkexch02.maartenskliniek.nl> <002101cce8e2$bb478060$31d68120$@gmail.com> <70FC3ACFFB46314EBEAF9101EA45F50E06D145F312@smkexch02.maartenskliniek.nl> Message-ID: Hi Sophie, If you specify a file and path, you don't need ./ in front of it, only when you try to execute a file in the current folder. In our local fieldtrip distribution for biosemi2ft, contrary to yours, apparently the extension .maci is missing so you need to specify the extension as well: If you are in the folder: ./biosemi2ft.maci (with optional parameters) or from anywhere else: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft.maci (with optional parameters) Gr. Philip On Feb 13, 2012, at 3:52 PM, Severens, Marianne wrote: > Hi Sophie > > I've checked the script that we use to startup the buffer in our lab. Apparently you need to type ./ before the command. This is what our script looks like: > cd to the /fieldtrip/realtime/acquisition/biosemi/ folder. > Then run the biosemi2ft: ./biosemi2ft (with optional parameters) > > I think you can also put a path in the gdf filename, so it does not save it in the fieldtrip folder, but you will have to check that. > > I hope this works for you! > Best, Marianne > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Sophie ADAMA [adama.sophie at gmail.com] > Sent: Saturday, February 11, 2012 6:29 PM > To: 'Email discussion list for the FieldTrip project' > Subject: Re: [FieldTrip] signal acquisition with Biosemi > > Hi Marianne, > > There are 3 biosemi2ft in that folder : biosemi2ft.cc, biosemi2ft.exe and biosemi2ft.maci; but when I type ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > in the command line, it says No such file or directory. > > Sophie > > From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Severens, Marianne > Sent: vendredi 10 février 2012 15:46 > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] signal acquisition with Biosemi > > Hi Sophie > > Are you sure that the correct version of the biosemi2ft (so the one for the mac) is in the folder that you are specifying? Maybe you can try it first without the optional parameters, so just > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > > Best, Marianne > > From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Sophie ADAMA > Sent: vrijdag 10 februari 2012 14:54 > To: 'Email discussion list for the FieldTrip project' > Subject: Re: [FieldTrip] signal acquisition with Biosemi > > Hi, > > I tried it on Windows too, and it works perfectly. > > But I’m a Mac girl ☺ and I will be happy if someone could help me. > > Thank you > > > From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) > Sent: vendredi 10 février 2012 06:26 > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] signal acquisition with Biosemi > > Hello, > > I tried the biosemi2tf.exe command it works well on Windows. > > But, unfortunately I don't know about the Mac OS. > > Best, > > Hamza > On Thu, Feb 9, 2012 at 9:37 PM, Sophie ADAMA > wrote: > Hi, > > Thanks for your response. > > I tried that but I get this: command not found. I am using Mac OS Lion. > > Any suggestions? > > Thanks > > Sophie > Le 09.02.12 17:56, Robert Oostenveld a écrit : > On behalf of Philip... > > > On 9 Feb 2012, at 15:31, Philip van den Broek wrote: > > > Dear Sophie and Hamza, > > The connection between the Biosemi Active2 system and the FieldTrip buffer is handled by interfacing software biosemi2ft (part of fieldtrip), and should be started from the terminal (mac) or command prompt (windows). > > The interfacing software is located in the FieldTrip folder: ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > > The BioSemi system needs a configuration (.cfg) file in which some acquisition-related settings are specified. Configuration files for the BioSemi system specify for example from how many channels data should be streamed and/or recorded, and whether the data should be downsampled. For more information about configuration files for different acquisition systems, see the Fieldtrip website. > > To start the buffer that connects to the Biosemi Active2, open the terminal (Mac) or command prompt (PC) and in the folder where you would like to save your data execute (change path according to your system and location of fieldtrip toolbox): > > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft > > > > : configuration file > > : base name of the gdf file. The suffix .gdf and session counters will be added automatically. > > : optional, default is 'localhost', specify '-' to spawn a local buffer (recommended) > > : optional, default is 1972 > > an example: > > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg myfile - 1972 > > Note that the manually specified name of the file will overwrite any existing file, so make sure myfile.gdf doesn't exist. > Once this is running, you get access to the data through the fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip fileio functions give you access to the data: > ft_read_header('buffer://localhost:1972'), or > ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100,........ > For further information, see fieldtrip website. > > (more info on how we use the system at our department can be found here: http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) > > Hope this helps you to get things running in your place. If you have any further questions, just let me know. > > Best regards, > > Philip van den Broek > Radboud University Nijmegen > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > > P.O. Box 9104, 6500 HE Nijmegen > Montessorilaan 3, 6525 HR Nijmegen > The Netherlands > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > ________________________________ > Disclaimer > Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. > > Sint Maartenskliniek > Hengstdal 3, > 6574 NA Ubbergen (bij Nijmegen) > Telefoon 024-3659 911 > Telefax 024-3659 204 > KvK nummer 41055111 > > Disclaimer > Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. > > Sint Maartenskliniek > Hengstdal 3, > 6574 NA Ubbergen (bij Nijmegen) > Telefoon 024-3659 911 > Telefax 024-3659 204 > KvK nummer 41055111 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From sysoevao at psychiatry.wustl.edu Mon Feb 13 21:49:17 2012 From: sysoevao at psychiatry.wustl.edu (Sysoeva, Olga Vladimirovna) Date: Mon, 13 Feb 2012 14:49:17 -0600 Subject: [FieldTrip] one/two-tails analysis Message-ID: <76DC57362137854CB9592B496182D5FA09D91CC315@wusmexmbx2.medpriv.wucon.wustl.edu> Dear group, I do face some weird results during my analysis. Usually I do t-test analysis to compare 2 condions/groups and use 2-tails, as far as I do not have any preliminary hypothesis about the direction of the effect. So my script looks something like Script 1 (see below). Important here is that I do keep the default parameters, cfg.tail = 0; cfg.clustertail = 0; To my understanding of statistic, if you have the two-tail effect, and group 1 has bigger mean than gr2, you should have the effect with one-tail as well and even more significant. But what I discovered just today that if I change this parameter to 1, cfg.tail = 1; cfg.clustertail = 1; in order to look spesifically for the one-tail effect (gr1 is bigger than gr2), my very significant 2 tail effect just disappeared completely. Is it a bug? Your comments are appreciated. Best reGards, Olga. Script 1 cfg = []; cfg.method = 'montecarlo'; % use the Monte Carlo Method to calculate the significance probability cfg.statistic = 'indepsamplesT'; % use the independent samples T-statistic as a measure to evaluate % the effect at the sample level % cfg.statistic = 'indepsamplesF'; % use the independent samples T-statistic as a measure to evaluate % cfg.computecritval = 'yes' % the effect at the sample level cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; % alpha level of the sample-specific test statistic that will be used for thresholding cfg.clusterstatistic = 'maxsum'; % test statistic that will be evaluated under the permutation distribution. cfg.minnbchan = 1; % minimum number of neighborhood channels that is required for a selected % sample to be included in the clustering algorithm (default=0). cfg.tail = 0; % -1, 1 or 0 (default = 0); one-sided or two-sided test cfg.clustertail = 0; cfg.alpha = 0.05; % alpha level of the permutation test cfg.numrandomization = 1000; % number of draws from the permutation distribution cfg.neighbourdist = 0.2; %cfg.neighbours = cfg_n; cfg.channel = {'all', '-HEOG', '-VEOG', '-EKG'}; cfg.latency = [0. 0.5]; cfg.layout = 'C:\Matlab_programs\Fieldtrip\My_Fieldtrip\EEG1010_modified32.lay'; subj1 = length(GROUP {nGroup1,1}); subj2 = length(GROUP {nGroup2,1}); design = zeros(1,subj1+subj2); design(1,1:subj1) = 1; design(1,subj1+1:subj1+subj2) = 2; cfg.design = design; cfg.ivar = 1; [stat] = ft_timelockstatistics(cfg, peak1_gr1 , peak1_gr2 ); ____________________________________________________________________________ Olga Sysoeva, Research Associate, PhD Psychiatry Department, Washington University School of Medicine Campus Box 8134 660 South Euclid Ave Saint Louis, MO 63110-9909 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From adama.sophie at gmail.com Tue Feb 14 15:06:21 2012 From: adama.sophie at gmail.com (Sophie ADAMA) Date: Tue, 14 Feb 2012 15:06:21 +0100 Subject: [FieldTrip] signal acquisition with Biosemi In-Reply-To: References: <134d01cce683$8b529090$a1f7b1b0$@gmail.com> <09E1CB40-CC51-4710-A16C-4B49660C00BB@donders.ru.nl> <8B6B86C5-3D11-4CFF-987A-6D9C6163DF7A@donders.ru.nl> <4F342065.8050707@gmail.com> <016201cce7fb$6a4b9e90$3ee2dbb0$@gmail.com> <70FC3ACFFB46314EBEAF9101EA45F50E06D8EC7A0C@smkexch02.maartenskliniek.nl> <002101cce8e2$bb478060$31d68120$@gmail.com> <70FC3ACFFB46314EBEAF9101EA45F50E06D145F312@smkexch02.maartenskliniek.nl> Message-ID: <4F3A6A5D.1050101@gmail.com> Hi everybody, I tried all this but it still doesn't work. The latest error I got was: *Access denied* Sincerly, Sophie Le 13.02.12 19:08, Philip van den Broek a écrit : > Hi Sophie, > > If you specify a file and path, you don't need ./ in front of it, only > when you try to execute a file in the current folder. In our local > fieldtrip distribution for biosemi2ft, contrary to yours, apparently > the extension .maci is missing so you need to specify the extension as > well: > If you are in the folder: > ./biosemi2ft.maci (with optional parameters) > > or from anywhere else: > ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft.maci (with > optional parameters) > > Gr. Philip > > On Feb 13, 2012, at 3:52 PM, Severens, Marianne wrote: > >> Hi Sophie >> >> I've checked the script that we use to startup the buffer in our lab. >> Apparently you need to type ./ before the command. This is what our >> script looks like: >> cd to the /fieldtrip/realtime/acquisition/biosemi/ folder. >> Then run the biosemi2ft: ./biosemi2ft (with optional parameters) >> >> I think you can also put a path in the gdf filename, so it does not >> save it in the fieldtrip folder, but you will have to check that. >> >> I hope this works for you! >> Best, Marianne >> ________________________________________ >> From: fieldtrip-bounces at donders.ru.nl >> >> [fieldtrip-bounces at donders.ru.nl >> ] On Behalf Of Sophie ADAMA >> [adama.sophie at gmail.com ] >> Sent: Saturday, February 11, 2012 6:29 PM >> To: 'Email discussion list for the FieldTrip project' >> Subject: Re: [FieldTrip] signal acquisition with Biosemi >> >> Hi Marianne, >> >> There are 3 biosemi2ft in that folder : biosemi2ft.cc, biosemi2ft.exe >> and biosemi2ft.maci; but when I type >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft >> in the command line, it says No such file or directory. >> >> Sophie >> >> From: fieldtrip-bounces at donders.ru.nl >> >> [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Severens, Marianne >> Sent: vendredi 10 février 2012 15:46 >> To: Email discussion list for the FieldTrip project >> Subject: Re: [FieldTrip] signal acquisition with Biosemi >> >> Hi Sophie >> >> Are you sure that the correct version of the biosemi2ft (so the one >> for the mac) is in the folder that you are specifying? Maybe you can >> try it first without the optional parameters, so just >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft >> >> Best, Marianne >> >> From: fieldtrip-bounces at donders.ru.nl >> >> [mailto:fieldtrip-bounces at donders.ru.nl] >> On Behalf Of Sophie ADAMA >> Sent: vrijdag 10 februari 2012 14:54 >> To: 'Email discussion list for the FieldTrip project' >> Subject: Re: [FieldTrip] signal acquisition with Biosemi >> >> Hi, >> >> I tried it on Windows too, and it works perfectly. >> >> But I'm a Mac girl ? and I will be happy if someone could help me. >> >> Thank you >> >> >> From: fieldtrip-bounces at donders.ru.nl >> >> [mailto:fieldtrip-bounces at donders.ru.nl] >> On Behalf Of Hamza Fawzi Altakroury (Student) >> Sent: vendredi 10 février 2012 06:26 >> To: Email discussion list for the FieldTrip project >> Subject: Re: [FieldTrip] signal acquisition with Biosemi >> >> Hello, >> >> I tried the biosemi2tf.exe command it works well on Windows. >> >> But, unfortunately I don't know about the Mac OS. >> >> Best, >> >> Hamza >> On Thu, Feb 9, 2012 at 9:37 PM, Sophie ADAMA > > wrote: >> Hi, >> >> Thanks for your response. >> >> I tried that but I get this: command not found. I am using Mac OS Lion. >> >> Any suggestions? >> >> Thanks >> >> Sophie >> Le 09.02.12 17:56, Robert Oostenveld a écrit : >> On behalf of Philip... >> >> >> On 9 Feb 2012, at 15:31, Philip van den Broek wrote: >> >> >> Dear Sophie and Hamza, >> >> The connection between the Biosemi Active2 system and the FieldTrip >> buffer is handled by interfacing software biosemi2ft (part of >> fieldtrip), and should be started from the terminal (mac) or command >> prompt (windows). >> >> The interfacing software is located in the FieldTrip folder: >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft >> >> The BioSemi system needs a configuration (.cfg) file in which some >> acquisition-related settings are specified. Configuration files for >> the BioSemi system specify for example from how many channels data >> should be streamed and/or recorded, and whether the data should be >> downsampled. For more information about configuration files for >> different acquisition systems, see the Fieldtrip >> website. >> >> To start the buffer that connects to the Biosemi Active2, open the >> terminal (Mac) or command prompt (PC) and in the folder where you >> would like to save your data execute (change path according to your >> system and location of fieldtrip toolbox): >> >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft >> >> >> >> >> : configuration file >> >> : base name of the gdf file. The suffix .gdf and session >> counters will be added automatically. >> >> : optional, default is 'localhost', specify '-' to spawn a >> local buffer (recommended) >> >> : optional, default is 1972 >> >> an example: >> >> ../fieldtrip/realtime/acquisition/biosemi/biosemi2ft myconfig.cfg >> myfile - 1972 >> >> Note that the manually specified name of the file will overwrite any >> existing file, so make sure myfile.gdf doesn't exist. >> Once this is running, you get access to the data through the >> fieldtrip buffer filled with data by biosemi2ft, i.e., fieldtrip >> fileio functions give you access to the data: >> ft_read_header('buffer://localhost:1972' >> ), or >> ft_read_data('buffer://localhost:1972','begsample',1,'endsample',100 >> ,........ >> For further information, see fieldtrip website. >> >> (more info on how we use the system at our department can be found >> here: >> http://www.nici.ru.nl/brainstream/twiki/bin/view/BrainStreamDocs/DocsSectionsInstallation) >> >> Hope this helps you to get things running in your place. If you have >> any further questions, just let me know. >> >> Best regards, >> >> Philip van den Broek >> Radboud University Nijmegen >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognition >> >> P.O. Box 9104, 6500 HE Nijmegen >> Montessorilaan 3, 6525 HR Nijmegen >> The Netherlands >> >> >> >> _______________________________________________ >> >> fieldtrip mailing list >> >> fieldtrip at donders.ru.nl >> >> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Hamza Fawzi Altakroury >> Graduate student - MA >> Faculty of Engineering and Natural Sciences >> Sabanc? University >> >> ________________________________ >> Disclaimer >> Vrijgave van de informatie verzonden met dit e-mail bericht is >> geaccordeerd door de ontvanger en/of zijn behandelend arts. >> Verstrekking van deze informatie is conform het Privacy reglement van >> de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de >> geadresseerde. Gebruik van deze informatie door anderen dan de >> geadresseerde is, zonder voorafgaande schriftelijke toestemming van >> de rechthebbende , verboden. De Sint Maartenskliniek staat niet in >> voor de juiste en volledige overbrenging van de inhoud van een >> gezonden e-mail, noch voor de ontvangst daarvan. >> >> Sint Maartenskliniek >> Hengstdal 3, >> 6574 NA Ubbergen (bij Nijmegen) >> Telefoon 024-3659 911 >> Telefax 024-3659 204 >> KvK nummer 41055111 >> >> Disclaimer >> Vrijgave van de informatie verzonden met dit e-mail bericht is >> geaccordeerd door de ontvanger en/of zijn behandelend arts. >> Verstrekking van deze informatie is conform het Privacy reglement van >> de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de >> geadresseerde. Gebruik van deze informatie door anderen dan de >> geadresseerde is, zonder voorafgaande schriftelijke toestemming van >> de rechthebbende , verboden. De Sint Maartenskliniek staat niet in >> voor de juiste en volledige overbrenging van de inhoud van een >> gezonden e-mail, noch voor de ontvangst daarvan. >> >> Sint Maartenskliniek >> Hengstdal 3, >> 6574 NA Ubbergen (bij Nijmegen) >> Telefoon 024-3659 911 >> Telefax 024-3659 204 >> KvK nummer 41055111 >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From sla.samiee at gmail.com Tue Feb 14 17:42:50 2012 From: sla.samiee at gmail.com (Soheila Samiee) Date: Tue, 14 Feb 2012 11:42:50 -0500 Subject: [FieldTrip] A problem in real-time processing of MEG signal using field trip buffer Message-ID: Dear group, I use FieldTrip for real-time processing of MEG signals using shared memory and field trip buffer in a machine other than acquisition system. I use matlab for reading the buffer and processing the data. During my data acquisition and sending it to other computer with *acq2ft*in linux, I face a problem. After sending some blocks of data, this message: "*Internal Converter thread does not keep up with load*" is shown in the terminal of *acq2ft* and in my matlab session I see an error : "ERROR: the buffer returned an error (517)". It does not depend on sampling rate of data in acquisition system. The problem often solve when I restart the computer which receives the data, but after some minutes of transferring the data I see the message again. Would you please help me in solving this problem? Best Wishes, Soheila -------------- next part -------------- An HTML attachment was scrubbed... URL: From akiko.ikkai at gmail.com Wed Feb 15 17:45:37 2012 From: akiko.ikkai at gmail.com (Akiko Ikkai) Date: Wed, 15 Feb 2012 11:45:37 -0500 Subject: [FieldTrip] volume conduction model missing .mat In-Reply-To: References: <2341406D-6422-4FD3-AD3C-73D1BF70B6CF@mac.com> Message-ID: Dear Fieldtrip users, Thank you Patrick, Nathan & Gio for your inputs. My MRI anatomical images need extensive cleaning (enhance contrasts, get rid of non-zero voxels outside the brain, etc...) before segmentation, as well as adjusting cfg.threshold for each tissue type during segmentation and each subject. At least testing with SPM standard MRI, segmentation and forward modeling works OK now. Individual subject's MRI, though, is still problematic, and I have a question for Fieldtrip developers: could you let me know whether "Create BEM headmodel for EEG ( http://fieldtrip.fcdonders.nl/example/create_bem_headmodel_for_eeg )" routine is what you recommend, or it's integrated into a newer function with newer cfg options? Is there a page I missed on the web? Thank you so much for your time! Akiko On Fri, Feb 10, 2012 at 4:36 AM, Gio Piantoni wrote: > Hi Akiki and Patrick, > > I agree with Nathan about segmentation problems. I had the same > problem when two of the three meshes intersected each other. Before > you run the forward model, you should check the segmentation (bnd) > using ft_plot_mesh. > ft_plot_mesh(bnd(1), 'facealpha', .5) > hold on > ft_plot_mesh(bnd(2), 'facecolor', 'r') > You will see that the two meshes intersect with each other. Depending > on how you created the meshes, you should fix the parameters in such a > way that they don't intersect. For example, ft_volumesegment has a > cfg.threshold option (you can check how the segmentation went with > ft_sourceplot) and ft_prepare_mesh_new has cfg.thresholdseg and > cfg.smoothseg. > > I think that the meshes in SPM are computed on an (affine-transformed) > template and not on the anatomically derived meshes. The template is > more robust and that's why the two surfaces do not intersect. > > In general, the segmentation depends on the quality of your MRIs and > you should really visually check the segmentation and meshes. When > those look ok, the BEM forward model usually works. Hope this helps. > > Cheers, > > Gio > > On Fri, Feb 10, 2012 at 09:00, Nathan Weisz wrote: > > Hi Akiki, > > > > I am not a headmodel expert. > > but looking at the output message, it seems your segementation did not go > > too well (see the "intersect" message). my intuition is then then the > next > > temporary file *.ama is not created and ft_prepare_bemmodel then simply > says > > ciao. > > > > perhaps you want to check / redo the segmentation? > > > > good luck, > > nathan > > > > > > On 09.02.2012, at 23:04, Akiko Ikkai wrote: > > > > Hi, > > > > I'm trying to create a volume conduction model for my EEG study based on > > anatomical MRI, and having trouble with ft_prepare_bemmodel > > > > when I run > > cfg = []; > > cfg.tissue = [7 4 1]; % value for brain, skull, and scalp > > cfg.conductivity = [1 1/80 1]*.33; % after standard_BEM.zip data > > cfg.isolatedsource = true; > > cfg.method = 'dipoli'; > > cfg.sourceunits = 'mm'; > > cfg.mriunits = 'mm'; > > vol = ft_prepare_bemmodel(cfg, seg4bem); > > > > I get the following error message while ft_prepare_bemmodel is running: > > > > Fatal error in dipoli: interface > > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and > > /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect > > at vertex 1402 of > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri > > > > Warning: an error ocurred while running dipoli > >> In dipoli at 94 > > In ft_prepare_bemmodel at 112 > > Error using ==> fread > > Invalid file identifier. Use fopen to generate a valid file identifier. > > Warning: File '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' > not > > found. > >> In dipoli at 102 > > In ft_prepare_bemmodel at 112 > > > > > > and the output vol is missing .mat, which causes an error > > during ft_sourceanalysis. > >>> vol > > vol = > > cond: [0.3300 0.0041 0.3300] > > bnd: [1x3 struct] > > source: 3 > > skin_surface: 3 > > skin: 1 > > type: 'dipoli' > > > > Does anyone know how to correct for "fatal error" so > > that ft_prepare_bemmodel creates the correct volume conduction model? I > > opened .tri file and removed line 1402, but got the same results. > > > > Thanks in advance! Akiko > > > > -- > > Akiko Ikkai, Ph.D. > > Postdoctoral Fellow > > Department of Psychological and Brain Sciences > > Johns Hopkins University > > Ames Hall, 3400 N. Charles St. > > Baltimore, MD 21218 > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Akiko Ikkai, Ph.D. Postdoctoral Fellow Department of Psychological and Brain Sciences Johns Hopkins University Ames Hall, 3400 N. Charles St. Baltimore, MD 21218 -------------- next part -------------- An HTML attachment was scrubbed... URL: From shayda.malekpour at gmail.com Wed Feb 15 21:19:50 2012 From: shayda.malekpour at gmail.com (Shayda Malekpour) Date: Wed, 15 Feb 2012 14:19:50 -0600 Subject: [FieldTrip] A question Message-ID: Dear All, I am using fieldtrip on MEG data set. I want to know if I do not remove any ICA component, will the data be the same as the original data, or is there is a filter somewhere in the software that changes the data? If so how much does it change it (What is their relative difference?) Thanks, Sheida -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu Feb 16 09:28:43 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 16 Feb 2012 09:28:43 +0100 Subject: [FieldTrip] A question In-Reply-To: References: Message-ID: Dear Sheida, You probably need to provide a bit more information before anyone is able to help you. In general, if you perform ICA, you get out component timecourses and mixing/unmixing matrices. If you keep all your components, and multiply them with the mixing matrix, you should get all your original channel timecourses out again. So: if you don't change the data, the data will not be changed :) Best, Eelke On 15 February 2012 21:19, Shayda Malekpour wrote: > Dear All, > > I am using fieldtrip on MEG data set. > I want to know if I do not remove any ICA component,  will the data be  the > same as the original data, or is there is a filter somewhere in the software > that changes the data? If so how much does it change it (What is their > relative difference?) > > Thanks, > > Sheida > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Thu Feb 16 10:36:05 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 16 Feb 2012 10:36:05 +0100 Subject: [FieldTrip] A problem in real-time processing of MEG signal using field trip buffer In-Reply-To: References: Message-ID: <4F3CCE05.4050109@donders.ru.nl> Dear Soheila, we were facing the same problem here. Presumably, there is some problem in the shared memory module that the buffer is using. Right now, however, we could not find out where the error precisely comes from, so our best work around is to restart the computer prior recording and optimize settings, such as channels and sampling/decimation rate of acq2ft. In our lab, we managed to find near-optimal settings, so that the buffer crashes only rarely (actually, I never saw it crashing when the acquisition computer was freshly restarted). Note that a lower number of channels or higher decimation does not mean that it runs more stable. It seems to be literally a trial-and-error approach :/ In order to track this down further, we need some more information, e.g. what MEG system are you using? What's your sampling rate, how many channels do you put into the buffer, and what's your decimation rate? It would be great if you could send me that information so that we can maybe try to track this down. Best regards, Jörn On 2/14/2012 5:42 PM, Soheila Samiee wrote: > Dear group, > > I use FieldTrip for real-time processing of MEG signals using shared > memory and field trip buffer in a machine other than acquisition > system. I use matlab for reading the buffer and processing the data. > During my data acquisition and sending it to other computer with > /acq2ft/ in linux, I face a problem. After sending some blocks of > data, this message: "/Internal Converter thread does not keep up with > load/" is shown in the terminal of /acq2ft/ and in my matlab session I > see an error : "ERROR: the buffer returned an error (517)". It does > not depend on sampling rate of data in acquisition system. The problem > often solve when I restart the computer which receives the data, but > after some minutes of transferring the data I see the message again. > > Would you please help me in solving this problem? > Best Wishes, > Soheila > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.piantoni at nin.knaw.nl Thu Feb 16 11:52:45 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Thu, 16 Feb 2012 11:52:45 +0100 Subject: [FieldTrip] volume conduction model missing .mat In-Reply-To: References: <2341406D-6422-4FD3-AD3C-73D1BF70B6CF@mac.com> Message-ID: Hi Akiko, What do you mean "problematic" exactly? From my understanding, there are 4 steps to get from the MRI to the forward model. 1. from MRI to segmentation 2. from segmentation to mesh (bnd) 3. from mesh to headmodel 4. from headmodel to forward model Here is the code I use. It seems to work fine, but experts might want to chip in and improve it. 1. from MRI to segmentation %-----------------% %-read MRI mrifile = '/path/to/your/mri.nii.gz'; mri = ft_read_mri(mrifile); %-----------------% %-----------------% %-segmenting the volume, Tissue Probability Maps % It takes time to run 'tpm' cfg1 = []; cfg1.threshold = []; cfg1.output = 'tpm'; cfg1.coordsys = 'spm'; tpm = ft_volumesegment(cfg1, mri); tpm.anatomy = mri.anatomy; %-----------------% %-----------------% %-segmenting the volume % this is faster after tpm cfg1 = []; cfg1.threshold = 1; % 1 is default, my MRI scalps were noisy, so I had to make it lower. cfg1.output = 'scalp'; cfg1.coordsys = 'spm'; segscalp = ft_volumesegment(cfg1, tpm); cfg1 = []; cfg1.threshold = []; cfg1.output = {'skull' 'brain'}; cfg1.coordsys = 'spm'; segment = ft_volumesegment(cfg1, tpm); segment.scalp = segscalp.scalp; %-----------------% Check the output with ft_sourceplot 2. from segmentation to mesh (bnd) %-----------------% %-prepare mesh for skull and brain (easy) cfg2 = []; cfg2.tissue = {'skull', 'brain'}; cfg2.numvertices = [1200 1000]; cfg2.transform = segment.transform; bnd = ft_prepare_mesh_new(cfg2, segment); %-----------------% %-----------------% %-prepare mesh for scalp (we need to be more liberal with threshold, bc of poor quality of MRI) cfg2 = []; cfg2.tissue = {'scalp'}; cfg2.numvertices = 2500; cfg2.thresholdseg = 0.1; cfg2.transform = segment.transform; scalp = ft_prepare_mesh_new(cfg2, segment); %-----------------% %-----------------% %-combine scalp and bnd bnd = [scalp bnd]; ft_plot_mesh(bnd(1), 'facealpha', .5) hold on ft_plot_mesh(bnd(2), 'facecolor', 'red') %-----------------% If bnd is good, no intersection between meshes and the outline looks nice, the following should run without problems. Please, do check your bnd. Segmentation and ft_prepare_mesh_new work really well. Another approach to get nice meshes is to skip step 1 and 2 and use Freesurfer/MNE. You can read the meshes in fieldtrip (ft_read_headshape, I think). The meshes are in the "bem" folder of Freesurfer, but I don't remember off the top of my head which files you should read ("outer_skull, inner_skull", I think). These meshes have a very very high resolution, you can scale them down with "reducepatch" in Matlab. 3. from mesh to headmodel %-----------------% %-headmodel cfg3 = []; cfg3.method = 'bem_dipoli'; cfg3.conductivity = [0.33 0.0042 0.33]; vol = ft_prepare_headmodel(cfg3, bnd); %-----------------% You can really pick your favorite here: dipoli, openmeeg, bemcp. This will take time (the more time, the more points on your meshes). 4. from headmodel to forward model You last problem is to get electrodes and headmodel in the same space. The template in SPM is already in MNI space, your individual MRIs probably not. You can realign them to MNI space before step 1 using SPM or FSL. elec = ft_read_sens(sensfile); elec = ft_convert_units(elec, 'mm'); %-------% %-simple transformation (based on visual realignment) % elecM is an affine matrix that you can get from ft_electroderealign % electrodes do not need to match the scalp perfectly, but they should be pretty close by. elec.chanpos = warp_apply(elecM, elec.chanpos); elec.elecpos = warp_apply(elecM, elec.elecpos); %-------% [vol, elec] = ft_prepare_vol_sens(vol, elec); % now you should check that the electrodes are on the scalp. %-----------------% %-----------------% %-prepare leadfield cfg4 = []; cfg4.elec = elec; cfg4.vol = vol; cfg4.grid.xgrid = -70:10:70; cfg4.grid.ygrid = -110:10:80; cfg4.grid.zgrid = -60:10:90; cfg4.inwardshift = 1; % to avoid dipoles on the border of bnd(3), which are very instable cfg4.grid.tight = 'no'; cfg4.feedback = 'none'; lead = ft_prepare_leadfield(cfg4, []); % use ft_plot_topo3d and ft_plot_dipole to check whether the projection of your dipole onto the scalp makes sense. %-----------------% "lead" should be your subject-specific, electrode-specific leadfield. There are quite a few parameters that you can change, but a clean segmentation and non-intersecting, smooth and realistic-looking meshes are a must. Then, using dipoli, openmeeg or bemcp should not change your forward model too much. Sorry if some points are not clear, but you should really look at your MRI/segmentation/meshes/electrodes/forward model as much as possible. Hope this will get you started. I appreciate any feedback on improving the code, this is just my personal attempt. Cheers Gio On Wed, Feb 15, 2012 at 17:45, Akiko Ikkai wrote: > Dear Fieldtrip users, > > Thank you Patrick, Nathan & Gio for your inputs. My MRI anatomical images > need extensive cleaning (enhance contrasts, get rid of non-zero voxels > outside the brain, etc...) before segmentation, as well as adjusting > cfg.threshold for each tissue type during segmentation and each subject. At > least testing with SPM standard MRI, segmentation and forward modeling works > OK now. > > Individual subject's MRI, though, is still problematic, and I have a > question for Fieldtrip developers: could you let me know whether "Create BEM > headmodel for EEG ( >  http://fieldtrip.fcdonders.nl/example/create_bem_headmodel_for_eeg )" > routine is what you recommend, or it's integrated into a newer function with > newer cfg options? Is there a page I missed on the web? > > Thank you so much for your time! > Akiko > > On Fri, Feb 10, 2012 at 4:36 AM, Gio Piantoni > wrote: >> >> Hi Akiki and Patrick, >> >> I agree with Nathan about segmentation problems. I had the same >> problem when two of the three meshes intersected each other. Before >> you run the forward model, you should check the segmentation (bnd) >> using ft_plot_mesh. >> ft_plot_mesh(bnd(1), 'facealpha', .5) >> hold on >> ft_plot_mesh(bnd(2), 'facecolor', 'r') >> You will see that the two meshes intersect with each other. Depending >> on how you created the meshes, you should fix the parameters in such a >> way that they don't intersect. For example, ft_volumesegment has a >> cfg.threshold option (you can check how the segmentation went with >> ft_sourceplot) and ft_prepare_mesh_new has cfg.thresholdseg and >> cfg.smoothseg. >> >> I think that the meshes in SPM are computed on an (affine-transformed) >> template and not on the anatomically derived meshes. The template is >> more robust and that's why the two surfaces do not intersect. >> >> In general, the segmentation depends on the quality of your MRIs and >> you should really visually check the segmentation and meshes. When >> those look ok, the BEM forward model usually works. Hope this helps. >> >> Cheers, >> >> Gio >> >> On Fri, Feb 10, 2012 at 09:00, Nathan Weisz wrote: >> > Hi Akiki, >> > >> > I am not a headmodel expert. >> > but looking at the output message, it seems your segementation did not >> > go >> > too well (see the "intersect" message). my intuition is then then the >> > next >> > temporary file *.ama is not created and ft_prepare_bemmodel then simply >> > says >> > ciao. >> > >> > perhaps you want to check / redo the segmentation? >> > >> > good luck, >> > nathan >> > >> > >> > On 09.02.2012, at 23:04, Akiko Ikkai wrote: >> > >> > Hi, >> > >> > I'm trying to create a volume conduction model for my EEG study based on >> > anatomical MRI, and having trouble with ft_prepare_bemmodel >> > >> > when I run >> > cfg                = []; >> > cfg.tissue         = [7 4 1]; % value for brain, skull, and scalp >> > cfg.conductivity   = [1 1/80 1]*.33; % after standard_BEM.zip data >> > cfg.isolatedsource = true; >> > cfg.method         = 'dipoli'; >> > cfg.sourceunits = 'mm'; >> > cfg.mriunits = 'mm'; >> > vol = ft_prepare_bemmodel(cfg, seg4bem); >> > >> > I get the following error message while ft_prepare_bemmodel is running: >> > >> > Fatal error in dipoli:  interface >> > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and >> > /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect >> >  at vertex 1402 of >> > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri >> > >> > Warning: an error ocurred while running dipoli >> >> In dipoli at 94 >> >   In ft_prepare_bemmodel at 112 >> > Error using ==> fread >> > Invalid file identifier.  Use fopen to generate a valid file identifier. >> > Warning: File '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' >> > not >> > found. >> >> In dipoli at 102 >> >   In ft_prepare_bemmodel at 112 >> > >> > >> > and the output vol is missing .mat, which causes an error >> > during ft_sourceanalysis. >> >>> vol >> > vol = >> >             cond: [0.3300 0.0041 0.3300] >> >              bnd: [1x3 struct] >> >           source: 3 >> >     skin_surface: 3 >> >             skin: 1 >> >             type: 'dipoli' >> > >> > Does anyone know how to correct for "fatal error" so >> > that ft_prepare_bemmodel creates the correct volume conduction model? I >> > opened .tri file and removed line 1402, but got the same results. >> > >> > Thanks in advance! Akiko >> > >> > -- >> > Akiko Ikkai, Ph.D. >> > Postdoctoral Fellow >> > Department of Psychological and Brain Sciences >> > Johns Hopkins University >> > Ames Hall, 3400 N. Charles St. >> > Baltimore, MD 21218 >> > >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > >> > >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Akiko Ikkai, Ph.D. > Postdoctoral Fellow > Department of Psychological and Brain Sciences > Johns Hopkins University > Ames Hall, 3400 N. Charles St. > Baltimore, MD 21218 > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From politzerahless at gmail.com Thu Feb 16 12:35:13 2012 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Thu, 16 Feb 2012 05:35:13 -0600 Subject: [FieldTrip] A question Message-ID: Hi Shayda, FieldTrip does not apply a filter by default, and I am not aware of any other 'hidden' transformations that happen. You can specify a filter when importing the data with ft_preprocessing(), and there are several different kinds of filters available, which will affect your data in different ways-- see http://fieldtrip.fcdonders.nl/reference/ft_preprocessing. The best thing to do is to import your data without using a filter and, if possible, use whatever tool comes with your MEG software to import that raw data into MATLAB as well (for example, for CTF this would be ds2txt), then you can plot them together to make sure there are no differences--when I have tried this with EEG data, fieldtrip hasn't changed them. Of course, if you want to use a filter, you can also try several filters (you can either filter within your system's software and then import straight to Fieldtrip, or use one of Fieldtrip's filters during import) and plot them to see how they affect your data. Best, Steve Politzer-Ahles > > Message: 2 > Date: Wed, 15 Feb 2012 14:19:50 -0600 > From: Shayda Malekpour > To: fieldtrip at donders.ru.nl > Subject: [FieldTrip] A question > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > Dear All, > > I am using fieldtrip on MEG data set. > I want to know if I do not remove any ICA component, will the data be the > same as the original data, or is there is a filter somewhere in the > software that changes the data? If so how much does it change it (What is > their relative difference?) > > Thanks, > > Sheida > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120215/ba4458d8/attachment-0001.html > > > > ------------------------------ > > Message: 3 > Date: Thu, 16 Feb 2012 09:28:43 +0100 > From: Eelke Spaak > To: Email discussion list for the FieldTrip project > > Subject: Re: [FieldTrip] A question > Message-ID: > > > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Sheida, > > You probably need to provide a bit more information before anyone is > able to help you. In general, if you perform ICA, you get out > component timecourses and mixing/unmixing matrices. If you keep all > your components, and multiply them with the mixing matrix, you should > get all your original channel timecourses out again. So: if you don't > change the data, the data will not be changed :) > > Best, > Eelke > > On 15 February 2012 21:19, Shayda Malekpour > wrote: > > Dear All, > > > > I am using fieldtrip on MEG data set. > > I want to know if I do not remove any ICA component,? will the data be? > the > > same as the original data, or is there is a filter somewhere in the > software > > that changes the data? If so how much does it change it (What is their > > relative difference?) > > > > Thanks, > > > > Sheida > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > ------------------------------ > > Message: 4 > Date: Thu, 16 Feb 2012 10:36:05 +0100 > From: "J?rn M. Horschig" > To: Email discussion list for the FieldTrip project > > Subject: Re: [FieldTrip] A problem in real-time processing of MEG > signal using field trip buffer > Message-ID: <4F3CCE05.4050109 at donders.ru.nl> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Dear Soheila, > > we were facing the same problem here. Presumably, there is some problem > in the shared memory module that the buffer is using. Right now, > however, we could not find out where the error precisely comes from, so > our best work around is to restart the computer prior recording and > optimize settings, such as channels and sampling/decimation rate of > acq2ft. In our lab, we managed to find near-optimal settings, so that > the buffer crashes only rarely (actually, I never saw it crashing when > the acquisition computer was freshly restarted). Note that a lower > number of channels or higher decimation does not mean that it runs more > stable. It seems to be literally a trial-and-error approach :/ > > In order to track this down further, we need some more information, e.g. > what MEG system are you using? What's your sampling rate, how many > channels do you put into the buffer, and what's your decimation rate? It > would be great if you could send me that information so that we can > maybe try to track this down. > > Best regards, > J?rn > > On 2/14/2012 5:42 PM, Soheila Samiee wrote: > > Dear group, > > > > I use FieldTrip for real-time processing of MEG signals using shared > > memory and field trip buffer in a machine other than acquisition > > system. I use matlab for reading the buffer and processing the data. > > During my data acquisition and sending it to other computer with > > /acq2ft/ in linux, I face a problem. After sending some blocks of > > data, this message: "/Internal Converter thread does not keep up with > > load/" is shown in the terminal of /acq2ft/ and in my matlab session I > > see an error : "ERROR: the buffer returned an error (517)". It does > > not depend on sampling rate of data in acquisition system. The problem > > often solve when I restart the computer which receives the data, but > > after some minutes of transferring the data I see the message again. > > > > Would you please help me in solving this problem? > > Best Wishes, > > Soheila > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > J?rn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120216/c01be767/attachment.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 15, Issue 17 > ***************************************** > -- Stephen Politzer-Ahles University of Kansas Linguistics Department http://www.linguistics.ku.edu/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Feb 16 12:39:25 2012 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 16 Feb 2012 12:39:25 +0100 Subject: [FieldTrip] A question In-Reply-To: References: Message-ID: Dear All, All true, except that ICA implemented by FT does demean the data before unmixing by default. Use cfg.demean = 'no' if you don't want to. cheers, stephen On 16 February 2012 12:35, Stephen Politzer-Ahles wrote: > Hi Shayda, > > FieldTrip does not apply a filter by default, and I am not aware of any > other 'hidden' transformations that happen. You can specify a filter when > importing the data with ft_preprocessing(), and there are several different > kinds of filters available, which will affect your data in different ways-- > see http://fieldtrip.fcdonders.nl/reference/ft_preprocessing. The best thing > to do is to import your data without using a filter and, if possible, use > whatever tool comes with your MEG software to import that raw data into > MATLAB as well (for example, for CTF this would be ds2txt), then you can > plot them together to make sure there are no differences--when I have tried > this with EEG data, fieldtrip hasn't changed them. Of course, if you want to > use a filter, you can also try several filters (you can either filter within > your system's software and then import straight to Fieldtrip, or use one of > Fieldtrip's filters during import) and plot them to see how they affect your > data. > > Best, > Steve Politzer-Ahles > > >> >> >> Message: 2 >> Date: Wed, 15 Feb 2012 14:19:50 -0600 >> From: Shayda Malekpour >> To: fieldtrip at donders.ru.nl >> Subject: [FieldTrip] A question >> Message-ID: >> >>   >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Dear All, >> >> I am using fieldtrip on MEG data set. >> I want to know if I do not remove any ICA component,  will the data be >>  the >> same as the original data, or is there is a filter somewhere in the >> software that changes the data? If so how much does it change it (What is >> their relative difference?) >> >> Thanks, >> >> Sheida >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> >> >> ------------------------------ >> >> Message: 3 >> Date: Thu, 16 Feb 2012 09:28:43 +0100 >> From: Eelke Spaak >> To: Email discussion list for the FieldTrip project >>         >> Subject: Re: [FieldTrip] A question >> Message-ID: >> >>   >> Content-Type: text/plain; charset=ISO-8859-1 >> >> >> Dear Sheida, >> >> You probably need to provide a bit more information before anyone is >> able to help you. In general, if you perform ICA, you get out >> component timecourses and mixing/unmixing matrices. If you keep all >> your components, and multiply them with the mixing matrix, you should >> get all your original channel timecourses out again. So: if you don't >> change the data, the data will not be changed :) >> >> Best, >> Eelke >> >> On 15 February 2012 21:19, Shayda Malekpour >> wrote: >> > Dear All, >> > >> > I am using fieldtrip on MEG data set. >> > I want to know if I do not remove any ICA component,? will the data be? >> > the >> >> > same as the original data, or is there is a filter somewhere in the >> > software >> > that changes the data? If so how much does it change it (What is their >> > relative difference?) >> > >> > Thanks, >> > >> > Sheida >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> ------------------------------ >> >> Message: 4 >> Date: Thu, 16 Feb 2012 10:36:05 +0100 >> From: "J?rn M. Horschig" >> To: Email discussion list for the FieldTrip project >>         >> Subject: Re: [FieldTrip] A problem in real-time processing of MEG >>        signal using field trip buffer >> Message-ID: <4F3CCE05.4050109 at donders.ru.nl> >> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" >> >> Dear Soheila, >> >> we were facing the same problem here. Presumably, there is some problem >> in the shared memory module that the buffer is using. Right now, >> however, we could not find out where the error precisely comes from, so >> our best work around is to restart the computer prior recording and >> optimize settings, such as channels and sampling/decimation rate of >> acq2ft. In our lab, we managed to find near-optimal settings, so that >> the buffer crashes only rarely (actually, I never saw it crashing when >> the acquisition computer was freshly restarted). Note that a lower >> number of channels or higher decimation does not mean that it runs more >> stable.  It seems to be literally a trial-and-error approach :/ >> >> In order to track this down further, we need some more information, e.g. >> what MEG system are you using? What's your sampling rate, how many >> channels do you put into the buffer, and what's your decimation rate? It >> would be great if you could send me that information so that we can >> maybe try to track this down. >> >> Best regards, >> J?rn >> >> On 2/14/2012 5:42 PM, Soheila Samiee wrote: >> > Dear group, >> > >> > I use FieldTrip for real-time processing of MEG signals using shared >> > memory and field trip buffer in a machine other than acquisition >> > system. I use matlab for reading the buffer and processing the data. >> > During my data acquisition and sending it to other computer with >> > /acq2ft/ in linux, I face a problem. After sending some blocks of >> > data, this message: "/Internal Converter thread does not keep up with >> > load/" is shown in the terminal of /acq2ft/ and in my matlab session I >> > see an error : "ERROR: the buffer returned an error (517)". It does >> > not depend on sampling rate of data in acquisition system. The problem >> > often solve when I restart the computer which receives the data, but >> > after some minutes of transferring the data I see the message again. >> > >> > Would you please help me in solving this problem? >> > Best Wishes, >> > Soheila >> >> > >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -- >> J?rn M. Horschig >> PhD Student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> Neuronal Oscillations Group >> >> P.O. Box 9101 >> NL-6500 HB Nijmegen >> The Netherlands >> >> Contact: >> E-Mail: jm.horschig at donders.ru.nl >> Tel:    +31-(0)24-36-68493 >> Web: http://www.ru.nl/donders >> >> Visiting address: >> Trigon, room 2.30 >> Kapittelweg 29 >> NL-6525 EN Nijmegen >> The Netherlands >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> >> >> ------------------------------ >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> End of fieldtrip Digest, Vol 15, Issue 17 >> ***************************************** > > > > > -- > Stephen Politzer-Ahles > University of Kansas > Linguistics Department > http://www.linguistics.ku.edu/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From carsten.wolters at uni-muenster.de Thu Feb 16 14:01:36 2012 From: carsten.wolters at uni-muenster.de (Dr. Carsten Wolters) Date: Thu, 16 Feb 2012 14:01:36 +0100 Subject: [FieldTrip] =?iso-8859-1?q?Postdoctoral_research_associate_positi?= =?iso-8859-1?q?on_available__at_the_University_of_M=FCnster?= Message-ID: <4F3CFE30.4050502@uni-muenster.de> Neuroscientist with focus on MR image analysis The Medical Faculty of the University of Münster is searching for a postdoctoral research associate at the 'Translational Research Imaging Center' (TRIC), where a new 3T MR-system for neuroimaging research will be put into operation soon. This position is focused on image processing and optimization to support the interdisciplinary working groups from the faculties of Medicine and Psychology. The position (TVL13) is initially limited to 3 years with possibility of extension. The area of responsibility includes the analysis of structural and functional MR data and the post-processing of fMRI- and DTI- measurements as well as the implementation of new post-processing methods for imaging and spectroscopy. Furthermore, the applicant should be interested in integration of different neuroimaging methods (multimodal integration). Besides an interdisciplinary and team-oriented working style, a high degree of mathematical and statistical knowledge is required. The applicant should possess a master degree (or equivalent) in natural or engineering sciences and a PhD and should be qualified by his scientific work and his own research that will also be pursued at the University of Münster. Applications of women and disabled applicants are explicitly welcome and will be preferred at same qualification, merits and achievements. For further questions please consult Dr. rer. nat. H. Kugel, the responsible senior physicist at the TRIC (Email: kugel at uni-muenster.de, Phone:+49/( 0)251 / 83-56145). The position will be open until filled. Applications should contain a personal statement of research background and interests, CV, list of publications and grants as well as the names of three referees and preprints of the three most important publications. Applications should be send to: *Dekan der Medizinischen Fakultät der Westfälischen Wilhelms-Universität Münster, Albert-Schweitzer-Campus 1, Gebäude D3, 48149 Münster * -- PD.Dr.rer.nat. Carsten Wolters Institute for Biomagnetism and Biosignalanalysis University of Muenster, 48149 Muenster, Germany Tel.: +49/(0)251-83-56904 Fax: +49/(0)251-83-56874 http://biomag.uni-muenster.de -------------- next part -------------- A non-text attachment was scrubbed... Name: MRTPostprocessing_Englisch.pdf Type: application/x-pdf Size: 166979 bytes Desc: not available URL: From jpnv2006 at gmail.com Thu Feb 16 17:35:28 2012 From: jpnv2006 at gmail.com (Juan Pablo Neira) Date: Thu, 16 Feb 2012 17:35:28 +0100 Subject: [FieldTrip] Align EEG electrode positions to BEM headmodel Question Message-ID: Hello, I am trying to align EEG electrodes to an individual MRI and a BEM model.  I am using the example: "Align EEG electrode positions to BEM headmodel" http://fieldtrip.fcdonders.nl/example/align_eeg_electrode_positions_to_bem_headmodel But I am having the next problem in "% align using fiducials" part: * Template structure (label, chanpos and elecpos) - sens_t structure (label, chanpos and elecpos) elec_mni.label = {'Nz', 'LPA', 'RPA'}; elec_mni.chanpos = [   head_Nas   head_Lpa   head_Rpa   ]; elec_mni.elecpos = [   head_Nas   head_Lpa   head_Rpa   ]; elec_mni.unit = 'mm'; % align using fiducials cfg = []; cfg.method = 'fiducial'; cfg.template= elec_mni; cfg.elec     = sens_t; cfg.casesensitive  = 'no';%'yes' or 'no' sens_aligned = ft_electroderealign(cfg); %Error message: %----------------------------------------------------- ??? Subscripted assignment between dissimilar structures. Error in ==> ft_electroderealign at 183     tmp(i) = ft_datatype_sens(template(i)); % ensure up-to-date sensor     descriptions (Oct 2011) %------------------------------------------------------- I have some questions that maybe can help to find the error: -  According to the example in the webpage, there are 2 functions from the private directory used:  electrodenormalize.m & warp_apply.m, but electrodenormalize.m never was used. Also in "% align using fiducials" the method used was 'realignfiducial', but that method is not available in electroderealign function. Is it possible the example is using the wrong function? - How should be the structure of the fiducials in the main sensor structure (sens_t). As 3 more electrodes (label+fid, chanpos+fid and elecpos+fid) or in a different place, for example sens_t.fid.pnt and sens_t.fid.label? By the way I am using Matlab 2011 and fieldtrip version 20120208 Best regards and thanks for the help. Jua Pablo Neira Vesga Christian Albrechts Universität Clinic Kiel, Germany From kd889 at nyu.edu Fri Feb 17 18:08:53 2012 From: kd889 at nyu.edu (Keith Doelling) Date: Fri, 17 Feb 2012 12:08:53 -0500 Subject: [FieldTrip] ft_channelrepair replaces channel data with NaNs after running PCA Message-ID: Hi guys, I'm struggling with my attempts to interpolate channel data for some bad channels. I put in the following code: cfg=[]; cfg.badchannel = 15; cfg.missingchannel = []; cfg.neighbours = neighbours; cfg.trials = 'all'; cleanchdata = ft_channelrepair(cfg,cleandata); the function the displays the following: "the input is raw data with 157 channels and 80 trials repairing channel AG015 using neighbour AG010 using neighbour AG014 using neighbour AG062 using neighbour AG092" suggesting that neighbours have been selected successfully. but a call to chdata.trial(1){15,:) just returns a bunch of NaNs rather than interpolated data I need. I found another email thread similar to this but that solution doesn't seem to apply to me as the neighbours seemed to have been selected successfully. The other interesting caveat is that ft_channelrepair seems to work fine if i run it without having run pca (to reject eyeblink and heartbeat components) beforehand. The code for the component analysis and the subsequent rejection are in separate loops. The PCA is saved into a .mat file and then loaded again when i'm ready to reject the bad components. But for simplicity's sake the important code looks like this. % principle component analysis run with 32 components cfg = []; cfg.channel = (1:157); cfg.runica.pca=32; pca_data = ft_componentanalysis(cfg,data); % view components in order to select bad ones cfg = []; cfg.layout = layout; % specify the layout file that should be used for plotting cfg.viewmode = 'component'; ft_databrowser(cfg, pca_data); waitfor(gcf); % type bad components as user input % for example: if runica002 and runica0003 should be rejected, type "2,3" into the dialogue box badcomps = inputdlg({'Bad Components:'}); badcomps = str2double(csv2cell(badcomps{1})); % reject bad components cfg = []; cfg.component = badcomps; cleandata = ft_rejectcomponent(cfg,pca_data); the variable 'cleandata' i get out from this code is the same cleandata i put in to ft_channelrepair. Are there any ideas as to what I've done wrong here? Let me know if I need to give you guys more information. Thanks for your help, Keith -- Keith Doelling Lab Manager and Research Assistant David Poeppel Lab New York University -------------- next part -------------- An HTML attachment was scrubbed... URL: From karl.doron at gmail.com Sat Feb 18 02:16:50 2012 From: karl.doron at gmail.com (Karl Doron) Date: Fri, 17 Feb 2012 17:16:50 -0800 Subject: [FieldTrip] help with channel combination In-Reply-To: References: Message-ID: Hello, I'm trying to run ft_connectivityanalysis on a reduced set of MEG channels, i.e., left and right posterior channels. Because neighboring channels are highly correlated, I'd like to exclude them and look only at "inter-hemispheric" connections. I'm having some troubling getting ft_channelcombination to produce this set of channels. I have 43 channels per hemisphere giving n(n-1)/2 connections. I made an NX2 matrix using repmat.m and passed it as cfg.channelcmb; however the output of ft_connectivityanalysis gave a vector for 'cohspctrm' rather than a chan_chan_freq matrix. Thanks for any suggestions. Karl Doron UC Santa Barbara -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Sat Feb 18 10:24:02 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Sat, 18 Feb 2012 10:24:02 +0100 Subject: [FieldTrip] help with channel combination In-Reply-To: References: Message-ID: Hi Karl, This is perfectly fine behavior. ft_connectivityanalysis either outputs a 'chan_chan_freq' matrix, or a 'chancmb_freq' matrix. The former will be the output when the input freq-structure contains fourier-spectra, and the cfg lacks a channelcmb field. Ft_connectivityanalysis then computes connectivity between all channel pairs, which can conveniently be stored in a square matrix 'chan_chan' for each frequency. If the freq-structure contains cross-spectra (and power-spectra), or if you specify a cfg.channelcmb in combination with fourierspectra in the input, you will get the connectivity data to be 'chancmb_freq', i.e. each row in the matrix contains a spectrum. The reason for this is that it is a priori unlikely that the channelcmb-array defines a set of channel pairs that can be represented in a square all-to-all matrix. If it is your intention to end up with a square matrix, you may want to consider first doing a subselection of channels, i.e. computing your fourierspectra only on the subset of channels you want to use in a later step, and then call ft_connectivityanalysis without a channelcmb field in the cfg. See for some additional information about the different representation of frequency domain data: http://fieldtrip.fcdonders.nl/faq/in_what_way_can_frequency_domain_data_be_represented_in_fieldtrip Cheers, Jan-Mathijs On Feb 18, 2012, at 2:16 AM, Karl Doron wrote: > Hello, > > I'm trying to run ft_connectivityanalysis on a reduced set of MEG channels, i.e., left and right posterior channels. Because neighboring channels are highly correlated, I'd like to exclude them and look only at "inter-hemispheric" connections. > > I'm having some troubling getting ft_channelcombination to produce this set of channels. I have 43 channels per hemisphere giving n(n-1)/2 connections. I made an NX2 matrix using repmat.m and passed it as cfg.channelcmb; however the output of ft_connectivityanalysis gave a vector for 'cohspctrm' rather than a chan_chan_freq matrix. > > Thanks for any suggestions. > > Karl Doron > UC Santa Barbara > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhaoyizhe at gmail.com Mon Feb 20 11:51:07 2012 From: zhaoyizhe at gmail.com (zhaoyizhe) Date: Mon, 20 Feb 2012 18:51:07 +0800 Subject: [FieldTrip] question about ft_sourceinterpolate Message-ID: <52DE5EF7-93B4-4261-AAC9-A1550A37C986@gmail.com> Dear all, I have a problem in function of 'ft_sourceinterpolate'. I run the scrips below, and data from the ftp sever as the test data. the result is below: ??? Error using ==> ft_checkconfig at 162 The field cfg.parameter is required cfg.parameter='all' has been tried. the result is below: ??? Reference to non-existent field 'all'. Would you mind tell me how to deal with it? Thanks a lot in advance. -------------------------------------- close clc clear load source mri = ft_read_mri('Subject01.mri'); cfg = []; cfg.downsample = 2; sourcePostInt = ft_sourceinterpolate(cfg, sourcePost , mri); -------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From mark.noordenbos at gmail.com Mon Feb 20 12:25:46 2012 From: mark.noordenbos at gmail.com (Mark Noordenbos) Date: Mon, 20 Feb 2012 12:25:46 +0100 Subject: [FieldTrip] clusterstatistics Message-ID: Dear Fieldtrippers, I have a question about how to report the findings using clusterstatistics. I used the cluster method to determine at which channels activity is significant different from zero. The cluster method revealed a significant cluster ranging from about 258-370 ms (using ft_clusterplot). If I only look at a certain channel (e.g., Fz) the activity is only significant during 272-322 ms. The time interval of the cluster is determined by the first and the last sample where the activity is significant, regardless if a certain channel shows significant activity during the complete time interval. For instance, if a certain channel shows significant activity only at sample X and another channel only at sample X+100, the cluster ranges from sample X to X+100. My problem is how to report the finding of the significant cluster. If I report that a significant cluster was found from 258-370 ms and show a plot of the activity at Fz (272-322 ms). Then the time intervals and p-values do not correspond. The stat structure contains only the p-value for the time interval of the cluster and not of the individual channels. Any suggestions or examples of how to report clusterstatistics. Regards, Mark -- Mark Noordenbos, MSc Radboud University Nijmegen Behavioural Science Institute P.O. Box 9104, Room A05.36 6500 HE Nijmegen The Netherlands Email: m.noordenbos at bsi.ru.nl Telephone: +31 24 3612070 Fax: +31 24 3616211 http://www.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From Lilla.Magyari at mpi.nl Mon Feb 20 14:44:57 2012 From: Lilla.Magyari at mpi.nl (Magyari, Lilla) Date: Mon, 20 Feb 2012 14:44:57 +0100 Subject: [FieldTrip] question about ft_sourceinterpolate In-Reply-To: <52DE5EF7-93B4-4261-AAC9-A1550A37C986@gmail.com> References: <52DE5EF7-93B4-4261-AAC9-A1550A37C986@gmail.com> Message-ID: <4F424E59.9030609@mpi.nl> Hi, ft_sourceinterpolate is probably requires the specific field of your functional data that should be interpolated. I do not know what kind of source-reconstruction you did on your data, and what kind of fields your data has (sourcePost), but it will be probably the "avg.pow" field. So, I suggest to try this: cfg.parameter = 'avg.pow'; Best, Lilla zhaoyizhe wrote: > Dear all, > > I have a problem in function of 'ft_sourceinterpolate'. > > I run the scrips below, and data from the ftp sever as the test data. > > the result is below: > ??? Error using ==> ft_checkconfig at 162 > The field cfg.parameter is required > > > cfg.parameter='all' has been tried. > the result is below: > ??? Reference to non-existent field 'all'. > > Would you mind tell me how to deal with it? Thanks a lot in advance. > > > -------------------------------------- > close > clc > clear > > > load source > mri = ft_read_mri('Subject01.mri'); > > cfg = []; > cfg.downsample = 2; > sourcePostInt = ft_sourceinterpolate(cfg, sourcePost , mri); > > -------------------------------------- > > > ------------------------------------------------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- PhD student Language and Cognition Group research assistant Neurobiology of Language Group Max Planck Institute for Psycholinguistics Nijmegen, P.O. Box 310, 6500AH, the Netherlands Phone: 0031 24 3521561 From zhaoyizhe at gmail.com Mon Feb 20 15:22:41 2012 From: zhaoyizhe at gmail.com (zhaoyizhe) Date: Mon, 20 Feb 2012 22:22:41 +0800 Subject: [FieldTrip] question about ft_sourceinterpolate In-Reply-To: <4F424E59.9030609@mpi.nl> References: <52DE5EF7-93B4-4261-AAC9-A1550A37C986@gmail.com> <4F424E59.9030609@mpi.nl> Message-ID: <64945130-6612-4591-B986-69C2A3904F69@gmail.com> Hi, Lilla, Thank you for your timely help! The problem has been solved! Cheers, Yizhe From sla.samiee at gmail.com Mon Feb 20 17:21:58 2012 From: sla.samiee at gmail.com (Soheila Samiee) Date: Mon, 20 Feb 2012 11:21:58 -0500 Subject: [FieldTrip] A problem in real-time processing of MEG signal using field trip buffer In-Reply-To: <4F3CCE05.4050109@donders.ru.nl> References: <4F3CCE05.4050109@donders.ru.nl> Message-ID: Dear Jörn, Thanks for your answer. I use CTF/VSM MedTech System. I use 364 channels and the sampling rate is 1200. The decimation rate is 1. As I saw in my recording there are two reasons for crashing in matlab session one of them is about transferring data which rarely occurs when the system is freshly restarted and the second one is related to reading data from buffer. When the number of samples of data which should be read is high we may see such problem. I wanted to check the timing of MEG System data stream and I used a m-file similar to what is published in fieldtrip website ( http://fieldtrip.fcdonders.nl/example/measuring_the_timing_delay_and_jitter_for_a_real-time_application), I attach the mfile to this email. When I run it step by step there is no problem, but when I run the whole file the problem of crashing matlab is occurred exactly when "i=2" and we are on the line of reading the data (*dat = buffer('get_dat', [s(i-1),s(i)],host,port); *). The problem occurs even if I restarted the computer just before running this file. On the other hand, although when the computer is freshly restarted we won't see any crash in matlab session during transferring data, but sometimes we see the message of "*Internal Converter thread does not keep up with load*" in the *acq2ft *terminal in acquisition system. This problem is depend on the rate of sending the data which is related to number of the channels and sampling rate, when we have more sampling rate or more number of channels we will see this message more times and when this message show on the screen, no data transfer to field trip buffer and we can't read data on the other computer. I appreciate it if you help me solve both of these problems about matlab crash and error in data transferring. All the best, Soheila On Thu, Feb 16, 2012 at 4:36 AM, "Jörn M. Horschig" < jm.horschig at donders.ru.nl> wrote: > Dear Soheila, > > we were facing the same problem here. Presumably, there is some problem in > the shared memory module that the buffer is using. Right now, however, we > could not find out where the error precisely comes from, so our best work > around is to restart the computer prior recording and optimize settings, > such as channels and sampling/decimation rate of acq2ft. In our lab, we > managed to find near-optimal settings, so that the buffer crashes only > rarely (actually, I never saw it crashing when the acquisition computer was > freshly restarted). Note that a lower number of channels or higher > decimation does not mean that it runs more stable. It seems to be > literally a trial-and-error approach :/ > > In order to track this down further, we need some more information, e.g. > what MEG system are you using? What's your sampling rate, how many channels > do you put into the buffer, and what's your decimation rate? It would be > great if you could send me that information so that we can maybe try to > track this down. > > Best regards, > Jörn > > > On 2/14/2012 5:42 PM, Soheila Samiee wrote: > > Dear group, > > I use FieldTrip for real-time processing of MEG signals using shared > memory and field trip buffer in a machine other than acquisition system. I > use matlab for reading the buffer and processing the data. > During my data acquisition and sending it to other computer with *acq2ft*in linux, I face a problem. After sending some blocks of data, this > message: "*Internal Converter thread does not keep up with load*" is > shown in the terminal of *acq2ft* and in my matlab session I see an error > : "ERROR: the buffer returned an error (517)". It does not depend on > sampling rate of data in acquisition system. The problem often solve when I > restart the computer which receives the data, but after some minutes of > transferring the data I see the message again. > > Would you please help me in solving this problem? > Best Wishes, > Soheila > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: DataStreamTiming.m Type: text/x-objcsrc Size: 1005 bytes Desc: not available URL: From g.piantoni at nin.knaw.nl Mon Feb 20 18:41:22 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Mon, 20 Feb 2012 18:41:22 +0100 Subject: [FieldTrip] clusterstatistics In-Reply-To: References: Message-ID: Hi Mark, It seems to me that clusterstatistics is giving the appropriate answer. Indeed it takes advantage of the information which can be sparse over multiple channels/frequency/time bins. The only criterion is that this activity is contiguous. I don't follow your example about significant activity at X and X+100 on two different channels. There should be some continuity between the two. As you mentioned, the cluster can span one channels between 0 and 100 and in another neighboring channel between 50 and 150. The cluster will correctly include both channels and the time window between 0 and 150. This is because there is some overlap in time between the two channels. If you think in terms of activity, you can report that activity is significantly different from baseline between 258 and 370 ms, over your channels. The p-value only belongs to the cluster, not to the single time point or channel. If you use bonferroni correction, you can attach single p-values to each timepoint/channel. If you have a priori hypothesis that you expect activity in Fz, you can specify a single channel in timelockstatistics. Depending your data, you might see more power (because you're testing fewer channels at the same time). Hope this helps, Gio -- 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.giovannipiantoni.com On Mon, Feb 20, 2012 at 12:25, Mark Noordenbos wrote: > Dear Fieldtrippers, > > > I have a question about how to report the findings using clusterstatistics. > I used the cluster method to determine at which channels activity is > significant different from zero. > > The cluster method revealed a significant cluster ranging from about 258-370 > ms (using ft_clusterplot). If I only look at a certain channel (e.g., Fz) > the activity is only significant during 272-322 ms. > > > The time interval of the cluster is determined by the first and the last > sample where the activity is significant, regardless if a certain channel > shows significant activity during the complete time interval. For instance, > if a certain channel shows significant activity only at sample X and another > channel only at sample X+100, the cluster ranges from sample X to X+100. > > > My problem is how to report the finding of the significant cluster. If I > report that a significant cluster was found from 258-370 ms and show a plot > of the activity at Fz (272-322 ms). Then the time intervals and p-values do > not correspond. The stat structure contains only the p-value for the time > interval of the cluster and not of the individual channels. > > > Any suggestions or examples of how to report clusterstatistics. > > > Regards, > Mark > > -- > Mark Noordenbos, MSc > > Radboud University Nijmegen > Behavioural Science Institute > > P.O. Box 9104, Room A05.36 > 6500 HE Nijmegen > The Netherlands > > Email: m.noordenbos at bsi.ru.nl > Telephone: +31 24 3612070 > Fax:          +31 24 3616211 > > http://www.ru.nl > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From drivolta81 at gmail.com Tue Feb 21 11:17:00 2012 From: drivolta81 at gmail.com (Davide Rivolta) Date: Tue, 21 Feb 2012 11:17:00 +0100 Subject: [FieldTrip] CTF to SPM Message-ID: Dear all, I wish to ask whether there is a way to import anatomical CTF files (.V2) into SPM. Thanks, Davide -- Davide Rivolta, PhD -------------- next part -------------- An HTML attachment was scrubbed... URL: From tomh at kurage.nimh.nih.gov Tue Feb 21 17:16:51 2012 From: tomh at kurage.nimh.nih.gov (Tom Holroyd (NIH/NIMH) [E]) Date: Tue, 21 Feb 2012 11:16:51 -0500 Subject: [FieldTrip] CTF to SPM In-Reply-To: References: Message-ID: <4F43C373.9090105@kurage.nimh.nih.gov> You can use AFNI to convert v2 .mri files to .nii files. Not v3 though, use CTF's MRIViewer to convert v3 format to v2 format and then use AFNI. I assume SPM can read .nii files. Davide Rivolta wrote: > Dear all, > > I wish to ask whether there is a way to import anatomical CTF files > (.V2) into SPM. >
Dr. Tom
--
How long have I investigated this one thing, the brain of the leech, so that here the slippery truth might no longer slip from me! Here is my domain! Thus spoke Zarathustra. From jan.schoffelen at donders.ru.nl Tue Feb 21 18:05:06 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 21 Feb 2012 18:05:06 +0100 Subject: [FieldTrip] CTF to SPM In-Reply-To: References: Message-ID: <3672CA8D-132F-4664-8251-56DF2F97FA73@donders.ru.nl> Hi Davide, If you use ft_read_mri to read in your *.mri you can use ft_volumewrite to save the volumetric data as nifti. You can look into the documentation of ft_volumewrite to see how this works. Best, Jan-Mathijs On Feb 21, 2012, at 11:17 AM, Davide Rivolta wrote: > Dear all, > > I wish to ask whether there is a way to import anatomical CTF files (.V2) into SPM. > > Thanks, > Davide > > > -- > Davide Rivolta, PhD > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From kd889 at nyu.edu Tue Feb 21 18:48:10 2012 From: kd889 at nyu.edu (Keith Doelling) Date: Tue, 21 Feb 2012 12:48:10 -0500 Subject: [FieldTrip] ft_channelrepair replaces channel data with NaNs after running PCA In-Reply-To: References: Message-ID: Hi guys, For those that are interested I figured out the problem. Somewhere in the process of running component analysis and then component rejection, fieldtrip was taking .chanpos and .chanori in my .grad field and replacing all the values with NaNs. I fixed the problem by adding cleandata.grad = data.grad just after component rejection. It would be great though, if some one could look at the ft_componentanalysis and ft_rejectcomponent functions and figure out why the grad information is being lost. Thanks! Keith On Fri, Feb 17, 2012 at 12:08 PM, Keith Doelling wrote: > Hi guys, > > I'm struggling with my attempts to interpolate channel data for some bad > channels. I put in the following code: > > > cfg=[]; > cfg.badchannel = 15; > cfg.missingchannel = []; > cfg.neighbours = neighbours; > cfg.trials = 'all'; > cleanchdata = ft_channelrepair(cfg,cleandata); > > > the function the displays the following: > > "the input is raw data with 157 channels and 80 trials > repairing channel AG015 > using neighbour AG010 > using neighbour AG014 > using neighbour AG062 > using neighbour AG092" > > suggesting that neighbours have been selected successfully. > > but a call to chdata.trial(1){15,:) just returns a bunch of NaNs rather > than interpolated data I need. > > I found another email thread similar to this but that solution doesn't > seem to apply to me as the neighbours seemed to have been selected > successfully. > > The other interesting caveat is that ft_channelrepair seems to work fine > if i run it without having run pca (to reject eyeblink and heartbeat > components) beforehand. > > The code for the component analysis and the subsequent rejection are in > separate loops. The PCA is saved into a .mat file and then loaded again > when i'm ready to reject the bad components. But for simplicity's sake the > important code looks like this. > > > % principle component analysis run with 32 components > cfg = []; > cfg.channel = (1:157); > cfg.runica.pca=32; > pca_data = ft_componentanalysis(cfg,data); > > % view components in order to select bad ones > cfg = []; > cfg.layout = layout; % specify the layout file that should be used > for plotting > cfg.viewmode = 'component'; > ft_databrowser(cfg, pca_data); > waitfor(gcf); > > % type bad components as user input > % for example: if runica002 and runica0003 should be rejected, type > "2,3" into the dialogue box > badcomps = inputdlg({'Bad Components:'}); > badcomps = str2double(csv2cell(badcomps{1})); > > % reject bad components > cfg = []; > cfg.component = badcomps; > cleandata = ft_rejectcomponent(cfg,pca_data); > > > the variable 'cleandata' i get out from this code is the same cleandata i > put in to ft_channelrepair. > > Are there any ideas as to what I've done wrong here? Let me know if I need > to give you guys more information. > > Thanks for your help, > Keith > > -- > Keith Doelling > Lab Manager and Research Assistant > David Poeppel Lab > New York University > > -- Keith Doelling Lab Manager and Research Assistant David Poeppel Lab New York University -------------- next part -------------- An HTML attachment was scrubbed... URL: From akiko.ikkai at gmail.com Tue Feb 21 18:52:27 2012 From: akiko.ikkai at gmail.com (Akiko Ikkai) Date: Tue, 21 Feb 2012 12:52:27 -0500 Subject: [FieldTrip] volume conduction model missing .mat In-Reply-To: References: <2341406D-6422-4FD3-AD3C-73D1BF70B6CF@mac.com> Message-ID: Hi Gio, Thank you for sharing your script. cfg.output = 'tpm' for ft_volumesegment seems to make a big difference, and now I could go all the way to actually running beamformer on my data! Of course, I had to add a few things. For example, in order to clean up segmented images, I added lines as seg2.brain(:,:,1:4)=0; seg2.skull(:,:,1:2)=0; to make sure scalp, skull and brain do not intersept at neck. Also did something like below for each tissue type (otherwise the resulting beamformer was too small on the brain) newsbrain = imdilate(seg2.brain,strel_bol(1)); seg2.brain = newsbrain; Fieldtrip developers, are there documentations for "cfg.output = 'tpm' " for segmentation? ft_segmentation help page simply says it's a default option. Thanks for your help! Akiko On Thu, Feb 16, 2012 at 5:52 AM, Gio Piantoni wrote: > Hi Akiko, > > What do you mean "problematic" exactly? From my understanding, there > are 4 steps to get from the MRI to the forward model. > 1. from MRI to segmentation > 2. from segmentation to mesh (bnd) > 3. from mesh to headmodel > 4. from headmodel to forward model > > Here is the code I use. It seems to work fine, but experts might want > to chip in and improve it. > 1. from MRI to segmentation > > %-----------------% > %-read MRI > mrifile = '/path/to/your/mri.nii.gz'; > mri = ft_read_mri(mrifile); > %-----------------% > > %-----------------% > %-segmenting the volume, Tissue Probability Maps > % It takes time to run 'tpm' > cfg1 = []; > cfg1.threshold = []; > cfg1.output = 'tpm'; > cfg1.coordsys = 'spm'; > tpm = ft_volumesegment(cfg1, mri); > tpm.anatomy = mri.anatomy; > %-----------------% > > %-----------------% > %-segmenting the volume > % this is faster after tpm > cfg1 = []; > cfg1.threshold = 1; % 1 is default, my MRI scalps were noisy, so I had > to make it lower. > cfg1.output = 'scalp'; > cfg1.coordsys = 'spm'; > segscalp = ft_volumesegment(cfg1, tpm); > > cfg1 = []; > cfg1.threshold = []; > cfg1.output = {'skull' 'brain'}; > cfg1.coordsys = 'spm'; > segment = ft_volumesegment(cfg1, tpm); > segment.scalp = segscalp.scalp; > %-----------------% > > Check the output with ft_sourceplot > > 2. from segmentation to mesh (bnd) > > %-----------------% > %-prepare mesh for skull and brain (easy) > cfg2 = []; > cfg2.tissue = {'skull', 'brain'}; > cfg2.numvertices = [1200 1000]; > cfg2.transform = segment.transform; > bnd = ft_prepare_mesh_new(cfg2, segment); > %-----------------% > > %-----------------% > %-prepare mesh for scalp (we need to be more liberal with threshold, > bc of poor quality of MRI) > cfg2 = []; > cfg2.tissue = {'scalp'}; > cfg2.numvertices = 2500; > cfg2.thresholdseg = 0.1; > cfg2.transform = segment.transform; > scalp = ft_prepare_mesh_new(cfg2, segment); > %-----------------% > > %-----------------% > %-combine scalp and bnd > bnd = [scalp bnd]; > ft_plot_mesh(bnd(1), 'facealpha', .5) > hold on > ft_plot_mesh(bnd(2), 'facecolor', 'red') > %-----------------% > > If bnd is good, no intersection between meshes and the outline looks > nice, the following should run without problems. Please, do check your > bnd. > Segmentation and ft_prepare_mesh_new work really well. Another > approach to get nice meshes is to skip step 1 and 2 and use > Freesurfer/MNE. You can read the meshes in fieldtrip > (ft_read_headshape, I think). The meshes are in the "bem" folder of > Freesurfer, but I don't remember off the top of my head which files > you should read ("outer_skull, inner_skull", I think). > These meshes have a very very high resolution, you can scale them down > with "reducepatch" in Matlab. > > 3. from mesh to headmodel > %-----------------% > %-headmodel > cfg3 = []; > cfg3.method = 'bem_dipoli'; > cfg3.conductivity = [0.33 0.0042 0.33]; > vol = ft_prepare_headmodel(cfg3, bnd); > %-----------------% > > You can really pick your favorite here: dipoli, openmeeg, bemcp. This > will take time (the more time, the more points on your meshes). > > 4. from headmodel to forward model > You last problem is to get electrodes and headmodel in the same space. > The template in SPM is already in MNI space, your individual MRIs > probably not. You can realign them to MNI space before step 1 using > SPM or FSL. > > elec = ft_read_sens(sensfile); > elec = ft_convert_units(elec, 'mm'); > > %-------% > %-simple transformation (based on visual realignment) > % elecM is an affine matrix that you can get from ft_electroderealign > % electrodes do not need to match the scalp perfectly, but they should > be pretty close by. > elec.chanpos = warp_apply(elecM, elec.chanpos); > elec.elecpos = warp_apply(elecM, elec.elecpos); > %-------% > > [vol, elec] = ft_prepare_vol_sens(vol, elec); > % now you should check that the electrodes are on the scalp. > %-----------------% > > %-----------------% > %-prepare leadfield > cfg4 = []; > cfg4.elec = elec; > cfg4.vol = vol; > cfg4.grid.xgrid = -70:10:70; > cfg4.grid.ygrid = -110:10:80; > cfg4.grid.zgrid = -60:10:90; > cfg4.inwardshift = 1; % to avoid dipoles on the border of bnd(3), > which are very instable > cfg4.grid.tight = 'no'; > cfg4.feedback = 'none'; > lead = ft_prepare_leadfield(cfg4, []); > % use ft_plot_topo3d and ft_plot_dipole to check whether the > projection of your dipole onto the scalp makes sense. > %-----------------% > > "lead" should be your subject-specific, electrode-specific leadfield. > There are quite a few parameters that you can change, but a clean > segmentation and non-intersecting, smooth and realistic-looking meshes > are a must. > Then, using dipoli, openmeeg or bemcp should not change your forward > model too much. > Sorry if some points are not clear, but you should really look at your > MRI/segmentation/meshes/electrodes/forward model as much as possible. > > Hope this will get you started. I appreciate any feedback on improving > the code, this is just my personal attempt. > > Cheers > > Gio > > On Wed, Feb 15, 2012 at 17:45, Akiko Ikkai wrote: > > Dear Fieldtrip users, > > > > Thank you Patrick, Nathan & Gio for your inputs. My MRI anatomical images > > need extensive cleaning (enhance contrasts, get rid of non-zero voxels > > outside the brain, etc...) before segmentation, as well as adjusting > > cfg.threshold for each tissue type during segmentation and each subject. > At > > least testing with SPM standard MRI, segmentation and forward modeling > works > > OK now. > > > > Individual subject's MRI, though, is still problematic, and I have a > > question for Fieldtrip developers: could you let me know whether "Create > BEM > > headmodel for EEG ( > > http://fieldtrip.fcdonders.nl/example/create_bem_headmodel_for_eeg )" > > routine is what you recommend, or it's integrated into a newer function > with > > newer cfg options? Is there a page I missed on the web? > > > > Thank you so much for your time! > > Akiko > > > > On Fri, Feb 10, 2012 at 4:36 AM, Gio Piantoni > > wrote: > >> > >> Hi Akiki and Patrick, > >> > >> I agree with Nathan about segmentation problems. I had the same > >> problem when two of the three meshes intersected each other. Before > >> you run the forward model, you should check the segmentation (bnd) > >> using ft_plot_mesh. > >> ft_plot_mesh(bnd(1), 'facealpha', .5) > >> hold on > >> ft_plot_mesh(bnd(2), 'facecolor', 'r') > >> You will see that the two meshes intersect with each other. Depending > >> on how you created the meshes, you should fix the parameters in such a > >> way that they don't intersect. For example, ft_volumesegment has a > >> cfg.threshold option (you can check how the segmentation went with > >> ft_sourceplot) and ft_prepare_mesh_new has cfg.thresholdseg and > >> cfg.smoothseg. > >> > >> I think that the meshes in SPM are computed on an (affine-transformed) > >> template and not on the anatomically derived meshes. The template is > >> more robust and that's why the two surfaces do not intersect. > >> > >> In general, the segmentation depends on the quality of your MRIs and > >> you should really visually check the segmentation and meshes. When > >> those look ok, the BEM forward model usually works. Hope this helps. > >> > >> Cheers, > >> > >> Gio > >> > >> On Fri, Feb 10, 2012 at 09:00, Nathan Weisz > wrote: > >> > Hi Akiki, > >> > > >> > I am not a headmodel expert. > >> > but looking at the output message, it seems your segementation did not > >> > go > >> > too well (see the "intersect" message). my intuition is then then the > >> > next > >> > temporary file *.ama is not created and ft_prepare_bemmodel then > simply > >> > says > >> > ciao. > >> > > >> > perhaps you want to check / redo the segmentation? > >> > > >> > good luck, > >> > nathan > >> > > >> > > >> > On 09.02.2012, at 23:04, Akiko Ikkai wrote: > >> > > >> > Hi, > >> > > >> > I'm trying to create a volume conduction model for my EEG study based > on > >> > anatomical MRI, and having trouble with ft_prepare_bemmodel > >> > > >> > when I run > >> > cfg = []; > >> > cfg.tissue = [7 4 1]; % value for brain, skull, and scalp > >> > cfg.conductivity = [1 1/80 1]*.33; % after standard_BEM.zip data > >> > cfg.isolatedsource = true; > >> > cfg.method = 'dipoli'; > >> > cfg.sourceunits = 'mm'; > >> > cfg.mriunits = 'mm'; > >> > vol = ft_prepare_bemmodel(cfg, seg4bem); > >> > > >> > I get the following error message while ft_prepare_bemmodel is > running: > >> > > >> > Fatal error in dipoli: interface > >> > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and > >> > /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect > >> > at vertex 1402 of > >> > /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri > >> > > >> > Warning: an error ocurred while running dipoli > >> >> In dipoli at 94 > >> > In ft_prepare_bemmodel at 112 > >> > Error using ==> fread > >> > Invalid file identifier. Use fopen to generate a valid file > identifier. > >> > Warning: File > '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' > >> > not > >> > found. > >> >> In dipoli at 102 > >> > In ft_prepare_bemmodel at 112 > >> > > >> > > >> > and the output vol is missing .mat, which causes an error > >> > during ft_sourceanalysis. > >> >>> vol > >> > vol = > >> > cond: [0.3300 0.0041 0.3300] > >> > bnd: [1x3 struct] > >> > source: 3 > >> > skin_surface: 3 > >> > skin: 1 > >> > type: 'dipoli' > >> > > >> > Does anyone know how to correct for "fatal error" so > >> > that ft_prepare_bemmodel creates the correct volume conduction model? > I > >> > opened .tri file and removed line 1402, but got the same results. > >> > > >> > Thanks in advance! Akiko > >> > > >> > -- > >> > Akiko Ikkai, Ph.D. > >> > Postdoctoral Fellow > >> > Department of Psychological and Brain Sciences > >> > Johns Hopkins University > >> > Ames Hall, 3400 N. Charles St. > >> > Baltimore, MD 21218 > >> > > >> > > >> > _______________________________________________ > >> > fieldtrip mailing list > >> > fieldtrip at donders.ru.nl > >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> > > >> > > >> > > >> > _______________________________________________ > >> > fieldtrip mailing list > >> > fieldtrip at donders.ru.nl > >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > -- > > Akiko Ikkai, Ph.D. > > Postdoctoral Fellow > > Department of Psychological and Brain Sciences > > Johns Hopkins University > > Ames Hall, 3400 N. Charles St. > > Baltimore, MD 21218 > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Akiko Ikkai, Ph.D. Postdoctoral Fellow Department of Psychological and Brain Sciences Johns Hopkins University Ames Hall, 3400 N. Charles St. Baltimore, MD 21218 -------------- next part -------------- An HTML attachment was scrubbed... URL: From drivolta81 at gmail.com Wed Feb 22 10:05:01 2012 From: drivolta81 at gmail.com (Davide Rivolta) Date: Wed, 22 Feb 2012 10:05:01 +0100 Subject: [FieldTrip] CTF to SPM In-Reply-To: <3672CA8D-132F-4664-8251-56DF2F97FA73@donders.ru.nl> References: <3672CA8D-132F-4664-8251-56DF2F97FA73@donders.ru.nl> Message-ID: Thank you for the replies. I am trying with ft_volumewrite. I have a small problem. the configuration wants me to specify the cfg.parameter, that is a "string, describing the functional data to be processed, e.g. 'pow', 'coh' or 'nai' ". I am a bit confused, since I have anatomical data, and I am not sure what to put here. Any ideas? Thanks a lot, Davide On Tue, Feb 21, 2012 at 6:05 PM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Hi Davide, > > If you use ft_read_mri to read in your *.mri you can use ft_volumewrite to > save the volumetric data as nifti. You can look into the documentation of > ft_volumewrite to see how this works. > > Best, > > Jan-Mathijs > > On Feb 21, 2012, at 11:17 AM, Davide Rivolta wrote: > > Dear all, > > > I wish to ask whether there is a way to import anatomical CTF files (.V2) > into SPM. > > > Thanks, > Davide > > > -- > Davide Rivolta, PhD > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Davide Rivolta, PhD -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Feb 22 10:47:02 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 22 Feb 2012 10:47:02 +0100 Subject: [FieldTrip] CTF to SPM In-Reply-To: References: <3672CA8D-132F-4664-8251-56DF2F97FA73@donders.ru.nl> Message-ID: <056A85D1-7E54-44B6-9CFA-DCB2BA88C27B@donders.ru.nl> Dear Davide, Did you try 'anatomy' ? BW, Jan-Mathijs On Feb 22, 2012, at 10:05 AM, Davide Rivolta wrote: > Thank you for the replies. > I am trying with ft_volumewrite. > > I have a small problem. the configuration wants me to specify the cfg.parameter, that is a "string, describing the functional data to be processed, e.g. 'pow', 'coh' or 'nai' ". > I am a bit confused, since I have anatomical data, and I am not sure what to put here. > > Any ideas? > > Thanks a lot, > Davide > > > On Tue, Feb 21, 2012 at 6:05 PM, jan-mathijs schoffelen wrote: > Hi Davide, > > If you use ft_read_mri to read in your *.mri you can use ft_volumewrite to save the volumetric data as nifti. You can look into the documentation of ft_volumewrite to see how this works. > > Best, > > Jan-Mathijs > > On Feb 21, 2012, at 11:17 AM, Davide Rivolta wrote: > >> Dear all, >> >> I wish to ask whether there is a way to import anatomical CTF files (.V2) into SPM. >> >> Thanks, >> Davide >> >> >> -- >> Davide Rivolta, PhD >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Davide Rivolta, PhD > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From drivolta81 at gmail.com Wed Feb 22 11:04:11 2012 From: drivolta81 at gmail.com (Davide Rivolta) Date: Wed, 22 Feb 2012 11:04:11 +0100 Subject: [FieldTrip] CTF to SPM In-Reply-To: <056A85D1-7E54-44B6-9CFA-DCB2BA88C27B@donders.ru.nl> References: <3672CA8D-132F-4664-8251-56DF2F97FA73@donders.ru.nl> <056A85D1-7E54-44B6-9CFA-DCB2BA88C27B@donders.ru.nl> Message-ID: Thanks again for the help. I still get an error regarding the name. Maybe is silly. This is my script: for i = 1:size(mri,1) fullname = strcat(inpath, mri{i,1}, '_V2.mri'); mri_V2 = ft_read_mri(fullname); cfg = []; cfg.parameter = 'anatomy'; cfg.filename = mri_V2; cfg.filetype = 'nifti'; ft_volumewrite(cfg, mri_V2); end; ?? Error using ==> fileparts at 17 Input must be a row vector of characters. Error in ==> ft_volumewrite at 411 [pathstr, name, ext] = fileparts(cfg.filename); Thanks again, Davide On Wed, Feb 22, 2012 at 10:47 AM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Dear Davide, > > Did you try 'anatomy' ? > > BW, > > Jan-Mathijs > > > On Feb 22, 2012, at 10:05 AM, Davide Rivolta wrote: > > Thank you for the replies. > I am trying with ft_volumewrite. > > I have a small problem. the configuration wants me to specify the > cfg.parameter, that is a "string, describing the functional data to be > processed, e.g. 'pow', 'coh' or 'nai' ". > I am a bit confused, since I have anatomical data, and I am not sure what > to put here. > > Any ideas? > > Thanks a lot, > Davide > > > On Tue, Feb 21, 2012 at 6:05 PM, jan-mathijs schoffelen < > jan.schoffelen at donders.ru.nl> wrote: > >> Hi Davide, >> >> If you use ft_read_mri to read in your *.mri you can use ft_volumewrite >> to save the volumetric data as nifti. You can look into the documentation >> of ft_volumewrite to see how this works. >> >> Best, >> >> Jan-Mathijs >> >> On Feb 21, 2012, at 11:17 AM, Davide Rivolta wrote: >> >> Dear all, >> >> >> I wish to ask whether there is a way to import anatomical CTF files (.V2) >> into SPM. >> >> >> Thanks, >> Davide >> >> >> -- >> Davide Rivolta, PhD >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Davide Rivolta, PhD > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Davide Rivolta, PhD -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Feb 22 12:04:45 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 22 Feb 2012 12:04:45 +0100 Subject: [FieldTrip] CTF to SPM In-Reply-To: References: <3672CA8D-132F-4664-8251-56DF2F97FA73@donders.ru.nl> <056A85D1-7E54-44B6-9CFA-DCB2BA88C27B@donders.ru.nl> Message-ID: Hi Davide, Perhaps putting the filename as a 'string' may do the trick. In that case it was indeed silly ;-). BW, JM On Feb 22, 2012, at 11:04 AM, Davide Rivolta wrote: > Thanks again for the help. I still get an error regarding the name. Maybe is silly. > > This is my script: > > > for i = 1:size(mri,1) > fullname = strcat(inpath, mri{i,1}, '_V2.mri'); > mri_V2 = ft_read_mri(fullname); > > cfg = []; > cfg.parameter = 'anatomy'; > cfg.filename = mri_V2; > cfg.filetype = 'nifti'; > ft_volumewrite(cfg, mri_V2); > > end; > > ?? Error using ==> fileparts at 17 > Input must be a row vector of characters. > Error in ==> ft_volumewrite at 411 > [pathstr, name, ext] = fileparts(cfg.filename); > > > > Thanks again, > Davide > > > > > On Wed, Feb 22, 2012 at 10:47 AM, jan-mathijs schoffelen wrote: > Dear Davide, > > Did you try 'anatomy' ? > > BW, > > Jan-Mathijs > > > On Feb 22, 2012, at 10:05 AM, Davide Rivolta wrote: > >> Thank you for the replies. >> I am trying with ft_volumewrite. >> >> I have a small problem. the configuration wants me to specify the cfg.parameter, that is a "string, describing the functional data to be processed, e.g. 'pow', 'coh' or 'nai' ". >> I am a bit confused, since I have anatomical data, and I am not sure what to put here. >> >> Any ideas? >> >> Thanks a lot, >> Davide >> >> >> On Tue, Feb 21, 2012 at 6:05 PM, jan-mathijs schoffelen wrote: >> Hi Davide, >> >> If you use ft_read_mri to read in your *.mri you can use ft_volumewrite to save the volumetric data as nifti. You can look into the documentation of ft_volumewrite to see how this works. >> >> Best, >> >> Jan-Mathijs >> >> On Feb 21, 2012, at 11:17 AM, Davide Rivolta wrote: >> >>> Dear all, >>> >>> I wish to ask whether there is a way to import anatomical CTF files (.V2) into SPM. >>> >>> Thanks, >>> Davide >>> >>> >>> -- >>> Davide Rivolta, PhD >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Davide Rivolta, PhD >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Davide Rivolta, PhD > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From drivolta81 at gmail.com Wed Feb 22 12:07:23 2012 From: drivolta81 at gmail.com (Davide Rivolta) Date: Wed, 22 Feb 2012 12:07:23 +0100 Subject: [FieldTrip] CTF to SPM In-Reply-To: References: <3672CA8D-132F-4664-8251-56DF2F97FA73@donders.ru.nl> <056A85D1-7E54-44B6-9CFA-DCB2BA88C27B@donders.ru.nl> Message-ID: Yep, I realized it after sending the email. It was silly indeed. It works fine now, Thanks, Davide On Wed, Feb 22, 2012 at 12:04 PM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Hi Davide, > > Perhaps putting the filename as a 'string' may do the trick. In that case > it was indeed silly ;-). > > BW, > > JM > > On Feb 22, 2012, at 11:04 AM, Davide Rivolta wrote: > > Thanks again for the help. I still get an error regarding the name. > Maybe is silly. > > This is my script: > > > for i = 1:size(mri,1) > fullname = strcat(inpath, mri{i,1}, '_V2.mri'); > mri_V2 = ft_read_mri(fullname); > > cfg = []; > cfg.parameter = 'anatomy'; > cfg.filename = mri_V2; > cfg.filetype = 'nifti'; > ft_volumewrite(cfg, mri_V2); > > end; > > ?? Error using ==> fileparts at 17 > Input must be a row vector of characters. > Error in ==> ft_volumewrite at 411 > [pathstr, name, ext] = fileparts(cfg.filename); > > > > Thanks again, > Davide > > > > > On Wed, Feb 22, 2012 at 10:47 AM, jan-mathijs schoffelen < > jan.schoffelen at donders.ru.nl> wrote: > >> Dear Davide, >> >> Did you try 'anatomy' ? >> >> BW, >> >> Jan-Mathijs >> >> >> On Feb 22, 2012, at 10:05 AM, Davide Rivolta wrote: >> >> Thank you for the replies. >> I am trying with ft_volumewrite. >> >> I have a small problem. the configuration wants me to specify the >> cfg.parameter, that is a "string, describing the functional data to be >> processed, e.g. 'pow', 'coh' or 'nai' ". >> I am a bit confused, since I have anatomical data, and I am not sure what >> to put here. >> >> Any ideas? >> >> Thanks a lot, >> Davide >> >> >> On Tue, Feb 21, 2012 at 6:05 PM, jan-mathijs schoffelen < >> jan.schoffelen at donders.ru.nl> wrote: >> >>> Hi Davide, >>> >>> If you use ft_read_mri to read in your *.mri you can use ft_volumewrite >>> to save the volumetric data as nifti. You can look into the documentation >>> of ft_volumewrite to see how this works. >>> >>> Best, >>> >>> Jan-Mathijs >>> >>> On Feb 21, 2012, at 11:17 AM, Davide Rivolta wrote: >>> >>> Dear all, >>> >>> >>> I wish to ask whether there is a way to import anatomical CTF files >>> (.V2) into SPM. >>> >>> >>> Thanks, >>> Davide >>> >>> >>> -- >>> Davide Rivolta, PhD >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> Jan-Mathijs Schoffelen, MD PhD >>> >>> Donders Institute for Brain, Cognition and Behaviour, >>> Centre for Cognitive Neuroimaging, >>> Radboud University Nijmegen, The Netherlands >>> >>> Max Planck Institute for Psycholinguistics, >>> Nijmegen, The Netherlands >>> >>> J.Schoffelen at donders.ru.nl >>> Telephone: +31-24-3614793 >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> Davide Rivolta, PhD >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Davide Rivolta, PhD > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Davide Rivolta, PhD -------------- next part -------------- An HTML attachment was scrubbed... URL: From jnortonf at uci.edu Thu Feb 23 04:28:24 2012 From: jnortonf at uci.edu (Jessamy Norton-Ford) Date: Wed, 22 Feb 2012 19:28:24 -0800 Subject: [FieldTrip] Fieldtrip tutorial error: trialfun Message-ID: Hello, I am new to Fieldtrip, and have run into the following problems running through the tutorial cfg = []; % empty configuration cfg.dataset = 'Subject01.ds'; % name of CTF dataset cfg.trialdef.eventtype = 'backpanel trigger'; cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 2; cfg.trialdef.eventvalue = 3; % event value of FIC cfg = ft_definetrial(cfg); Warning: no trialfun was specified, using trialfun_general > In ft_definetrial at 123 evaluating trialfunction 'trialfun_general' Warning: adding /Users/jessamynorton-ford/Documents/MATLAB/fieldtrip-20120222/external/ctf toolbox to your Matlab path readCTFds: Data set error : size of meg4 file(s) 0 bytes (from dir command) 179071200 bytes (from res4 file) reading the events from 'Subject01.ds/Subject01.res4' readCTFds: Data set error : size of meg4 file(s) 0 bytes (from dir command) 179071200 bytes (from res4 file) ??? Attempt to reference field of non-structure array. Error in ==> trialfun_general at 118 sel = ismember({event.type}, cfg.trialdef.eventtype); Error in ==> ft_definetrial at 166 [trl, event] = feval(cfg.trialfun, cfg); I found a somewhat similar issue on the boards from May 2011 ( http://mailman.science.ru.nl/pipermail/fieldtrip/2011-May/003827.html), and have since tried several instantiations of FieldTrip (though the version I was running when I first got the error was actually very new). So far I have tried: fieldtrip-20111004 fieldtrip-20111101 fieldtrip-20120220 fieldtrip-20120222 here is my ver info in case it is helpful: MATLAB Version 7.11.0.584 (R2010b) Operating System: Mac OS X Version: 10.6.2 Build: 10C540 Java VM Version: Java 1.6.0_15-b03-219 with Apple Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode ------------------------------------------------------------------------------------- Any suggestions of likely incompatibilities/mistakes on my part would be most helpful. Thank you, -- Jessamy Norton-Ford Doctoral Student, Department of Cognitive Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Feb 23 09:25:58 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 23 Feb 2012 09:25:58 +0100 Subject: [FieldTrip] Fieldtrip tutorial error: trialfun In-Reply-To: References: Message-ID: Dear Jessamy, This looks like you are calling the function from the wrong directory. I can reproduce your error when I call ft_redefinetrial from the following location: XXXXXX/Subject01.ds instead, you should call the function from: XXXXXX, i.e. one directory up (so type 'cd ../' to get there), or use an absolute path in cfg.dataset (i.e. cfg.dataset = '/XXXXXX/Subject01.ds') Best wishes, Jan-Mathijs On Feb 23, 2012, at 4:28 AM, Jessamy Norton-Ford wrote: > Hello, > > I am new to Fieldtrip, and have run into the following problems running through the tutorial > > cfg = []; % empty configuration > cfg.dataset = 'Subject01.ds'; % name of CTF dataset > cfg.trialdef.eventtype = 'backpanel trigger'; > cfg.trialdef.prestim = 1; > cfg.trialdef.poststim = 2; > cfg.trialdef.eventvalue = 3; % event value of FIC > cfg = ft_definetrial(cfg); > > Warning: no trialfun was specified, using trialfun_general > > > In ft_definetrial at 123 > evaluating trialfunction 'trialfun_general' > > Warning: adding > /Users/jessamynorton-ford/Documents/MATLAB/fieldtrip-20120222/external/ctf > toolbox to your Matlab path > > readCTFds: Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file) > > reading the events from 'Subject01.ds/Subject01.res4' > > readCTFds: Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file) > > ??? Attempt to reference field of non-structure array. > > Error in ==> trialfun_general at 118 > sel = ismember({event.type}, cfg.trialdef.eventtype); > > Error in ==> ft_definetrial at 166 > [trl, event] = feval(cfg.trialfun, cfg); > > I found a somewhat similar issue on the boards from May 2011 (http://mailman.science.ru.nl/pipermail/fieldtrip/2011-May/003827.html), and have since tried several instantiations of FieldTrip (though the version I was running when I first got the error was actually very new). So far I have tried: > > fieldtrip-20111004 > fieldtrip-20111101 > fieldtrip-20120220 > fieldtrip-20120222 > > here is my ver info in case it is helpful: > > MATLAB Version 7.11.0.584 (R2010b) > > Operating System: Mac OS X Version: 10.6.2 Build: 10C540 > Java VM Version: Java 1.6.0_15-b03-219 with Apple Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode > ------------------------------------------------------------------------------------- > > Any suggestions of likely incompatibilities/mistakes on my part would be most helpful. > > Thank you, > > -- > Jessamy Norton-Ford > Doctoral Student, Department of Cognitive Sciences > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Feb 23 10:11:29 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 23 Feb 2012 10:11:29 +0100 Subject: [FieldTrip] Fwd: ft_megplanar problem for planar gradient calculation References: Message-ID: Begin forwarded message: > > ---------- Forwarded message ---------- > From: Ion Lavado > Date: 2012/2/21 > Subject: ft_megplanar problem for planar gradient calculation > To: fieldtrip-request at donders.ru.nl > > > Hello, i'm doing the cluster based permutations tests on time-frequency data tutorial. I'm using an Elekta neuromag with 306 channels. My problem comes when i try to calculate the planar gradient. This is what i do: > > %************ READ WORD EVENT ************ > cfg = []; > cfg.dataset = '21_muti.fif'; > cfg.trialdef.eventtype = 'STI101'; > cfg.trialdef.prestim = 1; > cfg.trialdef.poststim = 1; > cfg.trialdef.eventvalue = 1; > cfg = ft_definetrial(cfg); > cfg.channel = {'MEG'}; > cfg.demean = 'yes'; > cfg.baselinewindow = [-0.5 0]; > dataMuti21_words = ft_preprocessing(cfg); > %************ READ PICTURES EVENT ************ > cfg = []; > cfg.dataset = '21_muti.fif'; > cfg.trialdef.eventtype = 'STI101'; > cfg.trialdef.prestim = 1; > cfg.trialdef.poststim = 1; > cfg.trialdef.eventvalue = 6; > cfg = ft_definetrial(cfg); > cfg.channel = {'MEG'}; > cfg.demean = 'yes'; > cfg.baselinewindow = [-0.5 0]; > dataMuti21_pictures = ft_preprocessing(cfg); > > > > %******* CALCULATE PLANAR GRADIENT ****** > cfg = []; > cfg.planarmethod = 'sincos'; > cfg_neighb.method = 'distance'; > cfg.grad = avg_words.grad; > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataMuti21_pictures); > avg_words_planar = ft_megplanar(cfg, dataMuti21_words); > avg_pictures_planar = ft_megplanar(cfg, dataMuti21_pictures); > > > HERE IS WHERE I GET THE ERROR: > ??? Error using ==> ft_checkdata at 359 > This function requires ctf151, ctf275, bti148, bti248, itab153, yokogawa160 or yokogawa64 data as input, but you are giving > neuromag306 data. > > Error in ==> ft_megplanar at 107 > data = ft_checkdata(data, 'datatype', {'raw' 'freq'}, 'feedback', 'yes', 'hassampleinfo', 'yes', 'ismeg', 'yes', 'senstype', > {'ctf151', 'ctf275', 'bti148', 'bti248', 'itab153', 'yokogawa160', 'yokoga > > > Can't i use neuromag306 data type sens for this function? any solution? THANKS IN ADVANCE > > Ion -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu Feb 23 10:19:25 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 23 Feb 2012 10:19:25 +0100 Subject: [FieldTrip] Fwd: ft_megplanar problem for planar gradient calculation In-Reply-To: References: Message-ID: Dear Ion, ft_megplanar is designed to estimate planar gradient information from axial gradiometer data. The Neuromag 306 system is equipped with planar gradiometers, so the data you have is already reflecting the planar magnetic gradient. In other words: there is no need to use ft_megplanar, in your case. Best, Eelke On 23 February 2012 10:11, jan-mathijs schoffelen wrote: > > > Begin forwarded message: > > > ---------- Forwarded message ---------- > From: Ion Lavado > Date: 2012/2/21 > Subject: ft_megplanar problem for planar gradient calculation > To: fieldtrip-request at donders.ru.nl > > > Hello, i'm doing the cluster based permutations tests on time-frequency data > tutorial. I'm using an Elekta neuromag with 306 channels. My problem comes > when i try to calculate the planar gradient. This is what i do: > > %************ READ WORD EVENT ************ > cfg = []; > cfg.dataset                 = '21_muti.fif'; > cfg.trialdef.eventtype      = 'STI101'; > cfg.trialdef.prestim        = 1; > cfg.trialdef.poststim       = 1; > cfg.trialdef.eventvalue     = 1; > cfg = ft_definetrial(cfg); > cfg.channel   = {'MEG'}; > cfg.demean        = 'yes'; > cfg.baselinewindow = [-0.5 0]; > dataMuti21_words = ft_preprocessing(cfg); > %************ READ PICTURES EVENT ************ > cfg = []; > cfg.dataset                 = '21_muti.fif'; > cfg.trialdef.eventtype      = 'STI101'; > cfg.trialdef.prestim        = 1; > cfg.trialdef.poststim       = 1; > cfg.trialdef.eventvalue     = 6; > cfg = ft_definetrial(cfg); > cfg.channel   = {'MEG'}; > cfg.demean        = 'yes'; > cfg.baselinewindow = [-0.5 0]; > dataMuti21_pictures = ft_preprocessing(cfg); > > > > %******* CALCULATE PLANAR GRADIENT ****** > cfg = []; > cfg.planarmethod = 'sincos'; > cfg_neighb.method    = 'distance'; > cfg.grad            = avg_words.grad; > cfg.neighbours       = ft_prepare_neighbours(cfg_neighb, > dataMuti21_pictures); > avg_words_planar = ft_megplanar(cfg, dataMuti21_words); > avg_pictures_planar = ft_megplanar(cfg, dataMuti21_pictures); > > > HERE IS WHERE I GET THE ERROR: > ??? Error using ==> ft_checkdata at 359 > This function requires ctf151, ctf275, bti148, bti248, itab153, yokogawa160 > or yokogawa64 data as input, but you are giving > neuromag306 data. > > Error in ==> ft_megplanar at 107 > data = ft_checkdata(data, 'datatype', {'raw' 'freq'}, 'feedback', 'yes', > 'hassampleinfo', 'yes', 'ismeg', 'yes', 'senstype', > {'ctf151', 'ctf275', 'bti148', 'bti248', 'itab153', 'yokogawa160', 'yokoga > > > Can't i use neuromag306 data type sens for this function? any solution? > THANKS IN ADVANCE > > Ion > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Thu Feb 23 10:20:29 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 23 Feb 2012 10:20:29 +0100 Subject: [FieldTrip] Fwd: ft_megplanar problem for planar gradient calculation In-Reply-To: References: Message-ID: <9F11307A-F697-4D9B-BBC4-694C00760EAC@donders.ru.nl> Dear Ion, In principle, you could do a synthetic planar grdient computation on the 102 magnetometer channels in your data. I don't think that this is supported by FieldTrip though. Obviously, you cannot do the planar gradient computation on the other 204 channels, because they already represent the magnetic field gradient. Best, Jan-Mathijs On Feb 23, 2012, at 10:11 AM, jan-mathijs schoffelen wrote: > > > Begin forwarded message: >> >> ---------- Forwarded message ---------- >> From: Ion Lavado >> Date: 2012/2/21 >> Subject: ft_megplanar problem for planar gradient calculation >> To: fieldtrip-request at donders.ru.nl >> >> >> Hello, i'm doing the cluster based permutations tests on time-frequency data tutorial. I'm using an Elekta neuromag with 306 channels. My problem comes when i try to calculate the planar gradient. This is what i do: >> >> %************ READ WORD EVENT ************ >> cfg = []; >> cfg.dataset = '21_muti.fif'; >> cfg.trialdef.eventtype = 'STI101'; >> cfg.trialdef.prestim = 1; >> cfg.trialdef.poststim = 1; >> cfg.trialdef.eventvalue = 1; >> cfg = ft_definetrial(cfg); >> cfg.channel = {'MEG'}; >> cfg.demean = 'yes'; >> cfg.baselinewindow = [-0.5 0]; >> dataMuti21_words = ft_preprocessing(cfg); >> %************ READ PICTURES EVENT ************ >> cfg = []; >> cfg.dataset = '21_muti.fif'; >> cfg.trialdef.eventtype = 'STI101'; >> cfg.trialdef.prestim = 1; >> cfg.trialdef.poststim = 1; >> cfg.trialdef.eventvalue = 6; >> cfg = ft_definetrial(cfg); >> cfg.channel = {'MEG'}; >> cfg.demean = 'yes'; >> cfg.baselinewindow = [-0.5 0]; >> dataMuti21_pictures = ft_preprocessing(cfg); >> >> >> >> %******* CALCULATE PLANAR GRADIENT ****** >> cfg = []; >> cfg.planarmethod = 'sincos'; >> cfg_neighb.method = 'distance'; >> cfg.grad = avg_words.grad; >> cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataMuti21_pictures); >> avg_words_planar = ft_megplanar(cfg, dataMuti21_words); >> avg_pictures_planar = ft_megplanar(cfg, dataMuti21_pictures); >> >> >> HERE IS WHERE I GET THE ERROR: >> ??? Error using ==> ft_checkdata at 359 >> This function requires ctf151, ctf275, bti148, bti248, itab153, yokogawa160 or yokogawa64 data as input, but you are giving >> neuromag306 data. >> >> Error in ==> ft_megplanar at 107 >> data = ft_checkdata(data, 'datatype', {'raw' 'freq'}, 'feedback', 'yes', 'hassampleinfo', 'yes', 'ismeg', 'yes', 'senstype', >> {'ctf151', 'ctf275', 'bti148', 'bti248', 'itab153', 'yokogawa160', 'yokoga >> >> >> Can't i use neuromag306 data type sens for this function? any solution? THANKS IN ADVANCE >> >> Ion > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Thu Feb 23 10:26:21 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 23 Feb 2012 10:26:21 +0100 Subject: [FieldTrip] Fwd: ft_megplanar problem for planar gradient calculation In-Reply-To: References: Message-ID: <4F46063D.9090501@donders.ru.nl> Hi, I might be mistaken since I am not using a neuromag system, but as far as I know a Neuromag system already has planar gradiometers? If so, then there would be no need to apply ft_megplanar (and actually, it would be an meaningless operation) Best, Jörn On 2/23/2012 10:11 AM, jan-mathijs schoffelen wrote: > > > Begin forwarded message: >> >> ---------- Forwarded message ---------- >> From: *Ion Lavado* > >> Date: 2012/2/21 >> Subject: ft_megplanar problem for planar gradient calculation >> To: fieldtrip-request at donders.ru.nl >> >> >> >> Hello, i'm doing the cluster based permutations tests on >> time-frequency data tutorial. I'm using an Elekta neuromag with 306 >> channels. My problem comes when i try to calculate the planar >> gradient. This is what i do: >> >> %************ READ WORD EVENT ************ >> cfg = []; >> cfg.dataset = '21_muti.fif'; >> cfg.trialdef.eventtype = 'STI101'; >> cfg.trialdef.prestim = 1; >> cfg.trialdef.poststim = 1; >> cfg.trialdef.eventvalue = 1; >> cfg = ft_definetrial(cfg); >> cfg.channel = {'MEG'}; >> cfg.demean = 'yes'; >> cfg.baselinewindow = [-0.5 0]; >> dataMuti21_words = ft_preprocessing(cfg); >> %************ READ PICTURES EVENT ************ >> cfg = []; >> cfg.dataset = '21_muti.fif'; >> cfg.trialdef.eventtype = 'STI101'; >> cfg.trialdef.prestim = 1; >> cfg.trialdef.poststim = 1; >> cfg.trialdef.eventvalue = 6; >> cfg = ft_definetrial(cfg); >> cfg.channel = {'MEG'}; >> cfg.demean = 'yes'; >> cfg.baselinewindow = [-0.5 0]; >> dataMuti21_pictures = ft_preprocessing(cfg); >> >> >> >> %******* CALCULATE PLANAR GRADIENT ****** >> cfg = []; >> cfg.planarmethod = 'sincos'; >> cfg_neighb.method = 'distance'; >> cfg.grad = avg_words.grad; >> cfg.neighbours = ft_prepare_neighbours(cfg_neighb, >> dataMuti21_pictures); >> avg_words_planar = ft_megplanar(cfg, dataMuti21_words); >> avg_pictures_planar = ft_megplanar(cfg, dataMuti21_pictures); >> >> >> HERE IS WHERE I GET THE ERROR: >> ??? Error using ==> ft_checkdata at 359 >> This function requires ctf151, ctf275, bti148, bti248, itab153, >> yokogawa160 or yokogawa64 data as input, but you are giving >> neuromag306 data. >> >> Error in ==> ft_megplanar at 107 >> data = ft_checkdata(data, 'datatype', {'raw' 'freq'}, 'feedback', >> 'yes', 'hassampleinfo', 'yes', 'ismeg', 'yes', 'senstype', >> {'ctf151', 'ctf275', 'bti148', 'bti248', 'itab153', 'yokogawa160', >> 'yokoga >> >> >> Can't i use neuromag306 data type sens for this function? any >> solution? THANKS IN ADVANCE >> >> Ion > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From Hanneke.vanDijk at med.uni-duesseldorf.de Thu Feb 23 10:51:00 2012 From: Hanneke.vanDijk at med.uni-duesseldorf.de (Hanneke.vanDijk at med.uni-duesseldorf.de) Date: Thu, 23 Feb 2012 10:51:00 +0100 Subject: [FieldTrip] [Fieldtrip] ft_megplanar problem for planar gradient calculation Message-ID: <72E993C35FB11743B79FF9286E5B6D8B029F8C31@Mail2-UKD.VMED.UKD> Dear Ion, If your ultimate goal is to combine the horizontal and vertical gradients you can do that later (after ft_timelockanalysis or ft_freqanalysis) using ft_combineplanar. You can skip the ft_megplanar step because the neuromag system already has planar gradiometers. I have done this numerous times and it works perfectly! Hope this helps, Hanneke __________________________________________ Dr. Hanneke van Dijk http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html Institute for Clinical Neuroscience, Heinrich Heine Universität Düsseldorf, Germany Hanneke.vanDijk at med.uni-duesseldorf.de Tel. +49 (0) 211 81 13074 __________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.reuderink at donders.ru.nl Thu Feb 23 13:27:35 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Thu, 23 Feb 2012 13:27:35 +0100 Subject: [FieldTrip] A question In-Reply-To: References: Message-ID: Further, it seems that the data is also scaled automatically, see http://code.google.com/p/fieldtrip/source/browse/trunk/ft_componentanalysis.m?spec=svn5313&r=5313#271 . Best, Boris On Thu, Feb 16, 2012 at 12:39 PM, Stephen Whitmarsh wrote: > Dear All, > > All true, except that ICA implemented by FT does demean the data > before unmixing by default. Use cfg.demean = 'no' if you don't want > to. > > cheers, > stephen > > On 16 February 2012 12:35, Stephen Politzer-Ahles > wrote: >> Hi Shayda, >> >> FieldTrip does not apply a filter by default, and I am not aware of any >> other 'hidden' transformations that happen. You can specify a filter when >> importing the data with ft_preprocessing(), and there are several different >> kinds of filters available, which will affect your data in different ways-- >> see http://fieldtrip.fcdonders.nl/reference/ft_preprocessing. The best thing >> to do is to import your data without using a filter and, if possible, use >> whatever tool comes with your MEG software to import that raw data into >> MATLAB as well (for example, for CTF this would be ds2txt), then you can >> plot them together to make sure there are no differences--when I have tried >> this with EEG data, fieldtrip hasn't changed them. Of course, if you want to >> use a filter, you can also try several filters (you can either filter within >> your system's software and then import straight to Fieldtrip, or use one of >> Fieldtrip's filters during import) and plot them to see how they affect your >> data. >> >> Best, >> Steve Politzer-Ahles >> >> >>> >>> >>> Message: 2 >>> Date: Wed, 15 Feb 2012 14:19:50 -0600 >>> From: Shayda Malekpour >>> To: fieldtrip at donders.ru.nl >>> Subject: [FieldTrip] A question >>> Message-ID: >>> >>>   >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> >>> Dear All, >>> >>> I am using fieldtrip on MEG data set. >>> I want to know if I do not remove any ICA component,  will the data be >>>  the >>> same as the original data, or is there is a filter somewhere in the >>> software that changes the data? If so how much does it change it (What is >>> their relative difference?) >>> >>> Thanks, >>> >>> Sheida >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: >>> >>> >>> ------------------------------ >>> >>> Message: 3 >>> Date: Thu, 16 Feb 2012 09:28:43 +0100 >>> From: Eelke Spaak >>> To: Email discussion list for the FieldTrip project >>>         >>> Subject: Re: [FieldTrip] A question >>> Message-ID: >>> >>>   >>> Content-Type: text/plain; charset=ISO-8859-1 >>> >>> >>> Dear Sheida, >>> >>> You probably need to provide a bit more information before anyone is >>> able to help you. In general, if you perform ICA, you get out >>> component timecourses and mixing/unmixing matrices. If you keep all >>> your components, and multiply them with the mixing matrix, you should >>> get all your original channel timecourses out again. So: if you don't >>> change the data, the data will not be changed :) >>> >>> Best, >>> Eelke >>> >>> On 15 February 2012 21:19, Shayda Malekpour >>> wrote: >>> > Dear All, >>> > >>> > I am using fieldtrip on MEG data set. >>> > I want to know if I do not remove any ICA component,? will the data be? >>> > the >>> >>> > same as the original data, or is there is a filter somewhere in the >>> > software >>> > that changes the data? If so how much does it change it (What is their >>> > relative difference?) >>> > >>> > Thanks, >>> > >>> > Sheida >>> > _______________________________________________ >>> > fieldtrip mailing list >>> > fieldtrip at donders.ru.nl >>> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> ------------------------------ >>> >>> Message: 4 >>> Date: Thu, 16 Feb 2012 10:36:05 +0100 >>> From: "J?rn M. Horschig" >>> To: Email discussion list for the FieldTrip project >>>         >>> Subject: Re: [FieldTrip] A problem in real-time processing of MEG >>>        signal using field trip buffer >>> Message-ID: <4F3CCE05.4050109 at donders.ru.nl> >>> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" >>> >>> Dear Soheila, >>> >>> we were facing the same problem here. Presumably, there is some problem >>> in the shared memory module that the buffer is using. Right now, >>> however, we could not find out where the error precisely comes from, so >>> our best work around is to restart the computer prior recording and >>> optimize settings, such as channels and sampling/decimation rate of >>> acq2ft. In our lab, we managed to find near-optimal settings, so that >>> the buffer crashes only rarely (actually, I never saw it crashing when >>> the acquisition computer was freshly restarted). Note that a lower >>> number of channels or higher decimation does not mean that it runs more >>> stable.  It seems to be literally a trial-and-error approach :/ >>> >>> In order to track this down further, we need some more information, e.g. >>> what MEG system are you using? What's your sampling rate, how many >>> channels do you put into the buffer, and what's your decimation rate? It >>> would be great if you could send me that information so that we can >>> maybe try to track this down. >>> >>> Best regards, >>> J?rn >>> >>> On 2/14/2012 5:42 PM, Soheila Samiee wrote: >>> > Dear group, >>> > >>> > I use FieldTrip for real-time processing of MEG signals using shared >>> > memory and field trip buffer in a machine other than acquisition >>> > system. I use matlab for reading the buffer and processing the data. >>> > During my data acquisition and sending it to other computer with >>> > /acq2ft/ in linux, I face a problem. After sending some blocks of >>> > data, this message: "/Internal Converter thread does not keep up with >>> > load/" is shown in the terminal of /acq2ft/ and in my matlab session I >>> > see an error : "ERROR: the buffer returned an error (517)". It does >>> > not depend on sampling rate of data in acquisition system. The problem >>> > often solve when I restart the computer which receives the data, but >>> > after some minutes of transferring the data I see the message again. >>> > >>> > Would you please help me in solving this problem? >>> > Best Wishes, >>> > Soheila >>> >>> > >>> > >>> > _______________________________________________ >>> > fieldtrip mailing list >>> > fieldtrip at donders.ru.nl >>> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> -- >>> J?rn M. Horschig >>> PhD Student >>> Donders Institute for Brain, Cognition and Behaviour >>> Centre for Cognitive Neuroimaging >>> Radboud University Nijmegen >>> Neuronal Oscillations Group >>> >>> P.O. Box 9101 >>> NL-6500 HB Nijmegen >>> The Netherlands >>> >>> Contact: >>> E-Mail: jm.horschig at donders.ru.nl >>> Tel:    +31-(0)24-36-68493 >>> Web: http://www.ru.nl/donders >>> >>> Visiting address: >>> Trigon, room 2.30 >>> Kapittelweg 29 >>> NL-6525 EN Nijmegen >>> The Netherlands >>> >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: >>> >>> >>> ------------------------------ >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> End of fieldtrip Digest, Vol 15, Issue 17 >>> ***************************************** >> >> >> >> >> -- >> Stephen Politzer-Ahles >> University of Kansas >> Linguistics Department >> http://www.linguistics.ku.edu/ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl From chrysa.lithari at gmail.com Fri Feb 24 11:08:40 2012 From: chrysa.lithari at gmail.com (Chrysa Lithari) Date: Fri, 24 Feb 2012 12:08:40 +0200 Subject: [FieldTrip] coregistration neuromag Message-ID: Hi to all, I just started using fieldtrip and I have the following question. I have the MRI and the polhemus data for each subject. The MRI is in dicom and I can also transform it to 'analyze' format using SPM. The polhemus data are in fif format, together with the functional data. How can I coregister these two types of data in fieldtrip? I searched in the tutorial and it is mentioned that normally MEG systems come with a software allowing to align MRI with the helmet, e.g. CTF. However, I have worked on Neuromag system and I have not done anything like this. How can I do it in Fieltrip? A step by step (AC-PC points, normalization, segmentation etc) guidance would be very helpful stating the functions I have to use and any precautions I have to consider during this process. Best regards and thanks in advance, Chrysa Lithari -- Chrysa Lithari - PhD candidate in Lab of Medical Informatics, Aristotle University of Thessaloniki, Greece - M.Sc. NeuroInformatics, Unversity of Patras, Greece - B.Sc. Computer Science, Aristotle University of Thessaloniki, Greece -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Fri Feb 24 11:24:26 2012 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Fri, 24 Feb 2012 10:24:26 +0000 Subject: [FieldTrip] coregistration neuromag In-Reply-To: References: Message-ID: Dear Chrysa, If you are using SPM already you could also generate a head model and do coregistration with SPM8 and then use it with Fieldtrip. See SPM manual for details. There are some example functions in the Beamforming toolbox in SPM where you can see how the SPM-Fieldtrip interfacing can be done. Best, Vladimir On Fri, Feb 24, 2012 at 10:08 AM, Chrysa Lithari wrote: > Hi to all, > > I just started using fieldtrip and I have the following question. > > I have the MRI and the polhemus data for each subject. > The MRI is in dicom and I can also transform it to 'analyze' format using > SPM. > The polhemus data are in fif format, together with the functional data. > How can I coregister these two types of data in fieldtrip? > I searched in the tutorial and it is mentioned that normally MEG systems > come with a software allowing to align MRI with the helmet, e.g. CTF. > However, I have worked on Neuromag system and I have not done anything like > this. How can I do it in Fieltrip? > A step by step (AC-PC points, normalization, segmentation etc) guidance > would be very helpful stating the functions I have to use and any > precautions I have to consider during this process. > > Best regards and thanks in advance, > Chrysa Lithari > > -- > Chrysa Lithari > - PhD candidate in Lab of Medical Informatics, Aristotle University of > Thessaloniki, Greece > - M.Sc. NeuroInformatics, Unversity of Patras, Greece > - B.Sc. Computer Science, Aristotle University of Thessaloniki, Greece > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From ole.jensen at donders.ru.nl Sun Feb 26 15:41:36 2012 From: ole.jensen at donders.ru.nl (Ole Jensen) Date: Sun, 26 Feb 2012 15:41:36 +0100 Subject: [FieldTrip] senior researcher position at the Donders Institute Message-ID: <4F4A44A0.4010201@donders.ru.nl> Dear colleagues, I would like to bring your attention to the position below. Alt the best, Ole Jensen http://www.neuosc.com ------------------------ *Senior Researcher for 'Neuronal Oscillations and Networks' (1,0 fte) * *Donders Institute, Centre for Cognitive Neuroimaging* *Vacancy number: 30.01.12* *Closing date: 15 April 2012* *Responsibilities* The Neuronal Oscillation group at the Donders Institute for Brain, Cognition and Behaviour has funding available for a senior researcher position. The position has a strong research component, but also includes additional management and teaching responsibilities. The management tasks involve active participation in structuring the research group, including supervision of MSc and PhD students (who will receive senior authorship where applicable). Further, you will contribute to grant writing. The research responsibilities focus on investigating the role of oscillatory neuronal activity involved in shaping the functional architecture of the working brain. This will be done in the context of advanced cognitive paradigms on attention, perception and memory. There will be a strong focus on the role of phase, network interactions and subcortical structures. You will have the following state-of-the-art equipment to your disposal: MEG, (f)MRI, EEG combined with TMS, and EEG combined with fMRI. A further aim is to link structural (e.g. DTI) and functional measurements. You will also participate in conceptually developing the framework for understanding the functional role of brain oscillations. *Work environment* The Donders Institute for Brain, Cognition and Behaviour consists of the Centre for Cognition, the Centre for Cognitive Neuroimaging and the Centre for Neuroscience. The mission of the Centre for Cognitive Neuroimaging is to conduct cutting-edge fundamental research in cognitive neuroscience. Much of the rapid progress in this field is being driven by the development of complex neuro-imaging techniques for measuring activity in the human working brain - an area in which the Centre plays a leading role. The research themes cover central cognitive functions such as perception, action, control, decision making, attention, memory, language, learning and plasticity. The internationally renowned centre currently hosts more than 100 PhD students and postdoctoral researchers from more than 20 countries, offering a stimulating and multidisciplinary research environment. The centre is equipped with three MRI scanners (7T, 3T, 1.5T), a 275-channel MEG system, an EEG-TMS laboratory, several (MR-compatible) EEG systems, and high-performance computational facilities. English is the lingua franca at the centre. You will work within the Neuronal Oscillations group. *What we expect from you* As a candidate for the position, you should have a PhD degree and several years of experience as postdoctoral researcher in a field related to cognitive neuroscience. Selection criteria will consider the record of published research, familiarity with neuroimaging techniques (fMRI, EEG, MEG, and/or TMS) and supervision experience. Proficiency in oral and written English is a prerequisite. You are expected to work in a team, sharing technical know-how and ideas. *What we have to offer* We offer you: - employment: 1,0 fte; - in addition to the salary: an 8% holiday allowance and an 8.3% end-of-year bonus; - the gross salary will be between EUR3,195 and EUR4,970 (scale 12), depending on experience; - salary scale 11 will apply during the first year; - duration of the contract: 6 years maximum. Are you interested in our excellentemployment conditions ? *Would you like to know more?* Further information on:DCCN Further information on:Neuronal Oscillations group Dr. Ole Jensen Telephone: +31 24 3610884 E-mail:ole.jensen at donders.ru.nl *Applications* Are you interested? It is Radboud University Nijmegen's policy to only accept applications by e-mail. Please send your application,/stating vacancy number 30.01.12/, tovacatures at dpo.ru.nl , for the attention of Dr. Ole Jensen, before 15 April 2012. For more information on the application procedure: +31 24 3611173 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tessa.vanleeuwen at fcdonders.ru.nl Mon Feb 27 10:33:50 2012 From: tessa.vanleeuwen at fcdonders.ru.nl (Tessa van Leeuwen) Date: Mon, 27 Feb 2012 10:33:50 +0100 (CET) Subject: [FieldTrip] adapting leadfields after PCA/ICA Message-ID: <1030785558.11966.1330335230620.JavaMail.root@draco.zimbra.ru.nl> Dear FieldTrip users, To save trials I plan on using ICA to remove eog artifacts from my MEG dataset. Because of the large number of channels (271) and limited trial-time (about 300 trials of 1.1 s in each run), we will most likely limit the number of possible components using PCA. The combined PCA/ICA data-cleaning step will have consequences for source reconstruction approaches that we would like to apply to the data later on, e.g. beamforming. When ICA components representing eyeblink artifacts have been removed from the data, how can the leadfield for source reconstruction be adapted to account for the alterations to the data? If anyone has more information about how to do this or can refer me to papers implementing such a pipeline, that would be highly appreciated. Thank you very much in advance for any tips. Best wishes, Tessa van Leeuwen From jan.schoffelen at donders.ru.nl Mon Feb 27 11:14:48 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 27 Feb 2012 11:14:48 +0100 Subject: [FieldTrip] adapting leadfields after PCA/ICA In-Reply-To: <1030785558.11966.1330335230620.JavaMail.root@draco.zimbra.ru.nl> References: <1030785558.11966.1330335230620.JavaMail.root@draco.zimbra.ru.nl> Message-ID: <9E6F733E-B395-486E-907F-C60674592371@donders.ru.nl> Hi Tessa, I imagine that you use ft_componentanalysis and ft_rejectcomponent sequentially in order to remove the eye blink topographies. If you use the data.grad in the output to ft_rejectcomponent for the computation of the leadfields you should be fine. The balancing matrix grad.tra will contain the information that will be used for the correction of the leadfields. Best wishes, Jan-Mathijs On Feb 27, 2012, at 10:33 AM, Tessa van Leeuwen wrote: > Dear FieldTrip users, > > To save trials I plan on using ICA to remove eog artifacts from my MEG dataset. Because of the large number of channels (271) and limited trial-time (about 300 trials of 1.1 s in each run), we will most likely limit the number of possible components using PCA. > > The combined PCA/ICA data-cleaning step will have consequences for source reconstruction approaches that we would like to apply to the data later on, e.g. beamforming. When ICA components representing eyeblink artifacts have been removed from the data, how can the leadfield for source reconstruction be adapted to account for the alterations to the data? > If anyone has more information about how to do this or can refer me to papers implementing such a pipeline, that would be highly appreciated. > > Thank you very much in advance for any tips. > > Best wishes, > Tessa van Leeuwen > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tessa.vanleeuwen at fcdonders.ru.nl Mon Feb 27 12:20:49 2012 From: tessa.vanleeuwen at fcdonders.ru.nl (Tessa van Leeuwen) Date: Mon, 27 Feb 2012 12:20:49 +0100 (CET) Subject: [FieldTrip] adapting leadfields after PCA/ICA In-Reply-To: <9E6F733E-B395-486E-907F-C60674592371@donders.ru.nl> Message-ID: <1972515496.15972.1330341648951.JavaMail.root@draco.zimbra.ru.nl> Hi Jan-Mathijs, Thank you for this quick and informative reply; we indeed use ft_componentanalysis and ft_rejectcomponent sequentially. I will make sure to save the grad structures for the later source analysis. Great! Thank you again, best, Tessa ----- "jan-mathijs schoffelen" wrote: > From: "jan-mathijs schoffelen" > To: "Email discussion list for the FieldTrip project" > Sent: Monday, February 27, 2012 11:14:48 AM > Subject: Re: [FieldTrip] adapting leadfields after PCA/ICA > > Hi Tessa, > I imagine that you use ft_componentanalysis and ft_rejectcomponent sequentially in order to remove the eye blink topographies. If you use the data.grad in the output to ft_rejectcomponent for the computation of the leadfields you should be fine. The balancing matrix grad.tra will contain the information that will be used for the correction of the leadfields. > Best wishes, > Jan-Mathijs > > On Feb 27, 2012, at 10:33 AM, Tessa van Leeuwen wrote: Dear FieldTrip users, > > To save trials I plan on using ICA to remove eog artifacts from my MEG dataset. Because of the large number of channels (271) and limited trial-time (about 300 trials of 1.1 s in each run), we will most likely limit the number of possible components using PCA. > > The combined PCA/ICA data-cleaning step will have consequences for source reconstruction approaches that we would like to apply to the data later on, e.g. beamforming. When ICA components representing eyeblink artifacts have been removed from the data, how can the leadfield for source reconstruction be adapted to account for the alterations to the data? > If anyone has more information about how to do this or can refer me to papers implementing such a pipeline, that would be highly appreciated. > > Thank you very much in advance for any tips. > > Best wishes, > Tessa van Leeuwen > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > Jan-Mathijs Schoffelen, MD PhD > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From max-philipp.stenner at med.ovgu.de Mon Feb 27 17:02:32 2012 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Mon, 27 Feb 2012 16:02:32 +0000 Subject: [FieldTrip] spm_eeg_ft2spm Message-ID: Dear fieldtrippers, I am trying to convert preprocessed/epoched fieldtrip data to spm8 using spm_eeg_ft2spm (for VB-ECD source analysis). I derived volume conduction models for my participants using spm_eeg_convert on data (that was not preprocessed/epoched) a while ago without encountering major problems. spm_eeg_ft2spm, however, requires an input argument "filename", for which I have tried various definitions (a result-filename, the original ft-datafile and filenames both with and without .dat of the same session of the spm_eeg_convert output). As I am not familiar with file_arrays and find little help within the function scripts, I was wondering whether anyone could tell me the (probably simple) solution to overcome the error 'mat2file' Cant open file. What does spm_eeg_ft2spm require as "filename" input? I am using fieldtrip-20111130 on a Windows7 PC. Thanks a lot, best Max From litvak.vladimir at gmail.com Mon Feb 27 17:18:37 2012 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Mon, 27 Feb 2012 16:18:37 +0000 Subject: [FieldTrip] spm_eeg_ft2spm In-Reply-To: References: Message-ID: <712F7AE2-5CF6-46D1-BEF3-AB699031DCD7@gmail.com> Hi Max, filename is the name for the new SPM dataset that you are generating. Not sure how volume conduction models are relevant here. Perhaps since we sit in the same building it'd be easier if you come to talk to me directly. Fieldtrip mailing list is not quite relevant for these issues as they are more SPM-related. Best, Vladimir On 27 Feb 2012, at 16:02, "Stenner, Max-Philipp" wrote: > Dear fieldtrippers, > > > > I am trying to convert preprocessed/epoched fieldtrip data to spm8 using spm_eeg_ft2spm (for VB-ECD source analysis). > > > > I derived volume conduction models for my participants using spm_eeg_convert on data (that was not preprocessed/epoched) a while ago without encountering major problems. spm_eeg_ft2spm, however, requires an input argument "filename", for which I have tried various definitions (a result-filename, the original ft-datafile and filenames both with and without .dat of the same session of the spm_eeg_convert output). As I am not familiar with file_arrays and find little help within the function scripts, I was wondering whether anyone could tell me the (probably simple) solution to overcome the error > > > > 'mat2file' Cant open file. > > > > What does spm_eeg_ft2spm require as "filename" input? > > > > I am using fieldtrip-20111130 on a Windows7 PC. > > > > Thanks a lot, > > best > > Max > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From s.bogels at psy.gla.ac.uk Tue Feb 28 13:12:47 2012 From: s.bogels at psy.gla.ac.uk (=?ISO-8859-1?Q?Sara_B=F6gels?=) Date: Tue, 28 Feb 2012 12:12:47 +0000 Subject: [FieldTrip] MNE: sourcespace and volume aligned? Message-ID: <4F4CC4BF.9030003@psy.gla.ac.uk> Hi all, I am working my way through the MNE tutorial and plotted the mesh and vol on top of each other at the end of the Freesurfer and MNE suite steps to check whether they are aligned. The volume seems to fit quite well into the mesh but is a bit smaller (see attached figures), but definitely not a factor 10. However, from the figure (5) in the tutorial, it seems as if the mesh has to be exactly on top of the volume. Does my plot show that the two are misaligned? If so, what might be the problem? I tried to use ft_determine_coordsys on the vol, but that gives me the error message: 'unknown units (dm)'. If I use it on the sourcespace I get the output that the units are 'cm'. Any help is appreciated. Thank you, Sara Bögels -------------- next part -------------- A non-text attachment was scrubbed... Name: mesh_vol_plot2.jpg Type: image/jpeg Size: 135822 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mesh_vol_plot.jpg Type: image/jpeg Size: 104188 bytes Desc: not available URL: From Lilla.Magyari at mpi.nl Tue Feb 28 14:52:55 2012 From: Lilla.Magyari at mpi.nl (Magyari, Lilla) Date: Tue, 28 Feb 2012 14:52:55 +0100 Subject: [FieldTrip] MNE: sourcespace and volume aligned? In-Reply-To: <4F4CC4BF.9030003@psy.gla.ac.uk> References: <4F4CC4BF.9030003@psy.gla.ac.uk> Message-ID: <4F4CDC37.6000504@mpi.nl> hi Sara, I think the alignment looks just good. The volume conductor is made from the (inside) skull surface, so it is a bit bigger indeed than the sourcespace. For me, it seems that there is also space between the vol and the sourcespace on the picture in the tutorial, but it is more difficult to see because it is colored. Probably, it wasn't plot with exactly the same piece of code than what is indicate above it. About the error message. I am wondering which version of Fieldtrip are you using? Because I had similar problems with my units when I used an earlier version of FieldTrip where the ft_convert_unit function worked a bit differently than now. In any case, we are simplifying this anatomical preprocessing pipeline (all things that you do in FieldTrip before using FreeSurfer) right now, so you can see the new version of the tutorial in a few days. Best, Lilla Sara Bögels wrote: > Hi all, > > I am working my way through the MNE tutorial and plotted the mesh and > vol on top of each other at the end of the Freesurfer and MNE suite > steps to check whether they are aligned. The volume seems to fit quite > well into the mesh but is a bit smaller (see attached figures), but > definitely not a factor 10. However, from the figure (5) in the > tutorial, it seems as if the mesh has to be exactly on top of the > volume. Does my plot show that the two are misaligned? If so, what might > be the problem? > > I tried to use ft_determine_coordsys on the vol, but that gives me the > error message: 'unknown units (dm)'. If I use it on the sourcespace I > get the output that the units are 'cm'. > > Any help is appreciated. > > Thank you, > Sara Bögels > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Andrew.Dykstra at med.uni-heidelberg.de Tue Feb 28 17:34:59 2012 From: Andrew.Dykstra at med.uni-heidelberg.de (Andrew R. Dykstra) Date: Tue, 28 Feb 2012 17:34:59 +0100 Subject: [FieldTrip] getting started with Neuromag 122 data Message-ID: Hi everyone, I'm new to Fieldtrip and would like to use it to process data collected on a Neuromag 122 system. However, I'm running into some fairly simple issues with regard to reading header information and events. Regarding header information, it seems that fieldtrip can read the fif file's header and raw data, but some fields in the header are not assigned correctly. For example, hdr.chantype returns 'unknown' for all channels in the data set (whereas they should be either 'meg_planar ' or trigger lines). Also, hdr.grad returns empty arrays. Regarding reading events, I read Yang Zhang's solution of using mne_make_combined_ event_file.m from the MNE stream and manually creating the event structure (from this list on Jan 8, 2010: http://mailman.science.ru.nl/pipermail/fieldtrip/2010-January/002551.html). This will should also work for me, but I was wondering if there is now a more streamlined way of accomplishing this in Fieldtrip, especially for fif files either containing or associated with an event list based on a text file with sample numbers, latencies, and event types. I did not see an option in ft_read_event to do this. Any suggestions would be much appreciated. Andy Andrew R. Dykstra, PhD Auditory Cognition Lab Neurologie und Poliklinik Universitätsklinikum Heidelberg Im Neuenheimer Feld 400 69120 Heidelberg "How small the cosmos. How paltry and puny compared to human consciousness . . . to a single individual recollection." - Vladimir Nabokov -------------- next part -------------- An HTML attachment was scrubbed... URL: From ali at cs.ru.nl Wed Feb 29 21:10:54 2012 From: ali at cs.ru.nl (Ali Bahramisharif) Date: Wed, 29 Feb 2012 21:10:54 +0100 Subject: [FieldTrip] question about MNI alignment Message-ID: Dear Fieldtrip users, I want to create MNI-aligned grids in individual head-space, and I follow the guidelines in : http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space?s[]=template&s[]=grid I do not know how old this page is, but I noticed that for example in the current version "cfg.coordinates" should be "cfg.coordsys". I have the following problems: 1- When I run "ft_plot_mesh(template_grid);", I get a cubic grid which is apparently different from the one shown in the page. 2- When I run, ft_plot_vol(hdm), it does not seem to be aligned to "ft_plot_sens(ft_read_sens(dataset{i}));" I checked my segmented volumes, and they seem to be fine, and I did not need to run flipdim. I am wondering whether my segmented data is correct or it should be flipped somewhere. Please let me know if anybody knows how to resolve this problem. Cheers, Ali