From Jan.Schoffelen at FCDONDERS.KUN.NL Wed Sep 1 12:01:17 2004 From: Jan.Schoffelen at FCDONDERS.KUN.NL (J.M. Schoffelen) Date: Wed, 1 Sep 2004 12:01:17 +0200 Subject: updat artifact-detection routines Message-ID: Dear Fieldtrippers, I updated some of the automatic artifact-detection routines, which make some things a bit more user friendly. Totally not according to the fieldtrip philosophy, there is now a GUI which enables you to browse through the data, if you select the feedback-option for the included artifact-types. I think that things are more or less self explanatory. Please report any bugs to me. Happy artifact-detecting, Jan-Mathijs -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.KUN.NL Fri Sep 3 17:03:57 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Fri, 3 Sep 2004 17:03:57 +0200 Subject: fieldtrip release 0.9.2 available Message-ID: Dear all, I am glad to announce the first version of FieldTrip that is available for everyone to download. On http://www.ru.nl/fcdonders/fieldtrip/ you can download the source code of version 0.9.2. It is still a beta version, since there are some more tests and minor changes that we want to do before we can call it version "1.0". But that should not limit you from already starting to use it. Happy fieldtripping! Robert PS for the people working in the F.C. Donders Centre nothing changes, the latest development version is still available on the /home/common network disk. ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From roberto at SMI.AUC.DK Mon Sep 6 18:03:57 2004 From: roberto at SMI.AUC.DK (Robert Oostenveld) Date: Mon, 6 Sep 2004 18:03:57 +0200 Subject: resampling strategies for beamformer scanning Message-ID: Hi FieldTrippers, I am re-working the resampling code (i.e. jacknife, randomization, etc.) in SOURCEANALYSIS and encountered a few problems that I would like to discuss with those of you who are actually using it. Could you please send me personally an email (so don't reply to the mailing list) if you are using any of the following combinations in SOURCEANALYSIS - jacknife with lcmv - bootstrap with lcmv or dics - singletrial with either lcmv or dics - rawtrial with either lcmv or dics or if you are using the option "cfg.trialweight" in SOURCEANALYSIS? If you are using randomization or resampling (between two conditions) you don't have to react. If you have no clue what this email is about, you also do not have to reply. best regards, Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From r.oostenveld at FCDONDERS.KUN.NL Wed Sep 8 08:43:13 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Wed, 8 Sep 2004 08:43:13 +0200 Subject: virtual channel In-Reply-To: <20040907164713.16475.qmail@web50909.mail.yahoo.com> Message-ID: On 7 Sep 2004, at 18:47, Bin Wu wrote: > There is a quick question: how to read virtual channel > data with your software? Thanks you for your help. Dear Bin Wu, I presume that you are referring to virtual channels in a CTF dataset? As far as I know, virtual channels are stored in the same manner as normal MEG and EEG channels, so selecting cfg.channel='all', or cfg.channel={'virt1', 'virt2', ...} (where virtX is the name of your channel) for preprocessing should do the trick. best regards, Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From tomh at KURAGE.NIMH.NIH.GOV Wed Sep 8 16:31:01 2004 From: tomh at KURAGE.NIMH.NIH.GOV (Tom Holroyd) Date: Wed, 8 Sep 2004 10:31:01 -0400 Subject: virtual channel In-Reply-To: <5B8900BE-0162-11D9-B907-000A95DBB2CC@fcdonders.kun.nl> Message-ID: > > There is a quick question: how to read virtual channel > > data with your software? Thanks you for your help. > > I presume that you are referring to virtual channels in a CTF dataset? > As far as I know, virtual channels are stored in the same manner as > normal MEG and EEG channels ... For SAM virtual channels, note that you will need to create a dataset with newDs that contains the virtual channels. The SAM software merely stores the weights in the .svl files, and the DataEditor only displays virtual channels but cannot save them. Also, the website here, http://kurage.nimh.nih.gov has a link to a program called newDs2, which includes a -band option and an -excludeMEG option, which are helpful for creating virtual channels. Recall that virtual channels are only valid in a certain passband, so something like newDs2 -band 20 80 -includeSAM stim,20-80Hz.wts -excludeMEG \ -marker stim -time -.2 .8 src.ds gamma.ds will do the filtering, clip the time segments (also needs to match the active window used to create the covariance), and create a dataset containing only the virtual channels, which will be named V0, V1, ... Dr. Tom Holroyd "A man of genius makes no mistakes. His errors are volitional and are the portals of discovery." -- James Joyce From r.oostenveld at FCDONDERS.KUN.NL Thu Sep 16 11:20:19 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Thu, 16 Sep 2004 11:20:19 +0200 Subject: Fieldtrip homepage has moved temporary Message-ID: Hi FieldTrippers, Due to the name change of the Katholieke Universiteit Nijmegen (KUN) to Radboud Universiteit (RU), all web and email addresses have been changed from xxx.ru.nl to xxx.kun.nl. Furthermore, two days ago the university IT department also introduced a new university-wide website on http://www.ru.nl. Thanks to this introduction, the links to the fieldtrip homepage do not work any more :-( This will be fixed as soon as possible, and I hope that we can get our old web adresses http://www.kun.nl/fcdonders/fieldtrip/ and http://www.ru.nl/fcdonders/fieldtrip/ back. In the meantime, the homepage of Fieldtrip (with documentation and downloads) is available from http://www2.ru.nl/fcdonders/fieldtrip Please point anyone who is interested to the temporary site on http://www2.ru.nl/fcdonders/fieldtrip. best regards, Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From r.oostenveld at FCDONDERS.KUN.NL Fri Sep 17 18:09:49 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Fri, 17 Sep 2004 18:09:49 +0200 Subject: new release (minor updates) Message-ID: Dear all I have just released FieldTrip version 0.9.3, which contains some minor updates relative to the previous release. I suggest that you only download it if you are actively working on implementing your own formats, regular users will not need to update. See http://www2.ru.nl/fcdonders/fieldtrip/download/ for the download. best regards, Robert PS since you are already subscribed to the mailing list, please do not check the "send update" and "add to list" boxes in the download form. ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From r.oostenveld at FCDONDERS.RU.NL Thu Sep 23 08:44:07 2004 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Thu, 23 Sep 2004 08:44:07 +0200 Subject: FieldTrip download request In-Reply-To: <001701c4a0e5$1361fbc0$3c1e5b83@vasan> Message-ID: Hi Sreenivasan, Could you be more specific: does Matlab give you errors, or is the problem with the trialdefinition? If you do hdr = read_fcdc_header(dataset); dat = read_fcdc_data(dataset, hdr, 1, 600); does hdr appear meaningfull and does dat look like the first 600 samples of all the channels that are in the dataset? best regards, Robert On 22 Sep 2004, at 22:45, R. Sreenivasan wrote: > I have difficulty in reading 295 channel CTF MEG data for Fieldtrip. I > would > appreciate if you can provide some input. > > -Sreenivasan > > ----- Original Message ----- > From: "Robert Oostenveld" > To: > Sent: Wednesday, September 22, 2004 3:23 PM > Subject: FieldTrip download request > > >> Thank you for your interest in the FieldTrip toolbox. >> You can download it here > http://www2.ru.nl/fcdonders/fieldtrip/d2o7834o/download.html > ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From Jan.Schoffelen at FCDONDERS.KUN.NL Wed Sep 1 12:01:17 2004 From: Jan.Schoffelen at FCDONDERS.KUN.NL (J.M. Schoffelen) Date: Wed, 1 Sep 2004 12:01:17 +0200 Subject: updat artifact-detection routines Message-ID: Dear Fieldtrippers, I updated some of the automatic artifact-detection routines, which make some things a bit more user friendly. Totally not according to the fieldtrip philosophy, there is now a GUI which enables you to browse through the data, if you select the feedback-option for the included artifact-types. I think that things are more or less self explanatory. Please report any bugs to me. Happy artifact-detecting, Jan-Mathijs -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.KUN.NL Fri Sep 3 17:03:57 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Fri, 3 Sep 2004 17:03:57 +0200 Subject: fieldtrip release 0.9.2 available Message-ID: Dear all, I am glad to announce the first version of FieldTrip that is available for everyone to download. On http://www.ru.nl/fcdonders/fieldtrip/ you can download the source code of version 0.9.2. It is still a beta version, since there are some more tests and minor changes that we want to do before we can call it version "1.0". But that should not limit you from already starting to use it. Happy fieldtripping! Robert PS for the people working in the F.C. Donders Centre nothing changes, the latest development version is still available on the /home/common network disk. ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From roberto at SMI.AUC.DK Mon Sep 6 18:03:57 2004 From: roberto at SMI.AUC.DK (Robert Oostenveld) Date: Mon, 6 Sep 2004 18:03:57 +0200 Subject: resampling strategies for beamformer scanning Message-ID: Hi FieldTrippers, I am re-working the resampling code (i.e. jacknife, randomization, etc.) in SOURCEANALYSIS and encountered a few problems that I would like to discuss with those of you who are actually using it. Could you please send me personally an email (so don't reply to the mailing list) if you are using any of the following combinations in SOURCEANALYSIS - jacknife with lcmv - bootstrap with lcmv or dics - singletrial with either lcmv or dics - rawtrial with either lcmv or dics or if you are using the option "cfg.trialweight" in SOURCEANALYSIS? If you are using randomization or resampling (between two conditions) you don't have to react. If you have no clue what this email is about, you also do not have to reply. best regards, Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From r.oostenveld at FCDONDERS.KUN.NL Wed Sep 8 08:43:13 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Wed, 8 Sep 2004 08:43:13 +0200 Subject: virtual channel In-Reply-To: <20040907164713.16475.qmail@web50909.mail.yahoo.com> Message-ID: On 7 Sep 2004, at 18:47, Bin Wu wrote: > There is a quick question: how to read virtual channel > data with your software? Thanks you for your help. Dear Bin Wu, I presume that you are referring to virtual channels in a CTF dataset? As far as I know, virtual channels are stored in the same manner as normal MEG and EEG channels, so selecting cfg.channel='all', or cfg.channel={'virt1', 'virt2', ...} (where virtX is the name of your channel) for preprocessing should do the trick. best regards, Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From tomh at KURAGE.NIMH.NIH.GOV Wed Sep 8 16:31:01 2004 From: tomh at KURAGE.NIMH.NIH.GOV (Tom Holroyd) Date: Wed, 8 Sep 2004 10:31:01 -0400 Subject: virtual channel In-Reply-To: <5B8900BE-0162-11D9-B907-000A95DBB2CC@fcdonders.kun.nl> Message-ID: > > There is a quick question: how to read virtual channel > > data with your software? Thanks you for your help. > > I presume that you are referring to virtual channels in a CTF dataset? > As far as I know, virtual channels are stored in the same manner as > normal MEG and EEG channels ... For SAM virtual channels, note that you will need to create a dataset with newDs that contains the virtual channels. The SAM software merely stores the weights in the .svl files, and the DataEditor only displays virtual channels but cannot save them. Also, the website here, http://kurage.nimh.nih.gov has a link to a program called newDs2, which includes a -band option and an -excludeMEG option, which are helpful for creating virtual channels. Recall that virtual channels are only valid in a certain passband, so something like newDs2 -band 20 80 -includeSAM stim,20-80Hz.wts -excludeMEG \ -marker stim -time -.2 .8 src.ds gamma.ds will do the filtering, clip the time segments (also needs to match the active window used to create the covariance), and create a dataset containing only the virtual channels, which will be named V0, V1, ... Dr. Tom Holroyd "A man of genius makes no mistakes. His errors are volitional and are the portals of discovery." -- James Joyce From r.oostenveld at FCDONDERS.KUN.NL Thu Sep 16 11:20:19 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Thu, 16 Sep 2004 11:20:19 +0200 Subject: Fieldtrip homepage has moved temporary Message-ID: Hi FieldTrippers, Due to the name change of the Katholieke Universiteit Nijmegen (KUN) to Radboud Universiteit (RU), all web and email addresses have been changed from xxx.ru.nl to xxx.kun.nl. Furthermore, two days ago the university IT department also introduced a new university-wide website on http://www.ru.nl. Thanks to this introduction, the links to the fieldtrip homepage do not work any more :-( This will be fixed as soon as possible, and I hope that we can get our old web adresses http://www.kun.nl/fcdonders/fieldtrip/ and http://www.ru.nl/fcdonders/fieldtrip/ back. In the meantime, the homepage of Fieldtrip (with documentation and downloads) is available from http://www2.ru.nl/fcdonders/fieldtrip Please point anyone who is interested to the temporary site on http://www2.ru.nl/fcdonders/fieldtrip. best regards, Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From r.oostenveld at FCDONDERS.KUN.NL Fri Sep 17 18:09:49 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Fri, 17 Sep 2004 18:09:49 +0200 Subject: new release (minor updates) Message-ID: Dear all I have just released FieldTrip version 0.9.3, which contains some minor updates relative to the previous release. I suggest that you only download it if you are actively working on implementing your own formats, regular users will not need to update. See http://www2.ru.nl/fcdonders/fieldtrip/download/ for the download. best regards, Robert PS since you are already subscribed to the mailing list, please do not check the "send update" and "add to list" boxes in the download form. ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From r.oostenveld at FCDONDERS.RU.NL Thu Sep 23 08:44:07 2004 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Thu, 23 Sep 2004 08:44:07 +0200 Subject: FieldTrip download request In-Reply-To: <001701c4a0e5$1361fbc0$3c1e5b83@vasan> Message-ID: Hi Sreenivasan, Could you be more specific: does Matlab give you errors, or is the problem with the trialdefinition? If you do hdr = read_fcdc_header(dataset); dat = read_fcdc_data(dataset, hdr, 1, 600); does hdr appear meaningfull and does dat look like the first 600 samples of all the channels that are in the dataset? best regards, Robert On 22 Sep 2004, at 22:45, R. Sreenivasan wrote: > I have difficulty in reading 295 channel CTF MEG data for Fieldtrip. I > would > appreciate if you can provide some input. > > -Sreenivasan > > ----- Original Message ----- > From: "Robert Oostenveld" > To: > Sent: Wednesday, September 22, 2004 3:23 PM > Subject: FieldTrip download request > > >> Thank you for your interest in the FieldTrip toolbox. >> You can download it here > http://www2.ru.nl/fcdonders/fieldtrip/d2o7834o/download.html > ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From Jan.Schoffelen at FCDONDERS.KUN.NL Wed Sep 1 12:01:17 2004 From: Jan.Schoffelen at FCDONDERS.KUN.NL (J.M. Schoffelen) Date: Wed, 1 Sep 2004 12:01:17 +0200 Subject: updat artifact-detection routines Message-ID: Dear Fieldtrippers, I updated some of the automatic artifact-detection routines, which make some things a bit more user friendly. Totally not according to the fieldtrip philosophy, there is now a GUI which enables you to browse through the data, if you select the feedback-option for the included artifact-types. I think that things are more or less self explanatory. Please report any bugs to me. Happy artifact-detecting, Jan-Mathijs -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.KUN.NL Fri Sep 3 17:03:57 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Fri, 3 Sep 2004 17:03:57 +0200 Subject: fieldtrip release 0.9.2 available Message-ID: Dear all, I am glad to announce the first version of FieldTrip that is available for everyone to download. On http://www.ru.nl/fcdonders/fieldtrip/ you can download the source code of version 0.9.2. It is still a beta version, since there are some more tests and minor changes that we want to do before we can call it version "1.0". But that should not limit you from already starting to use it. Happy fieldtripping! Robert PS for the people working in the F.C. Donders Centre nothing changes, the latest development version is still available on the /home/common network disk. ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From roberto at SMI.AUC.DK Mon Sep 6 18:03:57 2004 From: roberto at SMI.AUC.DK (Robert Oostenveld) Date: Mon, 6 Sep 2004 18:03:57 +0200 Subject: resampling strategies for beamformer scanning Message-ID: Hi FieldTrippers, I am re-working the resampling code (i.e. jacknife, randomization, etc.) in SOURCEANALYSIS and encountered a few problems that I would like to discuss with those of you who are actually using it. Could you please send me personally an email (so don't reply to the mailing list) if you are using any of the following combinations in SOURCEANALYSIS - jacknife with lcmv - bootstrap with lcmv or dics - singletrial with either lcmv or dics - rawtrial with either lcmv or dics or if you are using the option "cfg.trialweight" in SOURCEANALYSIS? If you are using randomization or resampling (between two conditions) you don't have to react. If you have no clue what this email is about, you also do not have to reply. best regards, Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From r.oostenveld at FCDONDERS.KUN.NL Wed Sep 8 08:43:13 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Wed, 8 Sep 2004 08:43:13 +0200 Subject: virtual channel In-Reply-To: <20040907164713.16475.qmail@web50909.mail.yahoo.com> Message-ID: On 7 Sep 2004, at 18:47, Bin Wu wrote: > There is a quick question: how to read virtual channel > data with your software? Thanks you for your help. Dear Bin Wu, I presume that you are referring to virtual channels in a CTF dataset? As far as I know, virtual channels are stored in the same manner as normal MEG and EEG channels, so selecting cfg.channel='all', or cfg.channel={'virt1', 'virt2', ...} (where virtX is the name of your channel) for preprocessing should do the trick. best regards, Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From tomh at KURAGE.NIMH.NIH.GOV Wed Sep 8 16:31:01 2004 From: tomh at KURAGE.NIMH.NIH.GOV (Tom Holroyd) Date: Wed, 8 Sep 2004 10:31:01 -0400 Subject: virtual channel In-Reply-To: <5B8900BE-0162-11D9-B907-000A95DBB2CC@fcdonders.kun.nl> Message-ID: > > There is a quick question: how to read virtual channel > > data with your software? Thanks you for your help. > > I presume that you are referring to virtual channels in a CTF dataset? > As far as I know, virtual channels are stored in the same manner as > normal MEG and EEG channels ... For SAM virtual channels, note that you will need to create a dataset with newDs that contains the virtual channels. The SAM software merely stores the weights in the .svl files, and the DataEditor only displays virtual channels but cannot save them. Also, the website here, http://kurage.nimh.nih.gov has a link to a program called newDs2, which includes a -band option and an -excludeMEG option, which are helpful for creating virtual channels. Recall that virtual channels are only valid in a certain passband, so something like newDs2 -band 20 80 -includeSAM stim,20-80Hz.wts -excludeMEG \ -marker stim -time -.2 .8 src.ds gamma.ds will do the filtering, clip the time segments (also needs to match the active window used to create the covariance), and create a dataset containing only the virtual channels, which will be named V0, V1, ... Dr. Tom Holroyd "A man of genius makes no mistakes. His errors are volitional and are the portals of discovery." -- James Joyce From r.oostenveld at FCDONDERS.KUN.NL Thu Sep 16 11:20:19 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Thu, 16 Sep 2004 11:20:19 +0200 Subject: Fieldtrip homepage has moved temporary Message-ID: Hi FieldTrippers, Due to the name change of the Katholieke Universiteit Nijmegen (KUN) to Radboud Universiteit (RU), all web and email addresses have been changed from xxx.ru.nl to xxx.kun.nl. Furthermore, two days ago the university IT department also introduced a new university-wide website on http://www.ru.nl. Thanks to this introduction, the links to the fieldtrip homepage do not work any more :-( This will be fixed as soon as possible, and I hope that we can get our old web adresses http://www.kun.nl/fcdonders/fieldtrip/ and http://www.ru.nl/fcdonders/fieldtrip/ back. In the meantime, the homepage of Fieldtrip (with documentation and downloads) is available from http://www2.ru.nl/fcdonders/fieldtrip Please point anyone who is interested to the temporary site on http://www2.ru.nl/fcdonders/fieldtrip. best regards, Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From r.oostenveld at FCDONDERS.KUN.NL Fri Sep 17 18:09:49 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Fri, 17 Sep 2004 18:09:49 +0200 Subject: new release (minor updates) Message-ID: Dear all I have just released FieldTrip version 0.9.3, which contains some minor updates relative to the previous release. I suggest that you only download it if you are actively working on implementing your own formats, regular users will not need to update. See http://www2.ru.nl/fcdonders/fieldtrip/download/ for the download. best regards, Robert PS since you are already subscribed to the mailing list, please do not check the "send update" and "add to list" boxes in the download form. ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From r.oostenveld at FCDONDERS.RU.NL Thu Sep 23 08:44:07 2004 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Thu, 23 Sep 2004 08:44:07 +0200 Subject: FieldTrip download request In-Reply-To: <001701c4a0e5$1361fbc0$3c1e5b83@vasan> Message-ID: Hi Sreenivasan, Could you be more specific: does Matlab give you errors, or is the problem with the trialdefinition? If you do hdr = read_fcdc_header(dataset); dat = read_fcdc_data(dataset, hdr, 1, 600); does hdr appear meaningfull and does dat look like the first 600 samples of all the channels that are in the dataset? best regards, Robert On 22 Sep 2004, at 22:45, R. Sreenivasan wrote: > I have difficulty in reading 295 channel CTF MEG data for Fieldtrip. I > would > appreciate if you can provide some input. > > -Sreenivasan > > ----- Original Message ----- > From: "Robert Oostenveld" > To: > Sent: Wednesday, September 22, 2004 3:23 PM > Subject: FieldTrip download request > > >> Thank you for your interest in the FieldTrip toolbox. >> You can download it here > http://www2.ru.nl/fcdonders/fieldtrip/d2o7834o/download.html > ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From Jan.Schoffelen at FCDONDERS.KUN.NL Wed Sep 1 12:01:17 2004 From: Jan.Schoffelen at FCDONDERS.KUN.NL (J.M. Schoffelen) Date: Wed, 1 Sep 2004 12:01:17 +0200 Subject: updat artifact-detection routines Message-ID: Dear Fieldtrippers, I updated some of the automatic artifact-detection routines, which make some things a bit more user friendly. Totally not according to the fieldtrip philosophy, there is now a GUI which enables you to browse through the data, if you select the feedback-option for the included artifact-types. I think that things are more or less self explanatory. Please report any bugs to me. Happy artifact-detecting, Jan-Mathijs -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.KUN.NL Fri Sep 3 17:03:57 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Fri, 3 Sep 2004 17:03:57 +0200 Subject: fieldtrip release 0.9.2 available Message-ID: Dear all, I am glad to announce the first version of FieldTrip that is available for everyone to download. On http://www.ru.nl/fcdonders/fieldtrip/ you can download the source code of version 0.9.2. It is still a beta version, since there are some more tests and minor changes that we want to do before we can call it version "1.0". But that should not limit you from already starting to use it. Happy fieldtripping! Robert PS for the people working in the F.C. Donders Centre nothing changes, the latest development version is still available on the /home/common network disk. ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From roberto at SMI.AUC.DK Mon Sep 6 18:03:57 2004 From: roberto at SMI.AUC.DK (Robert Oostenveld) Date: Mon, 6 Sep 2004 18:03:57 +0200 Subject: resampling strategies for beamformer scanning Message-ID: Hi FieldTrippers, I am re-working the resampling code (i.e. jacknife, randomization, etc.) in SOURCEANALYSIS and encountered a few problems that I would like to discuss with those of you who are actually using it. Could you please send me personally an email (so don't reply to the mailing list) if you are using any of the following combinations in SOURCEANALYSIS - jacknife with lcmv - bootstrap with lcmv or dics - singletrial with either lcmv or dics - rawtrial with either lcmv or dics or if you are using the option "cfg.trialweight" in SOURCEANALYSIS? If you are using randomization or resampling (between two conditions) you don't have to react. If you have no clue what this email is about, you also do not have to reply. best regards, Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From r.oostenveld at FCDONDERS.KUN.NL Wed Sep 8 08:43:13 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Wed, 8 Sep 2004 08:43:13 +0200 Subject: virtual channel In-Reply-To: <20040907164713.16475.qmail@web50909.mail.yahoo.com> Message-ID: On 7 Sep 2004, at 18:47, Bin Wu wrote: > There is a quick question: how to read virtual channel > data with your software? Thanks you for your help. Dear Bin Wu, I presume that you are referring to virtual channels in a CTF dataset? As far as I know, virtual channels are stored in the same manner as normal MEG and EEG channels, so selecting cfg.channel='all', or cfg.channel={'virt1', 'virt2', ...} (where virtX is the name of your channel) for preprocessing should do the trick. best regards, Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From tomh at KURAGE.NIMH.NIH.GOV Wed Sep 8 16:31:01 2004 From: tomh at KURAGE.NIMH.NIH.GOV (Tom Holroyd) Date: Wed, 8 Sep 2004 10:31:01 -0400 Subject: virtual channel In-Reply-To: <5B8900BE-0162-11D9-B907-000A95DBB2CC@fcdonders.kun.nl> Message-ID: > > There is a quick question: how to read virtual channel > > data with your software? Thanks you for your help. > > I presume that you are referring to virtual channels in a CTF dataset? > As far as I know, virtual channels are stored in the same manner as > normal MEG and EEG channels ... For SAM virtual channels, note that you will need to create a dataset with newDs that contains the virtual channels. The SAM software merely stores the weights in the .svl files, and the DataEditor only displays virtual channels but cannot save them. Also, the website here, http://kurage.nimh.nih.gov has a link to a program called newDs2, which includes a -band option and an -excludeMEG option, which are helpful for creating virtual channels. Recall that virtual channels are only valid in a certain passband, so something like newDs2 -band 20 80 -includeSAM stim,20-80Hz.wts -excludeMEG \ -marker stim -time -.2 .8 src.ds gamma.ds will do the filtering, clip the time segments (also needs to match the active window used to create the covariance), and create a dataset containing only the virtual channels, which will be named V0, V1, ... Dr. Tom Holroyd "A man of genius makes no mistakes. His errors are volitional and are the portals of discovery." -- James Joyce From r.oostenveld at FCDONDERS.KUN.NL Thu Sep 16 11:20:19 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Thu, 16 Sep 2004 11:20:19 +0200 Subject: Fieldtrip homepage has moved temporary Message-ID: Hi FieldTrippers, Due to the name change of the Katholieke Universiteit Nijmegen (KUN) to Radboud Universiteit (RU), all web and email addresses have been changed from xxx.ru.nl to xxx.kun.nl. Furthermore, two days ago the university IT department also introduced a new university-wide website on http://www.ru.nl. Thanks to this introduction, the links to the fieldtrip homepage do not work any more :-( This will be fixed as soon as possible, and I hope that we can get our old web adresses http://www.kun.nl/fcdonders/fieldtrip/ and http://www.ru.nl/fcdonders/fieldtrip/ back. In the meantime, the homepage of Fieldtrip (with documentation and downloads) is available from http://www2.ru.nl/fcdonders/fieldtrip Please point anyone who is interested to the temporary site on http://www2.ru.nl/fcdonders/fieldtrip. best regards, Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From r.oostenveld at FCDONDERS.KUN.NL Fri Sep 17 18:09:49 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Fri, 17 Sep 2004 18:09:49 +0200 Subject: new release (minor updates) Message-ID: Dear all I have just released FieldTrip version 0.9.3, which contains some minor updates relative to the previous release. I suggest that you only download it if you are actively working on implementing your own formats, regular users will not need to update. See http://www2.ru.nl/fcdonders/fieldtrip/download/ for the download. best regards, Robert PS since you are already subscribed to the mailing list, please do not check the "send update" and "add to list" boxes in the download form. ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links. From r.oostenveld at FCDONDERS.RU.NL Thu Sep 23 08:44:07 2004 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Thu, 23 Sep 2004 08:44:07 +0200 Subject: FieldTrip download request In-Reply-To: <001701c4a0e5$1361fbc0$3c1e5b83@vasan> Message-ID: Hi Sreenivasan, Could you be more specific: does Matlab give you errors, or is the problem with the trialdefinition? If you do hdr = read_fcdc_header(dataset); dat = read_fcdc_data(dataset, hdr, 1, 600); does hdr appear meaningfull and does dat look like the first 600 samples of all the channels that are in the dataset? best regards, Robert On 22 Sep 2004, at 22:45, R. Sreenivasan wrote: > I have difficulty in reading 295 channel CTF MEG data for Fieldtrip. I > would > appreciate if you can provide some input. > > -Sreenivasan > > ----- Original Message ----- > From: "Robert Oostenveld" > To: > Sent: Wednesday, September 22, 2004 3:23 PM > Subject: FieldTrip download request > > >> Thank you for your interest in the FieldTrip toolbox. >> You can download it here > http://www2.ru.nl/fcdonders/fieldtrip/d2o7834o/download.html > ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 ---------------------------------------------------------------------- N.B. Starting from 1 September 2004, the University of Nijmegen has changed its name to Radboud University Nijmegen. All web- and email-addresses ending in ".kun.nl" should therefore be changed into ".ru.nl". Please update your address book and links.