From r.oostenveld at FCDONDERS.RU.NL Mon Jan 3 12:11:00 2005 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 3 Jan 2005 12:11:00 +0100 Subject: FieldTrip Message-ID: Hi Litvak, Happy new year. Since you are asking some questions that also might be interesting to a wider audience, I will forward this mail to the FieldTrip discussion list as well. On 28 Dec 2004, at 11:06, Litvak Vladimir wrote: > Dear Robert, > > I've recently downloaded the FieldTrip toolbox and I have some > questions I hope you can help me with: > > 1) I've been working with EEGLAB for quite some time now and I know > you as a major contributor there as well. Why is FieldTrip developed > separately? Are there any plans to integrate the two toolboxes in the > future? I get that question more often and have just entered is in the FAQ. Please see http://www2.ru.nl/fcdonders/fieldtrip/faq.html#q7 Since both packages have a different aim, they will not be completely merged. But on some specific parts they will be more closely integrated. Fieldtrip and EEGLAB will share parts of their code and the upcoming "DIPFIT 2" module of EEGLAB will be completely based on Fieldtrip. > 2) We have a 64 channel Quickamp EEG system and also have a > possibility to get structural MRIs of our subjects. Would it be > possible to use the DICS method implemented in FieldTrip for analyzing > this data? How can I create a head model without using CTF software > (which I understand is something commercial that comes with your MEG > system)? The CTF software is commercial software for MEG, and therefore not of any use for your EEG. FieldTrip supports various headmodels. But DICS or other beamforming techniques are more sensitive to volume model errors than conventional dipole fitting methods. Therefore a sperical headmodel (as for example used in EEGLAB+DIPFIT) is not usefull. You should use a realistic shaped headmodel, for example using the boundary element method which is available in Fieldtrip. However, creating a realistic headmodel for EEG data from an individual anatomical MRI is difficult and requires quite some user interaction. At the FC Donders Centre we have two commercial packages that we can use for this: Curry and ASA. Therefore it has not been an issue for us sofar to implement an open source version of a BEM headmodel construction routine. > 3) How can I co-register the MRI scan with electrode positions > measured from the same subject? We didn't use capsules to mark the > reference points but I can mark them anatomically and we have the > measurements of the corresponding points with the electrode positions. You can do that using a homogenous transformation matrix (see http://www2.ru.nl/fcdonders/fieldtrip/faq.html#q5 and http://bishopw.loni.ucla.edu/AIR5/homogenous.html). In the private directory of FieldTrip you can find a function "headcoordinates.m" that will help you to compute this matrix. > 4) If there are no free tools available for creating a head model > would it be possible for me to get at least one model for a standard > MRI scan given our electrode positions? In principle you could do most of this using open source tools. You need to 1) segment the MRI, 2) create a triangulation and 3) compute the BEM system matrix. Step 1 and 2 are possible with various open source packages, although you probably will run into some problems with step 2. But I do not know an open source package that can perform step 3. Perhaps I could help you to construct a single BEM model based on a individual MRI, contact me if you are interested. best regards, Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD F.C. Donders Centre for Cognitive Neuroimaging Radboud University Nijmegen phone: +31-24-3619695 http://www.ru.nl/fcdonders/ ---------------------------------------------------------------------- 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 Tue Jan 25 09:13:15 2005 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 25 Jan 2005 09:13:15 +0100 Subject: FieldTrip question In-Reply-To: <41F51A7D.10406@med.uni-tuebingen.de> Message-ID: On 24 Jan 2005, at 16:55, Michael Zvyagintsev wrote: > Dear Colleagues, > I've just started to use fieldtrip for MEG data analysis. > I downloaded it and tried. But I found that during preprocessing there > are no files for 'remove_eog' and 'remove_mcg'. > Probably I downloaded something wrong, but it does not look like... > Could you send me these files or explain what to do with these steps. > Thanks, > Mikhail Zvyagintsev, MD, Bachelor of Informatic Dear Michael, The ECG removal was originally implemented for our MEG system (i.e. it has to remove the magnetocardiogram that we see in some subjects), but sofar we are not yet sufficiently confident about the results to include the remove_mcg subfunction that does the actial work in the release version. The EOG removal has not been implemented yet. Only a so called "hook" was implemented for it in the preprocessing routine so that someone who was willing to implement it could do it in a separate function without changes to the preprocessing function. Since both functions are not included in the release version, they are also not documented in the help and the default value for both is "no". I suggest for the moment that you stick to these default. Our usual procedure is to use the artefact detection routines (rejectartifact) and we reject the data in those trials (or parts of trials) that are contaminated by artefacts. best regards, Robert PS If you are particularly interested in this functionality, we can discuss whether and how to implement it in the release version. ---------------------------------------------------------------------- Robert Oostenveld, PhD F.C. Donders Centre for Cognitive Neuroimaging Radboud University Nijmegen phone: +31-24-3619695 http://www.ru.nl/fcdonders/ ---------------------------------------------------------------------- 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 ali.mazaheri at FCDONDERS.KUN.NL Fri Jan 28 00:32:04 2005 From: ali.mazaheri at FCDONDERS.KUN.NL (Ali Mazaheri) Date: Fri, 28 Jan 2005 00:32:04 +0100 Subject: preprocessing Message-ID: Hi, I am trying to once again preprocess some old data.. but I realize that I can't, even if I use the EXACT same parameters I used to preprocess only last month.. what could be the deal ? Once again I must emphasize that the exact same parameters were working on the same file only a month ago Here is the error I get : Error using ==> read_fcdc_data requested data segment extends over a discontinuous trial boundary Error in ==> \\bond\home\common\matlab\fieldtrip\artifact_jump.m On line 137 ==> dat = read_fcdc_data(cfg.datafile, hdr, trl (trllop,1), ... Error in ==> \\bond\home\common\matlab\fieldtrip\rejectartifact.m On line 224 ==> eval(sprintf('[cfg, %s] = artifact_%s(cfg);', cfg.artfctdef.type{type}, cfg.artfctdef.type{type})); Error in ==> \\bond\home\common\matlab\fieldtrip\preprocessing.m On line 242 ==> [cfg] = rejectartifact(cfg); Error in ==> Z:\MEG\20041201\cfgmaker.m On line 22 ==> data = preprocessing(cfg); From Jan.Schoffelen at FCDONDERS.RU.NL Fri Jan 28 08:17:53 2005 From: Jan.Schoffelen at FCDONDERS.RU.NL (J.M. Schoffelen) Date: Fri, 28 Jan 2005 08:17:53 +0100 Subject: preprocessing In-Reply-To: Message-ID: Hi Ali, 1 Please make sure you are running the latest fieldtrip-version on /home/common/matlab/fieldtrip, 2 Read the documentation of preprocessing and read_fcdc_data: -If your trial collection has been a pseudocontinuous one, you should add a field to your configuration which listens to the following name: cfg.datatype = 'continuous' -If your trial collection has not been a (pseudo)continuous one, but trial-based, the crash is put in on purpose, since several preprocessing steps such as filter padding, and artifact padding rely on the assumption that in the data, as it is in the datafile, the samples left and right of the trial-boundaries are contiguous in time. The extra check that is built in should make the users more aware of what they are doing. Yours, Jan-Mathijs PS: the change in preprocessing so far only pertains to the fcdc-users, all other users should be aware of how their data has been collected without the automatic check. The take home message is: beware when you start padding (which is automatically done at some places, especially in the artifact-routines, except when you put the relevant parameters to 0 in your configuration) when you have a trial based collection. -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Ali Mazaheri Sent: Friday, January 28, 2005 12:32 AM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] preprocessing Hi, I am trying to once again preprocess some old data.. but I realize that I can't, even if I use the EXACT same parameters I used to preprocess only last month.. what could be the deal ? Once again I must emphasize that the exact same parameters were working on the same file only a month ago Here is the error I get : Error using ==> read_fcdc_data requested data segment extends over a discontinuous trial boundary Error in ==> \\bond\home\common\matlab\fieldtrip\artifact_jump.m On line 137 ==> dat = read_fcdc_data(cfg.datafile, hdr, trl (trllop,1), ... Error in ==> \\bond\home\common\matlab\fieldtrip\rejectartifact.m On line 224 ==> eval(sprintf('[cfg, %s] = artifact_%s(cfg);', cfg.artfctdef.type{type}, cfg.artfctdef.type{type})); Error in ==> \\bond\home\common\matlab\fieldtrip\preprocessing.m On line 242 ==> [cfg] = rejectartifact(cfg); Error in ==> Z:\MEG\20041201\cfgmaker.m On line 22 ==> data = preprocessing(cfg); From schumat at UNI-MUENSTER.DE Mon Jan 31 08:24:58 2005 From: schumat at UNI-MUENSTER.DE (Matthias Schulz) Date: Mon, 31 Jan 2005 08:24:58 +0100 Subject: 275 CTF Channel datasets Message-ID: Dear Colleagues, I am a newcomer in the fieldtrip community. My question might therefore be silly. Recently, I tried to load a CTF 275-channel dataset to the fieldtrip environment but it did not work. However, it worked fine with a 151-Channel CTF dataset. Does some one have experience with 275 CTF Channel datasets and fieldtrip? And know how to remedy this problem? Kind regards, Matthias ---------------------------------------------------------------------- Dr. Matthias Schulz Department of Psychiatry & Psychotherapy, Institute for Biomagnetism & Biosignalanalysis University of Muenster phone: +49-251-8356651 ---------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Mon Jan 31 15:17:23 2005 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 31 Jan 2005 15:17:23 +0100 Subject: 275 CTF Channel datasets In-Reply-To: <20050131072459.4F7B136840@ZIVLNX01.uni-muenster.de> Message-ID: Hi Matthias, Welcome in our community ;-) I know that Tom Holroyd of the NIH and some of his colleagues) are working with FieldTrip on 275 channel CTF datasets, and I have also tested the code myself with 275ch CTF data. So I guess it should work... You could try hdr = read_fcdc_header('thenameoftheres4file'); dat = read_fcdc_data('thenameofthemeg4file', 1, 600); If that does not work, there is a real bug in FieldTrip. If you cannot get it to work, could you send me a zip file with your dataset, *EXCLUDING* the meg4 file. Then I can check whether the header information is read in correctly. That is the part of the dataset that might be binary incompatible, the binary format of the meg4 file is so simple that I cannot imagine that it is different for your new system. best regards, Robert PS pls don't send the zipfile to the discussion list, but to me directly On 31 Jan 2005, at 8:24, Matthias Schulz wrote: > Dear Colleagues, > >   > > I am a newcomer in the fieldtrip community. My question might > therefore be silly. Recently, I tried to load a CTF 275-channel > dataset to the fieldtrip environment but it did not work. However, it > worked fine with a 151-Channel CTF dataset. > > Does some one have experience with 275 CTF Channel datasets and > fieldtrip? And know how to remedy this problem? > >   > > Kind regards, Matthias > >   > >   > >   > > ---------------------------------------------------------------------- > >    Dr. Matthias Schulz > >    Department of Psychiatry & Psychotherapy, Institute for > Biomagnetism & Biosignalanalysis             > >    University of Muenster > > phone: +49-251-8356651 > > ---------------------------------------------------------------------- > >   > ---------------------------------------------------------------------- Robert Oostenveld, PhD F.C. Donders Centre for Cognitive Neuroimaging Radboud University Nijmegen phone: +31-24-3619695 http://www.ru.nl/fcdonders/ ---------------------------------------------------------------------- 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 Mon Jan 31 17:35:23 2005 From: tomh at KURAGE.NIMH.NIH.GOV (Tom Holroyd) Date: Mon, 31 Jan 2005 11:35:23 -0500 Subject: 275 CTF Channel datasets In-Reply-To: Message-ID: By the way, VSM is now releasing version 5 of the CTF MEG software. The dataset format has changed slightly. Code changes will be required. Datasets collected on CTF MEG systems with Acq version 5, using the new ECC (electronics control console), are going to be different. We just got this upgrade; we haven't gotten the new dataset libraries yet, though. But the old DataEditor just crashes when you try to read these new datasets. 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.RU.NL Mon Jan 3 12:11:00 2005 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 3 Jan 2005 12:11:00 +0100 Subject: FieldTrip Message-ID: Hi Litvak, Happy new year. Since you are asking some questions that also might be interesting to a wider audience, I will forward this mail to the FieldTrip discussion list as well. On 28 Dec 2004, at 11:06, Litvak Vladimir wrote: > Dear Robert, > > I've recently downloaded the FieldTrip toolbox and I have some > questions I hope you can help me with: > > 1) I've been working with EEGLAB for quite some time now and I know > you as a major contributor there as well. Why is FieldTrip developed > separately? Are there any plans to integrate the two toolboxes in the > future? I get that question more often and have just entered is in the FAQ. Please see http://www2.ru.nl/fcdonders/fieldtrip/faq.html#q7 Since both packages have a different aim, they will not be completely merged. But on some specific parts they will be more closely integrated. Fieldtrip and EEGLAB will share parts of their code and the upcoming "DIPFIT 2" module of EEGLAB will be completely based on Fieldtrip. > 2) We have a 64 channel Quickamp EEG system and also have a > possibility to get structural MRIs of our subjects. Would it be > possible to use the DICS method implemented in FieldTrip for analyzing > this data? How can I create a head model without using CTF software > (which I understand is something commercial that comes with your MEG > system)? The CTF software is commercial software for MEG, and therefore not of any use for your EEG. FieldTrip supports various headmodels. But DICS or other beamforming techniques are more sensitive to volume model errors than conventional dipole fitting methods. Therefore a sperical headmodel (as for example used in EEGLAB+DIPFIT) is not usefull. You should use a realistic shaped headmodel, for example using the boundary element method which is available in Fieldtrip. However, creating a realistic headmodel for EEG data from an individual anatomical MRI is difficult and requires quite some user interaction. At the FC Donders Centre we have two commercial packages that we can use for this: Curry and ASA. Therefore it has not been an issue for us sofar to implement an open source version of a BEM headmodel construction routine. > 3) How can I co-register the MRI scan with electrode positions > measured from the same subject? We didn't use capsules to mark the > reference points but I can mark them anatomically and we have the > measurements of the corresponding points with the electrode positions. You can do that using a homogenous transformation matrix (see http://www2.ru.nl/fcdonders/fieldtrip/faq.html#q5 and http://bishopw.loni.ucla.edu/AIR5/homogenous.html). In the private directory of FieldTrip you can find a function "headcoordinates.m" that will help you to compute this matrix. > 4) If there are no free tools available for creating a head model > would it be possible for me to get at least one model for a standard > MRI scan given our electrode positions? In principle you could do most of this using open source tools. You need to 1) segment the MRI, 2) create a triangulation and 3) compute the BEM system matrix. Step 1 and 2 are possible with various open source packages, although you probably will run into some problems with step 2. But I do not know an open source package that can perform step 3. Perhaps I could help you to construct a single BEM model based on a individual MRI, contact me if you are interested. best regards, Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD F.C. Donders Centre for Cognitive Neuroimaging Radboud University Nijmegen phone: +31-24-3619695 http://www.ru.nl/fcdonders/ ---------------------------------------------------------------------- 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 Tue Jan 25 09:13:15 2005 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 25 Jan 2005 09:13:15 +0100 Subject: FieldTrip question In-Reply-To: <41F51A7D.10406@med.uni-tuebingen.de> Message-ID: On 24 Jan 2005, at 16:55, Michael Zvyagintsev wrote: > Dear Colleagues, > I've just started to use fieldtrip for MEG data analysis. > I downloaded it and tried. But I found that during preprocessing there > are no files for 'remove_eog' and 'remove_mcg'. > Probably I downloaded something wrong, but it does not look like... > Could you send me these files or explain what to do with these steps. > Thanks, > Mikhail Zvyagintsev, MD, Bachelor of Informatic Dear Michael, The ECG removal was originally implemented for our MEG system (i.e. it has to remove the magnetocardiogram that we see in some subjects), but sofar we are not yet sufficiently confident about the results to include the remove_mcg subfunction that does the actial work in the release version. The EOG removal has not been implemented yet. Only a so called "hook" was implemented for it in the preprocessing routine so that someone who was willing to implement it could do it in a separate function without changes to the preprocessing function. Since both functions are not included in the release version, they are also not documented in the help and the default value for both is "no". I suggest for the moment that you stick to these default. Our usual procedure is to use the artefact detection routines (rejectartifact) and we reject the data in those trials (or parts of trials) that are contaminated by artefacts. best regards, Robert PS If you are particularly interested in this functionality, we can discuss whether and how to implement it in the release version. ---------------------------------------------------------------------- Robert Oostenveld, PhD F.C. Donders Centre for Cognitive Neuroimaging Radboud University Nijmegen phone: +31-24-3619695 http://www.ru.nl/fcdonders/ ---------------------------------------------------------------------- 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 ali.mazaheri at FCDONDERS.KUN.NL Fri Jan 28 00:32:04 2005 From: ali.mazaheri at FCDONDERS.KUN.NL (Ali Mazaheri) Date: Fri, 28 Jan 2005 00:32:04 +0100 Subject: preprocessing Message-ID: Hi, I am trying to once again preprocess some old data.. but I realize that I can't, even if I use the EXACT same parameters I used to preprocess only last month.. what could be the deal ? Once again I must emphasize that the exact same parameters were working on the same file only a month ago Here is the error I get : Error using ==> read_fcdc_data requested data segment extends over a discontinuous trial boundary Error in ==> \\bond\home\common\matlab\fieldtrip\artifact_jump.m On line 137 ==> dat = read_fcdc_data(cfg.datafile, hdr, trl (trllop,1), ... Error in ==> \\bond\home\common\matlab\fieldtrip\rejectartifact.m On line 224 ==> eval(sprintf('[cfg, %s] = artifact_%s(cfg);', cfg.artfctdef.type{type}, cfg.artfctdef.type{type})); Error in ==> \\bond\home\common\matlab\fieldtrip\preprocessing.m On line 242 ==> [cfg] = rejectartifact(cfg); Error in ==> Z:\MEG\20041201\cfgmaker.m On line 22 ==> data = preprocessing(cfg); From Jan.Schoffelen at FCDONDERS.RU.NL Fri Jan 28 08:17:53 2005 From: Jan.Schoffelen at FCDONDERS.RU.NL (J.M. Schoffelen) Date: Fri, 28 Jan 2005 08:17:53 +0100 Subject: preprocessing In-Reply-To: Message-ID: Hi Ali, 1 Please make sure you are running the latest fieldtrip-version on /home/common/matlab/fieldtrip, 2 Read the documentation of preprocessing and read_fcdc_data: -If your trial collection has been a pseudocontinuous one, you should add a field to your configuration which listens to the following name: cfg.datatype = 'continuous' -If your trial collection has not been a (pseudo)continuous one, but trial-based, the crash is put in on purpose, since several preprocessing steps such as filter padding, and artifact padding rely on the assumption that in the data, as it is in the datafile, the samples left and right of the trial-boundaries are contiguous in time. The extra check that is built in should make the users more aware of what they are doing. Yours, Jan-Mathijs PS: the change in preprocessing so far only pertains to the fcdc-users, all other users should be aware of how their data has been collected without the automatic check. The take home message is: beware when you start padding (which is automatically done at some places, especially in the artifact-routines, except when you put the relevant parameters to 0 in your configuration) when you have a trial based collection. -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Ali Mazaheri Sent: Friday, January 28, 2005 12:32 AM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] preprocessing Hi, I am trying to once again preprocess some old data.. but I realize that I can't, even if I use the EXACT same parameters I used to preprocess only last month.. what could be the deal ? Once again I must emphasize that the exact same parameters were working on the same file only a month ago Here is the error I get : Error using ==> read_fcdc_data requested data segment extends over a discontinuous trial boundary Error in ==> \\bond\home\common\matlab\fieldtrip\artifact_jump.m On line 137 ==> dat = read_fcdc_data(cfg.datafile, hdr, trl (trllop,1), ... Error in ==> \\bond\home\common\matlab\fieldtrip\rejectartifact.m On line 224 ==> eval(sprintf('[cfg, %s] = artifact_%s(cfg);', cfg.artfctdef.type{type}, cfg.artfctdef.type{type})); Error in ==> \\bond\home\common\matlab\fieldtrip\preprocessing.m On line 242 ==> [cfg] = rejectartifact(cfg); Error in ==> Z:\MEG\20041201\cfgmaker.m On line 22 ==> data = preprocessing(cfg); From schumat at UNI-MUENSTER.DE Mon Jan 31 08:24:58 2005 From: schumat at UNI-MUENSTER.DE (Matthias Schulz) Date: Mon, 31 Jan 2005 08:24:58 +0100 Subject: 275 CTF Channel datasets Message-ID: Dear Colleagues, I am a newcomer in the fieldtrip community. My question might therefore be silly. Recently, I tried to load a CTF 275-channel dataset to the fieldtrip environment but it did not work. However, it worked fine with a 151-Channel CTF dataset. Does some one have experience with 275 CTF Channel datasets and fieldtrip? And know how to remedy this problem? Kind regards, Matthias ---------------------------------------------------------------------- Dr. Matthias Schulz Department of Psychiatry & Psychotherapy, Institute for Biomagnetism & Biosignalanalysis University of Muenster phone: +49-251-8356651 ---------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Mon Jan 31 15:17:23 2005 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 31 Jan 2005 15:17:23 +0100 Subject: 275 CTF Channel datasets In-Reply-To: <20050131072459.4F7B136840@ZIVLNX01.uni-muenster.de> Message-ID: Hi Matthias, Welcome in our community ;-) I know that Tom Holroyd of the NIH and some of his colleagues) are working with FieldTrip on 275 channel CTF datasets, and I have also tested the code myself with 275ch CTF data. So I guess it should work... You could try hdr = read_fcdc_header('thenameoftheres4file'); dat = read_fcdc_data('thenameofthemeg4file', 1, 600); If that does not work, there is a real bug in FieldTrip. If you cannot get it to work, could you send me a zip file with your dataset, *EXCLUDING* the meg4 file. Then I can check whether the header information is read in correctly. That is the part of the dataset that might be binary incompatible, the binary format of the meg4 file is so simple that I cannot imagine that it is different for your new system. best regards, Robert PS pls don't send the zipfile to the discussion list, but to me directly On 31 Jan 2005, at 8:24, Matthias Schulz wrote: > Dear Colleagues, > >   > > I am a newcomer in the fieldtrip community. My question might > therefore be silly. Recently, I tried to load a CTF 275-channel > dataset to the fieldtrip environment but it did not work. However, it > worked fine with a 151-Channel CTF dataset. > > Does some one have experience with 275 CTF Channel datasets and > fieldtrip? And know how to remedy this problem? > >   > > Kind regards, Matthias > >   > >   > >   > > ---------------------------------------------------------------------- > >    Dr. Matthias Schulz > >    Department of Psychiatry & Psychotherapy, Institute for > Biomagnetism & Biosignalanalysis             > >    University of Muenster > > phone: +49-251-8356651 > > ---------------------------------------------------------------------- > >   > ---------------------------------------------------------------------- Robert Oostenveld, PhD F.C. Donders Centre for Cognitive Neuroimaging Radboud University Nijmegen phone: +31-24-3619695 http://www.ru.nl/fcdonders/ ---------------------------------------------------------------------- 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 Mon Jan 31 17:35:23 2005 From: tomh at KURAGE.NIMH.NIH.GOV (Tom Holroyd) Date: Mon, 31 Jan 2005 11:35:23 -0500 Subject: 275 CTF Channel datasets In-Reply-To: Message-ID: By the way, VSM is now releasing version 5 of the CTF MEG software. The dataset format has changed slightly. Code changes will be required. Datasets collected on CTF MEG systems with Acq version 5, using the new ECC (electronics control console), are going to be different. We just got this upgrade; we haven't gotten the new dataset libraries yet, though. But the old DataEditor just crashes when you try to read these new datasets. 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.RU.NL Mon Jan 3 12:11:00 2005 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 3 Jan 2005 12:11:00 +0100 Subject: FieldTrip Message-ID: Hi Litvak, Happy new year. Since you are asking some questions that also might be interesting to a wider audience, I will forward this mail to the FieldTrip discussion list as well. On 28 Dec 2004, at 11:06, Litvak Vladimir wrote: > Dear Robert, > > I've recently downloaded the FieldTrip toolbox and I have some > questions I hope you can help me with: > > 1) I've been working with EEGLAB for quite some time now and I know > you as a major contributor there as well. Why is FieldTrip developed > separately? Are there any plans to integrate the two toolboxes in the > future? I get that question more often and have just entered is in the FAQ. Please see http://www2.ru.nl/fcdonders/fieldtrip/faq.html#q7 Since both packages have a different aim, they will not be completely merged. But on some specific parts they will be more closely integrated. Fieldtrip and EEGLAB will share parts of their code and the upcoming "DIPFIT 2" module of EEGLAB will be completely based on Fieldtrip. > 2) We have a 64 channel Quickamp EEG system and also have a > possibility to get structural MRIs of our subjects. Would it be > possible to use the DICS method implemented in FieldTrip for analyzing > this data? How can I create a head model without using CTF software > (which I understand is something commercial that comes with your MEG > system)? The CTF software is commercial software for MEG, and therefore not of any use for your EEG. FieldTrip supports various headmodels. But DICS or other beamforming techniques are more sensitive to volume model errors than conventional dipole fitting methods. Therefore a sperical headmodel (as for example used in EEGLAB+DIPFIT) is not usefull. You should use a realistic shaped headmodel, for example using the boundary element method which is available in Fieldtrip. However, creating a realistic headmodel for EEG data from an individual anatomical MRI is difficult and requires quite some user interaction. At the FC Donders Centre we have two commercial packages that we can use for this: Curry and ASA. Therefore it has not been an issue for us sofar to implement an open source version of a BEM headmodel construction routine. > 3) How can I co-register the MRI scan with electrode positions > measured from the same subject? We didn't use capsules to mark the > reference points but I can mark them anatomically and we have the > measurements of the corresponding points with the electrode positions. You can do that using a homogenous transformation matrix (see http://www2.ru.nl/fcdonders/fieldtrip/faq.html#q5 and http://bishopw.loni.ucla.edu/AIR5/homogenous.html). In the private directory of FieldTrip you can find a function "headcoordinates.m" that will help you to compute this matrix. > 4) If there are no free tools available for creating a head model > would it be possible for me to get at least one model for a standard > MRI scan given our electrode positions? In principle you could do most of this using open source tools. You need to 1) segment the MRI, 2) create a triangulation and 3) compute the BEM system matrix. Step 1 and 2 are possible with various open source packages, although you probably will run into some problems with step 2. But I do not know an open source package that can perform step 3. Perhaps I could help you to construct a single BEM model based on a individual MRI, contact me if you are interested. best regards, Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD F.C. Donders Centre for Cognitive Neuroimaging Radboud University Nijmegen phone: +31-24-3619695 http://www.ru.nl/fcdonders/ ---------------------------------------------------------------------- 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 Tue Jan 25 09:13:15 2005 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 25 Jan 2005 09:13:15 +0100 Subject: FieldTrip question In-Reply-To: <41F51A7D.10406@med.uni-tuebingen.de> Message-ID: On 24 Jan 2005, at 16:55, Michael Zvyagintsev wrote: > Dear Colleagues, > I've just started to use fieldtrip for MEG data analysis. > I downloaded it and tried. But I found that during preprocessing there > are no files for 'remove_eog' and 'remove_mcg'. > Probably I downloaded something wrong, but it does not look like... > Could you send me these files or explain what to do with these steps. > Thanks, > Mikhail Zvyagintsev, MD, Bachelor of Informatic Dear Michael, The ECG removal was originally implemented for our MEG system (i.e. it has to remove the magnetocardiogram that we see in some subjects), but sofar we are not yet sufficiently confident about the results to include the remove_mcg subfunction that does the actial work in the release version. The EOG removal has not been implemented yet. Only a so called "hook" was implemented for it in the preprocessing routine so that someone who was willing to implement it could do it in a separate function without changes to the preprocessing function. Since both functions are not included in the release version, they are also not documented in the help and the default value for both is "no". I suggest for the moment that you stick to these default. Our usual procedure is to use the artefact detection routines (rejectartifact) and we reject the data in those trials (or parts of trials) that are contaminated by artefacts. best regards, Robert PS If you are particularly interested in this functionality, we can discuss whether and how to implement it in the release version. ---------------------------------------------------------------------- Robert Oostenveld, PhD F.C. Donders Centre for Cognitive Neuroimaging Radboud University Nijmegen phone: +31-24-3619695 http://www.ru.nl/fcdonders/ ---------------------------------------------------------------------- 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 ali.mazaheri at FCDONDERS.KUN.NL Fri Jan 28 00:32:04 2005 From: ali.mazaheri at FCDONDERS.KUN.NL (Ali Mazaheri) Date: Fri, 28 Jan 2005 00:32:04 +0100 Subject: preprocessing Message-ID: Hi, I am trying to once again preprocess some old data.. but I realize that I can't, even if I use the EXACT same parameters I used to preprocess only last month.. what could be the deal ? Once again I must emphasize that the exact same parameters were working on the same file only a month ago Here is the error I get : Error using ==> read_fcdc_data requested data segment extends over a discontinuous trial boundary Error in ==> \\bond\home\common\matlab\fieldtrip\artifact_jump.m On line 137 ==> dat = read_fcdc_data(cfg.datafile, hdr, trl (trllop,1), ... Error in ==> \\bond\home\common\matlab\fieldtrip\rejectartifact.m On line 224 ==> eval(sprintf('[cfg, %s] = artifact_%s(cfg);', cfg.artfctdef.type{type}, cfg.artfctdef.type{type})); Error in ==> \\bond\home\common\matlab\fieldtrip\preprocessing.m On line 242 ==> [cfg] = rejectartifact(cfg); Error in ==> Z:\MEG\20041201\cfgmaker.m On line 22 ==> data = preprocessing(cfg); From Jan.Schoffelen at FCDONDERS.RU.NL Fri Jan 28 08:17:53 2005 From: Jan.Schoffelen at FCDONDERS.RU.NL (J.M. Schoffelen) Date: Fri, 28 Jan 2005 08:17:53 +0100 Subject: preprocessing In-Reply-To: Message-ID: Hi Ali, 1 Please make sure you are running the latest fieldtrip-version on /home/common/matlab/fieldtrip, 2 Read the documentation of preprocessing and read_fcdc_data: -If your trial collection has been a pseudocontinuous one, you should add a field to your configuration which listens to the following name: cfg.datatype = 'continuous' -If your trial collection has not been a (pseudo)continuous one, but trial-based, the crash is put in on purpose, since several preprocessing steps such as filter padding, and artifact padding rely on the assumption that in the data, as it is in the datafile, the samples left and right of the trial-boundaries are contiguous in time. The extra check that is built in should make the users more aware of what they are doing. Yours, Jan-Mathijs PS: the change in preprocessing so far only pertains to the fcdc-users, all other users should be aware of how their data has been collected without the automatic check. The take home message is: beware when you start padding (which is automatically done at some places, especially in the artifact-routines, except when you put the relevant parameters to 0 in your configuration) when you have a trial based collection. -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Ali Mazaheri Sent: Friday, January 28, 2005 12:32 AM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] preprocessing Hi, I am trying to once again preprocess some old data.. but I realize that I can't, even if I use the EXACT same parameters I used to preprocess only last month.. what could be the deal ? Once again I must emphasize that the exact same parameters were working on the same file only a month ago Here is the error I get : Error using ==> read_fcdc_data requested data segment extends over a discontinuous trial boundary Error in ==> \\bond\home\common\matlab\fieldtrip\artifact_jump.m On line 137 ==> dat = read_fcdc_data(cfg.datafile, hdr, trl (trllop,1), ... Error in ==> \\bond\home\common\matlab\fieldtrip\rejectartifact.m On line 224 ==> eval(sprintf('[cfg, %s] = artifact_%s(cfg);', cfg.artfctdef.type{type}, cfg.artfctdef.type{type})); Error in ==> \\bond\home\common\matlab\fieldtrip\preprocessing.m On line 242 ==> [cfg] = rejectartifact(cfg); Error in ==> Z:\MEG\20041201\cfgmaker.m On line 22 ==> data = preprocessing(cfg); From schumat at UNI-MUENSTER.DE Mon Jan 31 08:24:58 2005 From: schumat at UNI-MUENSTER.DE (Matthias Schulz) Date: Mon, 31 Jan 2005 08:24:58 +0100 Subject: 275 CTF Channel datasets Message-ID: Dear Colleagues, I am a newcomer in the fieldtrip community. My question might therefore be silly. Recently, I tried to load a CTF 275-channel dataset to the fieldtrip environment but it did not work. However, it worked fine with a 151-Channel CTF dataset. Does some one have experience with 275 CTF Channel datasets and fieldtrip? And know how to remedy this problem? Kind regards, Matthias ---------------------------------------------------------------------- Dr. Matthias Schulz Department of Psychiatry & Psychotherapy, Institute for Biomagnetism & Biosignalanalysis University of Muenster phone: +49-251-8356651 ---------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Mon Jan 31 15:17:23 2005 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 31 Jan 2005 15:17:23 +0100 Subject: 275 CTF Channel datasets In-Reply-To: <20050131072459.4F7B136840@ZIVLNX01.uni-muenster.de> Message-ID: Hi Matthias, Welcome in our community ;-) I know that Tom Holroyd of the NIH and some of his colleagues) are working with FieldTrip on 275 channel CTF datasets, and I have also tested the code myself with 275ch CTF data. So I guess it should work... You could try hdr = read_fcdc_header('thenameoftheres4file'); dat = read_fcdc_data('thenameofthemeg4file', 1, 600); If that does not work, there is a real bug in FieldTrip. If you cannot get it to work, could you send me a zip file with your dataset, *EXCLUDING* the meg4 file. Then I can check whether the header information is read in correctly. That is the part of the dataset that might be binary incompatible, the binary format of the meg4 file is so simple that I cannot imagine that it is different for your new system. best regards, Robert PS pls don't send the zipfile to the discussion list, but to me directly On 31 Jan 2005, at 8:24, Matthias Schulz wrote: > Dear Colleagues, > >   > > I am a newcomer in the fieldtrip community. My question might > therefore be silly. Recently, I tried to load a CTF 275-channel > dataset to the fieldtrip environment but it did not work. However, it > worked fine with a 151-Channel CTF dataset. > > Does some one have experience with 275 CTF Channel datasets and > fieldtrip? And know how to remedy this problem? > >   > > Kind regards, Matthias > >   > >   > >   > > ---------------------------------------------------------------------- > >    Dr. Matthias Schulz > >    Department of Psychiatry & Psychotherapy, Institute for > Biomagnetism & Biosignalanalysis             > >    University of Muenster > > phone: +49-251-8356651 > > ---------------------------------------------------------------------- > >   > ---------------------------------------------------------------------- Robert Oostenveld, PhD F.C. Donders Centre for Cognitive Neuroimaging Radboud University Nijmegen phone: +31-24-3619695 http://www.ru.nl/fcdonders/ ---------------------------------------------------------------------- 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 Mon Jan 31 17:35:23 2005 From: tomh at KURAGE.NIMH.NIH.GOV (Tom Holroyd) Date: Mon, 31 Jan 2005 11:35:23 -0500 Subject: 275 CTF Channel datasets In-Reply-To: Message-ID: By the way, VSM is now releasing version 5 of the CTF MEG software. The dataset format has changed slightly. Code changes will be required. Datasets collected on CTF MEG systems with Acq version 5, using the new ECC (electronics control console), are going to be different. We just got this upgrade; we haven't gotten the new dataset libraries yet, though. But the old DataEditor just crashes when you try to read these new datasets. 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.RU.NL Mon Jan 3 12:11:00 2005 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 3 Jan 2005 12:11:00 +0100 Subject: FieldTrip Message-ID: Hi Litvak, Happy new year. Since you are asking some questions that also might be interesting to a wider audience, I will forward this mail to the FieldTrip discussion list as well. On 28 Dec 2004, at 11:06, Litvak Vladimir wrote: > Dear Robert, > > I've recently downloaded the FieldTrip toolbox and I have some > questions I hope you can help me with: > > 1) I've been working with EEGLAB for quite some time now and I know > you as a major contributor there as well. Why is FieldTrip developed > separately? Are there any plans to integrate the two toolboxes in the > future? I get that question more often and have just entered is in the FAQ. Please see http://www2.ru.nl/fcdonders/fieldtrip/faq.html#q7 Since both packages have a different aim, they will not be completely merged. But on some specific parts they will be more closely integrated. Fieldtrip and EEGLAB will share parts of their code and the upcoming "DIPFIT 2" module of EEGLAB will be completely based on Fieldtrip. > 2) We have a 64 channel Quickamp EEG system and also have a > possibility to get structural MRIs of our subjects. Would it be > possible to use the DICS method implemented in FieldTrip for analyzing > this data? How can I create a head model without using CTF software > (which I understand is something commercial that comes with your MEG > system)? The CTF software is commercial software for MEG, and therefore not of any use for your EEG. FieldTrip supports various headmodels. But DICS or other beamforming techniques are more sensitive to volume model errors than conventional dipole fitting methods. Therefore a sperical headmodel (as for example used in EEGLAB+DIPFIT) is not usefull. You should use a realistic shaped headmodel, for example using the boundary element method which is available in Fieldtrip. However, creating a realistic headmodel for EEG data from an individual anatomical MRI is difficult and requires quite some user interaction. At the FC Donders Centre we have two commercial packages that we can use for this: Curry and ASA. Therefore it has not been an issue for us sofar to implement an open source version of a BEM headmodel construction routine. > 3) How can I co-register the MRI scan with electrode positions > measured from the same subject? We didn't use capsules to mark the > reference points but I can mark them anatomically and we have the > measurements of the corresponding points with the electrode positions. You can do that using a homogenous transformation matrix (see http://www2.ru.nl/fcdonders/fieldtrip/faq.html#q5 and http://bishopw.loni.ucla.edu/AIR5/homogenous.html). In the private directory of FieldTrip you can find a function "headcoordinates.m" that will help you to compute this matrix. > 4) If there are no free tools available for creating a head model > would it be possible for me to get at least one model for a standard > MRI scan given our electrode positions? In principle you could do most of this using open source tools. You need to 1) segment the MRI, 2) create a triangulation and 3) compute the BEM system matrix. Step 1 and 2 are possible with various open source packages, although you probably will run into some problems with step 2. But I do not know an open source package that can perform step 3. Perhaps I could help you to construct a single BEM model based on a individual MRI, contact me if you are interested. best regards, Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD F.C. Donders Centre for Cognitive Neuroimaging Radboud University Nijmegen phone: +31-24-3619695 http://www.ru.nl/fcdonders/ ---------------------------------------------------------------------- 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 Tue Jan 25 09:13:15 2005 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 25 Jan 2005 09:13:15 +0100 Subject: FieldTrip question In-Reply-To: <41F51A7D.10406@med.uni-tuebingen.de> Message-ID: On 24 Jan 2005, at 16:55, Michael Zvyagintsev wrote: > Dear Colleagues, > I've just started to use fieldtrip for MEG data analysis. > I downloaded it and tried. But I found that during preprocessing there > are no files for 'remove_eog' and 'remove_mcg'. > Probably I downloaded something wrong, but it does not look like... > Could you send me these files or explain what to do with these steps. > Thanks, > Mikhail Zvyagintsev, MD, Bachelor of Informatic Dear Michael, The ECG removal was originally implemented for our MEG system (i.e. it has to remove the magnetocardiogram that we see in some subjects), but sofar we are not yet sufficiently confident about the results to include the remove_mcg subfunction that does the actial work in the release version. The EOG removal has not been implemented yet. Only a so called "hook" was implemented for it in the preprocessing routine so that someone who was willing to implement it could do it in a separate function without changes to the preprocessing function. Since both functions are not included in the release version, they are also not documented in the help and the default value for both is "no". I suggest for the moment that you stick to these default. Our usual procedure is to use the artefact detection routines (rejectartifact) and we reject the data in those trials (or parts of trials) that are contaminated by artefacts. best regards, Robert PS If you are particularly interested in this functionality, we can discuss whether and how to implement it in the release version. ---------------------------------------------------------------------- Robert Oostenveld, PhD F.C. Donders Centre for Cognitive Neuroimaging Radboud University Nijmegen phone: +31-24-3619695 http://www.ru.nl/fcdonders/ ---------------------------------------------------------------------- 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 ali.mazaheri at FCDONDERS.KUN.NL Fri Jan 28 00:32:04 2005 From: ali.mazaheri at FCDONDERS.KUN.NL (Ali Mazaheri) Date: Fri, 28 Jan 2005 00:32:04 +0100 Subject: preprocessing Message-ID: Hi, I am trying to once again preprocess some old data.. but I realize that I can't, even if I use the EXACT same parameters I used to preprocess only last month.. what could be the deal ? Once again I must emphasize that the exact same parameters were working on the same file only a month ago Here is the error I get : Error using ==> read_fcdc_data requested data segment extends over a discontinuous trial boundary Error in ==> \\bond\home\common\matlab\fieldtrip\artifact_jump.m On line 137 ==> dat = read_fcdc_data(cfg.datafile, hdr, trl (trllop,1), ... Error in ==> \\bond\home\common\matlab\fieldtrip\rejectartifact.m On line 224 ==> eval(sprintf('[cfg, %s] = artifact_%s(cfg);', cfg.artfctdef.type{type}, cfg.artfctdef.type{type})); Error in ==> \\bond\home\common\matlab\fieldtrip\preprocessing.m On line 242 ==> [cfg] = rejectartifact(cfg); Error in ==> Z:\MEG\20041201\cfgmaker.m On line 22 ==> data = preprocessing(cfg); From Jan.Schoffelen at FCDONDERS.RU.NL Fri Jan 28 08:17:53 2005 From: Jan.Schoffelen at FCDONDERS.RU.NL (J.M. Schoffelen) Date: Fri, 28 Jan 2005 08:17:53 +0100 Subject: preprocessing In-Reply-To: Message-ID: Hi Ali, 1 Please make sure you are running the latest fieldtrip-version on /home/common/matlab/fieldtrip, 2 Read the documentation of preprocessing and read_fcdc_data: -If your trial collection has been a pseudocontinuous one, you should add a field to your configuration which listens to the following name: cfg.datatype = 'continuous' -If your trial collection has not been a (pseudo)continuous one, but trial-based, the crash is put in on purpose, since several preprocessing steps such as filter padding, and artifact padding rely on the assumption that in the data, as it is in the datafile, the samples left and right of the trial-boundaries are contiguous in time. The extra check that is built in should make the users more aware of what they are doing. Yours, Jan-Mathijs PS: the change in preprocessing so far only pertains to the fcdc-users, all other users should be aware of how their data has been collected without the automatic check. The take home message is: beware when you start padding (which is automatically done at some places, especially in the artifact-routines, except when you put the relevant parameters to 0 in your configuration) when you have a trial based collection. -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Ali Mazaheri Sent: Friday, January 28, 2005 12:32 AM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] preprocessing Hi, I am trying to once again preprocess some old data.. but I realize that I can't, even if I use the EXACT same parameters I used to preprocess only last month.. what could be the deal ? Once again I must emphasize that the exact same parameters were working on the same file only a month ago Here is the error I get : Error using ==> read_fcdc_data requested data segment extends over a discontinuous trial boundary Error in ==> \\bond\home\common\matlab\fieldtrip\artifact_jump.m On line 137 ==> dat = read_fcdc_data(cfg.datafile, hdr, trl (trllop,1), ... Error in ==> \\bond\home\common\matlab\fieldtrip\rejectartifact.m On line 224 ==> eval(sprintf('[cfg, %s] = artifact_%s(cfg);', cfg.artfctdef.type{type}, cfg.artfctdef.type{type})); Error in ==> \\bond\home\common\matlab\fieldtrip\preprocessing.m On line 242 ==> [cfg] = rejectartifact(cfg); Error in ==> Z:\MEG\20041201\cfgmaker.m On line 22 ==> data = preprocessing(cfg); From schumat at UNI-MUENSTER.DE Mon Jan 31 08:24:58 2005 From: schumat at UNI-MUENSTER.DE (Matthias Schulz) Date: Mon, 31 Jan 2005 08:24:58 +0100 Subject: 275 CTF Channel datasets Message-ID: Dear Colleagues, I am a newcomer in the fieldtrip community. My question might therefore be silly. Recently, I tried to load a CTF 275-channel dataset to the fieldtrip environment but it did not work. However, it worked fine with a 151-Channel CTF dataset. Does some one have experience with 275 CTF Channel datasets and fieldtrip? And know how to remedy this problem? Kind regards, Matthias ---------------------------------------------------------------------- Dr. Matthias Schulz Department of Psychiatry & Psychotherapy, Institute for Biomagnetism & Biosignalanalysis University of Muenster phone: +49-251-8356651 ---------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Mon Jan 31 15:17:23 2005 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 31 Jan 2005 15:17:23 +0100 Subject: 275 CTF Channel datasets In-Reply-To: <20050131072459.4F7B136840@ZIVLNX01.uni-muenster.de> Message-ID: Hi Matthias, Welcome in our community ;-) I know that Tom Holroyd of the NIH and some of his colleagues) are working with FieldTrip on 275 channel CTF datasets, and I have also tested the code myself with 275ch CTF data. So I guess it should work... You could try hdr = read_fcdc_header('thenameoftheres4file'); dat = read_fcdc_data('thenameofthemeg4file', 1, 600); If that does not work, there is a real bug in FieldTrip. If you cannot get it to work, could you send me a zip file with your dataset, *EXCLUDING* the meg4 file. Then I can check whether the header information is read in correctly. That is the part of the dataset that might be binary incompatible, the binary format of the meg4 file is so simple that I cannot imagine that it is different for your new system. best regards, Robert PS pls don't send the zipfile to the discussion list, but to me directly On 31 Jan 2005, at 8:24, Matthias Schulz wrote: > Dear Colleagues, > >   > > I am a newcomer in the fieldtrip community. My question might > therefore be silly. Recently, I tried to load a CTF 275-channel > dataset to the fieldtrip environment but it did not work. However, it > worked fine with a 151-Channel CTF dataset. > > Does some one have experience with 275 CTF Channel datasets and > fieldtrip? And know how to remedy this problem? > >   > > Kind regards, Matthias > >   > >   > >   > > ---------------------------------------------------------------------- > >    Dr. Matthias Schulz > >    Department of Psychiatry & Psychotherapy, Institute for > Biomagnetism & Biosignalanalysis             > >    University of Muenster > > phone: +49-251-8356651 > > ---------------------------------------------------------------------- > >   > ---------------------------------------------------------------------- Robert Oostenveld, PhD F.C. Donders Centre for Cognitive Neuroimaging Radboud University Nijmegen phone: +31-24-3619695 http://www.ru.nl/fcdonders/ ---------------------------------------------------------------------- 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 Mon Jan 31 17:35:23 2005 From: tomh at KURAGE.NIMH.NIH.GOV (Tom Holroyd) Date: Mon, 31 Jan 2005 11:35:23 -0500 Subject: 275 CTF Channel datasets In-Reply-To: Message-ID: By the way, VSM is now releasing version 5 of the CTF MEG software. The dataset format has changed slightly. Code changes will be required. Datasets collected on CTF MEG systems with Acq version 5, using the new ECC (electronics control console), are going to be different. We just got this upgrade; we haven't gotten the new dataset libraries yet, though. But the old DataEditor just crashes when you try to read these new datasets. Dr. Tom Holroyd "A man of genius makes no mistakes. His errors are volitional and are the portals of discovery." -- James Joyce