From Jan.Schoffelen at FCDONDERS.RU.NL Tue Mar 1 09:15:31 2005 From: Jan.Schoffelen at FCDONDERS.RU.NL (J.M. Schoffelen) Date: Tue, 1 Mar 2005 09:15:31 +0100 Subject: Multiplot In-Reply-To: <05Feb28.172924cet.336456@nucleus.azvu.nl> Message-ID: Dear Teresa, What about taking your variable avg as an input to multiplotER? (in fact, that's how it works) Yours, Jan-Mathijs -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Montez, T. Sent: Monday, February 28, 2005 5:26 PM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] Multiplot Hi Fieldtrippers, The course is becoming closer, but I would like to solve the multiplot problem before that to prepare more interesting questions. I now tried: cfgpre = []; cfgpre.dataset = 'C:\Data\A002-EC_20021016_02.ds' cfgpre.trl= [[ones(1,2)]', [150*ones(1,2)]', [zeros(1,2)]'] cfgpre.channel='MEG' datatest = preprocessing(cfgpre) cfgpre.vartrllength=1 avg = timelockanalysis(cfgpre,datatest) cfgpre.yparam = 'avg' time=datatest.hdr.timeVec; cfgpre.xparam = 'time' multiplotER(cfgpre,datatest) and got the errors: ??? Error using ==> min Function 'min' is not defined for values of class 'cell'. Error in ==> C:\Matlab\FieldTrip\fieldtrip-0.9.5\multiplotER.m On line 117 ==> xmin = min(xvalues); Thanks, Teresa Montez From floris.delange at FCDONDERS.RU.NL Wed Mar 2 13:23:43 2005 From: floris.delange at FCDONDERS.RU.NL (Floris de Lange) Date: Wed, 2 Mar 2005 13:23:43 +0100 Subject: parametric modulation of power Message-ID: Dear Fieldtrippers, I have a (sort of conceptual) question on how to test for parametric modulations in power as a function of e.g. dificulty. I have a task which has 5 difficulty levels, so from 1=easy to 5=hard. I made 5 separate power-spectra, which could eg be named subj1_TFR{1} .. subj1_TFR{5}. I can of course inspect each power spectrum separately, and try to eye-ball whether there may be parametric increases or decreases in power with increasing difficulty level, but it would be nice if I could get a direct view on how 'linearly in/decreasing' the power spectrum per sensor and frequency is. Is this possible within Fieldtrip? Are there scripts around for doing such a linear regression analysis? Many thanks! All the best, Floris -------------- next part -------------- A non-text attachment was scrubbed... Name: floris.delange.vcf Type: text/x-vcard Size: 312 bytes Desc: not available URL: From maris at NICI.RU.NL Wed Mar 2 22:31:26 2005 From: maris at NICI.RU.NL (Eric Maris) Date: Wed, 2 Mar 2005 22:31:26 +0100 Subject: parametric modulation of power Message-ID: Dear Floris, > I have a (sort of conceptual) question on how to test for parametric > modulations in power as a function of e.g. dificulty. > > I have a task which has 5 difficulty levels, so from 1=easy to 5=hard. > I made 5 separate power-spectra, which could eg be named subj1_TFR{1} .. > subj1_TFR{5}. I can of course inspect each power spectrum separately, > and try to eye-ball whether there may be parametric increases or > decreases in power with increasing difficulty level, but it would be > nice if I could get a direct view on how 'linearly in/decreasing' the > power spectrum per sensor and frequency is. > Is this possible within Fieldtrip? Are there scripts around for doing > such a linear regression analysis? This is possible using using CLUSTERRANDANALYSIS. However, at present, only independent samples regression analyses are possible. In practice, this means that you can only analyse your data for each of the subjects separately (treating the trials as replications). Using CLUSTERRANDANALYSIS implies that you evaluate your effect using randomization inference. The nice thing about CLUSTERRANDANALYSIS is that it controls your family-wise error rate. Eric Maris From litvak at TECHUNIX.TECHNION.AC.IL Thu Mar 3 11:59:46 2005 From: litvak at TECHUNIX.TECHNION.AC.IL (Litvak Vladimir) Date: Thu, 3 Mar 2005 12:59:46 +0200 Subject: Statistical comparison of ERP waveforms In-Reply-To: <4225B04F.7070908@fcdonders.ru.nl> Message-ID: Dear Fieldtrip experts, I would like to perform statistical comparison between whole ERP waveforms (rather than just peaks). In my case I need paired ttest. My question is how should one solve the problem of false positives arising from multiple comparisons (all the timeframes)? Is far as I understood from the code the timelocked statistics function of Fieldtrip does not address this issue. I also looked in EEGLAB and it seems the same. Are there any good solutions (preferrable already implemented in Matlab)? Thanks, Vladimir Litvak From maris at NICI.RU.NL Thu Mar 3 16:38:02 2005 From: maris at NICI.RU.NL (Eric Maris) Date: Thu, 3 Mar 2005 16:38:02 +0100 Subject: Statistical comparison of ERP waveforms Message-ID: Hi Litvak, > I would like to perform statistical comparison between whole ERP waveforms > (rather than just peaks). In my case I need paired ttest. My question is > how should one solve the problem of false positives arising from multiple > comparisons (all the timeframes)? Is far as I understood from the code the > timelocked statistics function of Fieldtrip does not address this issue. I > also looked in EEGLAB and it seems the same. Are there any good solutions > (preferrable already implemented in Matlab)? In FIELDTRIP, we use randomization statistics to control the family-wise error rate. We have combined randomization statistics with a cluster-finding algorithm that drastically improves power in exploratory analyses. This has been implemented in the routine CLUSTERRANDANALYSIS which, unfortunately for you, is only available to users inside the FC Donders Center. We will make it available to the rest of the world in the summer of 2005. Eric Maris From shivakademane at YAHOO.COM Wed Mar 9 13:01:16 2005 From: shivakademane at YAHOO.COM (Shivaprakash) Date: Wed, 9 Mar 2005 04:01:16 -0800 Subject: req code Message-ID: field trippers, I am a student trying to implement in C the work done by- Lehmann, D. and Michel, C.M. (1990). Intracerebral dipole source localization for FFT power maps. Electroenceph. Clin. Neurophysiol. 76, 271-276. some how my programs are not working as explained in the paper. the following web ID has the codes but not in source code. http://www.puk.unibe.ch/tk2/Software.htm if any one has done the implementation send a copy of the source code to my ID. so that I can understand where I have gone wrong. --------------------------------- Celebrate Yahoo!'s 10th Birthday! Yahoo! Netrospective: 100 Moments of the Web -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Fri Mar 11 13:25:13 2005 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Fri, 11 Mar 2005 13:25:13 +0100 Subject: req code In-Reply-To: <20050309120116.87415.qmail@web21206.mail.yahoo.com> Message-ID: Dear Shivaprakash On 9 Mar 2005, at 13:01, Shivaprakash wrote: > I am a student trying to implement in C the work done by- > Lehmann, D. and Michel, C.M. (1990). Intracerebral dipole source > localization for FFT power maps. Electroenceph. Clin. Neurophysiol. > 76, 271-276. >   > some how my programs are not working as explained in the paper. the > following web ID has the codes but not in source code. > http://www.puk.unibe.ch/tk2/Software.htm >   > if any one has done the implementation send a copy of the source code > to my ID. so that I can understand where I have gone wrong. FieldTrip does implement frequency based source reconstructions using beamformer approaches, and frequency based dipole fitting in the way described by Lehman (1990) is not implemented in FieldTrip. Howvere, the method described by Lehman has subsequently been improved by Lutkenhoner and I suggest that you first look into that work: Lutkenhoner B. Frequency-domain localization of intracerebral dipolar sources. Electroencephalogr Clin Neurophysiol. 1992 Feb;82(2):112-8. If the implemented beamformer approach (see refs below) is not suitable for your data, then it would not be too difficult to implement a frequency based dipole fit algoritm based on the FREQANALYSIS and the DIPOLEFITTING code that is already present in our toolbox. However, FieldTrip is completely implemented in Matlab and not in C, and it will be a lot of work to reimplement it in C. My old and unsupported MSA library does contain a C-code implementation of the frequency dipole fit for EEG and MEG as described by Lutkenhoner, maybe you also want to take a look at that (http://oase.uci.kun.nl/~roberto/msa/) best regards, Robert refs: Gross J, Kujala J, Hamalainen M, Timmermann L, Schnitzler A, Salmelin R. Dynamic imaging of coherent sources: Studying neural interactions in the human brain. Proc Natl Acad Sci U S A. 2001 Jan 16;98(2):694-9. Van Veen BD, van Drongelen W, Yuchtman M, Suzuki A. Localization of brain electrical activity via linearly constrained minimum variance spatial filtering. IEEE Trans Biomed Eng. 1997 Sep;44(9):867-80. From maniar at CSHL.EDU Tue Mar 15 14:52:10 2005 From: maniar at CSHL.EDU (Maniar, Hiren) Date: Tue, 15 Mar 2005 08:52:10 -0500 Subject: CTF reading routines now GPL Message-ID: Hello Robert, I write in reference to the 2 script files you sent us, read_ctf_res4 & read_ctf_meg4. In read_ctf_res4, lines 230-234 & 254-258 apparently correct for some mis-oriented sensors. The question is whether it holds true for all CTF installations or simply the one at Donders? Would appreciate a clarification on this point. Thanks. Many thanks for the scripts. Regards, Hiren -----Original Message----- From: FieldTrip discussion list on behalf of Robert Oostenveld Sent: Fri 02/18/05 8:30 AM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] CTF reading routines now GPL Dear CTF-FieldTrip users, There are two files (read_ctf_res4 and read_ctf_meg4) in the FieldTrip release that were released as p-files instead of m-files. These two files originated from CTF, and since then have been modified and improved by us at the Donders (e.g. speed improvements and support for files >2GB). VSM MedTech Ltd. now has given us permission to release these files as wel in open source form under the GPL. They will be included as m-files in upcoming releases. For those of you who are interested, you'll also find them attached to this mail. best regards, Robert From r.oostenveld at FCDONDERS.RU.NL Tue Mar 15 17:50:06 2005 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 15 Mar 2005 17:50:06 +0100 Subject: CTF reading routines now GPL In-Reply-To: <44233CA5B57295409DA4423AECEFFEE738FBE0@mailbox01.cshl.edu> Message-ID: > I write in reference to the 2 script files you sent us, read_ctf_res4 > & read_ctf_meg4. In read_ctf_res4, lines 230-234 & 254-258 apparently > correct for some mis-oriented sensors. The question is whether it > holds true for all CTF installations or simply the one at Donders? > Would appreciate a clarification on this point. Thanks. Hi Hiren, No, it is not specific for the FCDC system. The res4 files of the 275 channel CTF system installed at the NIH also requires that the coil orientation of some (~130 of the 275) MEG sensors have to be flipped. Note that it does not affect the recorded data, but only the forward computed model-data in FieldTrip. I don't know how it is handeled in the CTF dipolefitting or SAM software itself, perhaps there is also a flag in the res4 header which I am not aware of that indicates whether the coil orientation is flipped. Robert From maniar at CSHL.EDU Tue Mar 15 19:49:00 2005 From: maniar at CSHL.EDU (Maniar, Hiren) Date: Tue, 15 Mar 2005 13:49:00 -0500 Subject: CTF reading routines now GPL Message-ID: Hi Robert, Many thanks for the quick clarification. Do appreciate it. Regards, Hiren -----Original Message----- From: FieldTrip discussion list on behalf of Robert Oostenveld Sent: Tue 03/15/05 11:50 AM To: FIELDTRIP at NIC.SURFNET.NL Subject: Re: [FIELDTRIP] CTF reading routines now GPL > I write in reference to the 2 script files you sent us, read_ctf_res4 > & read_ctf_meg4. In read_ctf_res4, lines 230-234 & 254-258 apparently > correct for some mis-oriented sensors. The question is whether it > holds true for all CTF installations or simply the one at Donders? > Would appreciate a clarification on this point. Thanks. Hi Hiren, No, it is not specific for the FCDC system. The res4 files of the 275 channel CTF system installed at the NIH also requires that the coil orientation of some (~130 of the 275) MEG sensors have to be flipped. Note that it does not affect the recorded data, but only the forward computed model-data in FieldTrip. I don't know how it is handeled in the CTF dipolefitting or SAM software itself, perhaps there is also a flag in the res4 header which I am not aware of that indicates whether the coil orientation is flipped. Robert From Jan.Schoffelen at FCDONDERS.RU.NL Tue Mar 1 09:15:31 2005 From: Jan.Schoffelen at FCDONDERS.RU.NL (J.M. Schoffelen) Date: Tue, 1 Mar 2005 09:15:31 +0100 Subject: Multiplot In-Reply-To: <05Feb28.172924cet.336456@nucleus.azvu.nl> Message-ID: Dear Teresa, What about taking your variable avg as an input to multiplotER? (in fact, that's how it works) Yours, Jan-Mathijs -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Montez, T. Sent: Monday, February 28, 2005 5:26 PM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] Multiplot Hi Fieldtrippers, The course is becoming closer, but I would like to solve the multiplot problem before that to prepare more interesting questions. I now tried: cfgpre = []; cfgpre.dataset = 'C:\Data\A002-EC_20021016_02.ds' cfgpre.trl= [[ones(1,2)]', [150*ones(1,2)]', [zeros(1,2)]'] cfgpre.channel='MEG' datatest = preprocessing(cfgpre) cfgpre.vartrllength=1 avg = timelockanalysis(cfgpre,datatest) cfgpre.yparam = 'avg' time=datatest.hdr.timeVec; cfgpre.xparam = 'time' multiplotER(cfgpre,datatest) and got the errors: ??? Error using ==> min Function 'min' is not defined for values of class 'cell'. Error in ==> C:\Matlab\FieldTrip\fieldtrip-0.9.5\multiplotER.m On line 117 ==> xmin = min(xvalues); Thanks, Teresa Montez From floris.delange at FCDONDERS.RU.NL Wed Mar 2 13:23:43 2005 From: floris.delange at FCDONDERS.RU.NL (Floris de Lange) Date: Wed, 2 Mar 2005 13:23:43 +0100 Subject: parametric modulation of power Message-ID: Dear Fieldtrippers, I have a (sort of conceptual) question on how to test for parametric modulations in power as a function of e.g. dificulty. I have a task which has 5 difficulty levels, so from 1=easy to 5=hard. I made 5 separate power-spectra, which could eg be named subj1_TFR{1} .. subj1_TFR{5}. I can of course inspect each power spectrum separately, and try to eye-ball whether there may be parametric increases or decreases in power with increasing difficulty level, but it would be nice if I could get a direct view on how 'linearly in/decreasing' the power spectrum per sensor and frequency is. Is this possible within Fieldtrip? Are there scripts around for doing such a linear regression analysis? Many thanks! All the best, Floris -------------- next part -------------- A non-text attachment was scrubbed... Name: floris.delange.vcf Type: text/x-vcard Size: 312 bytes Desc: not available URL: From maris at NICI.RU.NL Wed Mar 2 22:31:26 2005 From: maris at NICI.RU.NL (Eric Maris) Date: Wed, 2 Mar 2005 22:31:26 +0100 Subject: parametric modulation of power Message-ID: Dear Floris, > I have a (sort of conceptual) question on how to test for parametric > modulations in power as a function of e.g. dificulty. > > I have a task which has 5 difficulty levels, so from 1=easy to 5=hard. > I made 5 separate power-spectra, which could eg be named subj1_TFR{1} .. > subj1_TFR{5}. I can of course inspect each power spectrum separately, > and try to eye-ball whether there may be parametric increases or > decreases in power with increasing difficulty level, but it would be > nice if I could get a direct view on how 'linearly in/decreasing' the > power spectrum per sensor and frequency is. > Is this possible within Fieldtrip? Are there scripts around for doing > such a linear regression analysis? This is possible using using CLUSTERRANDANALYSIS. However, at present, only independent samples regression analyses are possible. In practice, this means that you can only analyse your data for each of the subjects separately (treating the trials as replications). Using CLUSTERRANDANALYSIS implies that you evaluate your effect using randomization inference. The nice thing about CLUSTERRANDANALYSIS is that it controls your family-wise error rate. Eric Maris From litvak at TECHUNIX.TECHNION.AC.IL Thu Mar 3 11:59:46 2005 From: litvak at TECHUNIX.TECHNION.AC.IL (Litvak Vladimir) Date: Thu, 3 Mar 2005 12:59:46 +0200 Subject: Statistical comparison of ERP waveforms In-Reply-To: <4225B04F.7070908@fcdonders.ru.nl> Message-ID: Dear Fieldtrip experts, I would like to perform statistical comparison between whole ERP waveforms (rather than just peaks). In my case I need paired ttest. My question is how should one solve the problem of false positives arising from multiple comparisons (all the timeframes)? Is far as I understood from the code the timelocked statistics function of Fieldtrip does not address this issue. I also looked in EEGLAB and it seems the same. Are there any good solutions (preferrable already implemented in Matlab)? Thanks, Vladimir Litvak From maris at NICI.RU.NL Thu Mar 3 16:38:02 2005 From: maris at NICI.RU.NL (Eric Maris) Date: Thu, 3 Mar 2005 16:38:02 +0100 Subject: Statistical comparison of ERP waveforms Message-ID: Hi Litvak, > I would like to perform statistical comparison between whole ERP waveforms > (rather than just peaks). In my case I need paired ttest. My question is > how should one solve the problem of false positives arising from multiple > comparisons (all the timeframes)? Is far as I understood from the code the > timelocked statistics function of Fieldtrip does not address this issue. I > also looked in EEGLAB and it seems the same. Are there any good solutions > (preferrable already implemented in Matlab)? In FIELDTRIP, we use randomization statistics to control the family-wise error rate. We have combined randomization statistics with a cluster-finding algorithm that drastically improves power in exploratory analyses. This has been implemented in the routine CLUSTERRANDANALYSIS which, unfortunately for you, is only available to users inside the FC Donders Center. We will make it available to the rest of the world in the summer of 2005. Eric Maris From shivakademane at YAHOO.COM Wed Mar 9 13:01:16 2005 From: shivakademane at YAHOO.COM (Shivaprakash) Date: Wed, 9 Mar 2005 04:01:16 -0800 Subject: req code Message-ID: field trippers, I am a student trying to implement in C the work done by- Lehmann, D. and Michel, C.M. (1990). Intracerebral dipole source localization for FFT power maps. Electroenceph. Clin. Neurophysiol. 76, 271-276. some how my programs are not working as explained in the paper. the following web ID has the codes but not in source code. http://www.puk.unibe.ch/tk2/Software.htm if any one has done the implementation send a copy of the source code to my ID. so that I can understand where I have gone wrong. --------------------------------- Celebrate Yahoo!'s 10th Birthday! Yahoo! Netrospective: 100 Moments of the Web -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Fri Mar 11 13:25:13 2005 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Fri, 11 Mar 2005 13:25:13 +0100 Subject: req code In-Reply-To: <20050309120116.87415.qmail@web21206.mail.yahoo.com> Message-ID: Dear Shivaprakash On 9 Mar 2005, at 13:01, Shivaprakash wrote: > I am a student trying to implement in C the work done by- > Lehmann, D. and Michel, C.M. (1990). Intracerebral dipole source > localization for FFT power maps. Electroenceph. Clin. Neurophysiol. > 76, 271-276. >   > some how my programs are not working as explained in the paper. the > following web ID has the codes but not in source code. > http://www.puk.unibe.ch/tk2/Software.htm >   > if any one has done the implementation send a copy of the source code > to my ID. so that I can understand where I have gone wrong. FieldTrip does implement frequency based source reconstructions using beamformer approaches, and frequency based dipole fitting in the way described by Lehman (1990) is not implemented in FieldTrip. Howvere, the method described by Lehman has subsequently been improved by Lutkenhoner and I suggest that you first look into that work: Lutkenhoner B. Frequency-domain localization of intracerebral dipolar sources. Electroencephalogr Clin Neurophysiol. 1992 Feb;82(2):112-8. If the implemented beamformer approach (see refs below) is not suitable for your data, then it would not be too difficult to implement a frequency based dipole fit algoritm based on the FREQANALYSIS and the DIPOLEFITTING code that is already present in our toolbox. However, FieldTrip is completely implemented in Matlab and not in C, and it will be a lot of work to reimplement it in C. My old and unsupported MSA library does contain a C-code implementation of the frequency dipole fit for EEG and MEG as described by Lutkenhoner, maybe you also want to take a look at that (http://oase.uci.kun.nl/~roberto/msa/) best regards, Robert refs: Gross J, Kujala J, Hamalainen M, Timmermann L, Schnitzler A, Salmelin R. Dynamic imaging of coherent sources: Studying neural interactions in the human brain. Proc Natl Acad Sci U S A. 2001 Jan 16;98(2):694-9. Van Veen BD, van Drongelen W, Yuchtman M, Suzuki A. Localization of brain electrical activity via linearly constrained minimum variance spatial filtering. IEEE Trans Biomed Eng. 1997 Sep;44(9):867-80. From maniar at CSHL.EDU Tue Mar 15 14:52:10 2005 From: maniar at CSHL.EDU (Maniar, Hiren) Date: Tue, 15 Mar 2005 08:52:10 -0500 Subject: CTF reading routines now GPL Message-ID: Hello Robert, I write in reference to the 2 script files you sent us, read_ctf_res4 & read_ctf_meg4. In read_ctf_res4, lines 230-234 & 254-258 apparently correct for some mis-oriented sensors. The question is whether it holds true for all CTF installations or simply the one at Donders? Would appreciate a clarification on this point. Thanks. Many thanks for the scripts. Regards, Hiren -----Original Message----- From: FieldTrip discussion list on behalf of Robert Oostenveld Sent: Fri 02/18/05 8:30 AM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] CTF reading routines now GPL Dear CTF-FieldTrip users, There are two files (read_ctf_res4 and read_ctf_meg4) in the FieldTrip release that were released as p-files instead of m-files. These two files originated from CTF, and since then have been modified and improved by us at the Donders (e.g. speed improvements and support for files >2GB). VSM MedTech Ltd. now has given us permission to release these files as wel in open source form under the GPL. They will be included as m-files in upcoming releases. For those of you who are interested, you'll also find them attached to this mail. best regards, Robert From r.oostenveld at FCDONDERS.RU.NL Tue Mar 15 17:50:06 2005 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 15 Mar 2005 17:50:06 +0100 Subject: CTF reading routines now GPL In-Reply-To: <44233CA5B57295409DA4423AECEFFEE738FBE0@mailbox01.cshl.edu> Message-ID: > I write in reference to the 2 script files you sent us, read_ctf_res4 > & read_ctf_meg4. In read_ctf_res4, lines 230-234 & 254-258 apparently > correct for some mis-oriented sensors. The question is whether it > holds true for all CTF installations or simply the one at Donders? > Would appreciate a clarification on this point. Thanks. Hi Hiren, No, it is not specific for the FCDC system. The res4 files of the 275 channel CTF system installed at the NIH also requires that the coil orientation of some (~130 of the 275) MEG sensors have to be flipped. Note that it does not affect the recorded data, but only the forward computed model-data in FieldTrip. I don't know how it is handeled in the CTF dipolefitting or SAM software itself, perhaps there is also a flag in the res4 header which I am not aware of that indicates whether the coil orientation is flipped. Robert From maniar at CSHL.EDU Tue Mar 15 19:49:00 2005 From: maniar at CSHL.EDU (Maniar, Hiren) Date: Tue, 15 Mar 2005 13:49:00 -0500 Subject: CTF reading routines now GPL Message-ID: Hi Robert, Many thanks for the quick clarification. Do appreciate it. Regards, Hiren -----Original Message----- From: FieldTrip discussion list on behalf of Robert Oostenveld Sent: Tue 03/15/05 11:50 AM To: FIELDTRIP at NIC.SURFNET.NL Subject: Re: [FIELDTRIP] CTF reading routines now GPL > I write in reference to the 2 script files you sent us, read_ctf_res4 > & read_ctf_meg4. In read_ctf_res4, lines 230-234 & 254-258 apparently > correct for some mis-oriented sensors. The question is whether it > holds true for all CTF installations or simply the one at Donders? > Would appreciate a clarification on this point. Thanks. Hi Hiren, No, it is not specific for the FCDC system. The res4 files of the 275 channel CTF system installed at the NIH also requires that the coil orientation of some (~130 of the 275) MEG sensors have to be flipped. Note that it does not affect the recorded data, but only the forward computed model-data in FieldTrip. I don't know how it is handeled in the CTF dipolefitting or SAM software itself, perhaps there is also a flag in the res4 header which I am not aware of that indicates whether the coil orientation is flipped. Robert From Jan.Schoffelen at FCDONDERS.RU.NL Tue Mar 1 09:15:31 2005 From: Jan.Schoffelen at FCDONDERS.RU.NL (J.M. Schoffelen) Date: Tue, 1 Mar 2005 09:15:31 +0100 Subject: Multiplot In-Reply-To: <05Feb28.172924cet.336456@nucleus.azvu.nl> Message-ID: Dear Teresa, What about taking your variable avg as an input to multiplotER? (in fact, that's how it works) Yours, Jan-Mathijs -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Montez, T. Sent: Monday, February 28, 2005 5:26 PM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] Multiplot Hi Fieldtrippers, The course is becoming closer, but I would like to solve the multiplot problem before that to prepare more interesting questions. I now tried: cfgpre = []; cfgpre.dataset = 'C:\Data\A002-EC_20021016_02.ds' cfgpre.trl= [[ones(1,2)]', [150*ones(1,2)]', [zeros(1,2)]'] cfgpre.channel='MEG' datatest = preprocessing(cfgpre) cfgpre.vartrllength=1 avg = timelockanalysis(cfgpre,datatest) cfgpre.yparam = 'avg' time=datatest.hdr.timeVec; cfgpre.xparam = 'time' multiplotER(cfgpre,datatest) and got the errors: ??? Error using ==> min Function 'min' is not defined for values of class 'cell'. Error in ==> C:\Matlab\FieldTrip\fieldtrip-0.9.5\multiplotER.m On line 117 ==> xmin = min(xvalues); Thanks, Teresa Montez From floris.delange at FCDONDERS.RU.NL Wed Mar 2 13:23:43 2005 From: floris.delange at FCDONDERS.RU.NL (Floris de Lange) Date: Wed, 2 Mar 2005 13:23:43 +0100 Subject: parametric modulation of power Message-ID: Dear Fieldtrippers, I have a (sort of conceptual) question on how to test for parametric modulations in power as a function of e.g. dificulty. I have a task which has 5 difficulty levels, so from 1=easy to 5=hard. I made 5 separate power-spectra, which could eg be named subj1_TFR{1} .. subj1_TFR{5}. I can of course inspect each power spectrum separately, and try to eye-ball whether there may be parametric increases or decreases in power with increasing difficulty level, but it would be nice if I could get a direct view on how 'linearly in/decreasing' the power spectrum per sensor and frequency is. Is this possible within Fieldtrip? Are there scripts around for doing such a linear regression analysis? Many thanks! All the best, Floris -------------- next part -------------- A non-text attachment was scrubbed... Name: floris.delange.vcf Type: text/x-vcard Size: 312 bytes Desc: not available URL: From maris at NICI.RU.NL Wed Mar 2 22:31:26 2005 From: maris at NICI.RU.NL (Eric Maris) Date: Wed, 2 Mar 2005 22:31:26 +0100 Subject: parametric modulation of power Message-ID: Dear Floris, > I have a (sort of conceptual) question on how to test for parametric > modulations in power as a function of e.g. dificulty. > > I have a task which has 5 difficulty levels, so from 1=easy to 5=hard. > I made 5 separate power-spectra, which could eg be named subj1_TFR{1} .. > subj1_TFR{5}. I can of course inspect each power spectrum separately, > and try to eye-ball whether there may be parametric increases or > decreases in power with increasing difficulty level, but it would be > nice if I could get a direct view on how 'linearly in/decreasing' the > power spectrum per sensor and frequency is. > Is this possible within Fieldtrip? Are there scripts around for doing > such a linear regression analysis? This is possible using using CLUSTERRANDANALYSIS. However, at present, only independent samples regression analyses are possible. In practice, this means that you can only analyse your data for each of the subjects separately (treating the trials as replications). Using CLUSTERRANDANALYSIS implies that you evaluate your effect using randomization inference. The nice thing about CLUSTERRANDANALYSIS is that it controls your family-wise error rate. Eric Maris From litvak at TECHUNIX.TECHNION.AC.IL Thu Mar 3 11:59:46 2005 From: litvak at TECHUNIX.TECHNION.AC.IL (Litvak Vladimir) Date: Thu, 3 Mar 2005 12:59:46 +0200 Subject: Statistical comparison of ERP waveforms In-Reply-To: <4225B04F.7070908@fcdonders.ru.nl> Message-ID: Dear Fieldtrip experts, I would like to perform statistical comparison between whole ERP waveforms (rather than just peaks). In my case I need paired ttest. My question is how should one solve the problem of false positives arising from multiple comparisons (all the timeframes)? Is far as I understood from the code the timelocked statistics function of Fieldtrip does not address this issue. I also looked in EEGLAB and it seems the same. Are there any good solutions (preferrable already implemented in Matlab)? Thanks, Vladimir Litvak From maris at NICI.RU.NL Thu Mar 3 16:38:02 2005 From: maris at NICI.RU.NL (Eric Maris) Date: Thu, 3 Mar 2005 16:38:02 +0100 Subject: Statistical comparison of ERP waveforms Message-ID: Hi Litvak, > I would like to perform statistical comparison between whole ERP waveforms > (rather than just peaks). In my case I need paired ttest. My question is > how should one solve the problem of false positives arising from multiple > comparisons (all the timeframes)? Is far as I understood from the code the > timelocked statistics function of Fieldtrip does not address this issue. I > also looked in EEGLAB and it seems the same. Are there any good solutions > (preferrable already implemented in Matlab)? In FIELDTRIP, we use randomization statistics to control the family-wise error rate. We have combined randomization statistics with a cluster-finding algorithm that drastically improves power in exploratory analyses. This has been implemented in the routine CLUSTERRANDANALYSIS which, unfortunately for you, is only available to users inside the FC Donders Center. We will make it available to the rest of the world in the summer of 2005. Eric Maris From shivakademane at YAHOO.COM Wed Mar 9 13:01:16 2005 From: shivakademane at YAHOO.COM (Shivaprakash) Date: Wed, 9 Mar 2005 04:01:16 -0800 Subject: req code Message-ID: field trippers, I am a student trying to implement in C the work done by- Lehmann, D. and Michel, C.M. (1990). Intracerebral dipole source localization for FFT power maps. Electroenceph. Clin. Neurophysiol. 76, 271-276. some how my programs are not working as explained in the paper. the following web ID has the codes but not in source code. http://www.puk.unibe.ch/tk2/Software.htm if any one has done the implementation send a copy of the source code to my ID. so that I can understand where I have gone wrong. --------------------------------- Celebrate Yahoo!'s 10th Birthday! Yahoo! Netrospective: 100 Moments of the Web -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Fri Mar 11 13:25:13 2005 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Fri, 11 Mar 2005 13:25:13 +0100 Subject: req code In-Reply-To: <20050309120116.87415.qmail@web21206.mail.yahoo.com> Message-ID: Dear Shivaprakash On 9 Mar 2005, at 13:01, Shivaprakash wrote: > I am a student trying to implement in C the work done by- > Lehmann, D. and Michel, C.M. (1990). Intracerebral dipole source > localization for FFT power maps. Electroenceph. Clin. Neurophysiol. > 76, 271-276. >   > some how my programs are not working as explained in the paper. the > following web ID has the codes but not in source code. > http://www.puk.unibe.ch/tk2/Software.htm >   > if any one has done the implementation send a copy of the source code > to my ID. so that I can understand where I have gone wrong. FieldTrip does implement frequency based source reconstructions using beamformer approaches, and frequency based dipole fitting in the way described by Lehman (1990) is not implemented in FieldTrip. Howvere, the method described by Lehman has subsequently been improved by Lutkenhoner and I suggest that you first look into that work: Lutkenhoner B. Frequency-domain localization of intracerebral dipolar sources. Electroencephalogr Clin Neurophysiol. 1992 Feb;82(2):112-8. If the implemented beamformer approach (see refs below) is not suitable for your data, then it would not be too difficult to implement a frequency based dipole fit algoritm based on the FREQANALYSIS and the DIPOLEFITTING code that is already present in our toolbox. However, FieldTrip is completely implemented in Matlab and not in C, and it will be a lot of work to reimplement it in C. My old and unsupported MSA library does contain a C-code implementation of the frequency dipole fit for EEG and MEG as described by Lutkenhoner, maybe you also want to take a look at that (http://oase.uci.kun.nl/~roberto/msa/) best regards, Robert refs: Gross J, Kujala J, Hamalainen M, Timmermann L, Schnitzler A, Salmelin R. Dynamic imaging of coherent sources: Studying neural interactions in the human brain. Proc Natl Acad Sci U S A. 2001 Jan 16;98(2):694-9. Van Veen BD, van Drongelen W, Yuchtman M, Suzuki A. Localization of brain electrical activity via linearly constrained minimum variance spatial filtering. IEEE Trans Biomed Eng. 1997 Sep;44(9):867-80. From maniar at CSHL.EDU Tue Mar 15 14:52:10 2005 From: maniar at CSHL.EDU (Maniar, Hiren) Date: Tue, 15 Mar 2005 08:52:10 -0500 Subject: CTF reading routines now GPL Message-ID: Hello Robert, I write in reference to the 2 script files you sent us, read_ctf_res4 & read_ctf_meg4. In read_ctf_res4, lines 230-234 & 254-258 apparently correct for some mis-oriented sensors. The question is whether it holds true for all CTF installations or simply the one at Donders? Would appreciate a clarification on this point. Thanks. Many thanks for the scripts. Regards, Hiren -----Original Message----- From: FieldTrip discussion list on behalf of Robert Oostenveld Sent: Fri 02/18/05 8:30 AM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] CTF reading routines now GPL Dear CTF-FieldTrip users, There are two files (read_ctf_res4 and read_ctf_meg4) in the FieldTrip release that were released as p-files instead of m-files. These two files originated from CTF, and since then have been modified and improved by us at the Donders (e.g. speed improvements and support for files >2GB). VSM MedTech Ltd. now has given us permission to release these files as wel in open source form under the GPL. They will be included as m-files in upcoming releases. For those of you who are interested, you'll also find them attached to this mail. best regards, Robert From r.oostenveld at FCDONDERS.RU.NL Tue Mar 15 17:50:06 2005 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 15 Mar 2005 17:50:06 +0100 Subject: CTF reading routines now GPL In-Reply-To: <44233CA5B57295409DA4423AECEFFEE738FBE0@mailbox01.cshl.edu> Message-ID: > I write in reference to the 2 script files you sent us, read_ctf_res4 > & read_ctf_meg4. In read_ctf_res4, lines 230-234 & 254-258 apparently > correct for some mis-oriented sensors. The question is whether it > holds true for all CTF installations or simply the one at Donders? > Would appreciate a clarification on this point. Thanks. Hi Hiren, No, it is not specific for the FCDC system. The res4 files of the 275 channel CTF system installed at the NIH also requires that the coil orientation of some (~130 of the 275) MEG sensors have to be flipped. Note that it does not affect the recorded data, but only the forward computed model-data in FieldTrip. I don't know how it is handeled in the CTF dipolefitting or SAM software itself, perhaps there is also a flag in the res4 header which I am not aware of that indicates whether the coil orientation is flipped. Robert From maniar at CSHL.EDU Tue Mar 15 19:49:00 2005 From: maniar at CSHL.EDU (Maniar, Hiren) Date: Tue, 15 Mar 2005 13:49:00 -0500 Subject: CTF reading routines now GPL Message-ID: Hi Robert, Many thanks for the quick clarification. Do appreciate it. Regards, Hiren -----Original Message----- From: FieldTrip discussion list on behalf of Robert Oostenveld Sent: Tue 03/15/05 11:50 AM To: FIELDTRIP at NIC.SURFNET.NL Subject: Re: [FIELDTRIP] CTF reading routines now GPL > I write in reference to the 2 script files you sent us, read_ctf_res4 > & read_ctf_meg4. In read_ctf_res4, lines 230-234 & 254-258 apparently > correct for some mis-oriented sensors. The question is whether it > holds true for all CTF installations or simply the one at Donders? > Would appreciate a clarification on this point. Thanks. Hi Hiren, No, it is not specific for the FCDC system. The res4 files of the 275 channel CTF system installed at the NIH also requires that the coil orientation of some (~130 of the 275) MEG sensors have to be flipped. Note that it does not affect the recorded data, but only the forward computed model-data in FieldTrip. I don't know how it is handeled in the CTF dipolefitting or SAM software itself, perhaps there is also a flag in the res4 header which I am not aware of that indicates whether the coil orientation is flipped. Robert