From Harsimrat.Singh at WARWICK.AC.UK Sun Jan 4 02:45:16 2009 From: Harsimrat.Singh at WARWICK.AC.UK (Singh, Harsimrat) Date: Sun, 4 Jan 2009 01:45:16 -0000 Subject: BCI2000 file read Message-ID: Hi I am trying to use some field trip functions for data recorded using BCI2000 (.dat) files. The data was recorded using brain vision amplifier. I understand that the function read_data doesnt read the BCI2000 files. Can anyone please suggest way around this ? Thanks in advance Regards Harsimrat ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Mon Jan 5 15:19:37 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 5 Jan 2009 15:19:37 +0100 Subject: BCI2000 file read In-Reply-To: <95B2B6BF8599AB4EA51DDC85904A15AAC6A16E@HOLLY.ads.warwick.ac.uk> Message-ID: Dear Harsimrat, It recently came to my attention that files written in older versions of BCI2000 are not completely compatible with newer versions of BCI2000. Is it possible for you to send me an example datafile that causes you the problem? The problem has to do with the file type detection and probably can be fixed quite easily. Please look here http://neuroimaging.ruhosting.nl/fieldtrip/doku.php?id=fieldtrip:contact for details on how to send the file. best regards, Robert On 4 Jan 2009, at 2:45, Singh, Harsimrat wrote: > Hi > > I am trying to use some field trip functions for data recorded using > BCI2000 (.dat) files. The data was recorded using brain vision > amplifier. > I understand that the function read_data doesnt read the BCI2000 > files. > Can anyone please suggest way around this ? > > Thanks in advance > Regards > Harsimrat > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From jason.sherfey at GMAIL.COM Tue Jan 6 01:15:16 2009 From: jason.sherfey at GMAIL.COM (Jason Sherfey) Date: Mon, 5 Jan 2009 16:15:16 -0800 Subject: freqanalysis_wltconvol Message-ID: Dear FieldTrip users, I have been using freqanalysis_wltconvol to compute the wavelet power spectrum for several months and recently began trying to understand the code. Reading past discussions on this listserv has been very helpful, but I can't figure out why it does the particular normalization that it does for the wavelet power calculation. This calculation can be found on line 299 of the 20081001 release. According to the comments at the beginning of the function, jansch "fixed [the] improper normalization of powdum" in Revision 1.17 on 2007/06/14. It seems to me that "powdum" is the wavelet power spectrum (P) and that "autspctrmacttap" is the signal's wavelet transform (T). If that is true, then the correction made on 2007/06/14 was the following: P = (2*|T| / fs)^2 became P = 2*|T|^2 / fs where fs = sampling frequency My current understanding (based on pp. 31-32 in Addison's text "The illustrated wavelet transform handbook") is that the wavelet energy density is given by E = |T|^2 and that P = E / (time period of the signal). Since the time period of the signal = (# of samples) / (sampling frequency), that would imply P = fs*|T|^2 / (# of samples). Thus, I thought |T|^2 should be multiplied by fs/(# of samples), but in the code it's instead multiplied by 2/fs. I am fairly new to wavelet analysis and suspect there's a small detail I don't understand. Does anyone know why the wavelet energy is normalized by 2/fs instead of fs/(# samples)? Thanks in advance, Jason ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From iversen at NSI.EDU Fri Jan 9 19:03:18 2009 From: iversen at NSI.EDU (John Iversen) Date: Fri, 9 Jan 2009 10:03:18 -0800 Subject: Q about integration with SPM8 In-Reply-To: <8d039c560901051615h68c88f7bw1356aea8be3b3295@mail.gmail.com> Message-ID: Hello, It's seems great that you there is not a partnership between Fieldtrip and SPM. Since SPM8 comes with its own version of fieldtrip, how will this be kept 'in sync' with the updates coming out of Donders? Having two different versions of fieldtrip seems like a potential headache. To avoid this issue, I was planning to have SPM8 use my existing Fieldtrip installation exclusively. Is there is any downside to this? What version of FT is included with SPM8? More generally, the SPM solution of renaming and wrappers seems rather involved. Couldn't managing the MATLAB search path ensure that there are no conflicts between versions? I'm sure you went this route for good reasons that I am unaware of, so I'd be happy to be enlightened. Thanks, as always, for a great set of tools, and support. Happy New Year to all. John John R. Iversen, PhD The Neurosciences Institute 10640 John Jay Hopkins Drive San Diego, CA 92121 (858)-626-2068 iversen at nsi.edu ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From v.litvak at ION.UCL.AC.UK Fri Jan 9 19:31:42 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Fri, 9 Jan 2009 18:31:42 +0000 Subject: Q about integration with SPM8 In-Reply-To: Message-ID: Dear John, On Fri, Jan 9, 2009 at 6:03 PM, John Iversen wrote: > Since SPM8 comes with its own version of fieldtrip, how will this be > kept 'in sync' with the updates coming out of Donders? This is done automatically presently on a daily basis, perhaps will be switched to a weekly update after the official release of SPM8. Critical updates are propagated immediately. So if you update SPM8, the version of FT in SPM8 will be from the same date. >Having two different > versions of fieldtrip seems like a potential headache. This is exactly what the wrappers are for. You can have your favorite FT version in the path with SPM but there will be no clashes as SPM will only use its internal version of FT. The same is true for your FT scripts - unless you explicitly call the wrappers with 'ft_...' your FT functions will come from your stand-alone FT installation and not from SPM. >To avoid this issue, > I was planning to have SPM8 use my existing Fieldtrip installation > exclusively. Is there is any downside to this? Yes because there is no guarantee that your particular FT version is compatible with your SPM version (unless you keep updating both which is redundant). The best way for you to work if you already have an FT version that works for you and don't want to update it for a while is to ignore the FT version that SPM uses and pretend it's not there. Wrappers will prevent any clashes as I explained. I hope my explanations are clear. If not, I'd be glad to answer any further questions. Best, Vladimir ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From christine.gruetzner at GOOGLEMAIL.COM Mon Jan 12 17:29:48 2009 From: christine.gruetzner at GOOGLEMAIL.COM (Christine Gruetzner) Date: Mon, 12 Jan 2009 17:29:48 +0100 Subject: Plotting individual source stat data Message-ID: Dear FieldTrip users, I'm trying to plot source stat data from individual subjects on the respective mri (according to the procedure suggested in the beamformer tutorial), but there seems to be a problem when I use sourceinterpolate (see below). Does anybody have an idea what's going wrong here? Thanks in advance! Best, Christine the input is source data with 4560 positions the input is volume data with dimensions [256 256 256] not downsampling anatomy not downsampling inside selecting subvolume of 0.0% interpolating ??? Attempted to access sel(1); index out of bounds because numel(sel)=0. Error in ==> sourceinterpolate>my_interpn at 380 progress(sel(1)/num, 'interpolating %.1f%%\n', 100*sel(1)/num); Error in ==> sourceinterpolate at 275 interp.inside( sel) = my_interpn(double(functional.inside), ax(sel), ay(sel), az(sel), 'nearest', cfg.feedback); Error in ==> PlotSourceData at 164 sourceinterp = sourceinterpolate(cfg, statdiff,mri); -- Christine Gruetzner, geb. Tillmann Max-Planck-Institut für Hirnforschung Abt. Neurophysiologie Deutschordenstr. 46 60528 Frankfurt am Main Germany Phone: +49 (0)69/6301-83225 E-Mail: tillmann at mpih-frankfurt.mpg.de http://www.mpih-frankfurt.mpg.de/global/Np/Staff/tillmann.htm ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Mon Jan 12 21:12:29 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 12 Jan 2009 21:12:29 +0100 Subject: Q about integration with SPM8 In-Reply-To: Message-ID: Hi John, Vladimir and I (and other spm developers) have considered this carefully, and the present spm8+fieldtrip mixture was the best we could come up with. The versions are automatically kept in synch, but the release schedule of fieldtrip is daily, whereas for spm8 it is less frequent. So the versions getting slightly out of sync on your computer is inevitable. With the latest 2008a and 2008b versions of Matlab there are better options for supporting such mixtures ofg packages (using "namespaces"), but since both spm and fieldtrip should work on older matlab versions, we cannot use those features yet. On 9 Jan 2009, at 19:31, Vladimir Litvak wrote: >> To avoid this issue, >> I was planning to have SPM8 use my existing Fieldtrip installation >> exclusively. Is there is any downside to this? > > Yes because there is no guarantee that your particular FT version is > compatible with your SPM version (unless you keep updating both which > is redundant). > > The best way for you to work if you already have an FT version that > works for you and don't want to update it for a while is to ignore the > FT version that SPM uses and pretend it's not there. Wrappers will > prevent any clashes as I explained. To add on Vladimirs comment: In practice it means that you delete the spm8/external/fieldtrip/private directory and keep the spm8/external/ fieldtrip directory for the wrappers. You can do the same for fileio and forwinv (also both in fieldtrip and spm8/external). Subsequently you should ensure that the ft_xxx wrappers in spm8, respectively the fileio_xxx and the forwinv_xxx wrappers are on your matlab path, just as your normal fieldtrip version. SPM8 will call those wrappers, which will call your standard fieldtrip functions. best Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From v.litvak at ION.UCL.AC.UK Mon Jan 12 23:13:14 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Mon, 12 Jan 2009 22:13:14 +0000 Subject: Q about integration with SPM8 In-Reply-To: Message-ID: Although what Robert described (deleting the private subdirectories) will do the trick, I don't see any reason to do it. I do see a reason not to do it because it may generate errors that will be very hard for us to reproduce and resolve. We are now often developing things in parallel where changes are made to FT to make some SPM feature work so if the two get slightly out of sync those new features will not work. Thus, I repeat my recommendation to leave things as they are. Don't you agree, Robert? There might be some problems with clashes if Robert starts naming some FT functions with the same names as wrappers in SPM. I don't know if there are any cases like this already. Vladimir On Mon, Jan 12, 2009 at 8:12 PM, Robert Oostenveld wrote: > Hi John, > > Vladimir and I (and other spm developers) have considered this carefully, > and the present spm8+fieldtrip mixture was the best we could come up with. > The versions are automatically kept in synch, but the release schedule of > fieldtrip is daily, whereas for spm8 it is less frequent. So the versions > getting slightly out of sync on your computer is inevitable. > > With the latest 2008a and 2008b versions of Matlab there are better options > for supporting such mixtures ofg packages (using "namespaces"), but since > both spm and fieldtrip should work on older matlab versions, we cannot use > those features yet. > > On 9 Jan 2009, at 19:31, Vladimir Litvak wrote: > >>> To avoid this issue, >>> I was planning to have SPM8 use my existing Fieldtrip installation >>> exclusively. Is there is any downside to this? >> >> Yes because there is no guarantee that your particular FT version is >> compatible with your SPM version (unless you keep updating both which >> is redundant). >> >> The best way for you to work if you already have an FT version that >> works for you and don't want to update it for a while is to ignore the >> FT version that SPM uses and pretend it's not there. Wrappers will >> prevent any clashes as I explained. > > To add on Vladimirs comment: In practice it means that you delete the > spm8/external/fieldtrip/private directory and keep the > spm8/external/fieldtrip directory for the wrappers. You can do the same for > fileio and forwinv (also both in fieldtrip and spm8/external). Subsequently > you should ensure that the ft_xxx wrappers in spm8, respectively the > fileio_xxx and the forwinv_xxx wrappers are on your matlab path, just as > your normal fieldtrip version. SPM8 will call those wrappers, which will > call your standard fieldtrip functions. > > best > Robert > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/fcdonders/fieldtrip. > > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From iversen at NSI.EDU Mon Jan 12 23:42:04 2009 From: iversen at NSI.EDU (John Iversen) Date: Mon, 12 Jan 2009 14:42:04 -0800 Subject: Q about integration with SPM8 In-Reply-To: Message-ID: Hi Robert and Vladimir, Thank you both for your responses. I very much appreciate the clarifications and suggestions for ways to proceed. Best regards, John On Jan 12, 2009, at 12:12 PM, Robert Oostenveld wrote: > Hi John, > > Vladimir and I (and other spm developers) have considered this > carefully, and the present spm8+fieldtrip mixture was the best we > could come up with. The versions are automatically kept in synch, > but the release schedule of fieldtrip is daily, whereas for spm8 it > is less frequent. So the versions getting slightly out of sync on > your computer is inevitable. > > With the latest 2008a and 2008b versions of Matlab there are better > options for supporting such mixtures ofg packages (using > "namespaces"), but since both spm and fieldtrip should work on older > matlab versions, we cannot use those features yet. > > On 9 Jan 2009, at 19:31, Vladimir Litvak wrote: > this >>> To avoid this issue, >>> I was planning to have SPM8 use my existing Fieldtrip installation >>> exclusively. Is there is any downside to? >> >> Yes because there is no guarantee that your particular FT version is >> compatible with your SPM version (unless you keep updating both which >> is redundant). >> >> The best way for you to work if you already have an FT version that >> works for you and don't want to update it for a while is to ignore >> the >> FT version that SPM uses and pretend it's not there. Wrappers will >> prevent any clashes as I explained. > > To add on Vladimirs comment: In practice it means that you delete > the spm8/external/fieldtrip/private directory and keep the spm8/ > external/fieldtrip directory for the wrappers. You can do the same > for fileio and forwinv (also both in fieldtrip and spm8/external). > Subsequently you should ensure that the ft_xxx wrappers in spm8, > respectively the fileio_xxx and the forwinv_xxx wrappers are on your > matlab path, just as your normal fieldtrip version. SPM8 will call > those wrappers, which will call your standard fieldtrip functions. > > best > Robert > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/fcdonders/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From iversen at NSI.EDU Tue Jan 13 00:04:33 2009 From: iversen at NSI.EDU (John Iversen) Date: Mon, 12 Jan 2009 15:04:33 -0800 Subject: Q about integration with SPM8 In-Reply-To: Message-ID: Sorry, my reply just crossed with yours. Ok, I'm now a bit confused as to the specifics of the co-evolution of the two projects. It sounds like the FT in SPM is a custom fit good at a particular moment in time, but that separate changes in either SPM or FT could bring some conflicts. That seems like a good argument to use the SPM version of FT. To clarify my perspective, what I didn't note in my original email, and I should have, is that the 'headache' I referred to is mainly due to the fact that I've made some modifications of my own on FT, and wasn't keen to need to fold them into two separate versions of FT that might be updated at different times. Granted that's a self-inflicted headache and perhaps at this point I should reconsider whether those modifications are in fact necessary. More generally, though, I like to tweak and be familiar with every detail of the code I'm using, so having two different versions is just that much more for my finite brain to keep track of. Of course, more generally the number one issue would be to avoid a situation in which two versions yielded different analysis results, but that doesn't seem to be a concern that either of you have expressed, so perhaps that is not something to worry about. So, now I'm considering just using the version of FT included in SPM for all my uses. I don't take advantage of the daily upgrades to FT, so the slower release schedule is fine. How does that sound? Thanks, John On Jan 12, 2009, at 2:13 PM, Vladimir Litvak wrote: > Although what Robert described (deleting the private subdirectories) > will do the trick, I don't see any reason to do it. I do see a reason > not to do it because it may generate errors that will be very hard for > us to reproduce and resolve. We are now often developing things in > parallel where changes are made to FT to make some SPM feature work so > if the two get slightly out of sync those new features will not work. > Thus, I repeat my recommendation to leave things as they are. Don't > you agree, Robert? > > There might be some problems with clashes if Robert starts naming some > FT functions with the same names as wrappers in SPM. I don't know if > there are any cases like this already. > > Vladimir > > > > On Mon, Jan 12, 2009 at 8:12 PM, Robert Oostenveld > wrote: >> Hi John, >> >> Vladimir and I (and other spm developers) have considered this >> carefully, >> and the present spm8+fieldtrip mixture was the best we could come >> up with. >> The versions are automatically kept in synch, but the release >> schedule of >> fieldtrip is daily, whereas for spm8 it is less frequent. So the >> versions >> getting slightly out of sync on your computer is inevitable. >> >> With the latest 2008a and 2008b versions of Matlab there are better >> options >> for supporting such mixtures ofg packages (using "namespaces"), but >> since >> both spm and fieldtrip should work on older matlab versions, we >> cannot use >> those features yet. >> >> On 9 Jan 2009, at 19:31, Vladimir Litvak wrote: >> >>>> To avoid this issue, >>>> I was planning to have SPM8 use my existing Fieldtrip installation >>>> exclusively. Is there is any downside to this? >>> >>> Yes because there is no guarantee that your particular FT version is >>> compatible with your SPM version (unless you keep updating both >>> which >>> is redundant). >>> >>> The best way for you to work if you already have an FT version that >>> works for you and don't want to update it for a while is to ignore >>> the >>> FT version that SPM uses and pretend it's not there. Wrappers will >>> prevent any clashes as I explained. >> >> To add on Vladimirs comment: In practice it means that you delete the >> spm8/external/fieldtrip/private directory and keep the >> spm8/external/fieldtrip directory for the wrappers. You can do the >> same for >> fileio and forwinv (also both in fieldtrip and spm8/external). >> Subsequently >> you should ensure that the ft_xxx wrappers in spm8, respectively the >> fileio_xxx and the forwinv_xxx wrappers are on your matlab path, >> just as >> your normal fieldtrip version. SPM8 will call those wrappers, which >> will >> call your standard fieldtrip functions. >> >> best >> Robert >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the >> FieldTrip toolbox, to share experiences and to discuss new ideas >> for MEG >> and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/fcdonders/fieldtrip. >> >> > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/fcdonders/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From v.litvak at ION.UCL.AC.UK Tue Jan 13 00:40:39 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Mon, 12 Jan 2009 23:40:39 +0000 Subject: Q about integration with SPM8 In-Reply-To: <5B9123D2-47A5-4884-BC50-08462FC09640@nsi.edu> Message-ID: Dear John, It's hard for me to follow your reasoning. On the one hand you want to keep using your old 'tweaked' FT, but on the other hand you want to switch to SPM's version which would not contain your modifications. Maybe there is something basic that I should reiterate. The actual analysis done in SPM is different than the analysis in FT. SPM proper presently used code from FT for data conversion and for computing lead fields. In both cases there are unlikely to be different results for different versions of the code. The reason all of FT is included in SPM and not just those specific parts is to make it possible for people to write some custom tools combining SPM and FT functions and distribute them to SPM users without the need to install external FT. If you just want to do your own analysis I don't see a good reason for you to use the FT included in SPM rather than the version you are presently working with. What I suggest is - just put both your old FT and SPM in the path and see how it goes. I don't foresee any problems. Note that you should keep updating SPM with patches from ftp://ftp.fil.ion.ucl.ac.uk/spm/spm8b_updates/ Best, Vladimir On Mon, Jan 12, 2009 at 11:04 PM, John Iversen wrote: > Sorry, my reply just crossed with yours. Ok, I'm now a bit confused as to > the specifics of the co-evolution of the two projects. It sounds like the FT > in SPM is a custom fit good at a particular moment in time, but that > separate changes in either SPM or FT could bring some conflicts. That seems > like a good argument to use the SPM version of FT. > > To clarify my perspective, what I didn't note in my original email, and I > should have, is that the 'headache' I referred to is mainly due to the fact > that I've made some modifications of my own on FT, and wasn't keen to need > to fold them into two separate versions of FT that might be updated at > different times. Granted that's a self-inflicted headache and perhaps at > this point I should reconsider whether those modifications are in fact > necessary. More generally, though, I like to tweak and be familiar with > every detail of the code I'm using, so having two different versions is just > that much more for my finite brain to keep track of. > > Of course, more generally the number one issue would be to avoid a situation > in which two versions yielded different analysis results, but that doesn't > seem to be a concern that either of you have expressed, so perhaps that is > not something to worry about. > > So, now I'm considering just using the version of FT included in SPM for all > my uses. I don't take advantage of the daily upgrades to FT, so the slower > release schedule is fine. How does that sound? > > Thanks, > > John > > On Jan 12, 2009, at 2:13 PM, Vladimir Litvak wrote: > >> Although what Robert described (deleting the private subdirectories) >> will do the trick, I don't see any reason to do it. I do see a reason >> not to do it because it may generate errors that will be very hard for >> us to reproduce and resolve. We are now often developing things in >> parallel where changes are made to FT to make some SPM feature work so >> if the two get slightly out of sync those new features will not work. >> Thus, I repeat my recommendation to leave things as they are. Don't >> you agree, Robert? >> >> There might be some problems with clashes if Robert starts naming some >> FT functions with the same names as wrappers in SPM. I don't know if >> there are any cases like this already. >> >> Vladimir >> >> >> >> On Mon, Jan 12, 2009 at 8:12 PM, Robert Oostenveld >> wrote: >>> >>> Hi John, >>> >>> Vladimir and I (and other spm developers) have considered this carefully, >>> and the present spm8+fieldtrip mixture was the best we could come up >>> with. >>> The versions are automatically kept in synch, but the release schedule of >>> fieldtrip is daily, whereas for spm8 it is less frequent. So the versions >>> getting slightly out of sync on your computer is inevitable. >>> >>> With the latest 2008a and 2008b versions of Matlab there are better >>> options >>> for supporting such mixtures ofg packages (using "namespaces"), but since >>> both spm and fieldtrip should work on older matlab versions, we cannot >>> use >>> those features yet. >>> >>> On 9 Jan 2009, at 19:31, Vladimir Litvak wrote: >>> >>>>> To avoid this issue, >>>>> I was planning to have SPM8 use my existing Fieldtrip installation >>>>> exclusively. Is there is any downside to this? >>>> >>>> Yes because there is no guarantee that your particular FT version is >>>> compatible with your SPM version (unless you keep updating both which >>>> is redundant). >>>> >>>> The best way for you to work if you already have an FT version that >>>> works for you and don't want to update it for a while is to ignore the >>>> FT version that SPM uses and pretend it's not there. Wrappers will >>>> prevent any clashes as I explained. >>> >>> To add on Vladimirs comment: In practice it means that you delete the >>> spm8/external/fieldtrip/private directory and keep the >>> spm8/external/fieldtrip directory for the wrappers. You can do the same >>> for >>> fileio and forwinv (also both in fieldtrip and spm8/external). >>> Subsequently >>> you should ensure that the ft_xxx wrappers in spm8, respectively the >>> fileio_xxx and the forwinv_xxx wrappers are on your matlab path, just as >>> your normal fieldtrip version. SPM8 will call those wrappers, which will >>> call your standard fieldtrip functions. >>> >>> best >>> Robert >>> >>> ---------------------------------- >>> The aim of this list is to facilitate the discussion between users of the >>> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG >>> and EEG analysis. See also >>> http://listserv.surfnet.nl/archives/fieldtrip.html and >>> http://www.ru.nl/fcdonders/fieldtrip. >>> >>> >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG >> and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/fcdonders/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/fcdonders/fieldtrip. > > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Tue Jan 13 09:43:07 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 13 Jan 2009 09:43:07 +0100 Subject: Q about integration with SPM8 In-Reply-To: <5B9123D2-47A5-4884-BC50-08462FC09640@nsi.edu> Message-ID: On 12 Jan 2009, at 23:13, Vladimir Litvak wrote: > if the two get slightly out of sync those new features will not work. > Thus, I repeat my recommendation to leave things as they are. Don't > you agree, Robert? depends on whether you are leaning towards the spm8 side or to the fieldtrip side. Debugging fieldtrip will be easier with a standard (and of course the latest) fieldtrip version, debugging spm8 is easier with the fieldtrip version included in spm8. The two are kept in sync as close as possible. So I don't expect major problems either way (except for the occasional bug that will hamper both). On 13 Jan 2009, at 0:04, John Iversen wrote: > So, now I'm considering just using the version of FT included in SPM > for all my uses. I don't take advantage of the daily upgrades to FT, > so the slower release schedule is fine. How does that sound? sounds fine to me. Actually, we (that is the fieldtrip developers) might decide in the future to change all fieldtrip function names to the spm ft_xxx scheme. At the moment that is too much work and would cause too much problems. But getting used to using the ft_xxx naming scheme in your own scripts might therefore in the future be handy. The reason that I prefer people to use the standard fieldtrip version is that it makes it much easier to find the help of the functions (which is not available in spm from the command line, due to the anonymous wrappers being in the way). Furthermore, the recently modified directory layout of fieldtrip clarifies how all pieces fit together (with an explicit distinction between public and private code and showing the various modules), whereas the directory layout in spm8 hides this (all interesting stuff goes into private). But as I said, the code is the same, every day an update from Nijmegen is sent to London, and you should just do whatever is the most comfortable for you. Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Tue Jan 13 10:10:18 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 13 Jan 2009 10:10:18 +0100 Subject: Plotting individual source stat data In-Reply-To: <841d3140901120829p3f8c7630q7c21e7c9a3da0e67@mail.gmail.com> Message-ID: Hi Christine On 12 Jan 2009, at 17:29, Christine Gruetzner wrote: > I'm trying to plot source stat data from individual subjects on the > respective mri (according to the procedure suggested in the > beamformer tutorial), but there seems to be a problem when I use > sourceinterpolate (see below). > > Does anybody have an idea what's going wrong here? > ... > the input is source data with 4560 positions > the input is volume data with dimensions [256 256 256] > not downsampling anatomy > not downsampling inside > selecting subvolume of 0.0% > interpolating > ??? Attempted to access sel(1); index out of bounds because > numel(sel)=0. To speed up the interpolation of the functional onto the anatomical data, the function determines the subvolume of the anatomical mri that is spanned by the functional data. Usually the anatomical mri covers the whole head (including chin and quite some air around the head), whereas the functional data only spans the brain. The functional data therefore takes only approximately 1/4 th of the volume of the anatomical mri. In your case it selects a subvolume of 0%, where I would expect a subvolume of 25%. That means that the functional data completely lies outside the space that is spanned by the anatomical MRI. Think of both volumes as a wireframe cube: normally the functional "cube" would be completely inside the anatomical "cube", but in this case it is completely outside. I suspect this to be due to a misspecification of the units (cm v.s. mm) of either functional or anatomical data. You should check your cfg.mriunits and cfg.sourceunits, or alternatively please read on: I have recentently been working on the autodetection of the units, which makes the manual specification unnecessary. The attached version of sourceinterpolate (not yet part of standard fieldtrip) should automatically detect the correct units (cm or mm) for the anatomical and functional data. Could you please try ot the attached version? Please rename your exsisting sourceinterpolate.m into sourceinterpolate_orig.m and then copy this function into your fieldtrip directory. I hope it solves your problem. best regards, Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: sourceinterpolate.m Type: application/octet-stream Size: 15957 bytes Desc: not available URL: -------------- next part -------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From astrid.steffen at UNI-KONSTANZ.DE Tue Jan 13 14:20:51 2009 From: astrid.steffen at UNI-KONSTANZ.DE (Astrid Steffen) Date: Tue, 13 Jan 2009 14:20:51 +0100 Subject: Besa2Fieldtrip Message-ID: Hi, I try to read MEG-files preprocessed in BESA into Fieldtrip therefore I use the Besa2Fieldtrip-function. I'm wondering where to obtain the grad-structure from: The sfp-files only contain headshape-information, the elp-files contain the location-information but cannot be decoded, and the pmg-file also cannot be read. At the moment, I use the 'read_fcdc_elec ' command. Do you have any suggestions how to solve this problem? Thank you & best regards Astrid ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From v.litvak at ION.UCL.AC.UK Tue Jan 13 15:51:06 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Tue, 13 Jan 2009 14:51:06 +0000 Subject: Besa2Fieldtrip In-Reply-To: <2F9766F6-007B-4C5B-89E4-664C169091C2@uni-konstanz.de> Message-ID: Dear Astrid, At the moment the only way you can obtain the grad struct is to read it from the original MEG datasets. You can then combine it with data read from BESA. There is no support for the way BESA stores MEG sensor locations (I suspect it's a proprietary format). Best, Vladimir On Tue, Jan 13, 2009 at 1:20 PM, Astrid Steffen wrote: > Hi, > > I try to read MEG-files preprocessed in BESA into Fieldtrip therefore I use > the Besa2Fieldtrip-function. I'm wondering where to obtain the > grad-structure from: The sfp-files only contain headshape-information, the > elp-files contain the location-information but cannot be decoded, and the > pmg-file also cannot be read. At the moment, I use the 'read_fcdc_elec ' > command. Do you have any suggestions how to solve this problem? > > Thank you & best regards > Astrid > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/fcdonders/fieldtrip. > > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From vvw at CALTECH.EDU Tue Jan 13 18:01:05 2009 From: vvw at CALTECH.EDU (Virginie van Wassenhove) Date: Tue, 13 Jan 2009 18:01:05 +0100 Subject: neuromag data analysis Message-ID: Hello Fieldtrip-ers and happy new year! I am trying to get some Neuromag (MEG) data analysis done with Fieldtrip - so far I had used fieldtrip for EEG. I can read the data fine (segmentation via meg-pd) but there are a couple of issues now. 1. when I try to filter or downsample I am receiving the following errors: %FILTER (lpf specified in cfg) blah = timelockanalysis(cfg,data_std_bc); the input is timelock data with 306 channels and 801 timebins applying preprocessing options ??? Undefined function or method 'butter' for input arguments of type 'double'. Error in ==> preproc_lowpassfilter at 80 [B, A] = butter(N, max(Flp)/Fn); Error in ==> preproc at 360 if strcmp(cfg.lpfilter, 'yes'), dat = preproc_lowpassfilter(dat, fsample, cfg.lpfreq, cfg.lpfiltord, cfg.lpfilttype, cfg.lpfiltdir); end Error in ==> timelockanalysis at 318 [data.trial{i}, data.label, data.time{i}, cfg.preproc] = preproc(data.trial{i}, data.label, data.fsample, cfg.preproc, data.offset(i)); ================================= %RESAMPLE ??? Error: File: isequal.m Line: 1 Column: 1 The input character is not valid in MATLAB statements or expressions. Error in ==> checkdata at 145 if ~isequal(feedback, 'no') Error in ==> resampledata at 60 data = checkdata(data, 'datatype', 'raw', 'feedback', 'yes'); ================================= The data structure looks fine to me: data_dev1 = hdr: [1x1 struct] label: {306x1 cell} trial: {1x101 cell} time: {1x101 cell} fsample: 1000 grad: [1x1 struct] cfg: [1x1 struct] data_dev1.grad = pnt: [510x3 double] ori: [510x3 double] tra: [306x510 double] unit: 'cm' label: {1x306 cell} Any idea on these error messages? 2. The second issue is that doing a timelockanalysis on these data returns no neg or pos clusters. There is no error message and the computations seem to run fine. Am I missing some steps in the preliminary stages of data analysis for MEG in fieldtrip? Thanks for any help you may provide, Virginie ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From v.litvak at ION.UCL.AC.UK Tue Jan 13 18:34:28 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Tue, 13 Jan 2009 17:34:28 +0000 Subject: neuromag data analysis In-Reply-To: Message-ID: Dear Virginie, It looks very much like the problem is in your Matlab. The first error is definitely a result of missing signal processing toolbox. The second one looks like a version thing, but I'm not sure. If I understand correctly the third one, it might have to do with the absence of image processing toolbox that is used to compute clusters. Best, Vladimir On Tue, Jan 13, 2009 at 5:01 PM, Virginie van Wassenhove wrote: > Hello Fieldtrip-ers and happy new year! > > I am trying to get some Neuromag (MEG) data analysis done with Fieldtrip - so > far I had used fieldtrip for EEG. I can read the data fine (segmentation via > meg-pd) but there are a couple of issues now. > > 1. when I try to filter or downsample I am receiving the following errors: > > %FILTER (lpf specified in cfg) > blah = timelockanalysis(cfg,data_std_bc); > the input is timelock data with 306 channels and 801 timebins > applying preprocessing options > ??? Undefined function or method 'butter' for input arguments of type 'double'. > > Error in ==> preproc_lowpassfilter at 80 > [B, A] = butter(N, max(Flp)/Fn); > > Error in ==> preproc at 360 > if strcmp(cfg.lpfilter, 'yes'), dat = preproc_lowpassfilter(dat, > fsample, cfg.lpfreq, cfg.lpfiltord, > cfg.lpfilttype, cfg.lpfiltdir); end > > Error in ==> timelockanalysis at 318 > [data.trial{i}, data.label, data.time{i}, cfg.preproc] = > preproc(data.trial{i}, data.label, > data.fsample, cfg.preproc, data.offset(i)); > ================================= > %RESAMPLE > ??? Error: File: isequal.m Line: 1 Column: 1 > The input character is not valid in MATLAB statements or expressions. > > Error in ==> checkdata at 145 > if ~isequal(feedback, 'no') > > Error in ==> resampledata at 60 > data = checkdata(data, 'datatype', 'raw', 'feedback', 'yes'); > > ================================= > The data structure looks fine to me: > > data_dev1 = > hdr: [1x1 struct] > label: {306x1 cell} > trial: {1x101 cell} > time: {1x101 cell} > fsample: 1000 > grad: [1x1 struct] > cfg: [1x1 struct] > > data_dev1.grad = > pnt: [510x3 double] > ori: [510x3 double] > tra: [306x510 double] > unit: 'cm' > label: {1x306 cell} > > > Any idea on these error messages? > > 2. The second issue is that doing a timelockanalysis on these data returns > no neg or pos clusters. There is no error message and the computations seem > to run fine. > > Am I missing some steps in the preliminary stages of data analysis for MEG > in fieldtrip? > > Thanks for any help you may provide, > > Virginie > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. > > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From vvw at CALTECH.EDU Tue Jan 13 19:14:39 2009 From: vvw at CALTECH.EDU (Virginie van Wassenhove) Date: Tue, 13 Jan 2009 10:14:39 -0800 Subject: neuromag data analysis In-Reply-To: Message-ID: Dear Vladimir, thanks for your quick reply. I had double-checked the signal processing toolboxes appear in my path so not sure what is going on there but will double-check this shortly... Virginie Virginie.van-Wassenhove at cea.fr Virginie.van.Wassenhove at gmail.com > Dear Virginie, > > It looks very much like the problem is in your Matlab. The first error > is definitely a result of missing signal processing toolbox. The > second one looks like a version thing, but I'm not sure. If I > understand correctly the third one, it might have to do with the > absence of image processing toolbox that is used to compute clusters. > > Best, > > Vladimir > > > > On Tue, Jan 13, 2009 at 5:01 PM, Virginie van Wassenhove > wrote: >> Hello Fieldtrip-ers and happy new year! >> >> I am trying to get some Neuromag (MEG) data analysis done with Fieldtrip >> - so >> far I had used fieldtrip for EEG. I can read the data fine (segmentation >> via >> meg-pd) but there are a couple of issues now. >> >> 1. when I try to filter or downsample I am receiving the following >> errors: >> >> %FILTER (lpf specified in cfg) >> blah = timelockanalysis(cfg,data_std_bc); >> the input is timelock data with 306 channels and 801 timebins >> applying preprocessing options >> ??? Undefined function or method 'butter' for input arguments of type >> 'double'. >> >> Error in ==> preproc_lowpassfilter at 80 >> [B, A] = butter(N, max(Flp)/Fn); >> >> Error in ==> preproc at 360 >> if strcmp(cfg.lpfilter, 'yes'), dat = preproc_lowpassfilter(dat, >> fsample, cfg.lpfreq, cfg.lpfiltord, >> cfg.lpfilttype, cfg.lpfiltdir); end >> >> Error in ==> timelockanalysis at 318 >> [data.trial{i}, data.label, data.time{i}, cfg.preproc] = >> preproc(data.trial{i}, data.label, >> data.fsample, cfg.preproc, data.offset(i)); >> ================================= >> %RESAMPLE >> ??? Error: File: isequal.m Line: 1 Column: 1 >> The input character is not valid in MATLAB statements or expressions. >> >> Error in ==> checkdata at 145 >> if ~isequal(feedback, 'no') >> >> Error in ==> resampledata at 60 >> data = checkdata(data, 'datatype', 'raw', 'feedback', 'yes'); >> >> ================================= >> The data structure looks fine to me: >> >> data_dev1 = >> hdr: [1x1 struct] >> label: {306x1 cell} >> trial: {1x101 cell} >> time: {1x101 cell} >> fsample: 1000 >> grad: [1x1 struct] >> cfg: [1x1 struct] >> >> data_dev1.grad = >> pnt: [510x3 double] >> ori: [510x3 double] >> tra: [306x510 double] >> unit: 'cm' >> label: {1x306 cell} >> >> >> Any idea on these error messages? >> >> 2. The second issue is that doing a timelockanalysis on these data >> returns >> no neg or pos clusters. There is no error message and the computations >> seem >> to run fine. >> >> Am I missing some steps in the preliminary stages of data analysis for >> MEG >> in fieldtrip? >> >> Thanks for any help you may provide, >> >> Virginie >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users of >> the FieldTrip toolbox, to share experiences and to discuss new ideas >> for MEG and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/fcdonders/fieldtrip. >> >> > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/fcdonders/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Tue Jan 20 17:59:47 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 20 Jan 2009 17:59:47 +0100 Subject: neuromag data analysis In-Reply-To: <2671.88.187.2.13.1231870479.squirrel@webmail.caltech.edu> Message-ID: Hi Virginie Something like this >> which medfilt1 /Applications/MATLAB-2007b/toolbox/signal/signal/medfilt1.m >> which butter /Applications/MATLAB-2007b/toolbox/signal/signal/butter.m and this >> which bwlabeln /Applications/MATLAB-2007b/toolbox/images/images/bwlabeln.m should be able to indicate to you whether the signal and image processing toolbox are available on your path. I'll add descriptive checks and error messages at the appropriate location in the code. best regards, Robert On 13 Jan 2009, at 19:14, Virginie van Wassenhove wrote: > Dear Vladimir, > > thanks for your quick reply. I had double-checked the signal > processing > toolboxes appear in my path so not sure what is going on there but > will > double-check this shortly... > > > Virginie ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From amrgermany at YAHOO.COM Tue Jan 20 18:59:42 2009 From: amrgermany at YAHOO.COM (Amr Ayoub) Date: Tue, 20 Jan 2009 09:59:42 -0800 Subject: Empty Beamform tutorial page Message-ID: Hello, Applying beamforming techniques in the frequency domain in the Tutorials gives an empty page. Here is the link: http://neuroimaging.ruhosting.nl/fieldtrip/doku.php?id=fieldtrip:documentation:tutorial:beamformer Thanks Regards, Amr ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bmewang at YAHOO.COM Wed Jan 21 23:01:50 2009 From: bmewang at YAHOO.COM (Wei Wang) Date: Wed, 21 Jan 2009 23:01:50 +0100 Subject: SPM2 and SPM5 Message-ID: Hi FieldTrip friends, We're starting to use FieldTrip for our MEG data analysis. The main problem I have is that the FieldTrip toolbox does not segment my MRI data properly, e.g. it will miss a lot of gray matters. What would be the general suggestions for this type of problem? Is it possible for me to fine tune the segmentation parameters. Also, it seemed to me that FieldTrip uses SPM2 for the segmentation. I'm wondering if FieldTrip is going to switch to SPM5 or not, assuming that SPM5 is more recent than SPM2. Another thing is that we have a Elekta Neuromag Vectorview 306-channel system, different from the CTF system that FCDC uses. If somebody has been able to do source localization successfully with FieldTrip toolbox and Neuromag MEG data, do you mind me asking you a couple of quick questions? Thank you very much and I appreciate the help! Wei ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From v.litvak at ION.UCL.AC.UK Thu Jan 22 00:41:59 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Wed, 21 Jan 2009 23:41:59 +0000 Subject: SPM2 and SPM5 In-Reply-To: Message-ID: Dear Wei, There is a lot of work being done now aimed at integrating Fieldtrip and SPM8. See http://neuroimaging.ruhosting.nl/fieldtrip/doku.php?id=fieldtrip:documentation:integrating_with_spm8 One of the features that will be available very soon (definitely by April 1, probably about a month from now) is the possibility to build subject-specific head models for MEG and EEG based on inverse-normalisation of template meshes, rather than segmentation. This will make it possible to get quite good head models even with suboptimal structural images (at least as good as those images possibly allow). Better support of Neuromag is also in the focus of our work right now. Neuromag is supported in Fieldtrip and SPM8 already using meg_pd toolbox and you can try analysing your data similarly to what you would do for CTF. However, there might be problems with some variants of Neuromag fif format, some of which are also platform dependent. We are working on developing a new Neuromag reader that will hopefully resolve these problems. So you may get started with the things that are already available and we hope that there will be improvements in these particular areas in the coming months. Best, Vladimir On Wed, Jan 21, 2009 at 10:01 PM, Wei Wang wrote: > Hi FieldTrip friends, > > We're starting to use FieldTrip for our MEG data analysis. The main problem I > have is that the FieldTrip toolbox does not segment my MRI data properly, > e.g. it will miss a lot of gray matters. What would be the general suggestions > for this type of problem? Is it possible for me to fine tune the segmentation > parameters. > > Also, it seemed to me that FieldTrip uses SPM2 for the segmentation. I'm > wondering if FieldTrip is going to switch to SPM5 or not, assuming that SPM5 > is more recent than SPM2. > > Another thing is that we have a Elekta Neuromag Vectorview 306-channel > system, different from the CTF system that FCDC uses. If somebody has > been able to do source localization successfully with FieldTrip toolbox and > Neuromag MEG data, do you mind me asking you a couple of quick questions? > > Thank you very much and I appreciate the help! > > Wei > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. > > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From bleichner.martin at GMAIL.COM Thu Jan 22 10:39:42 2009 From: bleichner.martin at GMAIL.COM (Martin Bleichner) Date: Thu, 22 Jan 2009 10:39:42 +0100 Subject: Permutation tests for time-frequency representations: Within trial experiments Message-ID: Hi there, I want to compute the permutation tests for time-frequency representations: within trial. In the tutorial it it stated that i have to select equal length intervals. 'To perform this comparison by means of a permutation test, we have to select equal-length non-overlapping time intervals in the baseline and the activation period.' However, my pre-stimulus and post-stimulus periods have a different length. My baseline is only 500 msec, while the post stimulus period is 1.5 and I am interested in the complete post-stimulus period. Are there possibilities to use unequal intervals? Would it make sense to split up the post stimulus period into 3 parts and compute the statistics for each post stimulus period? Thanks Best, Martin ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.maris at DONDERS.RU.NL Thu Jan 22 11:27:02 2009 From: e.maris at DONDERS.RU.NL (Eric Maris) Date: Thu, 22 Jan 2009 11:27:02 +0100 Subject: Permutation tests for time-frequency representations: Within trial experiments In-Reply-To: Message-ID: Hi Martin, I want to compute the permutation tests for time-frequency representations: within trial. In the tutorial it it stated that i have to select equal length intervals. 'To perform this comparison by means of a permutation test, we have to select equal-length non-overlapping time intervals in the baseline and the activation period.' However, my pre-stimulus and post-stimulus periods have a different length. My baseline is only 500 msec, while the post stimulus period is 1.5 and I am interested in the complete post-stimulus period. Are there possibilities to use unequal intervals? Would it make sense to split up the post stimulus period into 3 parts and compute the statistics for each post stimulus period? Yes, this is the way you should proceed. And, if you want to be safe on the statistical side, use Bonferroni correction (per-comparison alpha-level = 0.05/3) to accommodate for the fact that you run three tests instead of one. Good luck, Eric Maris Thanks Best, Martin ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Fri Jan 23 17:57:47 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Fri, 23 Jan 2009 17:57:47 +0100 Subject: SPM2 and SPM5 In-Reply-To: Message-ID: Hi Wei, On 21 Jan 2009, at 23:01, Wei Wang wrote: > Hi FieldTrip friends, > > We're starting to use FieldTrip for our MEG data analysis. The main > problem I > have is that the FieldTrip toolbox does not segment my MRI data > properly, > e.g. it will miss a lot of gray matters. What would be the general > suggestions > for this type of problem? Is it possible for me to fine tune the > segmentation > parameters. At the FCDC we are not really experts in segmentation. The volumesegment function contains defaults for SPM2 that work for our anatomical MRIs, i.e. for the particular sequence used on our MRI scanner whenever we send someone down to get a "MEG"-MRI. In SPM2/5/8 you of course have many more options for segmenting. The read_fcdc_mri function will read in anatomical MRIs' but also segmented MRIs. > Also, it seemed to me that FieldTrip uses SPM2 for the > segmentation. I'm > wondering if FieldTrip is going to switch to SPM5 or not, assuming > that SPM5 > is more recent than SPM2. There were some inconsistencies in the interface to the functions comparing SPM2 and SPM5, which is why we never swiched (and of course also because SPM2 already does the segmentation trick for us). We won't put effort into SPM5, but it is likely that the dependency on SPM2 functions will be replaced by the corresponding SPM8 functions. But it should also be easy to do the segmentation in SPM8 (e.g. with DARTEL) and read in the result for head-model generation and further processing in fieldtrip. MRI data formats are relatively simple to support, only the coordinate system alignment can be tricky. best regards, Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From mhamidi at WISC.EDU Fri Jan 23 21:12:08 2009 From: mhamidi at WISC.EDU (Massih Hamidi) Date: Fri, 23 Jan 2009 14:12:08 -0600 Subject: Measuring coherence at the source level Message-ID: Hi, I have used the beamformer technique with fieldtrip to produce source estimates of oscillatory activity in my EEG data. I've found two interesting sources and I'd like to know if there is any coherence (phase relationship) between the two. To test this, I would need to do phase coherence analyses at the scalp level between electrodes. Is there any way I could work backwards from the source estimate to the scalp electrode (i.e. which electrode describes each of the two sources best)? Or is there a better way to look at coherence between two brain regions? Thanks. -- Massih Hamidi Medical Scientist Training Program Neuroscience Training Program University of Wisconsin - Madison 1202 West Johnson St., Madison, WI 53706 608-265-3888 | mhamidi at wisc.edu ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Mon Jan 26 09:11:19 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 26 Jan 2009 09:11:19 +0100 Subject: Empty Beamform tutorial page In-Reply-To: <834428.63449.qm@web57416.mail.re1.yahoo.com> Message-ID: Hi Amr, Thanks for notifying us. Since moving to the new server there are some issues with the wiki. The caching of wiki pages fails somehow, which seems related to the neuroimaging.ruhosting.nl and fcdonders.ruhosting.nl confusion. In general (also to other users): if this happens the following workaround may help: If you fo to "edit" and then "preview" then you'll see the ful lcontent. I have upgraded the wiki CMS softare to the latest version, hopefully it solves the issue. best regards, Robert On 20 Jan 2009, at 18:59, Amr Ayoub wrote: > Hello, > > Applying beamforming techniques in the frequency domain in the > Tutorials gives an empty page. > Here is the link: > http://neuroimaging.ruhosting.nl/fieldtrip/doku.php?id=fieldtrip:documentation:tutorial:beamformer > > Thanks > Regards, > Amr > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From ana.acsousa at GMAIL.COM Mon Jan 26 12:07:39 2009 From: ana.acsousa at GMAIL.COM (Ana Carolina) Date: Mon, 26 Jan 2009 12:07:39 +0100 Subject: Ploting using easycap64ch-avg Message-ID: Dear FieldTrip users, I'm trying to plot EEG data using the easycap64ch-avg layout, but there seems to be a problem with the coordinate values because when I see the plot, the electrodes are not on the correct position. When I checked the values of the layout I saw that the values of the two first columns are not correct (I think), because if you think in all the electrodes that are in the same line like 35, 20, 8, 2, 1, 5, 14, 43 and 46 they should have the same value in the x- axis, but this doesn't happen. So, these and also all the other electrodes have small deviations like for example electrode 36 are not align whit the electrode 50 in y axis, etc. In this way I can't have a symmetrical plot of the electrodes. Does anybody have used this layout and have the same problem? Thanks in advance! regards, Ana Carolina ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Mon Jan 26 12:32:10 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 26 Jan 2009 12:32:10 +0100 Subject: Ploting using easycap64ch-avg In-Reply-To: <40538cdc0901260307u5a5a276dg4cd9978978fc1d1f@mail.gmail.com> Message-ID: Hi Ana, This is what I see. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Picture 1.png Type: image/png Size: 56013 bytes Desc: not available URL: -------------- next part -------------- It looks reasonable to me. The template layout files in fieldtrip/ template/*.lay that have "avg" in their name were all created by measuring the channel position on a few subjects' head with the polhemus tracker and averaging over those. Those measurements are not ideal, explaining the slight asymmetry. If you are not happy with this template layout (which I can imagine), I suggest you go to www.easycap.de, download a figure of the cap you are using, and use cfg =[] cfg.image = 'your_figure.gif' layout = prepare_layout(cfg); which will allow you to interactively click on each electrode position in the figure. You then also have to specify the outline of the head (including ears and nose) which will be displayed in black lines and the outline of the part of the head in which you want the interpolated data to show up (i.e. only the cricle of the head). best regards, Robert On 26 Jan 2009, at 12:07, Ana Carolina wrote: > Dear FieldTrip users, > > I'm trying to plot EEG data using the easycap64ch-avg layout, but > there seems to be a problem with the coordinate values because when > I see the plot, the electrodes are not on the correct position. When > I checked the values of the layout I saw that the values of the two > first columns are not correct (I think), because if you think in all > the electrodes that are in the same line like 35, 20, 8, 2, 1, 5, > 14, 43 and 46 they should have the same value in the x- axis, but > this doesn't happen. So, these and also all the other electrodes > have small deviations like for example electrode 36 are not align > whit the electrode 50 in y axis, etc. In this way I can't have a > symmetrical plot of the electrodes. > Does anybody have used this layout and have the same problem? > > Thanks in advance! > > regards, > Ana Carolina > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Mon Jan 26 14:45:31 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 26 Jan 2009 14:45:31 +0100 Subject: Workshop: Multimodal imaging in cognitive neuroscience Message-ID: Dear colleagues, The Donders Institute is pleased to announce: Multimodal imaging in cognitive neuroscience an international workshop of the Donders Institute 24 & 25 March 2009, the Netherlands The workshop aims at exploring how integrated multimodal neuroimaging could provide new ways of understanding brain functions. We will focus on two experimental situations that require integrated multimodal imaging: the quantification of the cerebral consequences of experimentally altered brain activity; and the analysis of dependencies between intrinsic and stimulus-driven cerebral dynamics. Speakers Sven Bestmann – Wellcome Centre for Neuroimaging, Institute of Neurology, University College, London Ralph D. Freeman – Vision Science Group, School of Optometry, and Helen Wills Neuroscience Institute, University of California, Berkeley Andreas Kleinschmidt – NeuroSpin, Gif-sur-Yvette, France David Leopold – Unit on Cognitive Neurophysiology and Imaging, Laboratory of Neuropsychology, National Institute of Mental health, USA Registration and further details http://www.ru.nl/donders/home/agenda/multimodel/ 24 & 25 March 2009 Donders Institute for Brain, Cognition and Behaviour Radboud University Nijmegen The Netherlands ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Multimodal_eFlyer.pdf Type: application/pdf Size: 211157 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.debener at UKE.UNI-HAMBURG.DE Tue Jan 27 10:49:30 2009 From: s.debener at UKE.UNI-HAMBURG.DE (Stefan Debener) Date: Tue, 27 Jan 2009 09:49:30 +0000 Subject: MEG/EEG post-doc position in Jena, Germany Message-ID: Post-Doc Position at the Biomagnetic Center Jena, Germany A two-year post-doc position is available at the Biomagnetic Center Jena. Biomagnetism has a long-standing tradition in Jena and the group consists of a young, interdisciplinary and international research team and a new head of department (Prof. S. Debener). The Biomag Center comprises several labs, including a new 306/128-channel whole-head MEG/EEG system (Neuromag). Areas of research are multisensory processing, somatosensory and pain research, cortical re-organization after cochlear implantation, neurocognition of temporal attention, and EEG-fMRI integration. The post-doc will have a strong interest in using independent component analysis for the analysis of EEG, MEG, and combined EEG-MEG recordings. Expertise in multichannel EEG or MEG analysis is mandatory, as well as a good theoretical background in biosignal processing, experimental neurosciences, or both. For further enquiries, please contact Stefan Debener. International applications are welcome. Please send your application (CV, list of publications, contact information for two references) to debener at biomag.uni-jena.de. Closing date is February 15, 2009. -- Prof. Dr. Stefan Debener Biomagnetic Center Dept. of Neurology University Hospital Jena Erlanger Allee 101 D-07747 Jena Germany Phone: +49-3641-9325770 Fax: +49-3641-9325772 Email: debener at biomag.uni-jena.de ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Tue Jan 27 17:54:48 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 27 Jan 2009 17:54:48 +0100 Subject: problems with wiki -> empty pages In-Reply-To: Message-ID: Dear all We are experiencing technical problems with the fieldtrip wiki. I had hoped that installing a new version of the software would fix it as I explained in a previous mail, and on Sunday that indeed seemed to solve it. But today the problems reappeared, even in more severe form. After trying to diagnose it and discussing it with some technical colleagues here and with some input from the ruhosting server system administrator (who is not part of our department), the working diagnosis is that there is a performance problem on the server hardware. The ruhosting machine is shared by many people, and it seems that high traffic in general (not the case on Sunday) combined with fieldtrip wiki edits (which happened a lot today) causes the hickups. These then result in empty pages in the cache and empty pages being displayed. Note that all the documents are still there. A workaround for the problem is to click the "edit" button and then click the "preview" button. That circumvents the caching, and for me results in a correect display of the page content. At the moment I cannot solve it, but tomorrow I'll again start bugging the sysadmin. I'll try to clear the cache as often as possible (because immediately after that, it looks OK). Sorry for the inconvenience, Robert On 27 Jan 2009, at 17:04, Vladimir Litvak wrote: > The problem is still there. I've just experienced it with the > statistics tutorial. Your suggestion works, but I'd like to send a > link to somebody so it'd be much simpler if you fix it. > > Vladimir > > On Mon, Jan 26, 2009 at 8:11 AM, Robert Oostenveld > wrote: >> Hi Amr, >> >> Thanks for notifying us. Since moving to the new server there are >> some >> issues with the wiki. The caching of wiki pages fails somehow, >> which seems >> related to the neuroimaging.ruhosting.nl and fcdonders.ruhosting.nl >> confusion. >> >> In general (also to other users): if this happens the following >> workaround >> may help: If you fo to "edit" and then "preview" then you'll see >> the ful >> lcontent. >> >> I have upgraded the wiki CMS softare to the latest version, >> hopefully it >> solves the issue. >> >> best regards, >> Robert > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From Harsimrat.Singh at WARWICK.AC.UK Sun Jan 4 02:45:16 2009 From: Harsimrat.Singh at WARWICK.AC.UK (Singh, Harsimrat) Date: Sun, 4 Jan 2009 01:45:16 -0000 Subject: BCI2000 file read Message-ID: Hi I am trying to use some field trip functions for data recorded using BCI2000 (.dat) files. The data was recorded using brain vision amplifier. I understand that the function read_data doesnt read the BCI2000 files. Can anyone please suggest way around this ? Thanks in advance Regards Harsimrat ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Mon Jan 5 15:19:37 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 5 Jan 2009 15:19:37 +0100 Subject: BCI2000 file read In-Reply-To: <95B2B6BF8599AB4EA51DDC85904A15AAC6A16E@HOLLY.ads.warwick.ac.uk> Message-ID: Dear Harsimrat, It recently came to my attention that files written in older versions of BCI2000 are not completely compatible with newer versions of BCI2000. Is it possible for you to send me an example datafile that causes you the problem? The problem has to do with the file type detection and probably can be fixed quite easily. Please look here http://neuroimaging.ruhosting.nl/fieldtrip/doku.php?id=fieldtrip:contact for details on how to send the file. best regards, Robert On 4 Jan 2009, at 2:45, Singh, Harsimrat wrote: > Hi > > I am trying to use some field trip functions for data recorded using > BCI2000 (.dat) files. The data was recorded using brain vision > amplifier. > I understand that the function read_data doesnt read the BCI2000 > files. > Can anyone please suggest way around this ? > > Thanks in advance > Regards > Harsimrat > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From jason.sherfey at GMAIL.COM Tue Jan 6 01:15:16 2009 From: jason.sherfey at GMAIL.COM (Jason Sherfey) Date: Mon, 5 Jan 2009 16:15:16 -0800 Subject: freqanalysis_wltconvol Message-ID: Dear FieldTrip users, I have been using freqanalysis_wltconvol to compute the wavelet power spectrum for several months and recently began trying to understand the code. Reading past discussions on this listserv has been very helpful, but I can't figure out why it does the particular normalization that it does for the wavelet power calculation. This calculation can be found on line 299 of the 20081001 release. According to the comments at the beginning of the function, jansch "fixed [the] improper normalization of powdum" in Revision 1.17 on 2007/06/14. It seems to me that "powdum" is the wavelet power spectrum (P) and that "autspctrmacttap" is the signal's wavelet transform (T). If that is true, then the correction made on 2007/06/14 was the following: P = (2*|T| / fs)^2 became P = 2*|T|^2 / fs where fs = sampling frequency My current understanding (based on pp. 31-32 in Addison's text "The illustrated wavelet transform handbook") is that the wavelet energy density is given by E = |T|^2 and that P = E / (time period of the signal). Since the time period of the signal = (# of samples) / (sampling frequency), that would imply P = fs*|T|^2 / (# of samples). Thus, I thought |T|^2 should be multiplied by fs/(# of samples), but in the code it's instead multiplied by 2/fs. I am fairly new to wavelet analysis and suspect there's a small detail I don't understand. Does anyone know why the wavelet energy is normalized by 2/fs instead of fs/(# samples)? Thanks in advance, Jason ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From iversen at NSI.EDU Fri Jan 9 19:03:18 2009 From: iversen at NSI.EDU (John Iversen) Date: Fri, 9 Jan 2009 10:03:18 -0800 Subject: Q about integration with SPM8 In-Reply-To: <8d039c560901051615h68c88f7bw1356aea8be3b3295@mail.gmail.com> Message-ID: Hello, It's seems great that you there is not a partnership between Fieldtrip and SPM. Since SPM8 comes with its own version of fieldtrip, how will this be kept 'in sync' with the updates coming out of Donders? Having two different versions of fieldtrip seems like a potential headache. To avoid this issue, I was planning to have SPM8 use my existing Fieldtrip installation exclusively. Is there is any downside to this? What version of FT is included with SPM8? More generally, the SPM solution of renaming and wrappers seems rather involved. Couldn't managing the MATLAB search path ensure that there are no conflicts between versions? I'm sure you went this route for good reasons that I am unaware of, so I'd be happy to be enlightened. Thanks, as always, for a great set of tools, and support. Happy New Year to all. John John R. Iversen, PhD The Neurosciences Institute 10640 John Jay Hopkins Drive San Diego, CA 92121 (858)-626-2068 iversen at nsi.edu ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From v.litvak at ION.UCL.AC.UK Fri Jan 9 19:31:42 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Fri, 9 Jan 2009 18:31:42 +0000 Subject: Q about integration with SPM8 In-Reply-To: Message-ID: Dear John, On Fri, Jan 9, 2009 at 6:03 PM, John Iversen wrote: > Since SPM8 comes with its own version of fieldtrip, how will this be > kept 'in sync' with the updates coming out of Donders? This is done automatically presently on a daily basis, perhaps will be switched to a weekly update after the official release of SPM8. Critical updates are propagated immediately. So if you update SPM8, the version of FT in SPM8 will be from the same date. >Having two different > versions of fieldtrip seems like a potential headache. This is exactly what the wrappers are for. You can have your favorite FT version in the path with SPM but there will be no clashes as SPM will only use its internal version of FT. The same is true for your FT scripts - unless you explicitly call the wrappers with 'ft_...' your FT functions will come from your stand-alone FT installation and not from SPM. >To avoid this issue, > I was planning to have SPM8 use my existing Fieldtrip installation > exclusively. Is there is any downside to this? Yes because there is no guarantee that your particular FT version is compatible with your SPM version (unless you keep updating both which is redundant). The best way for you to work if you already have an FT version that works for you and don't want to update it for a while is to ignore the FT version that SPM uses and pretend it's not there. Wrappers will prevent any clashes as I explained. I hope my explanations are clear. If not, I'd be glad to answer any further questions. Best, Vladimir ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From christine.gruetzner at GOOGLEMAIL.COM Mon Jan 12 17:29:48 2009 From: christine.gruetzner at GOOGLEMAIL.COM (Christine Gruetzner) Date: Mon, 12 Jan 2009 17:29:48 +0100 Subject: Plotting individual source stat data Message-ID: Dear FieldTrip users, I'm trying to plot source stat data from individual subjects on the respective mri (according to the procedure suggested in the beamformer tutorial), but there seems to be a problem when I use sourceinterpolate (see below). Does anybody have an idea what's going wrong here? Thanks in advance! Best, Christine the input is source data with 4560 positions the input is volume data with dimensions [256 256 256] not downsampling anatomy not downsampling inside selecting subvolume of 0.0% interpolating ??? Attempted to access sel(1); index out of bounds because numel(sel)=0. Error in ==> sourceinterpolate>my_interpn at 380 progress(sel(1)/num, 'interpolating %.1f%%\n', 100*sel(1)/num); Error in ==> sourceinterpolate at 275 interp.inside( sel) = my_interpn(double(functional.inside), ax(sel), ay(sel), az(sel), 'nearest', cfg.feedback); Error in ==> PlotSourceData at 164 sourceinterp = sourceinterpolate(cfg, statdiff,mri); -- Christine Gruetzner, geb. Tillmann Max-Planck-Institut für Hirnforschung Abt. Neurophysiologie Deutschordenstr. 46 60528 Frankfurt am Main Germany Phone: +49 (0)69/6301-83225 E-Mail: tillmann at mpih-frankfurt.mpg.de http://www.mpih-frankfurt.mpg.de/global/Np/Staff/tillmann.htm ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Mon Jan 12 21:12:29 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 12 Jan 2009 21:12:29 +0100 Subject: Q about integration with SPM8 In-Reply-To: Message-ID: Hi John, Vladimir and I (and other spm developers) have considered this carefully, and the present spm8+fieldtrip mixture was the best we could come up with. The versions are automatically kept in synch, but the release schedule of fieldtrip is daily, whereas for spm8 it is less frequent. So the versions getting slightly out of sync on your computer is inevitable. With the latest 2008a and 2008b versions of Matlab there are better options for supporting such mixtures ofg packages (using "namespaces"), but since both spm and fieldtrip should work on older matlab versions, we cannot use those features yet. On 9 Jan 2009, at 19:31, Vladimir Litvak wrote: >> To avoid this issue, >> I was planning to have SPM8 use my existing Fieldtrip installation >> exclusively. Is there is any downside to this? > > Yes because there is no guarantee that your particular FT version is > compatible with your SPM version (unless you keep updating both which > is redundant). > > The best way for you to work if you already have an FT version that > works for you and don't want to update it for a while is to ignore the > FT version that SPM uses and pretend it's not there. Wrappers will > prevent any clashes as I explained. To add on Vladimirs comment: In practice it means that you delete the spm8/external/fieldtrip/private directory and keep the spm8/external/ fieldtrip directory for the wrappers. You can do the same for fileio and forwinv (also both in fieldtrip and spm8/external). Subsequently you should ensure that the ft_xxx wrappers in spm8, respectively the fileio_xxx and the forwinv_xxx wrappers are on your matlab path, just as your normal fieldtrip version. SPM8 will call those wrappers, which will call your standard fieldtrip functions. best Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From v.litvak at ION.UCL.AC.UK Mon Jan 12 23:13:14 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Mon, 12 Jan 2009 22:13:14 +0000 Subject: Q about integration with SPM8 In-Reply-To: Message-ID: Although what Robert described (deleting the private subdirectories) will do the trick, I don't see any reason to do it. I do see a reason not to do it because it may generate errors that will be very hard for us to reproduce and resolve. We are now often developing things in parallel where changes are made to FT to make some SPM feature work so if the two get slightly out of sync those new features will not work. Thus, I repeat my recommendation to leave things as they are. Don't you agree, Robert? There might be some problems with clashes if Robert starts naming some FT functions with the same names as wrappers in SPM. I don't know if there are any cases like this already. Vladimir On Mon, Jan 12, 2009 at 8:12 PM, Robert Oostenveld wrote: > Hi John, > > Vladimir and I (and other spm developers) have considered this carefully, > and the present spm8+fieldtrip mixture was the best we could come up with. > The versions are automatically kept in synch, but the release schedule of > fieldtrip is daily, whereas for spm8 it is less frequent. So the versions > getting slightly out of sync on your computer is inevitable. > > With the latest 2008a and 2008b versions of Matlab there are better options > for supporting such mixtures ofg packages (using "namespaces"), but since > both spm and fieldtrip should work on older matlab versions, we cannot use > those features yet. > > On 9 Jan 2009, at 19:31, Vladimir Litvak wrote: > >>> To avoid this issue, >>> I was planning to have SPM8 use my existing Fieldtrip installation >>> exclusively. Is there is any downside to this? >> >> Yes because there is no guarantee that your particular FT version is >> compatible with your SPM version (unless you keep updating both which >> is redundant). >> >> The best way for you to work if you already have an FT version that >> works for you and don't want to update it for a while is to ignore the >> FT version that SPM uses and pretend it's not there. Wrappers will >> prevent any clashes as I explained. > > To add on Vladimirs comment: In practice it means that you delete the > spm8/external/fieldtrip/private directory and keep the > spm8/external/fieldtrip directory for the wrappers. You can do the same for > fileio and forwinv (also both in fieldtrip and spm8/external). Subsequently > you should ensure that the ft_xxx wrappers in spm8, respectively the > fileio_xxx and the forwinv_xxx wrappers are on your matlab path, just as > your normal fieldtrip version. SPM8 will call those wrappers, which will > call your standard fieldtrip functions. > > best > Robert > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/fcdonders/fieldtrip. > > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From iversen at NSI.EDU Mon Jan 12 23:42:04 2009 From: iversen at NSI.EDU (John Iversen) Date: Mon, 12 Jan 2009 14:42:04 -0800 Subject: Q about integration with SPM8 In-Reply-To: Message-ID: Hi Robert and Vladimir, Thank you both for your responses. I very much appreciate the clarifications and suggestions for ways to proceed. Best regards, John On Jan 12, 2009, at 12:12 PM, Robert Oostenveld wrote: > Hi John, > > Vladimir and I (and other spm developers) have considered this > carefully, and the present spm8+fieldtrip mixture was the best we > could come up with. The versions are automatically kept in synch, > but the release schedule of fieldtrip is daily, whereas for spm8 it > is less frequent. So the versions getting slightly out of sync on > your computer is inevitable. > > With the latest 2008a and 2008b versions of Matlab there are better > options for supporting such mixtures ofg packages (using > "namespaces"), but since both spm and fieldtrip should work on older > matlab versions, we cannot use those features yet. > > On 9 Jan 2009, at 19:31, Vladimir Litvak wrote: > this >>> To avoid this issue, >>> I was planning to have SPM8 use my existing Fieldtrip installation >>> exclusively. Is there is any downside to? >> >> Yes because there is no guarantee that your particular FT version is >> compatible with your SPM version (unless you keep updating both which >> is redundant). >> >> The best way for you to work if you already have an FT version that >> works for you and don't want to update it for a while is to ignore >> the >> FT version that SPM uses and pretend it's not there. Wrappers will >> prevent any clashes as I explained. > > To add on Vladimirs comment: In practice it means that you delete > the spm8/external/fieldtrip/private directory and keep the spm8/ > external/fieldtrip directory for the wrappers. You can do the same > for fileio and forwinv (also both in fieldtrip and spm8/external). > Subsequently you should ensure that the ft_xxx wrappers in spm8, > respectively the fileio_xxx and the forwinv_xxx wrappers are on your > matlab path, just as your normal fieldtrip version. SPM8 will call > those wrappers, which will call your standard fieldtrip functions. > > best > Robert > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/fcdonders/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From iversen at NSI.EDU Tue Jan 13 00:04:33 2009 From: iversen at NSI.EDU (John Iversen) Date: Mon, 12 Jan 2009 15:04:33 -0800 Subject: Q about integration with SPM8 In-Reply-To: Message-ID: Sorry, my reply just crossed with yours. Ok, I'm now a bit confused as to the specifics of the co-evolution of the two projects. It sounds like the FT in SPM is a custom fit good at a particular moment in time, but that separate changes in either SPM or FT could bring some conflicts. That seems like a good argument to use the SPM version of FT. To clarify my perspective, what I didn't note in my original email, and I should have, is that the 'headache' I referred to is mainly due to the fact that I've made some modifications of my own on FT, and wasn't keen to need to fold them into two separate versions of FT that might be updated at different times. Granted that's a self-inflicted headache and perhaps at this point I should reconsider whether those modifications are in fact necessary. More generally, though, I like to tweak and be familiar with every detail of the code I'm using, so having two different versions is just that much more for my finite brain to keep track of. Of course, more generally the number one issue would be to avoid a situation in which two versions yielded different analysis results, but that doesn't seem to be a concern that either of you have expressed, so perhaps that is not something to worry about. So, now I'm considering just using the version of FT included in SPM for all my uses. I don't take advantage of the daily upgrades to FT, so the slower release schedule is fine. How does that sound? Thanks, John On Jan 12, 2009, at 2:13 PM, Vladimir Litvak wrote: > Although what Robert described (deleting the private subdirectories) > will do the trick, I don't see any reason to do it. I do see a reason > not to do it because it may generate errors that will be very hard for > us to reproduce and resolve. We are now often developing things in > parallel where changes are made to FT to make some SPM feature work so > if the two get slightly out of sync those new features will not work. > Thus, I repeat my recommendation to leave things as they are. Don't > you agree, Robert? > > There might be some problems with clashes if Robert starts naming some > FT functions with the same names as wrappers in SPM. I don't know if > there are any cases like this already. > > Vladimir > > > > On Mon, Jan 12, 2009 at 8:12 PM, Robert Oostenveld > wrote: >> Hi John, >> >> Vladimir and I (and other spm developers) have considered this >> carefully, >> and the present spm8+fieldtrip mixture was the best we could come >> up with. >> The versions are automatically kept in synch, but the release >> schedule of >> fieldtrip is daily, whereas for spm8 it is less frequent. So the >> versions >> getting slightly out of sync on your computer is inevitable. >> >> With the latest 2008a and 2008b versions of Matlab there are better >> options >> for supporting such mixtures ofg packages (using "namespaces"), but >> since >> both spm and fieldtrip should work on older matlab versions, we >> cannot use >> those features yet. >> >> On 9 Jan 2009, at 19:31, Vladimir Litvak wrote: >> >>>> To avoid this issue, >>>> I was planning to have SPM8 use my existing Fieldtrip installation >>>> exclusively. Is there is any downside to this? >>> >>> Yes because there is no guarantee that your particular FT version is >>> compatible with your SPM version (unless you keep updating both >>> which >>> is redundant). >>> >>> The best way for you to work if you already have an FT version that >>> works for you and don't want to update it for a while is to ignore >>> the >>> FT version that SPM uses and pretend it's not there. Wrappers will >>> prevent any clashes as I explained. >> >> To add on Vladimirs comment: In practice it means that you delete the >> spm8/external/fieldtrip/private directory and keep the >> spm8/external/fieldtrip directory for the wrappers. You can do the >> same for >> fileio and forwinv (also both in fieldtrip and spm8/external). >> Subsequently >> you should ensure that the ft_xxx wrappers in spm8, respectively the >> fileio_xxx and the forwinv_xxx wrappers are on your matlab path, >> just as >> your normal fieldtrip version. SPM8 will call those wrappers, which >> will >> call your standard fieldtrip functions. >> >> best >> Robert >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the >> FieldTrip toolbox, to share experiences and to discuss new ideas >> for MEG >> and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/fcdonders/fieldtrip. >> >> > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/fcdonders/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From v.litvak at ION.UCL.AC.UK Tue Jan 13 00:40:39 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Mon, 12 Jan 2009 23:40:39 +0000 Subject: Q about integration with SPM8 In-Reply-To: <5B9123D2-47A5-4884-BC50-08462FC09640@nsi.edu> Message-ID: Dear John, It's hard for me to follow your reasoning. On the one hand you want to keep using your old 'tweaked' FT, but on the other hand you want to switch to SPM's version which would not contain your modifications. Maybe there is something basic that I should reiterate. The actual analysis done in SPM is different than the analysis in FT. SPM proper presently used code from FT for data conversion and for computing lead fields. In both cases there are unlikely to be different results for different versions of the code. The reason all of FT is included in SPM and not just those specific parts is to make it possible for people to write some custom tools combining SPM and FT functions and distribute them to SPM users without the need to install external FT. If you just want to do your own analysis I don't see a good reason for you to use the FT included in SPM rather than the version you are presently working with. What I suggest is - just put both your old FT and SPM in the path and see how it goes. I don't foresee any problems. Note that you should keep updating SPM with patches from ftp://ftp.fil.ion.ucl.ac.uk/spm/spm8b_updates/ Best, Vladimir On Mon, Jan 12, 2009 at 11:04 PM, John Iversen wrote: > Sorry, my reply just crossed with yours. Ok, I'm now a bit confused as to > the specifics of the co-evolution of the two projects. It sounds like the FT > in SPM is a custom fit good at a particular moment in time, but that > separate changes in either SPM or FT could bring some conflicts. That seems > like a good argument to use the SPM version of FT. > > To clarify my perspective, what I didn't note in my original email, and I > should have, is that the 'headache' I referred to is mainly due to the fact > that I've made some modifications of my own on FT, and wasn't keen to need > to fold them into two separate versions of FT that might be updated at > different times. Granted that's a self-inflicted headache and perhaps at > this point I should reconsider whether those modifications are in fact > necessary. More generally, though, I like to tweak and be familiar with > every detail of the code I'm using, so having two different versions is just > that much more for my finite brain to keep track of. > > Of course, more generally the number one issue would be to avoid a situation > in which two versions yielded different analysis results, but that doesn't > seem to be a concern that either of you have expressed, so perhaps that is > not something to worry about. > > So, now I'm considering just using the version of FT included in SPM for all > my uses. I don't take advantage of the daily upgrades to FT, so the slower > release schedule is fine. How does that sound? > > Thanks, > > John > > On Jan 12, 2009, at 2:13 PM, Vladimir Litvak wrote: > >> Although what Robert described (deleting the private subdirectories) >> will do the trick, I don't see any reason to do it. I do see a reason >> not to do it because it may generate errors that will be very hard for >> us to reproduce and resolve. We are now often developing things in >> parallel where changes are made to FT to make some SPM feature work so >> if the two get slightly out of sync those new features will not work. >> Thus, I repeat my recommendation to leave things as they are. Don't >> you agree, Robert? >> >> There might be some problems with clashes if Robert starts naming some >> FT functions with the same names as wrappers in SPM. I don't know if >> there are any cases like this already. >> >> Vladimir >> >> >> >> On Mon, Jan 12, 2009 at 8:12 PM, Robert Oostenveld >> wrote: >>> >>> Hi John, >>> >>> Vladimir and I (and other spm developers) have considered this carefully, >>> and the present spm8+fieldtrip mixture was the best we could come up >>> with. >>> The versions are automatically kept in synch, but the release schedule of >>> fieldtrip is daily, whereas for spm8 it is less frequent. So the versions >>> getting slightly out of sync on your computer is inevitable. >>> >>> With the latest 2008a and 2008b versions of Matlab there are better >>> options >>> for supporting such mixtures ofg packages (using "namespaces"), but since >>> both spm and fieldtrip should work on older matlab versions, we cannot >>> use >>> those features yet. >>> >>> On 9 Jan 2009, at 19:31, Vladimir Litvak wrote: >>> >>>>> To avoid this issue, >>>>> I was planning to have SPM8 use my existing Fieldtrip installation >>>>> exclusively. Is there is any downside to this? >>>> >>>> Yes because there is no guarantee that your particular FT version is >>>> compatible with your SPM version (unless you keep updating both which >>>> is redundant). >>>> >>>> The best way for you to work if you already have an FT version that >>>> works for you and don't want to update it for a while is to ignore the >>>> FT version that SPM uses and pretend it's not there. Wrappers will >>>> prevent any clashes as I explained. >>> >>> To add on Vladimirs comment: In practice it means that you delete the >>> spm8/external/fieldtrip/private directory and keep the >>> spm8/external/fieldtrip directory for the wrappers. You can do the same >>> for >>> fileio and forwinv (also both in fieldtrip and spm8/external). >>> Subsequently >>> you should ensure that the ft_xxx wrappers in spm8, respectively the >>> fileio_xxx and the forwinv_xxx wrappers are on your matlab path, just as >>> your normal fieldtrip version. SPM8 will call those wrappers, which will >>> call your standard fieldtrip functions. >>> >>> best >>> Robert >>> >>> ---------------------------------- >>> The aim of this list is to facilitate the discussion between users of the >>> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG >>> and EEG analysis. See also >>> http://listserv.surfnet.nl/archives/fieldtrip.html and >>> http://www.ru.nl/fcdonders/fieldtrip. >>> >>> >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG >> and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/fcdonders/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/fcdonders/fieldtrip. > > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Tue Jan 13 09:43:07 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 13 Jan 2009 09:43:07 +0100 Subject: Q about integration with SPM8 In-Reply-To: <5B9123D2-47A5-4884-BC50-08462FC09640@nsi.edu> Message-ID: On 12 Jan 2009, at 23:13, Vladimir Litvak wrote: > if the two get slightly out of sync those new features will not work. > Thus, I repeat my recommendation to leave things as they are. Don't > you agree, Robert? depends on whether you are leaning towards the spm8 side or to the fieldtrip side. Debugging fieldtrip will be easier with a standard (and of course the latest) fieldtrip version, debugging spm8 is easier with the fieldtrip version included in spm8. The two are kept in sync as close as possible. So I don't expect major problems either way (except for the occasional bug that will hamper both). On 13 Jan 2009, at 0:04, John Iversen wrote: > So, now I'm considering just using the version of FT included in SPM > for all my uses. I don't take advantage of the daily upgrades to FT, > so the slower release schedule is fine. How does that sound? sounds fine to me. Actually, we (that is the fieldtrip developers) might decide in the future to change all fieldtrip function names to the spm ft_xxx scheme. At the moment that is too much work and would cause too much problems. But getting used to using the ft_xxx naming scheme in your own scripts might therefore in the future be handy. The reason that I prefer people to use the standard fieldtrip version is that it makes it much easier to find the help of the functions (which is not available in spm from the command line, due to the anonymous wrappers being in the way). Furthermore, the recently modified directory layout of fieldtrip clarifies how all pieces fit together (with an explicit distinction between public and private code and showing the various modules), whereas the directory layout in spm8 hides this (all interesting stuff goes into private). But as I said, the code is the same, every day an update from Nijmegen is sent to London, and you should just do whatever is the most comfortable for you. Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Tue Jan 13 10:10:18 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 13 Jan 2009 10:10:18 +0100 Subject: Plotting individual source stat data In-Reply-To: <841d3140901120829p3f8c7630q7c21e7c9a3da0e67@mail.gmail.com> Message-ID: Hi Christine On 12 Jan 2009, at 17:29, Christine Gruetzner wrote: > I'm trying to plot source stat data from individual subjects on the > respective mri (according to the procedure suggested in the > beamformer tutorial), but there seems to be a problem when I use > sourceinterpolate (see below). > > Does anybody have an idea what's going wrong here? > ... > the input is source data with 4560 positions > the input is volume data with dimensions [256 256 256] > not downsampling anatomy > not downsampling inside > selecting subvolume of 0.0% > interpolating > ??? Attempted to access sel(1); index out of bounds because > numel(sel)=0. To speed up the interpolation of the functional onto the anatomical data, the function determines the subvolume of the anatomical mri that is spanned by the functional data. Usually the anatomical mri covers the whole head (including chin and quite some air around the head), whereas the functional data only spans the brain. The functional data therefore takes only approximately 1/4 th of the volume of the anatomical mri. In your case it selects a subvolume of 0%, where I would expect a subvolume of 25%. That means that the functional data completely lies outside the space that is spanned by the anatomical MRI. Think of both volumes as a wireframe cube: normally the functional "cube" would be completely inside the anatomical "cube", but in this case it is completely outside. I suspect this to be due to a misspecification of the units (cm v.s. mm) of either functional or anatomical data. You should check your cfg.mriunits and cfg.sourceunits, or alternatively please read on: I have recentently been working on the autodetection of the units, which makes the manual specification unnecessary. The attached version of sourceinterpolate (not yet part of standard fieldtrip) should automatically detect the correct units (cm or mm) for the anatomical and functional data. Could you please try ot the attached version? Please rename your exsisting sourceinterpolate.m into sourceinterpolate_orig.m and then copy this function into your fieldtrip directory. I hope it solves your problem. best regards, Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: sourceinterpolate.m Type: application/octet-stream Size: 15957 bytes Desc: not available URL: -------------- next part -------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From astrid.steffen at UNI-KONSTANZ.DE Tue Jan 13 14:20:51 2009 From: astrid.steffen at UNI-KONSTANZ.DE (Astrid Steffen) Date: Tue, 13 Jan 2009 14:20:51 +0100 Subject: Besa2Fieldtrip Message-ID: Hi, I try to read MEG-files preprocessed in BESA into Fieldtrip therefore I use the Besa2Fieldtrip-function. I'm wondering where to obtain the grad-structure from: The sfp-files only contain headshape-information, the elp-files contain the location-information but cannot be decoded, and the pmg-file also cannot be read. At the moment, I use the 'read_fcdc_elec ' command. Do you have any suggestions how to solve this problem? Thank you & best regards Astrid ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From v.litvak at ION.UCL.AC.UK Tue Jan 13 15:51:06 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Tue, 13 Jan 2009 14:51:06 +0000 Subject: Besa2Fieldtrip In-Reply-To: <2F9766F6-007B-4C5B-89E4-664C169091C2@uni-konstanz.de> Message-ID: Dear Astrid, At the moment the only way you can obtain the grad struct is to read it from the original MEG datasets. You can then combine it with data read from BESA. There is no support for the way BESA stores MEG sensor locations (I suspect it's a proprietary format). Best, Vladimir On Tue, Jan 13, 2009 at 1:20 PM, Astrid Steffen wrote: > Hi, > > I try to read MEG-files preprocessed in BESA into Fieldtrip therefore I use > the Besa2Fieldtrip-function. I'm wondering where to obtain the > grad-structure from: The sfp-files only contain headshape-information, the > elp-files contain the location-information but cannot be decoded, and the > pmg-file also cannot be read. At the moment, I use the 'read_fcdc_elec ' > command. Do you have any suggestions how to solve this problem? > > Thank you & best regards > Astrid > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/fcdonders/fieldtrip. > > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From vvw at CALTECH.EDU Tue Jan 13 18:01:05 2009 From: vvw at CALTECH.EDU (Virginie van Wassenhove) Date: Tue, 13 Jan 2009 18:01:05 +0100 Subject: neuromag data analysis Message-ID: Hello Fieldtrip-ers and happy new year! I am trying to get some Neuromag (MEG) data analysis done with Fieldtrip - so far I had used fieldtrip for EEG. I can read the data fine (segmentation via meg-pd) but there are a couple of issues now. 1. when I try to filter or downsample I am receiving the following errors: %FILTER (lpf specified in cfg) blah = timelockanalysis(cfg,data_std_bc); the input is timelock data with 306 channels and 801 timebins applying preprocessing options ??? Undefined function or method 'butter' for input arguments of type 'double'. Error in ==> preproc_lowpassfilter at 80 [B, A] = butter(N, max(Flp)/Fn); Error in ==> preproc at 360 if strcmp(cfg.lpfilter, 'yes'), dat = preproc_lowpassfilter(dat, fsample, cfg.lpfreq, cfg.lpfiltord, cfg.lpfilttype, cfg.lpfiltdir); end Error in ==> timelockanalysis at 318 [data.trial{i}, data.label, data.time{i}, cfg.preproc] = preproc(data.trial{i}, data.label, data.fsample, cfg.preproc, data.offset(i)); ================================= %RESAMPLE ??? Error: File: isequal.m Line: 1 Column: 1 The input character is not valid in MATLAB statements or expressions. Error in ==> checkdata at 145 if ~isequal(feedback, 'no') Error in ==> resampledata at 60 data = checkdata(data, 'datatype', 'raw', 'feedback', 'yes'); ================================= The data structure looks fine to me: data_dev1 = hdr: [1x1 struct] label: {306x1 cell} trial: {1x101 cell} time: {1x101 cell} fsample: 1000 grad: [1x1 struct] cfg: [1x1 struct] data_dev1.grad = pnt: [510x3 double] ori: [510x3 double] tra: [306x510 double] unit: 'cm' label: {1x306 cell} Any idea on these error messages? 2. The second issue is that doing a timelockanalysis on these data returns no neg or pos clusters. There is no error message and the computations seem to run fine. Am I missing some steps in the preliminary stages of data analysis for MEG in fieldtrip? Thanks for any help you may provide, Virginie ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From v.litvak at ION.UCL.AC.UK Tue Jan 13 18:34:28 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Tue, 13 Jan 2009 17:34:28 +0000 Subject: neuromag data analysis In-Reply-To: Message-ID: Dear Virginie, It looks very much like the problem is in your Matlab. The first error is definitely a result of missing signal processing toolbox. The second one looks like a version thing, but I'm not sure. If I understand correctly the third one, it might have to do with the absence of image processing toolbox that is used to compute clusters. Best, Vladimir On Tue, Jan 13, 2009 at 5:01 PM, Virginie van Wassenhove wrote: > Hello Fieldtrip-ers and happy new year! > > I am trying to get some Neuromag (MEG) data analysis done with Fieldtrip - so > far I had used fieldtrip for EEG. I can read the data fine (segmentation via > meg-pd) but there are a couple of issues now. > > 1. when I try to filter or downsample I am receiving the following errors: > > %FILTER (lpf specified in cfg) > blah = timelockanalysis(cfg,data_std_bc); > the input is timelock data with 306 channels and 801 timebins > applying preprocessing options > ??? Undefined function or method 'butter' for input arguments of type 'double'. > > Error in ==> preproc_lowpassfilter at 80 > [B, A] = butter(N, max(Flp)/Fn); > > Error in ==> preproc at 360 > if strcmp(cfg.lpfilter, 'yes'), dat = preproc_lowpassfilter(dat, > fsample, cfg.lpfreq, cfg.lpfiltord, > cfg.lpfilttype, cfg.lpfiltdir); end > > Error in ==> timelockanalysis at 318 > [data.trial{i}, data.label, data.time{i}, cfg.preproc] = > preproc(data.trial{i}, data.label, > data.fsample, cfg.preproc, data.offset(i)); > ================================= > %RESAMPLE > ??? Error: File: isequal.m Line: 1 Column: 1 > The input character is not valid in MATLAB statements or expressions. > > Error in ==> checkdata at 145 > if ~isequal(feedback, 'no') > > Error in ==> resampledata at 60 > data = checkdata(data, 'datatype', 'raw', 'feedback', 'yes'); > > ================================= > The data structure looks fine to me: > > data_dev1 = > hdr: [1x1 struct] > label: {306x1 cell} > trial: {1x101 cell} > time: {1x101 cell} > fsample: 1000 > grad: [1x1 struct] > cfg: [1x1 struct] > > data_dev1.grad = > pnt: [510x3 double] > ori: [510x3 double] > tra: [306x510 double] > unit: 'cm' > label: {1x306 cell} > > > Any idea on these error messages? > > 2. The second issue is that doing a timelockanalysis on these data returns > no neg or pos clusters. There is no error message and the computations seem > to run fine. > > Am I missing some steps in the preliminary stages of data analysis for MEG > in fieldtrip? > > Thanks for any help you may provide, > > Virginie > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. > > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From vvw at CALTECH.EDU Tue Jan 13 19:14:39 2009 From: vvw at CALTECH.EDU (Virginie van Wassenhove) Date: Tue, 13 Jan 2009 10:14:39 -0800 Subject: neuromag data analysis In-Reply-To: Message-ID: Dear Vladimir, thanks for your quick reply. I had double-checked the signal processing toolboxes appear in my path so not sure what is going on there but will double-check this shortly... Virginie Virginie.van-Wassenhove at cea.fr Virginie.van.Wassenhove at gmail.com > Dear Virginie, > > It looks very much like the problem is in your Matlab. The first error > is definitely a result of missing signal processing toolbox. The > second one looks like a version thing, but I'm not sure. If I > understand correctly the third one, it might have to do with the > absence of image processing toolbox that is used to compute clusters. > > Best, > > Vladimir > > > > On Tue, Jan 13, 2009 at 5:01 PM, Virginie van Wassenhove > wrote: >> Hello Fieldtrip-ers and happy new year! >> >> I am trying to get some Neuromag (MEG) data analysis done with Fieldtrip >> - so >> far I had used fieldtrip for EEG. I can read the data fine (segmentation >> via >> meg-pd) but there are a couple of issues now. >> >> 1. when I try to filter or downsample I am receiving the following >> errors: >> >> %FILTER (lpf specified in cfg) >> blah = timelockanalysis(cfg,data_std_bc); >> the input is timelock data with 306 channels and 801 timebins >> applying preprocessing options >> ??? Undefined function or method 'butter' for input arguments of type >> 'double'. >> >> Error in ==> preproc_lowpassfilter at 80 >> [B, A] = butter(N, max(Flp)/Fn); >> >> Error in ==> preproc at 360 >> if strcmp(cfg.lpfilter, 'yes'), dat = preproc_lowpassfilter(dat, >> fsample, cfg.lpfreq, cfg.lpfiltord, >> cfg.lpfilttype, cfg.lpfiltdir); end >> >> Error in ==> timelockanalysis at 318 >> [data.trial{i}, data.label, data.time{i}, cfg.preproc] = >> preproc(data.trial{i}, data.label, >> data.fsample, cfg.preproc, data.offset(i)); >> ================================= >> %RESAMPLE >> ??? Error: File: isequal.m Line: 1 Column: 1 >> The input character is not valid in MATLAB statements or expressions. >> >> Error in ==> checkdata at 145 >> if ~isequal(feedback, 'no') >> >> Error in ==> resampledata at 60 >> data = checkdata(data, 'datatype', 'raw', 'feedback', 'yes'); >> >> ================================= >> The data structure looks fine to me: >> >> data_dev1 = >> hdr: [1x1 struct] >> label: {306x1 cell} >> trial: {1x101 cell} >> time: {1x101 cell} >> fsample: 1000 >> grad: [1x1 struct] >> cfg: [1x1 struct] >> >> data_dev1.grad = >> pnt: [510x3 double] >> ori: [510x3 double] >> tra: [306x510 double] >> unit: 'cm' >> label: {1x306 cell} >> >> >> Any idea on these error messages? >> >> 2. The second issue is that doing a timelockanalysis on these data >> returns >> no neg or pos clusters. There is no error message and the computations >> seem >> to run fine. >> >> Am I missing some steps in the preliminary stages of data analysis for >> MEG >> in fieldtrip? >> >> Thanks for any help you may provide, >> >> Virginie >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users of >> the FieldTrip toolbox, to share experiences and to discuss new ideas >> for MEG and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/fcdonders/fieldtrip. >> >> > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/fcdonders/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Tue Jan 20 17:59:47 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 20 Jan 2009 17:59:47 +0100 Subject: neuromag data analysis In-Reply-To: <2671.88.187.2.13.1231870479.squirrel@webmail.caltech.edu> Message-ID: Hi Virginie Something like this >> which medfilt1 /Applications/MATLAB-2007b/toolbox/signal/signal/medfilt1.m >> which butter /Applications/MATLAB-2007b/toolbox/signal/signal/butter.m and this >> which bwlabeln /Applications/MATLAB-2007b/toolbox/images/images/bwlabeln.m should be able to indicate to you whether the signal and image processing toolbox are available on your path. I'll add descriptive checks and error messages at the appropriate location in the code. best regards, Robert On 13 Jan 2009, at 19:14, Virginie van Wassenhove wrote: > Dear Vladimir, > > thanks for your quick reply. I had double-checked the signal > processing > toolboxes appear in my path so not sure what is going on there but > will > double-check this shortly... > > > Virginie ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From amrgermany at YAHOO.COM Tue Jan 20 18:59:42 2009 From: amrgermany at YAHOO.COM (Amr Ayoub) Date: Tue, 20 Jan 2009 09:59:42 -0800 Subject: Empty Beamform tutorial page Message-ID: Hello, Applying beamforming techniques in the frequency domain in the Tutorials gives an empty page. Here is the link: http://neuroimaging.ruhosting.nl/fieldtrip/doku.php?id=fieldtrip:documentation:tutorial:beamformer Thanks Regards, Amr ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bmewang at YAHOO.COM Wed Jan 21 23:01:50 2009 From: bmewang at YAHOO.COM (Wei Wang) Date: Wed, 21 Jan 2009 23:01:50 +0100 Subject: SPM2 and SPM5 Message-ID: Hi FieldTrip friends, We're starting to use FieldTrip for our MEG data analysis. The main problem I have is that the FieldTrip toolbox does not segment my MRI data properly, e.g. it will miss a lot of gray matters. What would be the general suggestions for this type of problem? Is it possible for me to fine tune the segmentation parameters. Also, it seemed to me that FieldTrip uses SPM2 for the segmentation. I'm wondering if FieldTrip is going to switch to SPM5 or not, assuming that SPM5 is more recent than SPM2. Another thing is that we have a Elekta Neuromag Vectorview 306-channel system, different from the CTF system that FCDC uses. If somebody has been able to do source localization successfully with FieldTrip toolbox and Neuromag MEG data, do you mind me asking you a couple of quick questions? Thank you very much and I appreciate the help! Wei ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From v.litvak at ION.UCL.AC.UK Thu Jan 22 00:41:59 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Wed, 21 Jan 2009 23:41:59 +0000 Subject: SPM2 and SPM5 In-Reply-To: Message-ID: Dear Wei, There is a lot of work being done now aimed at integrating Fieldtrip and SPM8. See http://neuroimaging.ruhosting.nl/fieldtrip/doku.php?id=fieldtrip:documentation:integrating_with_spm8 One of the features that will be available very soon (definitely by April 1, probably about a month from now) is the possibility to build subject-specific head models for MEG and EEG based on inverse-normalisation of template meshes, rather than segmentation. This will make it possible to get quite good head models even with suboptimal structural images (at least as good as those images possibly allow). Better support of Neuromag is also in the focus of our work right now. Neuromag is supported in Fieldtrip and SPM8 already using meg_pd toolbox and you can try analysing your data similarly to what you would do for CTF. However, there might be problems with some variants of Neuromag fif format, some of which are also platform dependent. We are working on developing a new Neuromag reader that will hopefully resolve these problems. So you may get started with the things that are already available and we hope that there will be improvements in these particular areas in the coming months. Best, Vladimir On Wed, Jan 21, 2009 at 10:01 PM, Wei Wang wrote: > Hi FieldTrip friends, > > We're starting to use FieldTrip for our MEG data analysis. The main problem I > have is that the FieldTrip toolbox does not segment my MRI data properly, > e.g. it will miss a lot of gray matters. What would be the general suggestions > for this type of problem? Is it possible for me to fine tune the segmentation > parameters. > > Also, it seemed to me that FieldTrip uses SPM2 for the segmentation. I'm > wondering if FieldTrip is going to switch to SPM5 or not, assuming that SPM5 > is more recent than SPM2. > > Another thing is that we have a Elekta Neuromag Vectorview 306-channel > system, different from the CTF system that FCDC uses. If somebody has > been able to do source localization successfully with FieldTrip toolbox and > Neuromag MEG data, do you mind me asking you a couple of quick questions? > > Thank you very much and I appreciate the help! > > Wei > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. > > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From bleichner.martin at GMAIL.COM Thu Jan 22 10:39:42 2009 From: bleichner.martin at GMAIL.COM (Martin Bleichner) Date: Thu, 22 Jan 2009 10:39:42 +0100 Subject: Permutation tests for time-frequency representations: Within trial experiments Message-ID: Hi there, I want to compute the permutation tests for time-frequency representations: within trial. In the tutorial it it stated that i have to select equal length intervals. 'To perform this comparison by means of a permutation test, we have to select equal-length non-overlapping time intervals in the baseline and the activation period.' However, my pre-stimulus and post-stimulus periods have a different length. My baseline is only 500 msec, while the post stimulus period is 1.5 and I am interested in the complete post-stimulus period. Are there possibilities to use unequal intervals? Would it make sense to split up the post stimulus period into 3 parts and compute the statistics for each post stimulus period? Thanks Best, Martin ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.maris at DONDERS.RU.NL Thu Jan 22 11:27:02 2009 From: e.maris at DONDERS.RU.NL (Eric Maris) Date: Thu, 22 Jan 2009 11:27:02 +0100 Subject: Permutation tests for time-frequency representations: Within trial experiments In-Reply-To: Message-ID: Hi Martin, I want to compute the permutation tests for time-frequency representations: within trial. In the tutorial it it stated that i have to select equal length intervals. 'To perform this comparison by means of a permutation test, we have to select equal-length non-overlapping time intervals in the baseline and the activation period.' However, my pre-stimulus and post-stimulus periods have a different length. My baseline is only 500 msec, while the post stimulus period is 1.5 and I am interested in the complete post-stimulus period. Are there possibilities to use unequal intervals? Would it make sense to split up the post stimulus period into 3 parts and compute the statistics for each post stimulus period? Yes, this is the way you should proceed. And, if you want to be safe on the statistical side, use Bonferroni correction (per-comparison alpha-level = 0.05/3) to accommodate for the fact that you run three tests instead of one. Good luck, Eric Maris Thanks Best, Martin ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Fri Jan 23 17:57:47 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Fri, 23 Jan 2009 17:57:47 +0100 Subject: SPM2 and SPM5 In-Reply-To: Message-ID: Hi Wei, On 21 Jan 2009, at 23:01, Wei Wang wrote: > Hi FieldTrip friends, > > We're starting to use FieldTrip for our MEG data analysis. The main > problem I > have is that the FieldTrip toolbox does not segment my MRI data > properly, > e.g. it will miss a lot of gray matters. What would be the general > suggestions > for this type of problem? Is it possible for me to fine tune the > segmentation > parameters. At the FCDC we are not really experts in segmentation. The volumesegment function contains defaults for SPM2 that work for our anatomical MRIs, i.e. for the particular sequence used on our MRI scanner whenever we send someone down to get a "MEG"-MRI. In SPM2/5/8 you of course have many more options for segmenting. The read_fcdc_mri function will read in anatomical MRIs' but also segmented MRIs. > Also, it seemed to me that FieldTrip uses SPM2 for the > segmentation. I'm > wondering if FieldTrip is going to switch to SPM5 or not, assuming > that SPM5 > is more recent than SPM2. There were some inconsistencies in the interface to the functions comparing SPM2 and SPM5, which is why we never swiched (and of course also because SPM2 already does the segmentation trick for us). We won't put effort into SPM5, but it is likely that the dependency on SPM2 functions will be replaced by the corresponding SPM8 functions. But it should also be easy to do the segmentation in SPM8 (e.g. with DARTEL) and read in the result for head-model generation and further processing in fieldtrip. MRI data formats are relatively simple to support, only the coordinate system alignment can be tricky. best regards, Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From mhamidi at WISC.EDU Fri Jan 23 21:12:08 2009 From: mhamidi at WISC.EDU (Massih Hamidi) Date: Fri, 23 Jan 2009 14:12:08 -0600 Subject: Measuring coherence at the source level Message-ID: Hi, I have used the beamformer technique with fieldtrip to produce source estimates of oscillatory activity in my EEG data. I've found two interesting sources and I'd like to know if there is any coherence (phase relationship) between the two. To test this, I would need to do phase coherence analyses at the scalp level between electrodes. Is there any way I could work backwards from the source estimate to the scalp electrode (i.e. which electrode describes each of the two sources best)? Or is there a better way to look at coherence between two brain regions? Thanks. -- Massih Hamidi Medical Scientist Training Program Neuroscience Training Program University of Wisconsin - Madison 1202 West Johnson St., Madison, WI 53706 608-265-3888 | mhamidi at wisc.edu ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Mon Jan 26 09:11:19 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 26 Jan 2009 09:11:19 +0100 Subject: Empty Beamform tutorial page In-Reply-To: <834428.63449.qm@web57416.mail.re1.yahoo.com> Message-ID: Hi Amr, Thanks for notifying us. Since moving to the new server there are some issues with the wiki. The caching of wiki pages fails somehow, which seems related to the neuroimaging.ruhosting.nl and fcdonders.ruhosting.nl confusion. In general (also to other users): if this happens the following workaround may help: If you fo to "edit" and then "preview" then you'll see the ful lcontent. I have upgraded the wiki CMS softare to the latest version, hopefully it solves the issue. best regards, Robert On 20 Jan 2009, at 18:59, Amr Ayoub wrote: > Hello, > > Applying beamforming techniques in the frequency domain in the > Tutorials gives an empty page. > Here is the link: > http://neuroimaging.ruhosting.nl/fieldtrip/doku.php?id=fieldtrip:documentation:tutorial:beamformer > > Thanks > Regards, > Amr > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From ana.acsousa at GMAIL.COM Mon Jan 26 12:07:39 2009 From: ana.acsousa at GMAIL.COM (Ana Carolina) Date: Mon, 26 Jan 2009 12:07:39 +0100 Subject: Ploting using easycap64ch-avg Message-ID: Dear FieldTrip users, I'm trying to plot EEG data using the easycap64ch-avg layout, but there seems to be a problem with the coordinate values because when I see the plot, the electrodes are not on the correct position. When I checked the values of the layout I saw that the values of the two first columns are not correct (I think), because if you think in all the electrodes that are in the same line like 35, 20, 8, 2, 1, 5, 14, 43 and 46 they should have the same value in the x- axis, but this doesn't happen. So, these and also all the other electrodes have small deviations like for example electrode 36 are not align whit the electrode 50 in y axis, etc. In this way I can't have a symmetrical plot of the electrodes. Does anybody have used this layout and have the same problem? Thanks in advance! regards, Ana Carolina ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Mon Jan 26 12:32:10 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 26 Jan 2009 12:32:10 +0100 Subject: Ploting using easycap64ch-avg In-Reply-To: <40538cdc0901260307u5a5a276dg4cd9978978fc1d1f@mail.gmail.com> Message-ID: Hi Ana, This is what I see. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Picture 1.png Type: image/png Size: 56013 bytes Desc: not available URL: -------------- next part -------------- It looks reasonable to me. The template layout files in fieldtrip/ template/*.lay that have "avg" in their name were all created by measuring the channel position on a few subjects' head with the polhemus tracker and averaging over those. Those measurements are not ideal, explaining the slight asymmetry. If you are not happy with this template layout (which I can imagine), I suggest you go to www.easycap.de, download a figure of the cap you are using, and use cfg =[] cfg.image = 'your_figure.gif' layout = prepare_layout(cfg); which will allow you to interactively click on each electrode position in the figure. You then also have to specify the outline of the head (including ears and nose) which will be displayed in black lines and the outline of the part of the head in which you want the interpolated data to show up (i.e. only the cricle of the head). best regards, Robert On 26 Jan 2009, at 12:07, Ana Carolina wrote: > Dear FieldTrip users, > > I'm trying to plot EEG data using the easycap64ch-avg layout, but > there seems to be a problem with the coordinate values because when > I see the plot, the electrodes are not on the correct position. When > I checked the values of the layout I saw that the values of the two > first columns are not correct (I think), because if you think in all > the electrodes that are in the same line like 35, 20, 8, 2, 1, 5, > 14, 43 and 46 they should have the same value in the x- axis, but > this doesn't happen. So, these and also all the other electrodes > have small deviations like for example electrode 36 are not align > whit the electrode 50 in y axis, etc. In this way I can't have a > symmetrical plot of the electrodes. > Does anybody have used this layout and have the same problem? > > Thanks in advance! > > regards, > Ana Carolina > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Mon Jan 26 14:45:31 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 26 Jan 2009 14:45:31 +0100 Subject: Workshop: Multimodal imaging in cognitive neuroscience Message-ID: Dear colleagues, The Donders Institute is pleased to announce: Multimodal imaging in cognitive neuroscience an international workshop of the Donders Institute 24 & 25 March 2009, the Netherlands The workshop aims at exploring how integrated multimodal neuroimaging could provide new ways of understanding brain functions. We will focus on two experimental situations that require integrated multimodal imaging: the quantification of the cerebral consequences of experimentally altered brain activity; and the analysis of dependencies between intrinsic and stimulus-driven cerebral dynamics. Speakers Sven Bestmann – Wellcome Centre for Neuroimaging, Institute of Neurology, University College, London Ralph D. Freeman – Vision Science Group, School of Optometry, and Helen Wills Neuroscience Institute, University of California, Berkeley Andreas Kleinschmidt – NeuroSpin, Gif-sur-Yvette, France David Leopold – Unit on Cognitive Neurophysiology and Imaging, Laboratory of Neuropsychology, National Institute of Mental health, USA Registration and further details http://www.ru.nl/donders/home/agenda/multimodel/ 24 & 25 March 2009 Donders Institute for Brain, Cognition and Behaviour Radboud University Nijmegen The Netherlands ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Multimodal_eFlyer.pdf Type: application/pdf Size: 211157 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.debener at UKE.UNI-HAMBURG.DE Tue Jan 27 10:49:30 2009 From: s.debener at UKE.UNI-HAMBURG.DE (Stefan Debener) Date: Tue, 27 Jan 2009 09:49:30 +0000 Subject: MEG/EEG post-doc position in Jena, Germany Message-ID: Post-Doc Position at the Biomagnetic Center Jena, Germany A two-year post-doc position is available at the Biomagnetic Center Jena. Biomagnetism has a long-standing tradition in Jena and the group consists of a young, interdisciplinary and international research team and a new head of department (Prof. S. Debener). The Biomag Center comprises several labs, including a new 306/128-channel whole-head MEG/EEG system (Neuromag). Areas of research are multisensory processing, somatosensory and pain research, cortical re-organization after cochlear implantation, neurocognition of temporal attention, and EEG-fMRI integration. The post-doc will have a strong interest in using independent component analysis for the analysis of EEG, MEG, and combined EEG-MEG recordings. Expertise in multichannel EEG or MEG analysis is mandatory, as well as a good theoretical background in biosignal processing, experimental neurosciences, or both. For further enquiries, please contact Stefan Debener. International applications are welcome. Please send your application (CV, list of publications, contact information for two references) to debener at biomag.uni-jena.de. Closing date is February 15, 2009. -- Prof. Dr. Stefan Debener Biomagnetic Center Dept. of Neurology University Hospital Jena Erlanger Allee 101 D-07747 Jena Germany Phone: +49-3641-9325770 Fax: +49-3641-9325772 Email: debener at biomag.uni-jena.de ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Tue Jan 27 17:54:48 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 27 Jan 2009 17:54:48 +0100 Subject: problems with wiki -> empty pages In-Reply-To: Message-ID: Dear all We are experiencing technical problems with the fieldtrip wiki. I had hoped that installing a new version of the software would fix it as I explained in a previous mail, and on Sunday that indeed seemed to solve it. But today the problems reappeared, even in more severe form. After trying to diagnose it and discussing it with some technical colleagues here and with some input from the ruhosting server system administrator (who is not part of our department), the working diagnosis is that there is a performance problem on the server hardware. The ruhosting machine is shared by many people, and it seems that high traffic in general (not the case on Sunday) combined with fieldtrip wiki edits (which happened a lot today) causes the hickups. These then result in empty pages in the cache and empty pages being displayed. Note that all the documents are still there. A workaround for the problem is to click the "edit" button and then click the "preview" button. That circumvents the caching, and for me results in a correect display of the page content. At the moment I cannot solve it, but tomorrow I'll again start bugging the sysadmin. I'll try to clear the cache as often as possible (because immediately after that, it looks OK). Sorry for the inconvenience, Robert On 27 Jan 2009, at 17:04, Vladimir Litvak wrote: > The problem is still there. I've just experienced it with the > statistics tutorial. Your suggestion works, but I'd like to send a > link to somebody so it'd be much simpler if you fix it. > > Vladimir > > On Mon, Jan 26, 2009 at 8:11 AM, Robert Oostenveld > wrote: >> Hi Amr, >> >> Thanks for notifying us. Since moving to the new server there are >> some >> issues with the wiki. The caching of wiki pages fails somehow, >> which seems >> related to the neuroimaging.ruhosting.nl and fcdonders.ruhosting.nl >> confusion. >> >> In general (also to other users): if this happens the following >> workaround >> may help: If you fo to "edit" and then "preview" then you'll see >> the ful >> lcontent. >> >> I have upgraded the wiki CMS softare to the latest version, >> hopefully it >> solves the issue. >> >> best regards, >> Robert > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From Harsimrat.Singh at WARWICK.AC.UK Sun Jan 4 02:45:16 2009 From: Harsimrat.Singh at WARWICK.AC.UK (Singh, Harsimrat) Date: Sun, 4 Jan 2009 01:45:16 -0000 Subject: BCI2000 file read Message-ID: Hi I am trying to use some field trip functions for data recorded using BCI2000 (.dat) files. The data was recorded using brain vision amplifier. I understand that the function read_data doesnt read the BCI2000 files. Can anyone please suggest way around this ? Thanks in advance Regards Harsimrat ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Mon Jan 5 15:19:37 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 5 Jan 2009 15:19:37 +0100 Subject: BCI2000 file read In-Reply-To: <95B2B6BF8599AB4EA51DDC85904A15AAC6A16E@HOLLY.ads.warwick.ac.uk> Message-ID: Dear Harsimrat, It recently came to my attention that files written in older versions of BCI2000 are not completely compatible with newer versions of BCI2000. Is it possible for you to send me an example datafile that causes you the problem? The problem has to do with the file type detection and probably can be fixed quite easily. Please look here http://neuroimaging.ruhosting.nl/fieldtrip/doku.php?id=fieldtrip:contact for details on how to send the file. best regards, Robert On 4 Jan 2009, at 2:45, Singh, Harsimrat wrote: > Hi > > I am trying to use some field trip functions for data recorded using > BCI2000 (.dat) files. The data was recorded using brain vision > amplifier. > I understand that the function read_data doesnt read the BCI2000 > files. > Can anyone please suggest way around this ? > > Thanks in advance > Regards > Harsimrat > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From jason.sherfey at GMAIL.COM Tue Jan 6 01:15:16 2009 From: jason.sherfey at GMAIL.COM (Jason Sherfey) Date: Mon, 5 Jan 2009 16:15:16 -0800 Subject: freqanalysis_wltconvol Message-ID: Dear FieldTrip users, I have been using freqanalysis_wltconvol to compute the wavelet power spectrum for several months and recently began trying to understand the code. Reading past discussions on this listserv has been very helpful, but I can't figure out why it does the particular normalization that it does for the wavelet power calculation. This calculation can be found on line 299 of the 20081001 release. According to the comments at the beginning of the function, jansch "fixed [the] improper normalization of powdum" in Revision 1.17 on 2007/06/14. It seems to me that "powdum" is the wavelet power spectrum (P) and that "autspctrmacttap" is the signal's wavelet transform (T). If that is true, then the correction made on 2007/06/14 was the following: P = (2*|T| / fs)^2 became P = 2*|T|^2 / fs where fs = sampling frequency My current understanding (based on pp. 31-32 in Addison's text "The illustrated wavelet transform handbook") is that the wavelet energy density is given by E = |T|^2 and that P = E / (time period of the signal). Since the time period of the signal = (# of samples) / (sampling frequency), that would imply P = fs*|T|^2 / (# of samples). Thus, I thought |T|^2 should be multiplied by fs/(# of samples), but in the code it's instead multiplied by 2/fs. I am fairly new to wavelet analysis and suspect there's a small detail I don't understand. Does anyone know why the wavelet energy is normalized by 2/fs instead of fs/(# samples)? Thanks in advance, Jason ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From iversen at NSI.EDU Fri Jan 9 19:03:18 2009 From: iversen at NSI.EDU (John Iversen) Date: Fri, 9 Jan 2009 10:03:18 -0800 Subject: Q about integration with SPM8 In-Reply-To: <8d039c560901051615h68c88f7bw1356aea8be3b3295@mail.gmail.com> Message-ID: Hello, It's seems great that you there is not a partnership between Fieldtrip and SPM. Since SPM8 comes with its own version of fieldtrip, how will this be kept 'in sync' with the updates coming out of Donders? Having two different versions of fieldtrip seems like a potential headache. To avoid this issue, I was planning to have SPM8 use my existing Fieldtrip installation exclusively. Is there is any downside to this? What version of FT is included with SPM8? More generally, the SPM solution of renaming and wrappers seems rather involved. Couldn't managing the MATLAB search path ensure that there are no conflicts between versions? I'm sure you went this route for good reasons that I am unaware of, so I'd be happy to be enlightened. Thanks, as always, for a great set of tools, and support. Happy New Year to all. John John R. Iversen, PhD The Neurosciences Institute 10640 John Jay Hopkins Drive San Diego, CA 92121 (858)-626-2068 iversen at nsi.edu ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From v.litvak at ION.UCL.AC.UK Fri Jan 9 19:31:42 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Fri, 9 Jan 2009 18:31:42 +0000 Subject: Q about integration with SPM8 In-Reply-To: Message-ID: Dear John, On Fri, Jan 9, 2009 at 6:03 PM, John Iversen wrote: > Since SPM8 comes with its own version of fieldtrip, how will this be > kept 'in sync' with the updates coming out of Donders? This is done automatically presently on a daily basis, perhaps will be switched to a weekly update after the official release of SPM8. Critical updates are propagated immediately. So if you update SPM8, the version of FT in SPM8 will be from the same date. >Having two different > versions of fieldtrip seems like a potential headache. This is exactly what the wrappers are for. You can have your favorite FT version in the path with SPM but there will be no clashes as SPM will only use its internal version of FT. The same is true for your FT scripts - unless you explicitly call the wrappers with 'ft_...' your FT functions will come from your stand-alone FT installation and not from SPM. >To avoid this issue, > I was planning to have SPM8 use my existing Fieldtrip installation > exclusively. Is there is any downside to this? Yes because there is no guarantee that your particular FT version is compatible with your SPM version (unless you keep updating both which is redundant). The best way for you to work if you already have an FT version that works for you and don't want to update it for a while is to ignore the FT version that SPM uses and pretend it's not there. Wrappers will prevent any clashes as I explained. I hope my explanations are clear. If not, I'd be glad to answer any further questions. Best, Vladimir ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From christine.gruetzner at GOOGLEMAIL.COM Mon Jan 12 17:29:48 2009 From: christine.gruetzner at GOOGLEMAIL.COM (Christine Gruetzner) Date: Mon, 12 Jan 2009 17:29:48 +0100 Subject: Plotting individual source stat data Message-ID: Dear FieldTrip users, I'm trying to plot source stat data from individual subjects on the respective mri (according to the procedure suggested in the beamformer tutorial), but there seems to be a problem when I use sourceinterpolate (see below). Does anybody have an idea what's going wrong here? Thanks in advance! Best, Christine the input is source data with 4560 positions the input is volume data with dimensions [256 256 256] not downsampling anatomy not downsampling inside selecting subvolume of 0.0% interpolating ??? Attempted to access sel(1); index out of bounds because numel(sel)=0. Error in ==> sourceinterpolate>my_interpn at 380 progress(sel(1)/num, 'interpolating %.1f%%\n', 100*sel(1)/num); Error in ==> sourceinterpolate at 275 interp.inside( sel) = my_interpn(double(functional.inside), ax(sel), ay(sel), az(sel), 'nearest', cfg.feedback); Error in ==> PlotSourceData at 164 sourceinterp = sourceinterpolate(cfg, statdiff,mri); -- Christine Gruetzner, geb. Tillmann Max-Planck-Institut für Hirnforschung Abt. Neurophysiologie Deutschordenstr. 46 60528 Frankfurt am Main Germany Phone: +49 (0)69/6301-83225 E-Mail: tillmann at mpih-frankfurt.mpg.de http://www.mpih-frankfurt.mpg.de/global/Np/Staff/tillmann.htm ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Mon Jan 12 21:12:29 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 12 Jan 2009 21:12:29 +0100 Subject: Q about integration with SPM8 In-Reply-To: Message-ID: Hi John, Vladimir and I (and other spm developers) have considered this carefully, and the present spm8+fieldtrip mixture was the best we could come up with. The versions are automatically kept in synch, but the release schedule of fieldtrip is daily, whereas for spm8 it is less frequent. So the versions getting slightly out of sync on your computer is inevitable. With the latest 2008a and 2008b versions of Matlab there are better options for supporting such mixtures ofg packages (using "namespaces"), but since both spm and fieldtrip should work on older matlab versions, we cannot use those features yet. On 9 Jan 2009, at 19:31, Vladimir Litvak wrote: >> To avoid this issue, >> I was planning to have SPM8 use my existing Fieldtrip installation >> exclusively. Is there is any downside to this? > > Yes because there is no guarantee that your particular FT version is > compatible with your SPM version (unless you keep updating both which > is redundant). > > The best way for you to work if you already have an FT version that > works for you and don't want to update it for a while is to ignore the > FT version that SPM uses and pretend it's not there. Wrappers will > prevent any clashes as I explained. To add on Vladimirs comment: In practice it means that you delete the spm8/external/fieldtrip/private directory and keep the spm8/external/ fieldtrip directory for the wrappers. You can do the same for fileio and forwinv (also both in fieldtrip and spm8/external). Subsequently you should ensure that the ft_xxx wrappers in spm8, respectively the fileio_xxx and the forwinv_xxx wrappers are on your matlab path, just as your normal fieldtrip version. SPM8 will call those wrappers, which will call your standard fieldtrip functions. best Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From v.litvak at ION.UCL.AC.UK Mon Jan 12 23:13:14 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Mon, 12 Jan 2009 22:13:14 +0000 Subject: Q about integration with SPM8 In-Reply-To: Message-ID: Although what Robert described (deleting the private subdirectories) will do the trick, I don't see any reason to do it. I do see a reason not to do it because it may generate errors that will be very hard for us to reproduce and resolve. We are now often developing things in parallel where changes are made to FT to make some SPM feature work so if the two get slightly out of sync those new features will not work. Thus, I repeat my recommendation to leave things as they are. Don't you agree, Robert? There might be some problems with clashes if Robert starts naming some FT functions with the same names as wrappers in SPM. I don't know if there are any cases like this already. Vladimir On Mon, Jan 12, 2009 at 8:12 PM, Robert Oostenveld wrote: > Hi John, > > Vladimir and I (and other spm developers) have considered this carefully, > and the present spm8+fieldtrip mixture was the best we could come up with. > The versions are automatically kept in synch, but the release schedule of > fieldtrip is daily, whereas for spm8 it is less frequent. So the versions > getting slightly out of sync on your computer is inevitable. > > With the latest 2008a and 2008b versions of Matlab there are better options > for supporting such mixtures ofg packages (using "namespaces"), but since > both spm and fieldtrip should work on older matlab versions, we cannot use > those features yet. > > On 9 Jan 2009, at 19:31, Vladimir Litvak wrote: > >>> To avoid this issue, >>> I was planning to have SPM8 use my existing Fieldtrip installation >>> exclusively. Is there is any downside to this? >> >> Yes because there is no guarantee that your particular FT version is >> compatible with your SPM version (unless you keep updating both which >> is redundant). >> >> The best way for you to work if you already have an FT version that >> works for you and don't want to update it for a while is to ignore the >> FT version that SPM uses and pretend it's not there. Wrappers will >> prevent any clashes as I explained. > > To add on Vladimirs comment: In practice it means that you delete the > spm8/external/fieldtrip/private directory and keep the > spm8/external/fieldtrip directory for the wrappers. You can do the same for > fileio and forwinv (also both in fieldtrip and spm8/external). Subsequently > you should ensure that the ft_xxx wrappers in spm8, respectively the > fileio_xxx and the forwinv_xxx wrappers are on your matlab path, just as > your normal fieldtrip version. SPM8 will call those wrappers, which will > call your standard fieldtrip functions. > > best > Robert > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/fcdonders/fieldtrip. > > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From iversen at NSI.EDU Mon Jan 12 23:42:04 2009 From: iversen at NSI.EDU (John Iversen) Date: Mon, 12 Jan 2009 14:42:04 -0800 Subject: Q about integration with SPM8 In-Reply-To: Message-ID: Hi Robert and Vladimir, Thank you both for your responses. I very much appreciate the clarifications and suggestions for ways to proceed. Best regards, John On Jan 12, 2009, at 12:12 PM, Robert Oostenveld wrote: > Hi John, > > Vladimir and I (and other spm developers) have considered this > carefully, and the present spm8+fieldtrip mixture was the best we > could come up with. The versions are automatically kept in synch, > but the release schedule of fieldtrip is daily, whereas for spm8 it > is less frequent. So the versions getting slightly out of sync on > your computer is inevitable. > > With the latest 2008a and 2008b versions of Matlab there are better > options for supporting such mixtures ofg packages (using > "namespaces"), but since both spm and fieldtrip should work on older > matlab versions, we cannot use those features yet. > > On 9 Jan 2009, at 19:31, Vladimir Litvak wrote: > this >>> To avoid this issue, >>> I was planning to have SPM8 use my existing Fieldtrip installation >>> exclusively. Is there is any downside to? >> >> Yes because there is no guarantee that your particular FT version is >> compatible with your SPM version (unless you keep updating both which >> is redundant). >> >> The best way for you to work if you already have an FT version that >> works for you and don't want to update it for a while is to ignore >> the >> FT version that SPM uses and pretend it's not there. Wrappers will >> prevent any clashes as I explained. > > To add on Vladimirs comment: In practice it means that you delete > the spm8/external/fieldtrip/private directory and keep the spm8/ > external/fieldtrip directory for the wrappers. You can do the same > for fileio and forwinv (also both in fieldtrip and spm8/external). > Subsequently you should ensure that the ft_xxx wrappers in spm8, > respectively the fileio_xxx and the forwinv_xxx wrappers are on your > matlab path, just as your normal fieldtrip version. SPM8 will call > those wrappers, which will call your standard fieldtrip functions. > > best > Robert > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/fcdonders/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From iversen at NSI.EDU Tue Jan 13 00:04:33 2009 From: iversen at NSI.EDU (John Iversen) Date: Mon, 12 Jan 2009 15:04:33 -0800 Subject: Q about integration with SPM8 In-Reply-To: Message-ID: Sorry, my reply just crossed with yours. Ok, I'm now a bit confused as to the specifics of the co-evolution of the two projects. It sounds like the FT in SPM is a custom fit good at a particular moment in time, but that separate changes in either SPM or FT could bring some conflicts. That seems like a good argument to use the SPM version of FT. To clarify my perspective, what I didn't note in my original email, and I should have, is that the 'headache' I referred to is mainly due to the fact that I've made some modifications of my own on FT, and wasn't keen to need to fold them into two separate versions of FT that might be updated at different times. Granted that's a self-inflicted headache and perhaps at this point I should reconsider whether those modifications are in fact necessary. More generally, though, I like to tweak and be familiar with every detail of the code I'm using, so having two different versions is just that much more for my finite brain to keep track of. Of course, more generally the number one issue would be to avoid a situation in which two versions yielded different analysis results, but that doesn't seem to be a concern that either of you have expressed, so perhaps that is not something to worry about. So, now I'm considering just using the version of FT included in SPM for all my uses. I don't take advantage of the daily upgrades to FT, so the slower release schedule is fine. How does that sound? Thanks, John On Jan 12, 2009, at 2:13 PM, Vladimir Litvak wrote: > Although what Robert described (deleting the private subdirectories) > will do the trick, I don't see any reason to do it. I do see a reason > not to do it because it may generate errors that will be very hard for > us to reproduce and resolve. We are now often developing things in > parallel where changes are made to FT to make some SPM feature work so > if the two get slightly out of sync those new features will not work. > Thus, I repeat my recommendation to leave things as they are. Don't > you agree, Robert? > > There might be some problems with clashes if Robert starts naming some > FT functions with the same names as wrappers in SPM. I don't know if > there are any cases like this already. > > Vladimir > > > > On Mon, Jan 12, 2009 at 8:12 PM, Robert Oostenveld > wrote: >> Hi John, >> >> Vladimir and I (and other spm developers) have considered this >> carefully, >> and the present spm8+fieldtrip mixture was the best we could come >> up with. >> The versions are automatically kept in synch, but the release >> schedule of >> fieldtrip is daily, whereas for spm8 it is less frequent. So the >> versions >> getting slightly out of sync on your computer is inevitable. >> >> With the latest 2008a and 2008b versions of Matlab there are better >> options >> for supporting such mixtures ofg packages (using "namespaces"), but >> since >> both spm and fieldtrip should work on older matlab versions, we >> cannot use >> those features yet. >> >> On 9 Jan 2009, at 19:31, Vladimir Litvak wrote: >> >>>> To avoid this issue, >>>> I was planning to have SPM8 use my existing Fieldtrip installation >>>> exclusively. Is there is any downside to this? >>> >>> Yes because there is no guarantee that your particular FT version is >>> compatible with your SPM version (unless you keep updating both >>> which >>> is redundant). >>> >>> The best way for you to work if you already have an FT version that >>> works for you and don't want to update it for a while is to ignore >>> the >>> FT version that SPM uses and pretend it's not there. Wrappers will >>> prevent any clashes as I explained. >> >> To add on Vladimirs comment: In practice it means that you delete the >> spm8/external/fieldtrip/private directory and keep the >> spm8/external/fieldtrip directory for the wrappers. You can do the >> same for >> fileio and forwinv (also both in fieldtrip and spm8/external). >> Subsequently >> you should ensure that the ft_xxx wrappers in spm8, respectively the >> fileio_xxx and the forwinv_xxx wrappers are on your matlab path, >> just as >> your normal fieldtrip version. SPM8 will call those wrappers, which >> will >> call your standard fieldtrip functions. >> >> best >> Robert >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users >> of the >> FieldTrip toolbox, to share experiences and to discuss new ideas >> for MEG >> and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/fcdonders/fieldtrip. >> >> > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/fcdonders/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From v.litvak at ION.UCL.AC.UK Tue Jan 13 00:40:39 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Mon, 12 Jan 2009 23:40:39 +0000 Subject: Q about integration with SPM8 In-Reply-To: <5B9123D2-47A5-4884-BC50-08462FC09640@nsi.edu> Message-ID: Dear John, It's hard for me to follow your reasoning. On the one hand you want to keep using your old 'tweaked' FT, but on the other hand you want to switch to SPM's version which would not contain your modifications. Maybe there is something basic that I should reiterate. The actual analysis done in SPM is different than the analysis in FT. SPM proper presently used code from FT for data conversion and for computing lead fields. In both cases there are unlikely to be different results for different versions of the code. The reason all of FT is included in SPM and not just those specific parts is to make it possible for people to write some custom tools combining SPM and FT functions and distribute them to SPM users without the need to install external FT. If you just want to do your own analysis I don't see a good reason for you to use the FT included in SPM rather than the version you are presently working with. What I suggest is - just put both your old FT and SPM in the path and see how it goes. I don't foresee any problems. Note that you should keep updating SPM with patches from ftp://ftp.fil.ion.ucl.ac.uk/spm/spm8b_updates/ Best, Vladimir On Mon, Jan 12, 2009 at 11:04 PM, John Iversen wrote: > Sorry, my reply just crossed with yours. Ok, I'm now a bit confused as to > the specifics of the co-evolution of the two projects. It sounds like the FT > in SPM is a custom fit good at a particular moment in time, but that > separate changes in either SPM or FT could bring some conflicts. That seems > like a good argument to use the SPM version of FT. > > To clarify my perspective, what I didn't note in my original email, and I > should have, is that the 'headache' I referred to is mainly due to the fact > that I've made some modifications of my own on FT, and wasn't keen to need > to fold them into two separate versions of FT that might be updated at > different times. Granted that's a self-inflicted headache and perhaps at > this point I should reconsider whether those modifications are in fact > necessary. More generally, though, I like to tweak and be familiar with > every detail of the code I'm using, so having two different versions is just > that much more for my finite brain to keep track of. > > Of course, more generally the number one issue would be to avoid a situation > in which two versions yielded different analysis results, but that doesn't > seem to be a concern that either of you have expressed, so perhaps that is > not something to worry about. > > So, now I'm considering just using the version of FT included in SPM for all > my uses. I don't take advantage of the daily upgrades to FT, so the slower > release schedule is fine. How does that sound? > > Thanks, > > John > > On Jan 12, 2009, at 2:13 PM, Vladimir Litvak wrote: > >> Although what Robert described (deleting the private subdirectories) >> will do the trick, I don't see any reason to do it. I do see a reason >> not to do it because it may generate errors that will be very hard for >> us to reproduce and resolve. We are now often developing things in >> parallel where changes are made to FT to make some SPM feature work so >> if the two get slightly out of sync those new features will not work. >> Thus, I repeat my recommendation to leave things as they are. Don't >> you agree, Robert? >> >> There might be some problems with clashes if Robert starts naming some >> FT functions with the same names as wrappers in SPM. I don't know if >> there are any cases like this already. >> >> Vladimir >> >> >> >> On Mon, Jan 12, 2009 at 8:12 PM, Robert Oostenveld >> wrote: >>> >>> Hi John, >>> >>> Vladimir and I (and other spm developers) have considered this carefully, >>> and the present spm8+fieldtrip mixture was the best we could come up >>> with. >>> The versions are automatically kept in synch, but the release schedule of >>> fieldtrip is daily, whereas for spm8 it is less frequent. So the versions >>> getting slightly out of sync on your computer is inevitable. >>> >>> With the latest 2008a and 2008b versions of Matlab there are better >>> options >>> for supporting such mixtures ofg packages (using "namespaces"), but since >>> both spm and fieldtrip should work on older matlab versions, we cannot >>> use >>> those features yet. >>> >>> On 9 Jan 2009, at 19:31, Vladimir Litvak wrote: >>> >>>>> To avoid this issue, >>>>> I was planning to have SPM8 use my existing Fieldtrip installation >>>>> exclusively. Is there is any downside to this? >>>> >>>> Yes because there is no guarantee that your particular FT version is >>>> compatible with your SPM version (unless you keep updating both which >>>> is redundant). >>>> >>>> The best way for you to work if you already have an FT version that >>>> works for you and don't want to update it for a while is to ignore the >>>> FT version that SPM uses and pretend it's not there. Wrappers will >>>> prevent any clashes as I explained. >>> >>> To add on Vladimirs comment: In practice it means that you delete the >>> spm8/external/fieldtrip/private directory and keep the >>> spm8/external/fieldtrip directory for the wrappers. You can do the same >>> for >>> fileio and forwinv (also both in fieldtrip and spm8/external). >>> Subsequently >>> you should ensure that the ft_xxx wrappers in spm8, respectively the >>> fileio_xxx and the forwinv_xxx wrappers are on your matlab path, just as >>> your normal fieldtrip version. SPM8 will call those wrappers, which will >>> call your standard fieldtrip functions. >>> >>> best >>> Robert >>> >>> ---------------------------------- >>> The aim of this list is to facilitate the discussion between users of the >>> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG >>> and EEG analysis. See also >>> http://listserv.surfnet.nl/archives/fieldtrip.html and >>> http://www.ru.nl/fcdonders/fieldtrip. >>> >>> >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG >> and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/fcdonders/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/fcdonders/fieldtrip. > > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Tue Jan 13 09:43:07 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 13 Jan 2009 09:43:07 +0100 Subject: Q about integration with SPM8 In-Reply-To: <5B9123D2-47A5-4884-BC50-08462FC09640@nsi.edu> Message-ID: On 12 Jan 2009, at 23:13, Vladimir Litvak wrote: > if the two get slightly out of sync those new features will not work. > Thus, I repeat my recommendation to leave things as they are. Don't > you agree, Robert? depends on whether you are leaning towards the spm8 side or to the fieldtrip side. Debugging fieldtrip will be easier with a standard (and of course the latest) fieldtrip version, debugging spm8 is easier with the fieldtrip version included in spm8. The two are kept in sync as close as possible. So I don't expect major problems either way (except for the occasional bug that will hamper both). On 13 Jan 2009, at 0:04, John Iversen wrote: > So, now I'm considering just using the version of FT included in SPM > for all my uses. I don't take advantage of the daily upgrades to FT, > so the slower release schedule is fine. How does that sound? sounds fine to me. Actually, we (that is the fieldtrip developers) might decide in the future to change all fieldtrip function names to the spm ft_xxx scheme. At the moment that is too much work and would cause too much problems. But getting used to using the ft_xxx naming scheme in your own scripts might therefore in the future be handy. The reason that I prefer people to use the standard fieldtrip version is that it makes it much easier to find the help of the functions (which is not available in spm from the command line, due to the anonymous wrappers being in the way). Furthermore, the recently modified directory layout of fieldtrip clarifies how all pieces fit together (with an explicit distinction between public and private code and showing the various modules), whereas the directory layout in spm8 hides this (all interesting stuff goes into private). But as I said, the code is the same, every day an update from Nijmegen is sent to London, and you should just do whatever is the most comfortable for you. Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Tue Jan 13 10:10:18 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 13 Jan 2009 10:10:18 +0100 Subject: Plotting individual source stat data In-Reply-To: <841d3140901120829p3f8c7630q7c21e7c9a3da0e67@mail.gmail.com> Message-ID: Hi Christine On 12 Jan 2009, at 17:29, Christine Gruetzner wrote: > I'm trying to plot source stat data from individual subjects on the > respective mri (according to the procedure suggested in the > beamformer tutorial), but there seems to be a problem when I use > sourceinterpolate (see below). > > Does anybody have an idea what's going wrong here? > ... > the input is source data with 4560 positions > the input is volume data with dimensions [256 256 256] > not downsampling anatomy > not downsampling inside > selecting subvolume of 0.0% > interpolating > ??? Attempted to access sel(1); index out of bounds because > numel(sel)=0. To speed up the interpolation of the functional onto the anatomical data, the function determines the subvolume of the anatomical mri that is spanned by the functional data. Usually the anatomical mri covers the whole head (including chin and quite some air around the head), whereas the functional data only spans the brain. The functional data therefore takes only approximately 1/4 th of the volume of the anatomical mri. In your case it selects a subvolume of 0%, where I would expect a subvolume of 25%. That means that the functional data completely lies outside the space that is spanned by the anatomical MRI. Think of both volumes as a wireframe cube: normally the functional "cube" would be completely inside the anatomical "cube", but in this case it is completely outside. I suspect this to be due to a misspecification of the units (cm v.s. mm) of either functional or anatomical data. You should check your cfg.mriunits and cfg.sourceunits, or alternatively please read on: I have recentently been working on the autodetection of the units, which makes the manual specification unnecessary. The attached version of sourceinterpolate (not yet part of standard fieldtrip) should automatically detect the correct units (cm or mm) for the anatomical and functional data. Could you please try ot the attached version? Please rename your exsisting sourceinterpolate.m into sourceinterpolate_orig.m and then copy this function into your fieldtrip directory. I hope it solves your problem. best regards, Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: sourceinterpolate.m Type: application/octet-stream Size: 15957 bytes Desc: not available URL: -------------- next part -------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From astrid.steffen at UNI-KONSTANZ.DE Tue Jan 13 14:20:51 2009 From: astrid.steffen at UNI-KONSTANZ.DE (Astrid Steffen) Date: Tue, 13 Jan 2009 14:20:51 +0100 Subject: Besa2Fieldtrip Message-ID: Hi, I try to read MEG-files preprocessed in BESA into Fieldtrip therefore I use the Besa2Fieldtrip-function. I'm wondering where to obtain the grad-structure from: The sfp-files only contain headshape-information, the elp-files contain the location-information but cannot be decoded, and the pmg-file also cannot be read. At the moment, I use the 'read_fcdc_elec ' command. Do you have any suggestions how to solve this problem? Thank you & best regards Astrid ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From v.litvak at ION.UCL.AC.UK Tue Jan 13 15:51:06 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Tue, 13 Jan 2009 14:51:06 +0000 Subject: Besa2Fieldtrip In-Reply-To: <2F9766F6-007B-4C5B-89E4-664C169091C2@uni-konstanz.de> Message-ID: Dear Astrid, At the moment the only way you can obtain the grad struct is to read it from the original MEG datasets. You can then combine it with data read from BESA. There is no support for the way BESA stores MEG sensor locations (I suspect it's a proprietary format). Best, Vladimir On Tue, Jan 13, 2009 at 1:20 PM, Astrid Steffen wrote: > Hi, > > I try to read MEG-files preprocessed in BESA into Fieldtrip therefore I use > the Besa2Fieldtrip-function. I'm wondering where to obtain the > grad-structure from: The sfp-files only contain headshape-information, the > elp-files contain the location-information but cannot be decoded, and the > pmg-file also cannot be read. At the moment, I use the 'read_fcdc_elec ' > command. Do you have any suggestions how to solve this problem? > > Thank you & best regards > Astrid > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/fcdonders/fieldtrip. > > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From vvw at CALTECH.EDU Tue Jan 13 18:01:05 2009 From: vvw at CALTECH.EDU (Virginie van Wassenhove) Date: Tue, 13 Jan 2009 18:01:05 +0100 Subject: neuromag data analysis Message-ID: Hello Fieldtrip-ers and happy new year! I am trying to get some Neuromag (MEG) data analysis done with Fieldtrip - so far I had used fieldtrip for EEG. I can read the data fine (segmentation via meg-pd) but there are a couple of issues now. 1. when I try to filter or downsample I am receiving the following errors: %FILTER (lpf specified in cfg) blah = timelockanalysis(cfg,data_std_bc); the input is timelock data with 306 channels and 801 timebins applying preprocessing options ??? Undefined function or method 'butter' for input arguments of type 'double'. Error in ==> preproc_lowpassfilter at 80 [B, A] = butter(N, max(Flp)/Fn); Error in ==> preproc at 360 if strcmp(cfg.lpfilter, 'yes'), dat = preproc_lowpassfilter(dat, fsample, cfg.lpfreq, cfg.lpfiltord, cfg.lpfilttype, cfg.lpfiltdir); end Error in ==> timelockanalysis at 318 [data.trial{i}, data.label, data.time{i}, cfg.preproc] = preproc(data.trial{i}, data.label, data.fsample, cfg.preproc, data.offset(i)); ================================= %RESAMPLE ??? Error: File: isequal.m Line: 1 Column: 1 The input character is not valid in MATLAB statements or expressions. Error in ==> checkdata at 145 if ~isequal(feedback, 'no') Error in ==> resampledata at 60 data = checkdata(data, 'datatype', 'raw', 'feedback', 'yes'); ================================= The data structure looks fine to me: data_dev1 = hdr: [1x1 struct] label: {306x1 cell} trial: {1x101 cell} time: {1x101 cell} fsample: 1000 grad: [1x1 struct] cfg: [1x1 struct] data_dev1.grad = pnt: [510x3 double] ori: [510x3 double] tra: [306x510 double] unit: 'cm' label: {1x306 cell} Any idea on these error messages? 2. The second issue is that doing a timelockanalysis on these data returns no neg or pos clusters. There is no error message and the computations seem to run fine. Am I missing some steps in the preliminary stages of data analysis for MEG in fieldtrip? Thanks for any help you may provide, Virginie ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From v.litvak at ION.UCL.AC.UK Tue Jan 13 18:34:28 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Tue, 13 Jan 2009 17:34:28 +0000 Subject: neuromag data analysis In-Reply-To: Message-ID: Dear Virginie, It looks very much like the problem is in your Matlab. The first error is definitely a result of missing signal processing toolbox. The second one looks like a version thing, but I'm not sure. If I understand correctly the third one, it might have to do with the absence of image processing toolbox that is used to compute clusters. Best, Vladimir On Tue, Jan 13, 2009 at 5:01 PM, Virginie van Wassenhove wrote: > Hello Fieldtrip-ers and happy new year! > > I am trying to get some Neuromag (MEG) data analysis done with Fieldtrip - so > far I had used fieldtrip for EEG. I can read the data fine (segmentation via > meg-pd) but there are a couple of issues now. > > 1. when I try to filter or downsample I am receiving the following errors: > > %FILTER (lpf specified in cfg) > blah = timelockanalysis(cfg,data_std_bc); > the input is timelock data with 306 channels and 801 timebins > applying preprocessing options > ??? Undefined function or method 'butter' for input arguments of type 'double'. > > Error in ==> preproc_lowpassfilter at 80 > [B, A] = butter(N, max(Flp)/Fn); > > Error in ==> preproc at 360 > if strcmp(cfg.lpfilter, 'yes'), dat = preproc_lowpassfilter(dat, > fsample, cfg.lpfreq, cfg.lpfiltord, > cfg.lpfilttype, cfg.lpfiltdir); end > > Error in ==> timelockanalysis at 318 > [data.trial{i}, data.label, data.time{i}, cfg.preproc] = > preproc(data.trial{i}, data.label, > data.fsample, cfg.preproc, data.offset(i)); > ================================= > %RESAMPLE > ??? Error: File: isequal.m Line: 1 Column: 1 > The input character is not valid in MATLAB statements or expressions. > > Error in ==> checkdata at 145 > if ~isequal(feedback, 'no') > > Error in ==> resampledata at 60 > data = checkdata(data, 'datatype', 'raw', 'feedback', 'yes'); > > ================================= > The data structure looks fine to me: > > data_dev1 = > hdr: [1x1 struct] > label: {306x1 cell} > trial: {1x101 cell} > time: {1x101 cell} > fsample: 1000 > grad: [1x1 struct] > cfg: [1x1 struct] > > data_dev1.grad = > pnt: [510x3 double] > ori: [510x3 double] > tra: [306x510 double] > unit: 'cm' > label: {1x306 cell} > > > Any idea on these error messages? > > 2. The second issue is that doing a timelockanalysis on these data returns > no neg or pos clusters. There is no error message and the computations seem > to run fine. > > Am I missing some steps in the preliminary stages of data analysis for MEG > in fieldtrip? > > Thanks for any help you may provide, > > Virginie > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. > > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From vvw at CALTECH.EDU Tue Jan 13 19:14:39 2009 From: vvw at CALTECH.EDU (Virginie van Wassenhove) Date: Tue, 13 Jan 2009 10:14:39 -0800 Subject: neuromag data analysis In-Reply-To: Message-ID: Dear Vladimir, thanks for your quick reply. I had double-checked the signal processing toolboxes appear in my path so not sure what is going on there but will double-check this shortly... Virginie Virginie.van-Wassenhove at cea.fr Virginie.van.Wassenhove at gmail.com > Dear Virginie, > > It looks very much like the problem is in your Matlab. The first error > is definitely a result of missing signal processing toolbox. The > second one looks like a version thing, but I'm not sure. If I > understand correctly the third one, it might have to do with the > absence of image processing toolbox that is used to compute clusters. > > Best, > > Vladimir > > > > On Tue, Jan 13, 2009 at 5:01 PM, Virginie van Wassenhove > wrote: >> Hello Fieldtrip-ers and happy new year! >> >> I am trying to get some Neuromag (MEG) data analysis done with Fieldtrip >> - so >> far I had used fieldtrip for EEG. I can read the data fine (segmentation >> via >> meg-pd) but there are a couple of issues now. >> >> 1. when I try to filter or downsample I am receiving the following >> errors: >> >> %FILTER (lpf specified in cfg) >> blah = timelockanalysis(cfg,data_std_bc); >> the input is timelock data with 306 channels and 801 timebins >> applying preprocessing options >> ??? Undefined function or method 'butter' for input arguments of type >> 'double'. >> >> Error in ==> preproc_lowpassfilter at 80 >> [B, A] = butter(N, max(Flp)/Fn); >> >> Error in ==> preproc at 360 >> if strcmp(cfg.lpfilter, 'yes'), dat = preproc_lowpassfilter(dat, >> fsample, cfg.lpfreq, cfg.lpfiltord, >> cfg.lpfilttype, cfg.lpfiltdir); end >> >> Error in ==> timelockanalysis at 318 >> [data.trial{i}, data.label, data.time{i}, cfg.preproc] = >> preproc(data.trial{i}, data.label, >> data.fsample, cfg.preproc, data.offset(i)); >> ================================= >> %RESAMPLE >> ??? Error: File: isequal.m Line: 1 Column: 1 >> The input character is not valid in MATLAB statements or expressions. >> >> Error in ==> checkdata at 145 >> if ~isequal(feedback, 'no') >> >> Error in ==> resampledata at 60 >> data = checkdata(data, 'datatype', 'raw', 'feedback', 'yes'); >> >> ================================= >> The data structure looks fine to me: >> >> data_dev1 = >> hdr: [1x1 struct] >> label: {306x1 cell} >> trial: {1x101 cell} >> time: {1x101 cell} >> fsample: 1000 >> grad: [1x1 struct] >> cfg: [1x1 struct] >> >> data_dev1.grad = >> pnt: [510x3 double] >> ori: [510x3 double] >> tra: [306x510 double] >> unit: 'cm' >> label: {1x306 cell} >> >> >> Any idea on these error messages? >> >> 2. The second issue is that doing a timelockanalysis on these data >> returns >> no neg or pos clusters. There is no error message and the computations >> seem >> to run fine. >> >> Am I missing some steps in the preliminary stages of data analysis for >> MEG >> in fieldtrip? >> >> Thanks for any help you may provide, >> >> Virginie >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users of >> the FieldTrip toolbox, to share experiences and to discuss new ideas >> for MEG and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/fcdonders/fieldtrip. >> >> > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/fcdonders/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Tue Jan 20 17:59:47 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 20 Jan 2009 17:59:47 +0100 Subject: neuromag data analysis In-Reply-To: <2671.88.187.2.13.1231870479.squirrel@webmail.caltech.edu> Message-ID: Hi Virginie Something like this >> which medfilt1 /Applications/MATLAB-2007b/toolbox/signal/signal/medfilt1.m >> which butter /Applications/MATLAB-2007b/toolbox/signal/signal/butter.m and this >> which bwlabeln /Applications/MATLAB-2007b/toolbox/images/images/bwlabeln.m should be able to indicate to you whether the signal and image processing toolbox are available on your path. I'll add descriptive checks and error messages at the appropriate location in the code. best regards, Robert On 13 Jan 2009, at 19:14, Virginie van Wassenhove wrote: > Dear Vladimir, > > thanks for your quick reply. I had double-checked the signal > processing > toolboxes appear in my path so not sure what is going on there but > will > double-check this shortly... > > > Virginie ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From amrgermany at YAHOO.COM Tue Jan 20 18:59:42 2009 From: amrgermany at YAHOO.COM (Amr Ayoub) Date: Tue, 20 Jan 2009 09:59:42 -0800 Subject: Empty Beamform tutorial page Message-ID: Hello, Applying beamforming techniques in the frequency domain in the Tutorials gives an empty page. Here is the link: http://neuroimaging.ruhosting.nl/fieldtrip/doku.php?id=fieldtrip:documentation:tutorial:beamformer Thanks Regards, Amr ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bmewang at YAHOO.COM Wed Jan 21 23:01:50 2009 From: bmewang at YAHOO.COM (Wei Wang) Date: Wed, 21 Jan 2009 23:01:50 +0100 Subject: SPM2 and SPM5 Message-ID: Hi FieldTrip friends, We're starting to use FieldTrip for our MEG data analysis. The main problem I have is that the FieldTrip toolbox does not segment my MRI data properly, e.g. it will miss a lot of gray matters. What would be the general suggestions for this type of problem? Is it possible for me to fine tune the segmentation parameters. Also, it seemed to me that FieldTrip uses SPM2 for the segmentation. I'm wondering if FieldTrip is going to switch to SPM5 or not, assuming that SPM5 is more recent than SPM2. Another thing is that we have a Elekta Neuromag Vectorview 306-channel system, different from the CTF system that FCDC uses. If somebody has been able to do source localization successfully with FieldTrip toolbox and Neuromag MEG data, do you mind me asking you a couple of quick questions? Thank you very much and I appreciate the help! Wei ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From v.litvak at ION.UCL.AC.UK Thu Jan 22 00:41:59 2009 From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak) Date: Wed, 21 Jan 2009 23:41:59 +0000 Subject: SPM2 and SPM5 In-Reply-To: Message-ID: Dear Wei, There is a lot of work being done now aimed at integrating Fieldtrip and SPM8. See http://neuroimaging.ruhosting.nl/fieldtrip/doku.php?id=fieldtrip:documentation:integrating_with_spm8 One of the features that will be available very soon (definitely by April 1, probably about a month from now) is the possibility to build subject-specific head models for MEG and EEG based on inverse-normalisation of template meshes, rather than segmentation. This will make it possible to get quite good head models even with suboptimal structural images (at least as good as those images possibly allow). Better support of Neuromag is also in the focus of our work right now. Neuromag is supported in Fieldtrip and SPM8 already using meg_pd toolbox and you can try analysing your data similarly to what you would do for CTF. However, there might be problems with some variants of Neuromag fif format, some of which are also platform dependent. We are working on developing a new Neuromag reader that will hopefully resolve these problems. So you may get started with the things that are already available and we hope that there will be improvements in these particular areas in the coming months. Best, Vladimir On Wed, Jan 21, 2009 at 10:01 PM, Wei Wang wrote: > Hi FieldTrip friends, > > We're starting to use FieldTrip for our MEG data analysis. The main problem I > have is that the FieldTrip toolbox does not segment my MRI data properly, > e.g. it will miss a lot of gray matters. What would be the general suggestions > for this type of problem? Is it possible for me to fine tune the segmentation > parameters. > > Also, it seemed to me that FieldTrip uses SPM2 for the segmentation. I'm > wondering if FieldTrip is going to switch to SPM5 or not, assuming that SPM5 > is more recent than SPM2. > > Another thing is that we have a Elekta Neuromag Vectorview 306-channel > system, different from the CTF system that FCDC uses. If somebody has > been able to do source localization successfully with FieldTrip toolbox and > Neuromag MEG data, do you mind me asking you a couple of quick questions? > > Thank you very much and I appreciate the help! > > Wei > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. > > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From bleichner.martin at GMAIL.COM Thu Jan 22 10:39:42 2009 From: bleichner.martin at GMAIL.COM (Martin Bleichner) Date: Thu, 22 Jan 2009 10:39:42 +0100 Subject: Permutation tests for time-frequency representations: Within trial experiments Message-ID: Hi there, I want to compute the permutation tests for time-frequency representations: within trial. In the tutorial it it stated that i have to select equal length intervals. 'To perform this comparison by means of a permutation test, we have to select equal-length non-overlapping time intervals in the baseline and the activation period.' However, my pre-stimulus and post-stimulus periods have a different length. My baseline is only 500 msec, while the post stimulus period is 1.5 and I am interested in the complete post-stimulus period. Are there possibilities to use unequal intervals? Would it make sense to split up the post stimulus period into 3 parts and compute the statistics for each post stimulus period? Thanks Best, Martin ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.maris at DONDERS.RU.NL Thu Jan 22 11:27:02 2009 From: e.maris at DONDERS.RU.NL (Eric Maris) Date: Thu, 22 Jan 2009 11:27:02 +0100 Subject: Permutation tests for time-frequency representations: Within trial experiments In-Reply-To: Message-ID: Hi Martin, I want to compute the permutation tests for time-frequency representations: within trial. In the tutorial it it stated that i have to select equal length intervals. 'To perform this comparison by means of a permutation test, we have to select equal-length non-overlapping time intervals in the baseline and the activation period.' However, my pre-stimulus and post-stimulus periods have a different length. My baseline is only 500 msec, while the post stimulus period is 1.5 and I am interested in the complete post-stimulus period. Are there possibilities to use unequal intervals? Would it make sense to split up the post stimulus period into 3 parts and compute the statistics for each post stimulus period? Yes, this is the way you should proceed. And, if you want to be safe on the statistical side, use Bonferroni correction (per-comparison alpha-level = 0.05/3) to accommodate for the fact that you run three tests instead of one. Good luck, Eric Maris Thanks Best, Martin ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Fri Jan 23 17:57:47 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Fri, 23 Jan 2009 17:57:47 +0100 Subject: SPM2 and SPM5 In-Reply-To: Message-ID: Hi Wei, On 21 Jan 2009, at 23:01, Wei Wang wrote: > Hi FieldTrip friends, > > We're starting to use FieldTrip for our MEG data analysis. The main > problem I > have is that the FieldTrip toolbox does not segment my MRI data > properly, > e.g. it will miss a lot of gray matters. What would be the general > suggestions > for this type of problem? Is it possible for me to fine tune the > segmentation > parameters. At the FCDC we are not really experts in segmentation. The volumesegment function contains defaults for SPM2 that work for our anatomical MRIs, i.e. for the particular sequence used on our MRI scanner whenever we send someone down to get a "MEG"-MRI. In SPM2/5/8 you of course have many more options for segmenting. The read_fcdc_mri function will read in anatomical MRIs' but also segmented MRIs. > Also, it seemed to me that FieldTrip uses SPM2 for the > segmentation. I'm > wondering if FieldTrip is going to switch to SPM5 or not, assuming > that SPM5 > is more recent than SPM2. There were some inconsistencies in the interface to the functions comparing SPM2 and SPM5, which is why we never swiched (and of course also because SPM2 already does the segmentation trick for us). We won't put effort into SPM5, but it is likely that the dependency on SPM2 functions will be replaced by the corresponding SPM8 functions. But it should also be easy to do the segmentation in SPM8 (e.g. with DARTEL) and read in the result for head-model generation and further processing in fieldtrip. MRI data formats are relatively simple to support, only the coordinate system alignment can be tricky. best regards, Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From mhamidi at WISC.EDU Fri Jan 23 21:12:08 2009 From: mhamidi at WISC.EDU (Massih Hamidi) Date: Fri, 23 Jan 2009 14:12:08 -0600 Subject: Measuring coherence at the source level Message-ID: Hi, I have used the beamformer technique with fieldtrip to produce source estimates of oscillatory activity in my EEG data. I've found two interesting sources and I'd like to know if there is any coherence (phase relationship) between the two. To test this, I would need to do phase coherence analyses at the scalp level between electrodes. Is there any way I could work backwards from the source estimate to the scalp electrode (i.e. which electrode describes each of the two sources best)? Or is there a better way to look at coherence between two brain regions? Thanks. -- Massih Hamidi Medical Scientist Training Program Neuroscience Training Program University of Wisconsin - Madison 1202 West Johnson St., Madison, WI 53706 608-265-3888 | mhamidi at wisc.edu ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Mon Jan 26 09:11:19 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 26 Jan 2009 09:11:19 +0100 Subject: Empty Beamform tutorial page In-Reply-To: <834428.63449.qm@web57416.mail.re1.yahoo.com> Message-ID: Hi Amr, Thanks for notifying us. Since moving to the new server there are some issues with the wiki. The caching of wiki pages fails somehow, which seems related to the neuroimaging.ruhosting.nl and fcdonders.ruhosting.nl confusion. In general (also to other users): if this happens the following workaround may help: If you fo to "edit" and then "preview" then you'll see the ful lcontent. I have upgraded the wiki CMS softare to the latest version, hopefully it solves the issue. best regards, Robert On 20 Jan 2009, at 18:59, Amr Ayoub wrote: > Hello, > > Applying beamforming techniques in the frequency domain in the > Tutorials gives an empty page. > Here is the link: > http://neuroimaging.ruhosting.nl/fieldtrip/doku.php?id=fieldtrip:documentation:tutorial:beamformer > > Thanks > Regards, > Amr > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From ana.acsousa at GMAIL.COM Mon Jan 26 12:07:39 2009 From: ana.acsousa at GMAIL.COM (Ana Carolina) Date: Mon, 26 Jan 2009 12:07:39 +0100 Subject: Ploting using easycap64ch-avg Message-ID: Dear FieldTrip users, I'm trying to plot EEG data using the easycap64ch-avg layout, but there seems to be a problem with the coordinate values because when I see the plot, the electrodes are not on the correct position. When I checked the values of the layout I saw that the values of the two first columns are not correct (I think), because if you think in all the electrodes that are in the same line like 35, 20, 8, 2, 1, 5, 14, 43 and 46 they should have the same value in the x- axis, but this doesn't happen. So, these and also all the other electrodes have small deviations like for example electrode 36 are not align whit the electrode 50 in y axis, etc. In this way I can't have a symmetrical plot of the electrodes. Does anybody have used this layout and have the same problem? Thanks in advance! regards, Ana Carolina ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Mon Jan 26 12:32:10 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 26 Jan 2009 12:32:10 +0100 Subject: Ploting using easycap64ch-avg In-Reply-To: <40538cdc0901260307u5a5a276dg4cd9978978fc1d1f@mail.gmail.com> Message-ID: Hi Ana, This is what I see. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Picture 1.png Type: image/png Size: 56013 bytes Desc: not available URL: -------------- next part -------------- It looks reasonable to me. The template layout files in fieldtrip/ template/*.lay that have "avg" in their name were all created by measuring the channel position on a few subjects' head with the polhemus tracker and averaging over those. Those measurements are not ideal, explaining the slight asymmetry. If you are not happy with this template layout (which I can imagine), I suggest you go to www.easycap.de, download a figure of the cap you are using, and use cfg =[] cfg.image = 'your_figure.gif' layout = prepare_layout(cfg); which will allow you to interactively click on each electrode position in the figure. You then also have to specify the outline of the head (including ears and nose) which will be displayed in black lines and the outline of the part of the head in which you want the interpolated data to show up (i.e. only the cricle of the head). best regards, Robert On 26 Jan 2009, at 12:07, Ana Carolina wrote: > Dear FieldTrip users, > > I'm trying to plot EEG data using the easycap64ch-avg layout, but > there seems to be a problem with the coordinate values because when > I see the plot, the electrodes are not on the correct position. When > I checked the values of the layout I saw that the values of the two > first columns are not correct (I think), because if you think in all > the electrodes that are in the same line like 35, 20, 8, 2, 1, 5, > 14, 43 and 46 they should have the same value in the x- axis, but > this doesn't happen. So, these and also all the other electrodes > have small deviations like for example electrode 36 are not align > whit the electrode 50 in y axis, etc. In this way I can't have a > symmetrical plot of the electrodes. > Does anybody have used this layout and have the same problem? > > Thanks in advance! > > regards, > Ana Carolina > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Mon Jan 26 14:45:31 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 26 Jan 2009 14:45:31 +0100 Subject: Workshop: Multimodal imaging in cognitive neuroscience Message-ID: Dear colleagues, The Donders Institute is pleased to announce: Multimodal imaging in cognitive neuroscience an international workshop of the Donders Institute 24 & 25 March 2009, the Netherlands The workshop aims at exploring how integrated multimodal neuroimaging could provide new ways of understanding brain functions. We will focus on two experimental situations that require integrated multimodal imaging: the quantification of the cerebral consequences of experimentally altered brain activity; and the analysis of dependencies between intrinsic and stimulus-driven cerebral dynamics. Speakers Sven Bestmann – Wellcome Centre for Neuroimaging, Institute of Neurology, University College, London Ralph D. Freeman – Vision Science Group, School of Optometry, and Helen Wills Neuroscience Institute, University of California, Berkeley Andreas Kleinschmidt – NeuroSpin, Gif-sur-Yvette, France David Leopold – Unit on Cognitive Neurophysiology and Imaging, Laboratory of Neuropsychology, National Institute of Mental health, USA Registration and further details http://www.ru.nl/donders/home/agenda/multimodel/ 24 & 25 March 2009 Donders Institute for Brain, Cognition and Behaviour Radboud University Nijmegen The Netherlands ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Multimodal_eFlyer.pdf Type: application/pdf Size: 211157 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.debener at UKE.UNI-HAMBURG.DE Tue Jan 27 10:49:30 2009 From: s.debener at UKE.UNI-HAMBURG.DE (Stefan Debener) Date: Tue, 27 Jan 2009 09:49:30 +0000 Subject: MEG/EEG post-doc position in Jena, Germany Message-ID: Post-Doc Position at the Biomagnetic Center Jena, Germany A two-year post-doc position is available at the Biomagnetic Center Jena. Biomagnetism has a long-standing tradition in Jena and the group consists of a young, interdisciplinary and international research team and a new head of department (Prof. S. Debener). The Biomag Center comprises several labs, including a new 306/128-channel whole-head MEG/EEG system (Neuromag). Areas of research are multisensory processing, somatosensory and pain research, cortical re-organization after cochlear implantation, neurocognition of temporal attention, and EEG-fMRI integration. The post-doc will have a strong interest in using independent component analysis for the analysis of EEG, MEG, and combined EEG-MEG recordings. Expertise in multichannel EEG or MEG analysis is mandatory, as well as a good theoretical background in biosignal processing, experimental neurosciences, or both. For further enquiries, please contact Stefan Debener. International applications are welcome. Please send your application (CV, list of publications, contact information for two references) to debener at biomag.uni-jena.de. Closing date is February 15, 2009. -- Prof. Dr. Stefan Debener Biomagnetic Center Dept. of Neurology University Hospital Jena Erlanger Allee 101 D-07747 Jena Germany Phone: +49-3641-9325770 Fax: +49-3641-9325772 Email: debener at biomag.uni-jena.de ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Tue Jan 27 17:54:48 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 27 Jan 2009 17:54:48 +0100 Subject: problems with wiki -> empty pages In-Reply-To: Message-ID: Dear all We are experiencing technical problems with the fieldtrip wiki. I had hoped that installing a new version of the software would fix it as I explained in a previous mail, and on Sunday that indeed seemed to solve it. But today the problems reappeared, even in more severe form. After trying to diagnose it and discussing it with some technical colleagues here and with some input from the ruhosting server system administrator (who is not part of our department), the working diagnosis is that there is a performance problem on the server hardware. The ruhosting machine is shared by many people, and it seems that high traffic in general (not the case on Sunday) combined with fieldtrip wiki edits (which happened a lot today) causes the hickups. These then result in empty pages in the cache and empty pages being displayed. Note that all the documents are still there. A workaround for the problem is to click the "edit" button and then click the "preview" button. That circumvents the caching, and for me results in a correect display of the page content. At the moment I cannot solve it, but tomorrow I'll again start bugging the sysadmin. I'll try to clear the cache as often as possible (because immediately after that, it looks OK). Sorry for the inconvenience, Robert On 27 Jan 2009, at 17:04, Vladimir Litvak wrote: > The problem is still there. I've just experienced it with the > statistics tutorial. Your suggestion works, but I'd like to send a > link to somebody so it'd be much simpler if you fix it. > > Vladimir > > On Mon, Jan 26, 2009 at 8:11 AM, Robert Oostenveld > wrote: >> Hi Amr, >> >> Thanks for notifying us. Since moving to the new server there are >> some >> issues with the wiki. The caching of wiki pages fails somehow, >> which seems >> related to the neuroimaging.ruhosting.nl and fcdonders.ruhosting.nl >> confusion. >> >> In general (also to other users): if this happens the following >> workaround >> may help: If you fo to "edit" and then "preview" then you'll see >> the ful >> lcontent. >> >> I have upgraded the wiki CMS softare to the latest version, >> hopefully it >> solves the issue. >> >> best regards, >> Robert > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.