From r.oostenveld at FCDONDERS.KUN.NL Thu Aug 5 09:24:22 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Thu, 5 Aug 2004 09:24:22 +0200 Subject: new functions Message-ID: Dear fieldtrippers, I have implemented three new functions that all relate to SOURECANALYSIS, and are especially relevant to help reduce memory requirements in randomization stats. SOURCE2GRID should help you to remove all the unneccesary items from a sourcestructure, so that you can use it in cfg.grid for sourceanalysis. SOURCE2SPARSE removes all dipole locations from a source structure that are outside teh head. Source strength at these locations is not computed anyway, so it does not make the computation faster, but those locations do take up memory. The reduced sourecspace (or precomputred grid) can take ~2x up to 10x as less memory as the full sourcespace. SOURCE2FULL is the opposite from source2sparse and it will add all outside locations again, recreating the complete source volume that you can plot, interpolate and export. I hope that they are all bug free, but they have not yet been tested extensively. Use with caution. best regards, Robert PS the functions are available as usual in the FC Donders internal /home/common/matlab/fieldtrip directory ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From r.oostenveld at FCDONDERS.KUN.NL Thu Aug 5 16:56:54 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Thu, 5 Aug 2004 16:56:54 +0200 Subject: statistical analysis over subjects Message-ID: Dear FieldTrippers, I have implemented a function called SOURCWRITE, which can read in functional data from an Analyze file. With this function, you can combine the functional data from multiple subjects _after_ aligning the subjects anatomical+functional data to a common anatomical template brain, and subsequently you can perform group-level statistics. The supports importing either a single condition or two conditions. In the case of two conditions, the function also supports randomization or permutation (needed for non-parametric testing). The function returns a structure that is equivalent to the output of the sourceanalysis function, and you can put the data into sourcestatistics directly. Some details for the realignment to a template brain with SPM and/or BrainVoyager have already been sorted out by JM and Markus Siegel, but there is still some work that needs to be done there. If you are interested in group-analysis contact me and we can try to get it to work completely. best regards, Robert From roberto at SMI.AUC.DK Fri Aug 6 10:58:28 2004 From: roberto at SMI.AUC.DK (Robert Oostenveld) Date: Fri, 6 Aug 2004 10:58:28 +0200 Subject: plotting headmodel Message-ID: Hi I implemented a new function in FieldTrip for plotting headmodels. Sofar it only works for CTF multiple-sphere models, but that is where it is needed most. The function is called HEADMODELPLOT, and it can make different visualisations of the gradiometers and the spheres which can help you to verify the correctness of your localSpheres.hdm files. Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From roberto at SMI.AUC.DK Fri Aug 6 11:14:33 2004 From: roberto at SMI.AUC.DK (Robert Oostenveld) Date: Fri, 6 Aug 2004 11:14:33 +0200 Subject: statistical analysis over subjects In-Reply-To: Message-ID: Hi A small correction on my mail of yesterday: the function is called SOURCEREAD and not sourcewrite. The sourcewrite function already existed and should be used to export your functional data to Analyze files prior to realiging. Robert On 5 Aug 2004, at 16:56, Robert Oostenveld wrote: > Dear FieldTrippers, > > I have implemented a function called SOURCWRITE, which can read in > functional data from an Analyze file. With this function, you can > combine the functional data from multiple subjects _after_ aligning the > subjects anatomical+functional data to a common anatomical template > brain, and subsequently you can perform group-level statistics. The > supports importing either a single condition or two conditions. In the > case of two conditions, the function also supports randomization or > permutation (needed for non-parametric testing). The function returns a > structure that is equivalent to the output of the sourceanalysis > function, and you can put the data into sourcestatistics directly. > > Some details for the realignment to a template brain with SPM and/or > BrainVoyager have already been sorted out by JM and Markus Siegel, but > there is still some work that needs to be done there. If you are > interested in group-analysis contact me and we can try to get it to > work completely. > > best regards, > Robert > ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From r.oostenveld at FCDONDERS.KUN.NL Mon Aug 16 12:11:24 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Mon, 16 Aug 2004 12:11:24 +0200 Subject: beamforming and precomputed leadfields Message-ID: Hi FieldTrippers, Last weeks BIOMAG was fun, and I got quite some new ideas that I already starten implementing. FieldTrip is definitely on the right track and gained a lot of attention. On the code level: I have made some modifications to the way that leadfields are kept and/or precomputed. The old options of SOURCANALYSIS are still supported, but there is also a new function PRECOMPUTE_LEADFIELD. I suggest that you use the new function if you want to perform resampling/randomization based source analysis and statistics. Furthermore, we discovered a "feature" of the beamformer method that is not so nice. Although it is not really a bug, but it might mess up your sourceanalysis results if you are using multisphere headmodels as most of us do. The problem has to do with the radial dipole component and noise projection. If you are at the moment busy with sourceanalysis, please contact me as soon as possible(!!) and I will explain it and show you the workaround that is already implemented. For the rest of you: I will explain it in more detail in this weeks thursday MEG meeting. best regards, Robert From r.oostenveld at FCDONDERS.KUN.NL Mon Aug 16 13:15:49 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Mon, 16 Aug 2004 13:15:49 +0200 Subject: randomization vs. permutation Message-ID: Hi FieldTrippers, As you all know, we are already heavily using randomization methods for our statistics (e.g. in SOURCEANALYSIS or in RANDCLUSTERANALYSIS). Likewise, jacknife and bootstrap estimates of variance are available in SOURECANALYSIS and FREQANALYSIS (for coherence). These methods (i.e. jacknife, bootstrap, randomization) can all be shared under the common umbrella of resampling theory, and there is another obvious resampling that sofar was not implemented yet: PERMUTATION. Whereas in randomization you throw all trials over both conditions together and then randomly re-assigned them to the two conditions, in permutation the trials in condition A and B are selectively swapped (at random) between conditions. Therefore the number of trials should be the same. Permutation actually is a specific instance of randomization. The null-hypothesis that you are testing using either the randomization or permutation is slightly different. Using randomization, you assume that all trials in condition A and condition B come from the same distribution. Using permutation, you only assume that the i-th trial of condition A comes from the same distribution as the i-th trial of condition B. Therefore permutation is a more natural choise for baseline vs. active comparisons (comparing the pre- and post-stimulus interval of every trial) and I also suspect that the permutation based approach will result in more statistical power. Of course you can only apply the permutation method if your data contains trials in A and B that can be directly compared. best regards, Robert From roberto at SMI.AUC.DK Thu Aug 19 09:16:25 2004 From: roberto at SMI.AUC.DK (Robert Oostenveld) Date: Thu, 19 Aug 2004 09:16:25 +0200 Subject: parametric sourcestatistics Message-ID: Hi, I have made some changes to SOURCESTATISTICS_PARAMETRIC that can result in backward incompatibilities: - removed nai and pseudo-t as methods (see SOURCDESCRIPTIVES) - changed interpretation of cfg.threshold for consistency with other functions - removed inconsistent and untested conversion from t- to z-score Although I have tried to check for those options and give a warning or error if you use them in your scripts, you still should be acutious if you think that these changes affect your analysis. Contact me if you have questions about it. best, Robert PS. About my previous mail regarding resampling methods (randomization/permutation): that mail only applied to the source-level analysis, those of you who are using CLUSTERRANDANALYSIS on the channel level already had the option for using permutation in a within-subject-design (as Eric pointed me out). ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From r.oostenveld at FCDONDERS.KUN.NL Thu Aug 19 12:35:57 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Thu, 19 Aug 2004 12:35:57 +0200 Subject: preprocessing cleanup Message-ID: Dear FieldTrippers, Related to the upcoming release of FieldTrip, I am busy cleaning up parts of the code that are not so clear at the moment. One of them is preprocessing and definetrial. Currently the preprocessing function is reading multiple datatypes at once and giving each of them a different treatment. This clearly reflects that preprocessing was initially written for MEG data and that other dataformats were added later. Specifically, these two sections in the help of preprocessing are what bothers me. % Specific preprocessing options for EMG channels are % cfg.emgchannel = cell-array with the label(s) of EMG channels % cfg.emghpfreq = high-pass frequency % cfg.emgrectify = 'yes' or 'no' % cfg.emghilbert = 'yes' or 'no' % % Specific preprocessing options for EEG channels are % cfg.eegchannel = cell-array with the label(s) of EEG channels % cfg.implicitref = 'label' or empty, add the implicit reference as zeros prior to rereferencing % cfg.refchannel = cell-array with new reference channel(s) % cfg.reref = 'no' or 'yes' All other preprocessing options are applied to MEG as well as to EMG and EOG channel groups, which means that you currently can NOT apply different filter settings for EMG and MEG channels, or apply baseline correction to only one of them. I would like to suggest the following changes 1) there will be no MEG/EEG/EMG specific options any more 2) preprocessing will treat all channels the same 3) if you want to apply different settings to different channel groups (e.g. to the MEG and the EEG channels), you should call preprocessing twice and concatenate the resulting raw data objects. These changes will facilitate further improvements of the preprocessing function, as well of the artifact detection routines. Regarding item 3: I can of course explain how to do it (or I could even write a general function for that). Important for item 3 is that it will not be neccessary to redo the artifact detection multiple times for the different channel groups that you want to concatenate. I would like to get your feedback on the following two items: At the moment I am only aware of Jan-Mathijs mixing different channel groups in his analyses, so please let me know if you are also using EMG and/or EEG channels and their specific preprocessing options. Furthermore, if you have particular opinions about this issue, let me know as soon as ppossible (either to me directly, through the fieldtrip list or at the thursday MEG meeting). If I don't get any objections, I will implement the changes as suggested. best regards, Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From Pascal.Fries at FCDONDERS.KUN.NL Thu Aug 19 12:41:46 2004 From: Pascal.Fries at FCDONDERS.KUN.NL (Pascal Fries) Date: Thu, 19 Aug 2004 12:41:46 +0200 Subject: preprocessing cleanup In-Reply-To: <8E475CF9-F1CB-11D8-9CB1-000A95DBB2CC@fcdonders.kun.nl> Message-ID: Hi Robert, I suggest that we discuss this at the fieldtrip meeting. Best, Pascal > -----Original Message----- > From: FieldTrip discussion list > [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Robert Oostenveld > Sent: Thursday, August 19, 2004 12:36 PM > To: FIELDTRIP at NIC.SURFNET.NL > Subject: [FIELDTRIP] preprocessing cleanup > > Dear FieldTrippers, > > Related to the upcoming release of FieldTrip, I am busy > cleaning up parts of the code that are not so clear at the > moment. One of them is preprocessing and definetrial. > Currently the preprocessing function is reading multiple > datatypes at once and giving each of them a different > treatment. This clearly reflects that preprocessing was > initially written for MEG data and that other dataformats > were added later. > Specifically, these two sections in the help of preprocessing > are what bothers me. > > % Specific preprocessing options for EMG channels are > % cfg.emgchannel = cell-array with the label(s) of EMG channels > % cfg.emghpfreq = high-pass frequency > % cfg.emgrectify = 'yes' or 'no' > % cfg.emghilbert = 'yes' or 'no' > % > % Specific preprocessing options for EEG channels are > % cfg.eegchannel = cell-array with the label(s) of EEG channels > % cfg.implicitref = 'label' or empty, add the implicit reference as > zeros prior to rereferencing > % cfg.refchannel = cell-array with new reference channel(s) > % cfg.reref = 'no' or 'yes' > > All other preprocessing options are applied to MEG as well as > to EMG and EOG channel groups, which means that you currently > can NOT apply different filter settings for EMG and MEG > channels, or apply baseline correction to only one of them. > > I would like to suggest the following changes > 1) there will be no MEG/EEG/EMG specific options any more > 2) preprocessing will treat all channels the same > 3) if you want to apply different settings to different > channel groups (e.g. to the MEG and the EEG channels), you > should call preprocessing twice and concatenate the resulting > raw data objects. > > These changes will facilitate further improvements of the > preprocessing function, as well of the artifact detection > routines. Regarding item 3: > I can of course explain how to do it (or I could even write a > general function for that). Important for item 3 is that it > will not be neccessary to redo the artifact detection > multiple times for the different channel groups that you want > to concatenate. > > I would like to get your feedback on the following two items: > At the moment I am only aware of Jan-Mathijs mixing different > channel groups in his analyses, so please let me know if you > are also using EMG and/or EEG channels and their specific > preprocessing options. Furthermore, if you have particular > opinions about this issue, let me know as soon as ppossible > (either to me directly, through the fieldtrip list or at the > thursday MEG meeting). If I don't get any objections, I will > implement the changes as suggested. > > best regards, > Robert > > > ---------------------------------------------------------------------- > Robert Oostenveld, PhD > Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark > > and > > F.C. Donders Centre for Cognitive Neuroimaging University > Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands > > Tel: +31 (0)24 3619695 > Fax: +31 (0)24 3610989 > From christian.forkstam at FCDONDERS.KUN.NL Thu Aug 19 13:06:15 2004 From: christian.forkstam at FCDONDERS.KUN.NL (christian forkstam) Date: Thu, 19 Aug 2004 13:06:15 +0200 Subject: preprocessing cleanup In-Reply-To: <8E475CF9-F1CB-11D8-9CB1-000A95DBB2CC@fcdonders.kun.nl> Message-ID: hey master fieldtripper, if i understand the proposed modification correctly it seems like a perfect idea to me. just to make sure i don't loose the possibility to rereference my EEG data i just want to secure this option. as far as i understan it does not hurt to include the possibility for both MEG/EEG/EMG analysis but you know that better. the options of concern: % cfg.implicitref = 'label' or empty, add the implicit reference as zeros prior to rereferencing % cfg.refchannel = cell-array with new reference channel(s) % cfg.reref = 'no' or 'yes' ...christian (soon out tripping the fields of a nothern swedish mountain area...) Robert Oostenveld wrote: > Dear FieldTrippers, > > Related to the upcoming release of FieldTrip, I am busy cleaning up > parts of the code that are not so clear at the moment. One of them is > preprocessing and definetrial. Currently the preprocessing function is > reading multiple datatypes at once and giving each of them a different > treatment. This clearly reflects that preprocessing was initially > written for MEG data and that other dataformats were added later. > Specifically, these two sections in the help of preprocessing are what > bothers me. > > % Specific preprocessing options for EMG channels are > % cfg.emgchannel = cell-array with the label(s) of EMG channels > % cfg.emghpfreq = high-pass frequency > % cfg.emgrectify = 'yes' or 'no' > % cfg.emghilbert = 'yes' or 'no' > % > % Specific preprocessing options for EEG channels are > % cfg.eegchannel = cell-array with the label(s) of EEG channels > % cfg.implicitref = 'label' or empty, add the implicit reference as > zeros prior to rereferencing > % cfg.refchannel = cell-array with new reference channel(s) > % cfg.reref = 'no' or 'yes' > > All other preprocessing options are applied to MEG as well as to EMG > and EOG channel groups, which means that you currently can NOT apply > different filter settings for EMG and MEG channels, or apply baseline > correction to only one of them. > > I would like to suggest the following changes > 1) there will be no MEG/EEG/EMG specific options any more > 2) preprocessing will treat all channels the same > 3) if you want to apply different settings to different channel > groups (e.g. to the MEG and the EEG channels), you should call > preprocessing twice and concatenate the resulting raw data objects. > > These changes will facilitate further improvements of the preprocessing > function, as well of the artifact detection routines. Regarding item 3: > I can of course explain how to do it (or I could even write a general > function for that). Important for item 3 is that it will not be > neccessary to redo the artifact detection multiple times for the > different channel groups that you want to concatenate. > > I would like to get your feedback on the following two items: At the > moment I am only aware of Jan-Mathijs mixing different channel groups > in his analyses, so please let me know if you are also using EMG and/or > EEG channels and their specific preprocessing options. Furthermore, if > you have particular opinions about this issue, let me know as soon as > ppossible (either to me directly, through the fieldtrip list or at the > thursday MEG meeting). If I don't get any objections, I will implement > the changes as suggested. > > best regards, > Robert > > > ---------------------------------------------------------------------- > Robert Oostenveld, PhD > Center for Sensory-Motor Interaction (SMI) > Aalborg University, Denmark > > and > > F.C. Donders Centre for Cognitive Neuroimaging > University Nijmegen > P.O. Box 9101 > NL-6500 AH Nijmegen > The Netherlands > > Tel: +31 (0)24 3619695 > Fax: +31 (0)24 3610989 From roberto at SMI.AUC.DK Thu Aug 19 13:33:55 2004 From: roberto at SMI.AUC.DK (Robert Oostenveld) Date: Thu, 19 Aug 2004 13:33:55 +0200 Subject: preprocessing cleanup In-Reply-To: <412489A7.6020000@fcdonders.kun.nl> Message-ID: Hi Christian, Rereferencing for EEG data will certainly remain included. My suggestion would be to implement rereferencing as a general option, i.e. cfg.implicitref cfg.refchannel cfg.reref would apply to all channels that are listed in cfg.channel, and cfg.eegchannel would be obsoleted. This does mean that people in principle could also apply nonsense rereferencing to MEG channels, but if they are that stupid... Robert On 19 Aug 2004, at 13:06, christian forkstam wrote: > hey master fieldtripper, > > if i understand the proposed modification correctly it seems like a > perfect idea to me. just to make sure i don't loose the possibility to > rereference my EEG data i just want to secure this option. as far as i > understan it does not hurt to include the possibility for both > MEG/EEG/EMG analysis but you know that better. > > the options of concern: > > % cfg.implicitref = 'label' or empty, add the implicit reference as > zeros prior to rereferencing > % cfg.refchannel = cell-array with new reference channel(s) > % cfg.reref = 'no' or 'yes' > > ...christian > (soon out tripping the fields of a nothern swedish mountain area...) > > > Robert Oostenveld wrote: >> Dear FieldTrippers, >> >> Related to the upcoming release of FieldTrip, I am busy cleaning up >> parts of the code that are not so clear at the moment. One of them is >> preprocessing and definetrial. Currently the preprocessing function is >> reading multiple datatypes at once and giving each of them a different >> treatment. This clearly reflects that preprocessing was initially >> written for MEG data and that other dataformats were added later. >> Specifically, these two sections in the help of preprocessing are what >> bothers me. >> >> % Specific preprocessing options for EMG channels are >> % cfg.emgchannel = cell-array with the label(s) of EMG channels >> % cfg.emghpfreq = high-pass frequency >> % cfg.emgrectify = 'yes' or 'no' >> % cfg.emghilbert = 'yes' or 'no' >> % >> % Specific preprocessing options for EEG channels are >> % cfg.eegchannel = cell-array with the label(s) of EEG channels >> % cfg.implicitref = 'label' or empty, add the implicit reference as >> zeros prior to rereferencing >> % cfg.refchannel = cell-array with new reference channel(s) >> % cfg.reref = 'no' or 'yes' >> >> All other preprocessing options are applied to MEG as well as to EMG >> and EOG channel groups, which means that you currently can NOT apply >> different filter settings for EMG and MEG channels, or apply baseline >> correction to only one of them. >> >> I would like to suggest the following changes >> 1) there will be no MEG/EEG/EMG specific options any more >> 2) preprocessing will treat all channels the same >> 3) if you want to apply different settings to different channel >> groups (e.g. to the MEG and the EEG channels), you should call >> preprocessing twice and concatenate the resulting raw data objects. >> >> These changes will facilitate further improvements of the >> preprocessing >> function, as well of the artifact detection routines. Regarding item >> 3: >> I can of course explain how to do it (or I could even write a general >> function for that). Important for item 3 is that it will not be >> neccessary to redo the artifact detection multiple times for the >> different channel groups that you want to concatenate. >> >> I would like to get your feedback on the following two items: At the >> moment I am only aware of Jan-Mathijs mixing different channel groups >> in his analyses, so please let me know if you are also using EMG >> and/or >> EEG channels and their specific preprocessing options. Furthermore, if >> you have particular opinions about this issue, let me know as soon as >> ppossible (either to me directly, through the fieldtrip list or at the >> thursday MEG meeting). If I don't get any objections, I will implement >> the changes as suggested. >> >> best regards, >> Robert >> >> >> ---------------------------------------------------------------------- >> Robert Oostenveld, PhD >> Center for Sensory-Motor Interaction (SMI) >> Aalborg University, Denmark >> >> and >> >> F.C. Donders Centre for Cognitive Neuroimaging >> University Nijmegen >> P.O. Box 9101 >> NL-6500 AH Nijmegen >> The Netherlands >> >> Tel: +31 (0)24 3619695 >> Fax: +31 (0)24 3610989 >> ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From r.oostenveld at FCDONDERS.KUN.NL Fri Aug 20 09:02:38 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Fri, 20 Aug 2004 09:02:38 +0200 Subject: preprocessing Message-ID: Hi FieldTrippers, Following yesterdays discussion, I have modified preprocessing according to my proposal: all channels are now treated the same. If you try to use one of the old options (eegchannel, emghilbert, etc.) it will give an error. The operation to separate out DEFINETRIAL and REJECTARTIFACT from preprosessing will mainly be in the documentation, and should also not affect your current configurations and scripts. Therefore I will proceed with that as well, but will not notify you of it specifically. best regards Robert From Pascal.Fries at FCDONDERS.KUN.NL Wed Aug 25 11:32:35 2004 From: Pascal.Fries at FCDONDERS.KUN.NL (Pascal Fries) Date: Wed, 25 Aug 2004 11:32:35 +0200 Subject: freqdescriptives In-Reply-To: Message-ID: Dear fieldtrippers, I have just committed a new function to fieldtrip: freqdescriptives. It is meant to replace the old and not really fieldtrip-like frqanajckstatistic. I have tested it, but please report bugs! Pascal Pascal Fries Principal Investigator Neuronal Coherence Group F. C. Donders Centre for Cognitive Neuroimaging University of Nijmegen Adelbertusplein 1 6525 EK Nijmegen The Netherlands Phone: (+31) (0)24 36 10657 Fax: (+31) (0)24 36 10989 e-mail: pascal.fries at fcdonders.kun.nl website: www.kun.nl/fcdonders/ From m.siegel at UKE.UNI-HAMBURG.DE Thu Aug 26 14:04:42 2004 From: m.siegel at UKE.UNI-HAMBURG.DE (Markus Siegel) Date: Thu, 26 Aug 2004 14:04:42 +0200 Subject: new functions in CVS Message-ID: Dear fieldtrippers, I have added sliceinterp.m and sourcestatistics_randomization.m to the CVS. No changes to sourcestatistics_randomization.m sliceinterp.m has now cfg.whitebg = 'yes' as defaul and a bug concerning user-colormaps has been fixed. Best, Markus Siegel From r.oostenveld at FCDONDERS.KUN.NL Thu Aug 5 09:24:22 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Thu, 5 Aug 2004 09:24:22 +0200 Subject: new functions Message-ID: Dear fieldtrippers, I have implemented three new functions that all relate to SOURECANALYSIS, and are especially relevant to help reduce memory requirements in randomization stats. SOURCE2GRID should help you to remove all the unneccesary items from a sourcestructure, so that you can use it in cfg.grid for sourceanalysis. SOURCE2SPARSE removes all dipole locations from a source structure that are outside teh head. Source strength at these locations is not computed anyway, so it does not make the computation faster, but those locations do take up memory. The reduced sourecspace (or precomputred grid) can take ~2x up to 10x as less memory as the full sourcespace. SOURCE2FULL is the opposite from source2sparse and it will add all outside locations again, recreating the complete source volume that you can plot, interpolate and export. I hope that they are all bug free, but they have not yet been tested extensively. Use with caution. best regards, Robert PS the functions are available as usual in the FC Donders internal /home/common/matlab/fieldtrip directory ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From r.oostenveld at FCDONDERS.KUN.NL Thu Aug 5 16:56:54 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Thu, 5 Aug 2004 16:56:54 +0200 Subject: statistical analysis over subjects Message-ID: Dear FieldTrippers, I have implemented a function called SOURCWRITE, which can read in functional data from an Analyze file. With this function, you can combine the functional data from multiple subjects _after_ aligning the subjects anatomical+functional data to a common anatomical template brain, and subsequently you can perform group-level statistics. The supports importing either a single condition or two conditions. In the case of two conditions, the function also supports randomization or permutation (needed for non-parametric testing). The function returns a structure that is equivalent to the output of the sourceanalysis function, and you can put the data into sourcestatistics directly. Some details for the realignment to a template brain with SPM and/or BrainVoyager have already been sorted out by JM and Markus Siegel, but there is still some work that needs to be done there. If you are interested in group-analysis contact me and we can try to get it to work completely. best regards, Robert From roberto at SMI.AUC.DK Fri Aug 6 10:58:28 2004 From: roberto at SMI.AUC.DK (Robert Oostenveld) Date: Fri, 6 Aug 2004 10:58:28 +0200 Subject: plotting headmodel Message-ID: Hi I implemented a new function in FieldTrip for plotting headmodels. Sofar it only works for CTF multiple-sphere models, but that is where it is needed most. The function is called HEADMODELPLOT, and it can make different visualisations of the gradiometers and the spheres which can help you to verify the correctness of your localSpheres.hdm files. Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From roberto at SMI.AUC.DK Fri Aug 6 11:14:33 2004 From: roberto at SMI.AUC.DK (Robert Oostenveld) Date: Fri, 6 Aug 2004 11:14:33 +0200 Subject: statistical analysis over subjects In-Reply-To: Message-ID: Hi A small correction on my mail of yesterday: the function is called SOURCEREAD and not sourcewrite. The sourcewrite function already existed and should be used to export your functional data to Analyze files prior to realiging. Robert On 5 Aug 2004, at 16:56, Robert Oostenveld wrote: > Dear FieldTrippers, > > I have implemented a function called SOURCWRITE, which can read in > functional data from an Analyze file. With this function, you can > combine the functional data from multiple subjects _after_ aligning the > subjects anatomical+functional data to a common anatomical template > brain, and subsequently you can perform group-level statistics. The > supports importing either a single condition or two conditions. In the > case of two conditions, the function also supports randomization or > permutation (needed for non-parametric testing). The function returns a > structure that is equivalent to the output of the sourceanalysis > function, and you can put the data into sourcestatistics directly. > > Some details for the realignment to a template brain with SPM and/or > BrainVoyager have already been sorted out by JM and Markus Siegel, but > there is still some work that needs to be done there. If you are > interested in group-analysis contact me and we can try to get it to > work completely. > > best regards, > Robert > ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From r.oostenveld at FCDONDERS.KUN.NL Mon Aug 16 12:11:24 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Mon, 16 Aug 2004 12:11:24 +0200 Subject: beamforming and precomputed leadfields Message-ID: Hi FieldTrippers, Last weeks BIOMAG was fun, and I got quite some new ideas that I already starten implementing. FieldTrip is definitely on the right track and gained a lot of attention. On the code level: I have made some modifications to the way that leadfields are kept and/or precomputed. The old options of SOURCANALYSIS are still supported, but there is also a new function PRECOMPUTE_LEADFIELD. I suggest that you use the new function if you want to perform resampling/randomization based source analysis and statistics. Furthermore, we discovered a "feature" of the beamformer method that is not so nice. Although it is not really a bug, but it might mess up your sourceanalysis results if you are using multisphere headmodels as most of us do. The problem has to do with the radial dipole component and noise projection. If you are at the moment busy with sourceanalysis, please contact me as soon as possible(!!) and I will explain it and show you the workaround that is already implemented. For the rest of you: I will explain it in more detail in this weeks thursday MEG meeting. best regards, Robert From r.oostenveld at FCDONDERS.KUN.NL Mon Aug 16 13:15:49 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Mon, 16 Aug 2004 13:15:49 +0200 Subject: randomization vs. permutation Message-ID: Hi FieldTrippers, As you all know, we are already heavily using randomization methods for our statistics (e.g. in SOURCEANALYSIS or in RANDCLUSTERANALYSIS). Likewise, jacknife and bootstrap estimates of variance are available in SOURECANALYSIS and FREQANALYSIS (for coherence). These methods (i.e. jacknife, bootstrap, randomization) can all be shared under the common umbrella of resampling theory, and there is another obvious resampling that sofar was not implemented yet: PERMUTATION. Whereas in randomization you throw all trials over both conditions together and then randomly re-assigned them to the two conditions, in permutation the trials in condition A and B are selectively swapped (at random) between conditions. Therefore the number of trials should be the same. Permutation actually is a specific instance of randomization. The null-hypothesis that you are testing using either the randomization or permutation is slightly different. Using randomization, you assume that all trials in condition A and condition B come from the same distribution. Using permutation, you only assume that the i-th trial of condition A comes from the same distribution as the i-th trial of condition B. Therefore permutation is a more natural choise for baseline vs. active comparisons (comparing the pre- and post-stimulus interval of every trial) and I also suspect that the permutation based approach will result in more statistical power. Of course you can only apply the permutation method if your data contains trials in A and B that can be directly compared. best regards, Robert From roberto at SMI.AUC.DK Thu Aug 19 09:16:25 2004 From: roberto at SMI.AUC.DK (Robert Oostenveld) Date: Thu, 19 Aug 2004 09:16:25 +0200 Subject: parametric sourcestatistics Message-ID: Hi, I have made some changes to SOURCESTATISTICS_PARAMETRIC that can result in backward incompatibilities: - removed nai and pseudo-t as methods (see SOURCDESCRIPTIVES) - changed interpretation of cfg.threshold for consistency with other functions - removed inconsistent and untested conversion from t- to z-score Although I have tried to check for those options and give a warning or error if you use them in your scripts, you still should be acutious if you think that these changes affect your analysis. Contact me if you have questions about it. best, Robert PS. About my previous mail regarding resampling methods (randomization/permutation): that mail only applied to the source-level analysis, those of you who are using CLUSTERRANDANALYSIS on the channel level already had the option for using permutation in a within-subject-design (as Eric pointed me out). ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From r.oostenveld at FCDONDERS.KUN.NL Thu Aug 19 12:35:57 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Thu, 19 Aug 2004 12:35:57 +0200 Subject: preprocessing cleanup Message-ID: Dear FieldTrippers, Related to the upcoming release of FieldTrip, I am busy cleaning up parts of the code that are not so clear at the moment. One of them is preprocessing and definetrial. Currently the preprocessing function is reading multiple datatypes at once and giving each of them a different treatment. This clearly reflects that preprocessing was initially written for MEG data and that other dataformats were added later. Specifically, these two sections in the help of preprocessing are what bothers me. % Specific preprocessing options for EMG channels are % cfg.emgchannel = cell-array with the label(s) of EMG channels % cfg.emghpfreq = high-pass frequency % cfg.emgrectify = 'yes' or 'no' % cfg.emghilbert = 'yes' or 'no' % % Specific preprocessing options for EEG channels are % cfg.eegchannel = cell-array with the label(s) of EEG channels % cfg.implicitref = 'label' or empty, add the implicit reference as zeros prior to rereferencing % cfg.refchannel = cell-array with new reference channel(s) % cfg.reref = 'no' or 'yes' All other preprocessing options are applied to MEG as well as to EMG and EOG channel groups, which means that you currently can NOT apply different filter settings for EMG and MEG channels, or apply baseline correction to only one of them. I would like to suggest the following changes 1) there will be no MEG/EEG/EMG specific options any more 2) preprocessing will treat all channels the same 3) if you want to apply different settings to different channel groups (e.g. to the MEG and the EEG channels), you should call preprocessing twice and concatenate the resulting raw data objects. These changes will facilitate further improvements of the preprocessing function, as well of the artifact detection routines. Regarding item 3: I can of course explain how to do it (or I could even write a general function for that). Important for item 3 is that it will not be neccessary to redo the artifact detection multiple times for the different channel groups that you want to concatenate. I would like to get your feedback on the following two items: At the moment I am only aware of Jan-Mathijs mixing different channel groups in his analyses, so please let me know if you are also using EMG and/or EEG channels and their specific preprocessing options. Furthermore, if you have particular opinions about this issue, let me know as soon as ppossible (either to me directly, through the fieldtrip list or at the thursday MEG meeting). If I don't get any objections, I will implement the changes as suggested. best regards, Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From Pascal.Fries at FCDONDERS.KUN.NL Thu Aug 19 12:41:46 2004 From: Pascal.Fries at FCDONDERS.KUN.NL (Pascal Fries) Date: Thu, 19 Aug 2004 12:41:46 +0200 Subject: preprocessing cleanup In-Reply-To: <8E475CF9-F1CB-11D8-9CB1-000A95DBB2CC@fcdonders.kun.nl> Message-ID: Hi Robert, I suggest that we discuss this at the fieldtrip meeting. Best, Pascal > -----Original Message----- > From: FieldTrip discussion list > [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Robert Oostenveld > Sent: Thursday, August 19, 2004 12:36 PM > To: FIELDTRIP at NIC.SURFNET.NL > Subject: [FIELDTRIP] preprocessing cleanup > > Dear FieldTrippers, > > Related to the upcoming release of FieldTrip, I am busy > cleaning up parts of the code that are not so clear at the > moment. One of them is preprocessing and definetrial. > Currently the preprocessing function is reading multiple > datatypes at once and giving each of them a different > treatment. This clearly reflects that preprocessing was > initially written for MEG data and that other dataformats > were added later. > Specifically, these two sections in the help of preprocessing > are what bothers me. > > % Specific preprocessing options for EMG channels are > % cfg.emgchannel = cell-array with the label(s) of EMG channels > % cfg.emghpfreq = high-pass frequency > % cfg.emgrectify = 'yes' or 'no' > % cfg.emghilbert = 'yes' or 'no' > % > % Specific preprocessing options for EEG channels are > % cfg.eegchannel = cell-array with the label(s) of EEG channels > % cfg.implicitref = 'label' or empty, add the implicit reference as > zeros prior to rereferencing > % cfg.refchannel = cell-array with new reference channel(s) > % cfg.reref = 'no' or 'yes' > > All other preprocessing options are applied to MEG as well as > to EMG and EOG channel groups, which means that you currently > can NOT apply different filter settings for EMG and MEG > channels, or apply baseline correction to only one of them. > > I would like to suggest the following changes > 1) there will be no MEG/EEG/EMG specific options any more > 2) preprocessing will treat all channels the same > 3) if you want to apply different settings to different > channel groups (e.g. to the MEG and the EEG channels), you > should call preprocessing twice and concatenate the resulting > raw data objects. > > These changes will facilitate further improvements of the > preprocessing function, as well of the artifact detection > routines. Regarding item 3: > I can of course explain how to do it (or I could even write a > general function for that). Important for item 3 is that it > will not be neccessary to redo the artifact detection > multiple times for the different channel groups that you want > to concatenate. > > I would like to get your feedback on the following two items: > At the moment I am only aware of Jan-Mathijs mixing different > channel groups in his analyses, so please let me know if you > are also using EMG and/or EEG channels and their specific > preprocessing options. Furthermore, if you have particular > opinions about this issue, let me know as soon as ppossible > (either to me directly, through the fieldtrip list or at the > thursday MEG meeting). If I don't get any objections, I will > implement the changes as suggested. > > best regards, > Robert > > > ---------------------------------------------------------------------- > Robert Oostenveld, PhD > Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark > > and > > F.C. Donders Centre for Cognitive Neuroimaging University > Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands > > Tel: +31 (0)24 3619695 > Fax: +31 (0)24 3610989 > From christian.forkstam at FCDONDERS.KUN.NL Thu Aug 19 13:06:15 2004 From: christian.forkstam at FCDONDERS.KUN.NL (christian forkstam) Date: Thu, 19 Aug 2004 13:06:15 +0200 Subject: preprocessing cleanup In-Reply-To: <8E475CF9-F1CB-11D8-9CB1-000A95DBB2CC@fcdonders.kun.nl> Message-ID: hey master fieldtripper, if i understand the proposed modification correctly it seems like a perfect idea to me. just to make sure i don't loose the possibility to rereference my EEG data i just want to secure this option. as far as i understan it does not hurt to include the possibility for both MEG/EEG/EMG analysis but you know that better. the options of concern: % cfg.implicitref = 'label' or empty, add the implicit reference as zeros prior to rereferencing % cfg.refchannel = cell-array with new reference channel(s) % cfg.reref = 'no' or 'yes' ...christian (soon out tripping the fields of a nothern swedish mountain area...) Robert Oostenveld wrote: > Dear FieldTrippers, > > Related to the upcoming release of FieldTrip, I am busy cleaning up > parts of the code that are not so clear at the moment. One of them is > preprocessing and definetrial. Currently the preprocessing function is > reading multiple datatypes at once and giving each of them a different > treatment. This clearly reflects that preprocessing was initially > written for MEG data and that other dataformats were added later. > Specifically, these two sections in the help of preprocessing are what > bothers me. > > % Specific preprocessing options for EMG channels are > % cfg.emgchannel = cell-array with the label(s) of EMG channels > % cfg.emghpfreq = high-pass frequency > % cfg.emgrectify = 'yes' or 'no' > % cfg.emghilbert = 'yes' or 'no' > % > % Specific preprocessing options for EEG channels are > % cfg.eegchannel = cell-array with the label(s) of EEG channels > % cfg.implicitref = 'label' or empty, add the implicit reference as > zeros prior to rereferencing > % cfg.refchannel = cell-array with new reference channel(s) > % cfg.reref = 'no' or 'yes' > > All other preprocessing options are applied to MEG as well as to EMG > and EOG channel groups, which means that you currently can NOT apply > different filter settings for EMG and MEG channels, or apply baseline > correction to only one of them. > > I would like to suggest the following changes > 1) there will be no MEG/EEG/EMG specific options any more > 2) preprocessing will treat all channels the same > 3) if you want to apply different settings to different channel > groups (e.g. to the MEG and the EEG channels), you should call > preprocessing twice and concatenate the resulting raw data objects. > > These changes will facilitate further improvements of the preprocessing > function, as well of the artifact detection routines. Regarding item 3: > I can of course explain how to do it (or I could even write a general > function for that). Important for item 3 is that it will not be > neccessary to redo the artifact detection multiple times for the > different channel groups that you want to concatenate. > > I would like to get your feedback on the following two items: At the > moment I am only aware of Jan-Mathijs mixing different channel groups > in his analyses, so please let me know if you are also using EMG and/or > EEG channels and their specific preprocessing options. Furthermore, if > you have particular opinions about this issue, let me know as soon as > ppossible (either to me directly, through the fieldtrip list or at the > thursday MEG meeting). If I don't get any objections, I will implement > the changes as suggested. > > best regards, > Robert > > > ---------------------------------------------------------------------- > Robert Oostenveld, PhD > Center for Sensory-Motor Interaction (SMI) > Aalborg University, Denmark > > and > > F.C. Donders Centre for Cognitive Neuroimaging > University Nijmegen > P.O. Box 9101 > NL-6500 AH Nijmegen > The Netherlands > > Tel: +31 (0)24 3619695 > Fax: +31 (0)24 3610989 From roberto at SMI.AUC.DK Thu Aug 19 13:33:55 2004 From: roberto at SMI.AUC.DK (Robert Oostenveld) Date: Thu, 19 Aug 2004 13:33:55 +0200 Subject: preprocessing cleanup In-Reply-To: <412489A7.6020000@fcdonders.kun.nl> Message-ID: Hi Christian, Rereferencing for EEG data will certainly remain included. My suggestion would be to implement rereferencing as a general option, i.e. cfg.implicitref cfg.refchannel cfg.reref would apply to all channels that are listed in cfg.channel, and cfg.eegchannel would be obsoleted. This does mean that people in principle could also apply nonsense rereferencing to MEG channels, but if they are that stupid... Robert On 19 Aug 2004, at 13:06, christian forkstam wrote: > hey master fieldtripper, > > if i understand the proposed modification correctly it seems like a > perfect idea to me. just to make sure i don't loose the possibility to > rereference my EEG data i just want to secure this option. as far as i > understan it does not hurt to include the possibility for both > MEG/EEG/EMG analysis but you know that better. > > the options of concern: > > % cfg.implicitref = 'label' or empty, add the implicit reference as > zeros prior to rereferencing > % cfg.refchannel = cell-array with new reference channel(s) > % cfg.reref = 'no' or 'yes' > > ...christian > (soon out tripping the fields of a nothern swedish mountain area...) > > > Robert Oostenveld wrote: >> Dear FieldTrippers, >> >> Related to the upcoming release of FieldTrip, I am busy cleaning up >> parts of the code that are not so clear at the moment. One of them is >> preprocessing and definetrial. Currently the preprocessing function is >> reading multiple datatypes at once and giving each of them a different >> treatment. This clearly reflects that preprocessing was initially >> written for MEG data and that other dataformats were added later. >> Specifically, these two sections in the help of preprocessing are what >> bothers me. >> >> % Specific preprocessing options for EMG channels are >> % cfg.emgchannel = cell-array with the label(s) of EMG channels >> % cfg.emghpfreq = high-pass frequency >> % cfg.emgrectify = 'yes' or 'no' >> % cfg.emghilbert = 'yes' or 'no' >> % >> % Specific preprocessing options for EEG channels are >> % cfg.eegchannel = cell-array with the label(s) of EEG channels >> % cfg.implicitref = 'label' or empty, add the implicit reference as >> zeros prior to rereferencing >> % cfg.refchannel = cell-array with new reference channel(s) >> % cfg.reref = 'no' or 'yes' >> >> All other preprocessing options are applied to MEG as well as to EMG >> and EOG channel groups, which means that you currently can NOT apply >> different filter settings for EMG and MEG channels, or apply baseline >> correction to only one of them. >> >> I would like to suggest the following changes >> 1) there will be no MEG/EEG/EMG specific options any more >> 2) preprocessing will treat all channels the same >> 3) if you want to apply different settings to different channel >> groups (e.g. to the MEG and the EEG channels), you should call >> preprocessing twice and concatenate the resulting raw data objects. >> >> These changes will facilitate further improvements of the >> preprocessing >> function, as well of the artifact detection routines. Regarding item >> 3: >> I can of course explain how to do it (or I could even write a general >> function for that). Important for item 3 is that it will not be >> neccessary to redo the artifact detection multiple times for the >> different channel groups that you want to concatenate. >> >> I would like to get your feedback on the following two items: At the >> moment I am only aware of Jan-Mathijs mixing different channel groups >> in his analyses, so please let me know if you are also using EMG >> and/or >> EEG channels and their specific preprocessing options. Furthermore, if >> you have particular opinions about this issue, let me know as soon as >> ppossible (either to me directly, through the fieldtrip list or at the >> thursday MEG meeting). If I don't get any objections, I will implement >> the changes as suggested. >> >> best regards, >> Robert >> >> >> ---------------------------------------------------------------------- >> Robert Oostenveld, PhD >> Center for Sensory-Motor Interaction (SMI) >> Aalborg University, Denmark >> >> and >> >> F.C. Donders Centre for Cognitive Neuroimaging >> University Nijmegen >> P.O. Box 9101 >> NL-6500 AH Nijmegen >> The Netherlands >> >> Tel: +31 (0)24 3619695 >> Fax: +31 (0)24 3610989 >> ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From r.oostenveld at FCDONDERS.KUN.NL Fri Aug 20 09:02:38 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Fri, 20 Aug 2004 09:02:38 +0200 Subject: preprocessing Message-ID: Hi FieldTrippers, Following yesterdays discussion, I have modified preprocessing according to my proposal: all channels are now treated the same. If you try to use one of the old options (eegchannel, emghilbert, etc.) it will give an error. The operation to separate out DEFINETRIAL and REJECTARTIFACT from preprosessing will mainly be in the documentation, and should also not affect your current configurations and scripts. Therefore I will proceed with that as well, but will not notify you of it specifically. best regards Robert From Pascal.Fries at FCDONDERS.KUN.NL Wed Aug 25 11:32:35 2004 From: Pascal.Fries at FCDONDERS.KUN.NL (Pascal Fries) Date: Wed, 25 Aug 2004 11:32:35 +0200 Subject: freqdescriptives In-Reply-To: Message-ID: Dear fieldtrippers, I have just committed a new function to fieldtrip: freqdescriptives. It is meant to replace the old and not really fieldtrip-like frqanajckstatistic. I have tested it, but please report bugs! Pascal Pascal Fries Principal Investigator Neuronal Coherence Group F. C. Donders Centre for Cognitive Neuroimaging University of Nijmegen Adelbertusplein 1 6525 EK Nijmegen The Netherlands Phone: (+31) (0)24 36 10657 Fax: (+31) (0)24 36 10989 e-mail: pascal.fries at fcdonders.kun.nl website: www.kun.nl/fcdonders/ From m.siegel at UKE.UNI-HAMBURG.DE Thu Aug 26 14:04:42 2004 From: m.siegel at UKE.UNI-HAMBURG.DE (Markus Siegel) Date: Thu, 26 Aug 2004 14:04:42 +0200 Subject: new functions in CVS Message-ID: Dear fieldtrippers, I have added sliceinterp.m and sourcestatistics_randomization.m to the CVS. No changes to sourcestatistics_randomization.m sliceinterp.m has now cfg.whitebg = 'yes' as defaul and a bug concerning user-colormaps has been fixed. Best, Markus Siegel From r.oostenveld at FCDONDERS.KUN.NL Thu Aug 5 09:24:22 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Thu, 5 Aug 2004 09:24:22 +0200 Subject: new functions Message-ID: Dear fieldtrippers, I have implemented three new functions that all relate to SOURECANALYSIS, and are especially relevant to help reduce memory requirements in randomization stats. SOURCE2GRID should help you to remove all the unneccesary items from a sourcestructure, so that you can use it in cfg.grid for sourceanalysis. SOURCE2SPARSE removes all dipole locations from a source structure that are outside teh head. Source strength at these locations is not computed anyway, so it does not make the computation faster, but those locations do take up memory. The reduced sourecspace (or precomputred grid) can take ~2x up to 10x as less memory as the full sourcespace. SOURCE2FULL is the opposite from source2sparse and it will add all outside locations again, recreating the complete source volume that you can plot, interpolate and export. I hope that they are all bug free, but they have not yet been tested extensively. Use with caution. best regards, Robert PS the functions are available as usual in the FC Donders internal /home/common/matlab/fieldtrip directory ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From r.oostenveld at FCDONDERS.KUN.NL Thu Aug 5 16:56:54 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Thu, 5 Aug 2004 16:56:54 +0200 Subject: statistical analysis over subjects Message-ID: Dear FieldTrippers, I have implemented a function called SOURCWRITE, which can read in functional data from an Analyze file. With this function, you can combine the functional data from multiple subjects _after_ aligning the subjects anatomical+functional data to a common anatomical template brain, and subsequently you can perform group-level statistics. The supports importing either a single condition or two conditions. In the case of two conditions, the function also supports randomization or permutation (needed for non-parametric testing). The function returns a structure that is equivalent to the output of the sourceanalysis function, and you can put the data into sourcestatistics directly. Some details for the realignment to a template brain with SPM and/or BrainVoyager have already been sorted out by JM and Markus Siegel, but there is still some work that needs to be done there. If you are interested in group-analysis contact me and we can try to get it to work completely. best regards, Robert From roberto at SMI.AUC.DK Fri Aug 6 10:58:28 2004 From: roberto at SMI.AUC.DK (Robert Oostenveld) Date: Fri, 6 Aug 2004 10:58:28 +0200 Subject: plotting headmodel Message-ID: Hi I implemented a new function in FieldTrip for plotting headmodels. Sofar it only works for CTF multiple-sphere models, but that is where it is needed most. The function is called HEADMODELPLOT, and it can make different visualisations of the gradiometers and the spheres which can help you to verify the correctness of your localSpheres.hdm files. Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From roberto at SMI.AUC.DK Fri Aug 6 11:14:33 2004 From: roberto at SMI.AUC.DK (Robert Oostenveld) Date: Fri, 6 Aug 2004 11:14:33 +0200 Subject: statistical analysis over subjects In-Reply-To: Message-ID: Hi A small correction on my mail of yesterday: the function is called SOURCEREAD and not sourcewrite. The sourcewrite function already existed and should be used to export your functional data to Analyze files prior to realiging. Robert On 5 Aug 2004, at 16:56, Robert Oostenveld wrote: > Dear FieldTrippers, > > I have implemented a function called SOURCWRITE, which can read in > functional data from an Analyze file. With this function, you can > combine the functional data from multiple subjects _after_ aligning the > subjects anatomical+functional data to a common anatomical template > brain, and subsequently you can perform group-level statistics. The > supports importing either a single condition or two conditions. In the > case of two conditions, the function also supports randomization or > permutation (needed for non-parametric testing). The function returns a > structure that is equivalent to the output of the sourceanalysis > function, and you can put the data into sourcestatistics directly. > > Some details for the realignment to a template brain with SPM and/or > BrainVoyager have already been sorted out by JM and Markus Siegel, but > there is still some work that needs to be done there. If you are > interested in group-analysis contact me and we can try to get it to > work completely. > > best regards, > Robert > ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From r.oostenveld at FCDONDERS.KUN.NL Mon Aug 16 12:11:24 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Mon, 16 Aug 2004 12:11:24 +0200 Subject: beamforming and precomputed leadfields Message-ID: Hi FieldTrippers, Last weeks BIOMAG was fun, and I got quite some new ideas that I already starten implementing. FieldTrip is definitely on the right track and gained a lot of attention. On the code level: I have made some modifications to the way that leadfields are kept and/or precomputed. The old options of SOURCANALYSIS are still supported, but there is also a new function PRECOMPUTE_LEADFIELD. I suggest that you use the new function if you want to perform resampling/randomization based source analysis and statistics. Furthermore, we discovered a "feature" of the beamformer method that is not so nice. Although it is not really a bug, but it might mess up your sourceanalysis results if you are using multisphere headmodels as most of us do. The problem has to do with the radial dipole component and noise projection. If you are at the moment busy with sourceanalysis, please contact me as soon as possible(!!) and I will explain it and show you the workaround that is already implemented. For the rest of you: I will explain it in more detail in this weeks thursday MEG meeting. best regards, Robert From r.oostenveld at FCDONDERS.KUN.NL Mon Aug 16 13:15:49 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Mon, 16 Aug 2004 13:15:49 +0200 Subject: randomization vs. permutation Message-ID: Hi FieldTrippers, As you all know, we are already heavily using randomization methods for our statistics (e.g. in SOURCEANALYSIS or in RANDCLUSTERANALYSIS). Likewise, jacknife and bootstrap estimates of variance are available in SOURECANALYSIS and FREQANALYSIS (for coherence). These methods (i.e. jacknife, bootstrap, randomization) can all be shared under the common umbrella of resampling theory, and there is another obvious resampling that sofar was not implemented yet: PERMUTATION. Whereas in randomization you throw all trials over both conditions together and then randomly re-assigned them to the two conditions, in permutation the trials in condition A and B are selectively swapped (at random) between conditions. Therefore the number of trials should be the same. Permutation actually is a specific instance of randomization. The null-hypothesis that you are testing using either the randomization or permutation is slightly different. Using randomization, you assume that all trials in condition A and condition B come from the same distribution. Using permutation, you only assume that the i-th trial of condition A comes from the same distribution as the i-th trial of condition B. Therefore permutation is a more natural choise for baseline vs. active comparisons (comparing the pre- and post-stimulus interval of every trial) and I also suspect that the permutation based approach will result in more statistical power. Of course you can only apply the permutation method if your data contains trials in A and B that can be directly compared. best regards, Robert From roberto at SMI.AUC.DK Thu Aug 19 09:16:25 2004 From: roberto at SMI.AUC.DK (Robert Oostenveld) Date: Thu, 19 Aug 2004 09:16:25 +0200 Subject: parametric sourcestatistics Message-ID: Hi, I have made some changes to SOURCESTATISTICS_PARAMETRIC that can result in backward incompatibilities: - removed nai and pseudo-t as methods (see SOURCDESCRIPTIVES) - changed interpretation of cfg.threshold for consistency with other functions - removed inconsistent and untested conversion from t- to z-score Although I have tried to check for those options and give a warning or error if you use them in your scripts, you still should be acutious if you think that these changes affect your analysis. Contact me if you have questions about it. best, Robert PS. About my previous mail regarding resampling methods (randomization/permutation): that mail only applied to the source-level analysis, those of you who are using CLUSTERRANDANALYSIS on the channel level already had the option for using permutation in a within-subject-design (as Eric pointed me out). ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From r.oostenveld at FCDONDERS.KUN.NL Thu Aug 19 12:35:57 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Thu, 19 Aug 2004 12:35:57 +0200 Subject: preprocessing cleanup Message-ID: Dear FieldTrippers, Related to the upcoming release of FieldTrip, I am busy cleaning up parts of the code that are not so clear at the moment. One of them is preprocessing and definetrial. Currently the preprocessing function is reading multiple datatypes at once and giving each of them a different treatment. This clearly reflects that preprocessing was initially written for MEG data and that other dataformats were added later. Specifically, these two sections in the help of preprocessing are what bothers me. % Specific preprocessing options for EMG channels are % cfg.emgchannel = cell-array with the label(s) of EMG channels % cfg.emghpfreq = high-pass frequency % cfg.emgrectify = 'yes' or 'no' % cfg.emghilbert = 'yes' or 'no' % % Specific preprocessing options for EEG channels are % cfg.eegchannel = cell-array with the label(s) of EEG channels % cfg.implicitref = 'label' or empty, add the implicit reference as zeros prior to rereferencing % cfg.refchannel = cell-array with new reference channel(s) % cfg.reref = 'no' or 'yes' All other preprocessing options are applied to MEG as well as to EMG and EOG channel groups, which means that you currently can NOT apply different filter settings for EMG and MEG channels, or apply baseline correction to only one of them. I would like to suggest the following changes 1) there will be no MEG/EEG/EMG specific options any more 2) preprocessing will treat all channels the same 3) if you want to apply different settings to different channel groups (e.g. to the MEG and the EEG channels), you should call preprocessing twice and concatenate the resulting raw data objects. These changes will facilitate further improvements of the preprocessing function, as well of the artifact detection routines. Regarding item 3: I can of course explain how to do it (or I could even write a general function for that). Important for item 3 is that it will not be neccessary to redo the artifact detection multiple times for the different channel groups that you want to concatenate. I would like to get your feedback on the following two items: At the moment I am only aware of Jan-Mathijs mixing different channel groups in his analyses, so please let me know if you are also using EMG and/or EEG channels and their specific preprocessing options. Furthermore, if you have particular opinions about this issue, let me know as soon as ppossible (either to me directly, through the fieldtrip list or at the thursday MEG meeting). If I don't get any objections, I will implement the changes as suggested. best regards, Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From Pascal.Fries at FCDONDERS.KUN.NL Thu Aug 19 12:41:46 2004 From: Pascal.Fries at FCDONDERS.KUN.NL (Pascal Fries) Date: Thu, 19 Aug 2004 12:41:46 +0200 Subject: preprocessing cleanup In-Reply-To: <8E475CF9-F1CB-11D8-9CB1-000A95DBB2CC@fcdonders.kun.nl> Message-ID: Hi Robert, I suggest that we discuss this at the fieldtrip meeting. Best, Pascal > -----Original Message----- > From: FieldTrip discussion list > [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Robert Oostenveld > Sent: Thursday, August 19, 2004 12:36 PM > To: FIELDTRIP at NIC.SURFNET.NL > Subject: [FIELDTRIP] preprocessing cleanup > > Dear FieldTrippers, > > Related to the upcoming release of FieldTrip, I am busy > cleaning up parts of the code that are not so clear at the > moment. One of them is preprocessing and definetrial. > Currently the preprocessing function is reading multiple > datatypes at once and giving each of them a different > treatment. This clearly reflects that preprocessing was > initially written for MEG data and that other dataformats > were added later. > Specifically, these two sections in the help of preprocessing > are what bothers me. > > % Specific preprocessing options for EMG channels are > % cfg.emgchannel = cell-array with the label(s) of EMG channels > % cfg.emghpfreq = high-pass frequency > % cfg.emgrectify = 'yes' or 'no' > % cfg.emghilbert = 'yes' or 'no' > % > % Specific preprocessing options for EEG channels are > % cfg.eegchannel = cell-array with the label(s) of EEG channels > % cfg.implicitref = 'label' or empty, add the implicit reference as > zeros prior to rereferencing > % cfg.refchannel = cell-array with new reference channel(s) > % cfg.reref = 'no' or 'yes' > > All other preprocessing options are applied to MEG as well as > to EMG and EOG channel groups, which means that you currently > can NOT apply different filter settings for EMG and MEG > channels, or apply baseline correction to only one of them. > > I would like to suggest the following changes > 1) there will be no MEG/EEG/EMG specific options any more > 2) preprocessing will treat all channels the same > 3) if you want to apply different settings to different > channel groups (e.g. to the MEG and the EEG channels), you > should call preprocessing twice and concatenate the resulting > raw data objects. > > These changes will facilitate further improvements of the > preprocessing function, as well of the artifact detection > routines. Regarding item 3: > I can of course explain how to do it (or I could even write a > general function for that). Important for item 3 is that it > will not be neccessary to redo the artifact detection > multiple times for the different channel groups that you want > to concatenate. > > I would like to get your feedback on the following two items: > At the moment I am only aware of Jan-Mathijs mixing different > channel groups in his analyses, so please let me know if you > are also using EMG and/or EEG channels and their specific > preprocessing options. Furthermore, if you have particular > opinions about this issue, let me know as soon as ppossible > (either to me directly, through the fieldtrip list or at the > thursday MEG meeting). If I don't get any objections, I will > implement the changes as suggested. > > best regards, > Robert > > > ---------------------------------------------------------------------- > Robert Oostenveld, PhD > Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark > > and > > F.C. Donders Centre for Cognitive Neuroimaging University > Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands > > Tel: +31 (0)24 3619695 > Fax: +31 (0)24 3610989 > From christian.forkstam at FCDONDERS.KUN.NL Thu Aug 19 13:06:15 2004 From: christian.forkstam at FCDONDERS.KUN.NL (christian forkstam) Date: Thu, 19 Aug 2004 13:06:15 +0200 Subject: preprocessing cleanup In-Reply-To: <8E475CF9-F1CB-11D8-9CB1-000A95DBB2CC@fcdonders.kun.nl> Message-ID: hey master fieldtripper, if i understand the proposed modification correctly it seems like a perfect idea to me. just to make sure i don't loose the possibility to rereference my EEG data i just want to secure this option. as far as i understan it does not hurt to include the possibility for both MEG/EEG/EMG analysis but you know that better. the options of concern: % cfg.implicitref = 'label' or empty, add the implicit reference as zeros prior to rereferencing % cfg.refchannel = cell-array with new reference channel(s) % cfg.reref = 'no' or 'yes' ...christian (soon out tripping the fields of a nothern swedish mountain area...) Robert Oostenveld wrote: > Dear FieldTrippers, > > Related to the upcoming release of FieldTrip, I am busy cleaning up > parts of the code that are not so clear at the moment. One of them is > preprocessing and definetrial. Currently the preprocessing function is > reading multiple datatypes at once and giving each of them a different > treatment. This clearly reflects that preprocessing was initially > written for MEG data and that other dataformats were added later. > Specifically, these two sections in the help of preprocessing are what > bothers me. > > % Specific preprocessing options for EMG channels are > % cfg.emgchannel = cell-array with the label(s) of EMG channels > % cfg.emghpfreq = high-pass frequency > % cfg.emgrectify = 'yes' or 'no' > % cfg.emghilbert = 'yes' or 'no' > % > % Specific preprocessing options for EEG channels are > % cfg.eegchannel = cell-array with the label(s) of EEG channels > % cfg.implicitref = 'label' or empty, add the implicit reference as > zeros prior to rereferencing > % cfg.refchannel = cell-array with new reference channel(s) > % cfg.reref = 'no' or 'yes' > > All other preprocessing options are applied to MEG as well as to EMG > and EOG channel groups, which means that you currently can NOT apply > different filter settings for EMG and MEG channels, or apply baseline > correction to only one of them. > > I would like to suggest the following changes > 1) there will be no MEG/EEG/EMG specific options any more > 2) preprocessing will treat all channels the same > 3) if you want to apply different settings to different channel > groups (e.g. to the MEG and the EEG channels), you should call > preprocessing twice and concatenate the resulting raw data objects. > > These changes will facilitate further improvements of the preprocessing > function, as well of the artifact detection routines. Regarding item 3: > I can of course explain how to do it (or I could even write a general > function for that). Important for item 3 is that it will not be > neccessary to redo the artifact detection multiple times for the > different channel groups that you want to concatenate. > > I would like to get your feedback on the following two items: At the > moment I am only aware of Jan-Mathijs mixing different channel groups > in his analyses, so please let me know if you are also using EMG and/or > EEG channels and their specific preprocessing options. Furthermore, if > you have particular opinions about this issue, let me know as soon as > ppossible (either to me directly, through the fieldtrip list or at the > thursday MEG meeting). If I don't get any objections, I will implement > the changes as suggested. > > best regards, > Robert > > > ---------------------------------------------------------------------- > Robert Oostenveld, PhD > Center for Sensory-Motor Interaction (SMI) > Aalborg University, Denmark > > and > > F.C. Donders Centre for Cognitive Neuroimaging > University Nijmegen > P.O. Box 9101 > NL-6500 AH Nijmegen > The Netherlands > > Tel: +31 (0)24 3619695 > Fax: +31 (0)24 3610989 From roberto at SMI.AUC.DK Thu Aug 19 13:33:55 2004 From: roberto at SMI.AUC.DK (Robert Oostenveld) Date: Thu, 19 Aug 2004 13:33:55 +0200 Subject: preprocessing cleanup In-Reply-To: <412489A7.6020000@fcdonders.kun.nl> Message-ID: Hi Christian, Rereferencing for EEG data will certainly remain included. My suggestion would be to implement rereferencing as a general option, i.e. cfg.implicitref cfg.refchannel cfg.reref would apply to all channels that are listed in cfg.channel, and cfg.eegchannel would be obsoleted. This does mean that people in principle could also apply nonsense rereferencing to MEG channels, but if they are that stupid... Robert On 19 Aug 2004, at 13:06, christian forkstam wrote: > hey master fieldtripper, > > if i understand the proposed modification correctly it seems like a > perfect idea to me. just to make sure i don't loose the possibility to > rereference my EEG data i just want to secure this option. as far as i > understan it does not hurt to include the possibility for both > MEG/EEG/EMG analysis but you know that better. > > the options of concern: > > % cfg.implicitref = 'label' or empty, add the implicit reference as > zeros prior to rereferencing > % cfg.refchannel = cell-array with new reference channel(s) > % cfg.reref = 'no' or 'yes' > > ...christian > (soon out tripping the fields of a nothern swedish mountain area...) > > > Robert Oostenveld wrote: >> Dear FieldTrippers, >> >> Related to the upcoming release of FieldTrip, I am busy cleaning up >> parts of the code that are not so clear at the moment. One of them is >> preprocessing and definetrial. Currently the preprocessing function is >> reading multiple datatypes at once and giving each of them a different >> treatment. This clearly reflects that preprocessing was initially >> written for MEG data and that other dataformats were added later. >> Specifically, these two sections in the help of preprocessing are what >> bothers me. >> >> % Specific preprocessing options for EMG channels are >> % cfg.emgchannel = cell-array with the label(s) of EMG channels >> % cfg.emghpfreq = high-pass frequency >> % cfg.emgrectify = 'yes' or 'no' >> % cfg.emghilbert = 'yes' or 'no' >> % >> % Specific preprocessing options for EEG channels are >> % cfg.eegchannel = cell-array with the label(s) of EEG channels >> % cfg.implicitref = 'label' or empty, add the implicit reference as >> zeros prior to rereferencing >> % cfg.refchannel = cell-array with new reference channel(s) >> % cfg.reref = 'no' or 'yes' >> >> All other preprocessing options are applied to MEG as well as to EMG >> and EOG channel groups, which means that you currently can NOT apply >> different filter settings for EMG and MEG channels, or apply baseline >> correction to only one of them. >> >> I would like to suggest the following changes >> 1) there will be no MEG/EEG/EMG specific options any more >> 2) preprocessing will treat all channels the same >> 3) if you want to apply different settings to different channel >> groups (e.g. to the MEG and the EEG channels), you should call >> preprocessing twice and concatenate the resulting raw data objects. >> >> These changes will facilitate further improvements of the >> preprocessing >> function, as well of the artifact detection routines. Regarding item >> 3: >> I can of course explain how to do it (or I could even write a general >> function for that). Important for item 3 is that it will not be >> neccessary to redo the artifact detection multiple times for the >> different channel groups that you want to concatenate. >> >> I would like to get your feedback on the following two items: At the >> moment I am only aware of Jan-Mathijs mixing different channel groups >> in his analyses, so please let me know if you are also using EMG >> and/or >> EEG channels and their specific preprocessing options. Furthermore, if >> you have particular opinions about this issue, let me know as soon as >> ppossible (either to me directly, through the fieldtrip list or at the >> thursday MEG meeting). If I don't get any objections, I will implement >> the changes as suggested. >> >> best regards, >> Robert >> >> >> ---------------------------------------------------------------------- >> Robert Oostenveld, PhD >> Center for Sensory-Motor Interaction (SMI) >> Aalborg University, Denmark >> >> and >> >> F.C. Donders Centre for Cognitive Neuroimaging >> University Nijmegen >> P.O. Box 9101 >> NL-6500 AH Nijmegen >> The Netherlands >> >> Tel: +31 (0)24 3619695 >> Fax: +31 (0)24 3610989 >> ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From r.oostenveld at FCDONDERS.KUN.NL Fri Aug 20 09:02:38 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Fri, 20 Aug 2004 09:02:38 +0200 Subject: preprocessing Message-ID: Hi FieldTrippers, Following yesterdays discussion, I have modified preprocessing according to my proposal: all channels are now treated the same. If you try to use one of the old options (eegchannel, emghilbert, etc.) it will give an error. The operation to separate out DEFINETRIAL and REJECTARTIFACT from preprosessing will mainly be in the documentation, and should also not affect your current configurations and scripts. Therefore I will proceed with that as well, but will not notify you of it specifically. best regards Robert From Pascal.Fries at FCDONDERS.KUN.NL Wed Aug 25 11:32:35 2004 From: Pascal.Fries at FCDONDERS.KUN.NL (Pascal Fries) Date: Wed, 25 Aug 2004 11:32:35 +0200 Subject: freqdescriptives In-Reply-To: Message-ID: Dear fieldtrippers, I have just committed a new function to fieldtrip: freqdescriptives. It is meant to replace the old and not really fieldtrip-like frqanajckstatistic. I have tested it, but please report bugs! Pascal Pascal Fries Principal Investigator Neuronal Coherence Group F. C. Donders Centre for Cognitive Neuroimaging University of Nijmegen Adelbertusplein 1 6525 EK Nijmegen The Netherlands Phone: (+31) (0)24 36 10657 Fax: (+31) (0)24 36 10989 e-mail: pascal.fries at fcdonders.kun.nl website: www.kun.nl/fcdonders/ From m.siegel at UKE.UNI-HAMBURG.DE Thu Aug 26 14:04:42 2004 From: m.siegel at UKE.UNI-HAMBURG.DE (Markus Siegel) Date: Thu, 26 Aug 2004 14:04:42 +0200 Subject: new functions in CVS Message-ID: Dear fieldtrippers, I have added sliceinterp.m and sourcestatistics_randomization.m to the CVS. No changes to sourcestatistics_randomization.m sliceinterp.m has now cfg.whitebg = 'yes' as defaul and a bug concerning user-colormaps has been fixed. Best, Markus Siegel From r.oostenveld at FCDONDERS.KUN.NL Thu Aug 5 09:24:22 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Thu, 5 Aug 2004 09:24:22 +0200 Subject: new functions Message-ID: Dear fieldtrippers, I have implemented three new functions that all relate to SOURECANALYSIS, and are especially relevant to help reduce memory requirements in randomization stats. SOURCE2GRID should help you to remove all the unneccesary items from a sourcestructure, so that you can use it in cfg.grid for sourceanalysis. SOURCE2SPARSE removes all dipole locations from a source structure that are outside teh head. Source strength at these locations is not computed anyway, so it does not make the computation faster, but those locations do take up memory. The reduced sourecspace (or precomputred grid) can take ~2x up to 10x as less memory as the full sourcespace. SOURCE2FULL is the opposite from source2sparse and it will add all outside locations again, recreating the complete source volume that you can plot, interpolate and export. I hope that they are all bug free, but they have not yet been tested extensively. Use with caution. best regards, Robert PS the functions are available as usual in the FC Donders internal /home/common/matlab/fieldtrip directory ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From r.oostenveld at FCDONDERS.KUN.NL Thu Aug 5 16:56:54 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Thu, 5 Aug 2004 16:56:54 +0200 Subject: statistical analysis over subjects Message-ID: Dear FieldTrippers, I have implemented a function called SOURCWRITE, which can read in functional data from an Analyze file. With this function, you can combine the functional data from multiple subjects _after_ aligning the subjects anatomical+functional data to a common anatomical template brain, and subsequently you can perform group-level statistics. The supports importing either a single condition or two conditions. In the case of two conditions, the function also supports randomization or permutation (needed for non-parametric testing). The function returns a structure that is equivalent to the output of the sourceanalysis function, and you can put the data into sourcestatistics directly. Some details for the realignment to a template brain with SPM and/or BrainVoyager have already been sorted out by JM and Markus Siegel, but there is still some work that needs to be done there. If you are interested in group-analysis contact me and we can try to get it to work completely. best regards, Robert From roberto at SMI.AUC.DK Fri Aug 6 10:58:28 2004 From: roberto at SMI.AUC.DK (Robert Oostenveld) Date: Fri, 6 Aug 2004 10:58:28 +0200 Subject: plotting headmodel Message-ID: Hi I implemented a new function in FieldTrip for plotting headmodels. Sofar it only works for CTF multiple-sphere models, but that is where it is needed most. The function is called HEADMODELPLOT, and it can make different visualisations of the gradiometers and the spheres which can help you to verify the correctness of your localSpheres.hdm files. Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From roberto at SMI.AUC.DK Fri Aug 6 11:14:33 2004 From: roberto at SMI.AUC.DK (Robert Oostenveld) Date: Fri, 6 Aug 2004 11:14:33 +0200 Subject: statistical analysis over subjects In-Reply-To: Message-ID: Hi A small correction on my mail of yesterday: the function is called SOURCEREAD and not sourcewrite. The sourcewrite function already existed and should be used to export your functional data to Analyze files prior to realiging. Robert On 5 Aug 2004, at 16:56, Robert Oostenveld wrote: > Dear FieldTrippers, > > I have implemented a function called SOURCWRITE, which can read in > functional data from an Analyze file. With this function, you can > combine the functional data from multiple subjects _after_ aligning the > subjects anatomical+functional data to a common anatomical template > brain, and subsequently you can perform group-level statistics. The > supports importing either a single condition or two conditions. In the > case of two conditions, the function also supports randomization or > permutation (needed for non-parametric testing). The function returns a > structure that is equivalent to the output of the sourceanalysis > function, and you can put the data into sourcestatistics directly. > > Some details for the realignment to a template brain with SPM and/or > BrainVoyager have already been sorted out by JM and Markus Siegel, but > there is still some work that needs to be done there. If you are > interested in group-analysis contact me and we can try to get it to > work completely. > > best regards, > Robert > ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From r.oostenveld at FCDONDERS.KUN.NL Mon Aug 16 12:11:24 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Mon, 16 Aug 2004 12:11:24 +0200 Subject: beamforming and precomputed leadfields Message-ID: Hi FieldTrippers, Last weeks BIOMAG was fun, and I got quite some new ideas that I already starten implementing. FieldTrip is definitely on the right track and gained a lot of attention. On the code level: I have made some modifications to the way that leadfields are kept and/or precomputed. The old options of SOURCANALYSIS are still supported, but there is also a new function PRECOMPUTE_LEADFIELD. I suggest that you use the new function if you want to perform resampling/randomization based source analysis and statistics. Furthermore, we discovered a "feature" of the beamformer method that is not so nice. Although it is not really a bug, but it might mess up your sourceanalysis results if you are using multisphere headmodels as most of us do. The problem has to do with the radial dipole component and noise projection. If you are at the moment busy with sourceanalysis, please contact me as soon as possible(!!) and I will explain it and show you the workaround that is already implemented. For the rest of you: I will explain it in more detail in this weeks thursday MEG meeting. best regards, Robert From r.oostenveld at FCDONDERS.KUN.NL Mon Aug 16 13:15:49 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Mon, 16 Aug 2004 13:15:49 +0200 Subject: randomization vs. permutation Message-ID: Hi FieldTrippers, As you all know, we are already heavily using randomization methods for our statistics (e.g. in SOURCEANALYSIS or in RANDCLUSTERANALYSIS). Likewise, jacknife and bootstrap estimates of variance are available in SOURECANALYSIS and FREQANALYSIS (for coherence). These methods (i.e. jacknife, bootstrap, randomization) can all be shared under the common umbrella of resampling theory, and there is another obvious resampling that sofar was not implemented yet: PERMUTATION. Whereas in randomization you throw all trials over both conditions together and then randomly re-assigned them to the two conditions, in permutation the trials in condition A and B are selectively swapped (at random) between conditions. Therefore the number of trials should be the same. Permutation actually is a specific instance of randomization. The null-hypothesis that you are testing using either the randomization or permutation is slightly different. Using randomization, you assume that all trials in condition A and condition B come from the same distribution. Using permutation, you only assume that the i-th trial of condition A comes from the same distribution as the i-th trial of condition B. Therefore permutation is a more natural choise for baseline vs. active comparisons (comparing the pre- and post-stimulus interval of every trial) and I also suspect that the permutation based approach will result in more statistical power. Of course you can only apply the permutation method if your data contains trials in A and B that can be directly compared. best regards, Robert From roberto at SMI.AUC.DK Thu Aug 19 09:16:25 2004 From: roberto at SMI.AUC.DK (Robert Oostenveld) Date: Thu, 19 Aug 2004 09:16:25 +0200 Subject: parametric sourcestatistics Message-ID: Hi, I have made some changes to SOURCESTATISTICS_PARAMETRIC that can result in backward incompatibilities: - removed nai and pseudo-t as methods (see SOURCDESCRIPTIVES) - changed interpretation of cfg.threshold for consistency with other functions - removed inconsistent and untested conversion from t- to z-score Although I have tried to check for those options and give a warning or error if you use them in your scripts, you still should be acutious if you think that these changes affect your analysis. Contact me if you have questions about it. best, Robert PS. About my previous mail regarding resampling methods (randomization/permutation): that mail only applied to the source-level analysis, those of you who are using CLUSTERRANDANALYSIS on the channel level already had the option for using permutation in a within-subject-design (as Eric pointed me out). ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From r.oostenveld at FCDONDERS.KUN.NL Thu Aug 19 12:35:57 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Thu, 19 Aug 2004 12:35:57 +0200 Subject: preprocessing cleanup Message-ID: Dear FieldTrippers, Related to the upcoming release of FieldTrip, I am busy cleaning up parts of the code that are not so clear at the moment. One of them is preprocessing and definetrial. Currently the preprocessing function is reading multiple datatypes at once and giving each of them a different treatment. This clearly reflects that preprocessing was initially written for MEG data and that other dataformats were added later. Specifically, these two sections in the help of preprocessing are what bothers me. % Specific preprocessing options for EMG channels are % cfg.emgchannel = cell-array with the label(s) of EMG channels % cfg.emghpfreq = high-pass frequency % cfg.emgrectify = 'yes' or 'no' % cfg.emghilbert = 'yes' or 'no' % % Specific preprocessing options for EEG channels are % cfg.eegchannel = cell-array with the label(s) of EEG channels % cfg.implicitref = 'label' or empty, add the implicit reference as zeros prior to rereferencing % cfg.refchannel = cell-array with new reference channel(s) % cfg.reref = 'no' or 'yes' All other preprocessing options are applied to MEG as well as to EMG and EOG channel groups, which means that you currently can NOT apply different filter settings for EMG and MEG channels, or apply baseline correction to only one of them. I would like to suggest the following changes 1) there will be no MEG/EEG/EMG specific options any more 2) preprocessing will treat all channels the same 3) if you want to apply different settings to different channel groups (e.g. to the MEG and the EEG channels), you should call preprocessing twice and concatenate the resulting raw data objects. These changes will facilitate further improvements of the preprocessing function, as well of the artifact detection routines. Regarding item 3: I can of course explain how to do it (or I could even write a general function for that). Important for item 3 is that it will not be neccessary to redo the artifact detection multiple times for the different channel groups that you want to concatenate. I would like to get your feedback on the following two items: At the moment I am only aware of Jan-Mathijs mixing different channel groups in his analyses, so please let me know if you are also using EMG and/or EEG channels and their specific preprocessing options. Furthermore, if you have particular opinions about this issue, let me know as soon as ppossible (either to me directly, through the fieldtrip list or at the thursday MEG meeting). If I don't get any objections, I will implement the changes as suggested. best regards, Robert ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From Pascal.Fries at FCDONDERS.KUN.NL Thu Aug 19 12:41:46 2004 From: Pascal.Fries at FCDONDERS.KUN.NL (Pascal Fries) Date: Thu, 19 Aug 2004 12:41:46 +0200 Subject: preprocessing cleanup In-Reply-To: <8E475CF9-F1CB-11D8-9CB1-000A95DBB2CC@fcdonders.kun.nl> Message-ID: Hi Robert, I suggest that we discuss this at the fieldtrip meeting. Best, Pascal > -----Original Message----- > From: FieldTrip discussion list > [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Robert Oostenveld > Sent: Thursday, August 19, 2004 12:36 PM > To: FIELDTRIP at NIC.SURFNET.NL > Subject: [FIELDTRIP] preprocessing cleanup > > Dear FieldTrippers, > > Related to the upcoming release of FieldTrip, I am busy > cleaning up parts of the code that are not so clear at the > moment. One of them is preprocessing and definetrial. > Currently the preprocessing function is reading multiple > datatypes at once and giving each of them a different > treatment. This clearly reflects that preprocessing was > initially written for MEG data and that other dataformats > were added later. > Specifically, these two sections in the help of preprocessing > are what bothers me. > > % Specific preprocessing options for EMG channels are > % cfg.emgchannel = cell-array with the label(s) of EMG channels > % cfg.emghpfreq = high-pass frequency > % cfg.emgrectify = 'yes' or 'no' > % cfg.emghilbert = 'yes' or 'no' > % > % Specific preprocessing options for EEG channels are > % cfg.eegchannel = cell-array with the label(s) of EEG channels > % cfg.implicitref = 'label' or empty, add the implicit reference as > zeros prior to rereferencing > % cfg.refchannel = cell-array with new reference channel(s) > % cfg.reref = 'no' or 'yes' > > All other preprocessing options are applied to MEG as well as > to EMG and EOG channel groups, which means that you currently > can NOT apply different filter settings for EMG and MEG > channels, or apply baseline correction to only one of them. > > I would like to suggest the following changes > 1) there will be no MEG/EEG/EMG specific options any more > 2) preprocessing will treat all channels the same > 3) if you want to apply different settings to different > channel groups (e.g. to the MEG and the EEG channels), you > should call preprocessing twice and concatenate the resulting > raw data objects. > > These changes will facilitate further improvements of the > preprocessing function, as well of the artifact detection > routines. Regarding item 3: > I can of course explain how to do it (or I could even write a > general function for that). Important for item 3 is that it > will not be neccessary to redo the artifact detection > multiple times for the different channel groups that you want > to concatenate. > > I would like to get your feedback on the following two items: > At the moment I am only aware of Jan-Mathijs mixing different > channel groups in his analyses, so please let me know if you > are also using EMG and/or EEG channels and their specific > preprocessing options. Furthermore, if you have particular > opinions about this issue, let me know as soon as ppossible > (either to me directly, through the fieldtrip list or at the > thursday MEG meeting). If I don't get any objections, I will > implement the changes as suggested. > > best regards, > Robert > > > ---------------------------------------------------------------------- > Robert Oostenveld, PhD > Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark > > and > > F.C. Donders Centre for Cognitive Neuroimaging University > Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands > > Tel: +31 (0)24 3619695 > Fax: +31 (0)24 3610989 > From christian.forkstam at FCDONDERS.KUN.NL Thu Aug 19 13:06:15 2004 From: christian.forkstam at FCDONDERS.KUN.NL (christian forkstam) Date: Thu, 19 Aug 2004 13:06:15 +0200 Subject: preprocessing cleanup In-Reply-To: <8E475CF9-F1CB-11D8-9CB1-000A95DBB2CC@fcdonders.kun.nl> Message-ID: hey master fieldtripper, if i understand the proposed modification correctly it seems like a perfect idea to me. just to make sure i don't loose the possibility to rereference my EEG data i just want to secure this option. as far as i understan it does not hurt to include the possibility for both MEG/EEG/EMG analysis but you know that better. the options of concern: % cfg.implicitref = 'label' or empty, add the implicit reference as zeros prior to rereferencing % cfg.refchannel = cell-array with new reference channel(s) % cfg.reref = 'no' or 'yes' ...christian (soon out tripping the fields of a nothern swedish mountain area...) Robert Oostenveld wrote: > Dear FieldTrippers, > > Related to the upcoming release of FieldTrip, I am busy cleaning up > parts of the code that are not so clear at the moment. One of them is > preprocessing and definetrial. Currently the preprocessing function is > reading multiple datatypes at once and giving each of them a different > treatment. This clearly reflects that preprocessing was initially > written for MEG data and that other dataformats were added later. > Specifically, these two sections in the help of preprocessing are what > bothers me. > > % Specific preprocessing options for EMG channels are > % cfg.emgchannel = cell-array with the label(s) of EMG channels > % cfg.emghpfreq = high-pass frequency > % cfg.emgrectify = 'yes' or 'no' > % cfg.emghilbert = 'yes' or 'no' > % > % Specific preprocessing options for EEG channels are > % cfg.eegchannel = cell-array with the label(s) of EEG channels > % cfg.implicitref = 'label' or empty, add the implicit reference as > zeros prior to rereferencing > % cfg.refchannel = cell-array with new reference channel(s) > % cfg.reref = 'no' or 'yes' > > All other preprocessing options are applied to MEG as well as to EMG > and EOG channel groups, which means that you currently can NOT apply > different filter settings for EMG and MEG channels, or apply baseline > correction to only one of them. > > I would like to suggest the following changes > 1) there will be no MEG/EEG/EMG specific options any more > 2) preprocessing will treat all channels the same > 3) if you want to apply different settings to different channel > groups (e.g. to the MEG and the EEG channels), you should call > preprocessing twice and concatenate the resulting raw data objects. > > These changes will facilitate further improvements of the preprocessing > function, as well of the artifact detection routines. Regarding item 3: > I can of course explain how to do it (or I could even write a general > function for that). Important for item 3 is that it will not be > neccessary to redo the artifact detection multiple times for the > different channel groups that you want to concatenate. > > I would like to get your feedback on the following two items: At the > moment I am only aware of Jan-Mathijs mixing different channel groups > in his analyses, so please let me know if you are also using EMG and/or > EEG channels and their specific preprocessing options. Furthermore, if > you have particular opinions about this issue, let me know as soon as > ppossible (either to me directly, through the fieldtrip list or at the > thursday MEG meeting). If I don't get any objections, I will implement > the changes as suggested. > > best regards, > Robert > > > ---------------------------------------------------------------------- > Robert Oostenveld, PhD > Center for Sensory-Motor Interaction (SMI) > Aalborg University, Denmark > > and > > F.C. Donders Centre for Cognitive Neuroimaging > University Nijmegen > P.O. Box 9101 > NL-6500 AH Nijmegen > The Netherlands > > Tel: +31 (0)24 3619695 > Fax: +31 (0)24 3610989 From roberto at SMI.AUC.DK Thu Aug 19 13:33:55 2004 From: roberto at SMI.AUC.DK (Robert Oostenveld) Date: Thu, 19 Aug 2004 13:33:55 +0200 Subject: preprocessing cleanup In-Reply-To: <412489A7.6020000@fcdonders.kun.nl> Message-ID: Hi Christian, Rereferencing for EEG data will certainly remain included. My suggestion would be to implement rereferencing as a general option, i.e. cfg.implicitref cfg.refchannel cfg.reref would apply to all channels that are listed in cfg.channel, and cfg.eegchannel would be obsoleted. This does mean that people in principle could also apply nonsense rereferencing to MEG channels, but if they are that stupid... Robert On 19 Aug 2004, at 13:06, christian forkstam wrote: > hey master fieldtripper, > > if i understand the proposed modification correctly it seems like a > perfect idea to me. just to make sure i don't loose the possibility to > rereference my EEG data i just want to secure this option. as far as i > understan it does not hurt to include the possibility for both > MEG/EEG/EMG analysis but you know that better. > > the options of concern: > > % cfg.implicitref = 'label' or empty, add the implicit reference as > zeros prior to rereferencing > % cfg.refchannel = cell-array with new reference channel(s) > % cfg.reref = 'no' or 'yes' > > ...christian > (soon out tripping the fields of a nothern swedish mountain area...) > > > Robert Oostenveld wrote: >> Dear FieldTrippers, >> >> Related to the upcoming release of FieldTrip, I am busy cleaning up >> parts of the code that are not so clear at the moment. One of them is >> preprocessing and definetrial. Currently the preprocessing function is >> reading multiple datatypes at once and giving each of them a different >> treatment. This clearly reflects that preprocessing was initially >> written for MEG data and that other dataformats were added later. >> Specifically, these two sections in the help of preprocessing are what >> bothers me. >> >> % Specific preprocessing options for EMG channels are >> % cfg.emgchannel = cell-array with the label(s) of EMG channels >> % cfg.emghpfreq = high-pass frequency >> % cfg.emgrectify = 'yes' or 'no' >> % cfg.emghilbert = 'yes' or 'no' >> % >> % Specific preprocessing options for EEG channels are >> % cfg.eegchannel = cell-array with the label(s) of EEG channels >> % cfg.implicitref = 'label' or empty, add the implicit reference as >> zeros prior to rereferencing >> % cfg.refchannel = cell-array with new reference channel(s) >> % cfg.reref = 'no' or 'yes' >> >> All other preprocessing options are applied to MEG as well as to EMG >> and EOG channel groups, which means that you currently can NOT apply >> different filter settings for EMG and MEG channels, or apply baseline >> correction to only one of them. >> >> I would like to suggest the following changes >> 1) there will be no MEG/EEG/EMG specific options any more >> 2) preprocessing will treat all channels the same >> 3) if you want to apply different settings to different channel >> groups (e.g. to the MEG and the EEG channels), you should call >> preprocessing twice and concatenate the resulting raw data objects. >> >> These changes will facilitate further improvements of the >> preprocessing >> function, as well of the artifact detection routines. Regarding item >> 3: >> I can of course explain how to do it (or I could even write a general >> function for that). Important for item 3 is that it will not be >> neccessary to redo the artifact detection multiple times for the >> different channel groups that you want to concatenate. >> >> I would like to get your feedback on the following two items: At the >> moment I am only aware of Jan-Mathijs mixing different channel groups >> in his analyses, so please let me know if you are also using EMG >> and/or >> EEG channels and their specific preprocessing options. Furthermore, if >> you have particular opinions about this issue, let me know as soon as >> ppossible (either to me directly, through the fieldtrip list or at the >> thursday MEG meeting). If I don't get any objections, I will implement >> the changes as suggested. >> >> best regards, >> Robert >> >> >> ---------------------------------------------------------------------- >> Robert Oostenveld, PhD >> Center for Sensory-Motor Interaction (SMI) >> Aalborg University, Denmark >> >> and >> >> F.C. Donders Centre for Cognitive Neuroimaging >> University Nijmegen >> P.O. Box 9101 >> NL-6500 AH Nijmegen >> The Netherlands >> >> Tel: +31 (0)24 3619695 >> Fax: +31 (0)24 3610989 >> ---------------------------------------------------------------------- Robert Oostenveld, PhD Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark and F.C. Donders Centre for Cognitive Neuroimaging University Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands Tel: +31 (0)24 3619695 Fax: +31 (0)24 3610989 From r.oostenveld at FCDONDERS.KUN.NL Fri Aug 20 09:02:38 2004 From: r.oostenveld at FCDONDERS.KUN.NL (Robert Oostenveld) Date: Fri, 20 Aug 2004 09:02:38 +0200 Subject: preprocessing Message-ID: Hi FieldTrippers, Following yesterdays discussion, I have modified preprocessing according to my proposal: all channels are now treated the same. If you try to use one of the old options (eegchannel, emghilbert, etc.) it will give an error. The operation to separate out DEFINETRIAL and REJECTARTIFACT from preprosessing will mainly be in the documentation, and should also not affect your current configurations and scripts. Therefore I will proceed with that as well, but will not notify you of it specifically. best regards Robert From Pascal.Fries at FCDONDERS.KUN.NL Wed Aug 25 11:32:35 2004 From: Pascal.Fries at FCDONDERS.KUN.NL (Pascal Fries) Date: Wed, 25 Aug 2004 11:32:35 +0200 Subject: freqdescriptives In-Reply-To: Message-ID: Dear fieldtrippers, I have just committed a new function to fieldtrip: freqdescriptives. It is meant to replace the old and not really fieldtrip-like frqanajckstatistic. I have tested it, but please report bugs! Pascal Pascal Fries Principal Investigator Neuronal Coherence Group F. C. Donders Centre for Cognitive Neuroimaging University of Nijmegen Adelbertusplein 1 6525 EK Nijmegen The Netherlands Phone: (+31) (0)24 36 10657 Fax: (+31) (0)24 36 10989 e-mail: pascal.fries at fcdonders.kun.nl website: www.kun.nl/fcdonders/ From m.siegel at UKE.UNI-HAMBURG.DE Thu Aug 26 14:04:42 2004 From: m.siegel at UKE.UNI-HAMBURG.DE (Markus Siegel) Date: Thu, 26 Aug 2004 14:04:42 +0200 Subject: new functions in CVS Message-ID: Dear fieldtrippers, I have added sliceinterp.m and sourcestatistics_randomization.m to the CVS. No changes to sourcestatistics_randomization.m sliceinterp.m has now cfg.whitebg = 'yes' as defaul and a bug concerning user-colormaps has been fixed. Best, Markus Siegel