From marco.rotonda at GMAIL.COM Tue Jun 1 11:48:44 2010 From: marco.rotonda at GMAIL.COM (Marco Rotonda) Date: Tue, 1 Jun 2010 11:48:44 +0200 Subject: cohrefchannel Message-ID: Hi again... I know that this could be quite a fool question but I still have this problem... I don't know if this could be the solution but if I make a new channel that is the mean of all the others? ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Tue Jun 1 12:22:26 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Tue, 1 Jun 2010 12:22:26 +0200 Subject: cohrefchannel In-Reply-To: Message-ID: Hi Marco, Doesn't it just work if you specify cfg.cohrefchannel = 'thenameofthereferencechannelyouthrewaway'? As far as I know the plotting routine needs to know which rows from the freq.labelcmb to select for plotting. For this it needs a channel name, but it does not need the original channel to be present in the data. Cheers, Jan-Mathijs On Jun 1, 2010, at 11:48 AM, Marco Rotonda wrote: > Hi again... > I know that this could be quite a fool question but I still have this > problem... I don't know if this could be the solution but if I make > a new > channel that is the mean of all the others? > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Matthias.Wacker at MTI.UNI-JENA.DE Tue Jun 1 15:00:15 2010 From: Matthias.Wacker at MTI.UNI-JENA.DE (Matthias Wacker) Date: Tue, 1 Jun 2010 15:00:15 +0200 Subject: Missing "subplots" in ft_multiplotER Message-ID: Dear Community, I have lasting problems with the ft_multiplotER routine. When I do a multiplot, the small plots themselves are missing (Snapshot.png). However, using the interactive mode, averaging over multiple channels with mouse interaction shows that the data is there (Snapshot2.png). What am I doing wrong? Or is it a known issue? %%%%%%% BEGIN CODE %%%%%%%% ... [data] = ft_preprocessing(cfg); ... %% time locked analysis cfg = []; avgData = ft_timelockanalysis(cfg, data); %% plot it % create layout lay = ft_prepare_layout([], data); % plot cfg = []; cfg.showlabels = 'yes'; cfg.fontsize = 6; cfg.layout = lay; cfg.interactive='yes'; ft_multiplotER(cfg, avgData); %%%%%%% END CODE %%%%%%%% Thanks for any help! Best regards, Matthias Wacker ____________________ Universitätsklinikum Jena Körperschaft des öffentlichen Rechts und Teilkörperschaft der Friedrich-Schiller-Universität Jena Bachstraße 18, 07743 Jena Verwaltungsratsvorsitzender: Prof. Dr. Thomas Deufel; Medizinischer Vorstand: Prof. Dr. Klaus Höffken; Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufmännischer Vorstand und Sprecher des Klinikumsvorstandes: Rudolf Kruse Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221; Gerichtsstand Jena Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Snapshot2.png Type: image/png Size: 41862 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Snapshot.png Type: image/png Size: 41348 bytes Desc: not available URL: From maglione.antongiulio at LIBERO.IT Tue Jun 1 15:39:33 2010 From: maglione.antongiulio at LIBERO.IT (Anton Giulio Maglione) Date: Tue, 1 Jun 2010 15:39:33 +0200 Subject: Make a leadfield from matlab structure Message-ID: Hi all! i have an MRI image in .img format. i made, with brainsuite software, tissue structure of the cortex, skull and skin (in matlab format). can i use some fieldtrip fuctions to make leadfield matrix?or should i make all the analysis only fieldtrip functions? best regards, giulio maglione -- " Un giorno, passeggiando nella foresta, ho visto una bestia. Quando mi sono avvicinato ho visto che era un uomo. Quando sono arrivato vicino a lui mi sono accorto che era mio fratello" (Proverbio tibetano) Vieni a trovarmi a quest'indirizzo: angima.blogspot.com oppure http://www.facebook.com/antongiulio.maglione?ref=name (Facebook) ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From gianpaolo.demarchi at UNITN.IT Tue Jun 1 16:01:14 2010 From: gianpaolo.demarchi at UNITN.IT (Gianpaolo Demarchi) Date: Tue, 1 Jun 2010 16:01:14 +0200 Subject: Missing "subplots" in ft_multiplotER In-Reply-To: <4C052081.CBF6.008E.0@mti.uni-jena.de> Message-ID: Dear Matthias, I encountered the same proble some time ago, and another user (Stephan Moratti) helped me a lot in solving it. You can look in the mailing list archives (i.e. use the "search" power ;-)), but for you convenience I repost here the link to the thread: https://listserv.surfnet.nl/scripts/wa.cgi?A2=ind1002&L=fieldtrip&T=0&F=&S=&P=4945 BTW, it's not a bug, but somehow a "feature", in the sense that forces you to select only one type of sensors to look at (with cfg.channel properly set for either magnetometers or gradiometers). Best, Gianpaolo ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From BelluscB at NINDS.NIH.GOV Thu Jun 3 18:00:29 2010 From: BelluscB at NINDS.NIH.GOV (Belluscio, Beth (NIH/NINDS) [E]) Date: Thu, 3 Jun 2010 12:00:29 -0400 Subject: evoked field amplitude Message-ID: I want to calculate the strength of the evoked fields in response to a series of stimuli. Initially, I tried doing this with the averaged data at sensors demonstrating an evoked field following the stimulus. However, I noticed that during the course of the response, the dipole of the source seemed to shift slightly, and that this dipole was not consistently oriented following successive stimuli. So I was concerned that by measuring only the response at the sensor, I would obtain a false sense of change in the underlying response. I decided to try looking at the response with the data converted into the corresponding planar gradient (I use a CTF MEG). However, I was unable to find a way to obtain values of the field within an ROI with this data set. Does anyone know how to do this? Lastly, it seems it might be best to compute the source and then evaluate the strength of the signal from an ROI in source-space. What are the pros/cons of using sensor space vs. source space to measure the amplitude of a response? Is there a convention within the field for the methodology for doing this? Beth Belluscio, MD-PhD Clinical Fellow Human Motor Control Section National Institute of Neurological Disorders and Stroke 301-402-3495 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sklein at BERKELEY.EDU Thu Jun 3 19:02:45 2010 From: sklein at BERKELEY.EDU (Stanley Klein) Date: Thu, 3 Jun 2010 10:02:45 -0700 Subject: evoked field amplitude In-Reply-To: <794DFDD3C128EF44AC49ADC58FD0090C02BA31C163@NIHMLBX10.nih.gov> Message-ID: Beth, you ask about going to source space. It's my understanding that people don't yet know how to reliably go from sensor space to source space. The problem is that neighboring cortical areas are often wired together and will fire together and since these neighboring areas will likely have different folding patterns and different time functions the inverse problem of going to sources has problems with both EEG and MEG because of how close these neighbors are to each other. There are two cases where there seem to be solutions, one is occipital cortex where V1, V2, V3, V3a have retinotopic organization that can be identified with fMRI/MRI. The idea here is that with tiny patches in a dartboard layout one can overwhelm the above ambiguity by making use of the topographic layout of cortex. Another area is in somatosensory and motor areas where the homunculus mapping also allows neighboring areas to be separated. Luckily fMRI can also identifying other regions that could be used in helping one go from sensors to sources. However, the above manipulations aren't easily carried out. In addition, there are many researchers who believe that ICA can help do the job. In summary it is healthy to be skeptical of some of the claims of success in going from sensors to sources. Stan On Thu, Jun 3, 2010 at 9:00 AM, Belluscio, Beth (NIH/NINDS) [E] < BelluscB at ninds.nih.gov> wrote: > I want to calculate the strength of the evoked fields in response to a > series of stimuli. Initially, I tried doing this with the averaged data at > sensors demonstrating an evoked field following the stimulus. However, I > noticed that during the course of the response, the dipole of the source > seemed to shift slightly, and that this dipole was not consistently oriented > following successive stimuli. So I was concerned that by measuring only the > response at the sensor, I would obtain a false sense of change in the > underlying response. > > I decided to try looking at the response with the data converted into the > corresponding planar gradient (I use a CTF MEG). However, I was unable to > find a way to obtain values of the field within an ROI with this data set. > Does anyone know how to do this? > > Lastly, it seems it might be best to compute the source and then evaluate > the strength of the signal from an ROI in source-space. What are the > pros/cons of using sensor space vs. source space to measure the amplitude of > a response? Is there a convention within the field for the methodology for > doing this? > > > > > > Beth Belluscio, MD-PhD > > Clinical Fellow > > Human Motor Control Section > > National Institute of Neurological Disorders and Stroke > > 301-402-3495 > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at MAC.COM Thu Jun 3 20:55:05 2010 From: nathanweisz at MAC.COM (Nathan Weisz) Date: Thu, 3 Jun 2010 20:55:05 +0200 Subject: evoked field amplitude In-Reply-To: <794DFDD3C128EF44AC49ADC58FD0090C02BA31C163@NIHMLBX10.nih.gov> Message-ID: > following the stimulus. However, I noticed that during the course of the response, the dipole of the source seemed to shift slightly, > it really depends what you mean by "shift slightly". small shifts shouldn't be a big deal (i hesitate to give a rule of thumb). your dipole doesn't just capture activity from that one spot. of course if the movement is huge then placing a single dipole somewhere to represent that activity does not make sense. > and that this dipole was not consistently oriented following successive stimuli. So I was concerned that by measuring only the response at the sensor, I would obtain a false sense of change in the underlying response. > the standard BESA approach e.g. would be to use a "regional source" i.e. a dipole with 3 orthogonal orientations. you can then calculate the vector magnitude (pythagoras). that should take care of a "rotating" dipole. this can also be done within fieldtrip if you don't have BESA. > the signal from an ROI in source-space. What are the pros/cons of using sensor space vs. source space to measure the amplitude of a response? > pro: - in case of "simple" activations (e.g. sensory evoked ERPs) you can reduce the information from >100 sensors to e.g. 2 sources. the dipole positions could also be standardized across subjects which may increase your power later when doing statistics (sensor positions are impossible to standardize without using offline tricks) - of course neighbouring sources capture almost identical activity (which is good regarding you issue of "slightly shifting" source; see above), however the mixing of diverse activities is far worse on a sensor level! cons: - some arbitrariness of placing sources in "cognitive" experiments. unless you have very good prior information where to expect activity to come from, doing sensor analysis first followed by some distributed sources solution seems more advisable. you could then still look at time courses of ROIs defined by your statistical contrast. in the end, there is no general cookbook-recipe and you should decide based on your experiment. the best situation is when your sensor and source data give converging results :-) best, nathan > > > > > Beth Belluscio, MD-PhD > > Clinical Fellow > > Human Motor Control Section > > National Institute of Neurological Disorders and Stroke > > 301-402-3495 > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Don.Rojas at UCDENVER.EDU Thu Jun 3 22:04:29 2010 From: Don.Rojas at UCDENVER.EDU (Rojas, Don) Date: Thu, 3 Jun 2010 14:04:29 -0600 Subject: evoked field amplitude In-Reply-To: Message-ID: I disagree somewhat with the idea that we don't know how to reliably go from sensor to source space. For datasets with large SNR sensory and motor evoked responses, constrained inverse solutions can be quite reliable and correspond very well in some cases with fMRI (whether evoked responses and fMRI "should" correspond to each other is a different question). The literature has many examples of this type of inverse. Some potential pros, depending on the validity of your source solution and your experiment: 1. Reduction of the number of comparisons made (e.g., 275 MEG sensors in the CTF system at NIMH can be reduced to several ECDs in some simple sensory experiments). 2. Independence of the source strength from the sensor-brain distance (signal amplitudes in MEG sensors in particular are highly dependent on how far away the head is from the sensory array and this can vary tremendously from subject to subject). 3. Higher signal to noise ratio, depending on the approach used. Some spatial filtering approaches such as SSP, beamforming, etc. can substantially reduce the impact of noise from non-brain source such as magnetic dental work artifacts in MEG, gamma-band range muscle activity in EEG, etc. Some potential cons: 1. Invalid source models can nullify any potential advantage. 2. In cognitive experiments, some potential sources may not have very large activity relative to the sensory evoked fields/potentials you measure, and depending on the preprocessing and inverse approaches, the source model may be biased towards the larger SNR responses. 3. Source modeling can be computationally and/or financially expensive, particularly when highly accurate individual anatomical MRI segmentations are needed to construct the conductor model. Best, Don __________________ Don Rojas, Ph.D. Director, Magnetoencephalography Laboratory University of Colorado Denver On 6/3/10 11:02 AM, "Stanley Klein" wrote: Beth, you ask about going to source space. It's my understanding that people don't yet know how to reliably go from sensor space to source space. The problem is that neighboring cortical areas are often wired together and will fire together and since these neighboring areas will likely have different folding patterns and different time functions the inverse problem of going to sources has problems with both EEG and MEG because of how close these neighbors are to each other. There are two cases where there seem to be solutions, one is occipital cortex where V1, V2, V3, V3a have retinotopic organization that can be identified with fMRI/MRI. The idea here is that with tiny patches in a dartboard layout one can overwhelm the above ambiguity by making use of the topographic layout of cortex. Another area is in somatosensory and motor areas where the homunculus mapping also allows neighboring areas to be separated. Luckily fMRI can also identifying other regions that could be used in helping one go from sensors to sources. However, the above manipulations aren't easily carried out. In addition, there are many researchers who believe that ICA can help do the job. In summary it is healthy to be skeptical of some of the claims of success in going from sensors to sources. Stan On Thu, Jun 3, 2010 at 9:00 AM, Belluscio, Beth (NIH/NINDS) [E] wrote: I want to calculate the strength of the evoked fields in response to a series of stimuli. Initially, I tried doing this with the averaged data at sensors demonstrating an evoked field following the stimulus. However, I noticed that during the course of the response, the dipole of the source seemed to shift slightly, and that this dipole was not consistently oriented following successive stimuli. So I was concerned that by measuring only the response at the sensor, I would obtain a false sense of change in the underlying response. I decided to try looking at the response with the data converted into the corresponding planar gradient (I use a CTF MEG). However, I was unable to find a way to obtain values of the field within an ROI with this data set. Does anyone know how to do this? Lastly, it seems it might be best to compute the source and then evaluate the strength of the signal from an ROI in source-space. What are the pros/cons of using sensor space vs. source space to measure the amplitude of a response? Is there a convention within the field for the methodology for doing this? Beth Belluscio, MD-PhD Clinical Fellow Human Motor Control Section National Institute of Neurological Disorders and Stroke 301-402-3495 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Jan.Hirschmann at MED.UNI-DUESSELDORF.DE Fri Jun 4 15:21:29 2010 From: Jan.Hirschmann at MED.UNI-DUESSELDORF.DE (Jan Hirschmann) Date: Fri, 4 Jun 2010 15:21:29 +0200 Subject: coordinates and volumelookup Message-ID: Dear all, I am using the function ft_volumelookup with the AFNI atlas to find out the areas belonging to certain MNI coordinates. Regarding this I have 3 little questions: 1) If I create a grid from template brain T1 (spm2) and multiply the .pos entries by 10 to convert to mm, as described in the example matlab scripts on the fieldtrip homepage, the .pos entries are MNI coordinates, right? 2) When I use volumelookup to look up coordinates (I am giving a mask as input which really has only 1 nonzero entry) I often get the result: "no label found". Are there really that many places in the brain which do not have a label in the atlas? 3) When using the function I get the warning: "homogenous transformation might be incorrect for AFNI file". Should I worry about this? Labelling structures I recognize with the tool, e.g. thalamus, works fine, so I guess labels and cords match. Thanks for your help! Jan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Jan.Hirschmann at MED.UNI-DUESSELDORF.DE Fri Jun 4 15:28:59 2010 From: Jan.Hirschmann at MED.UNI-DUESSELDORF.DE (Jan Hirschmann) Date: Fri, 4 Jun 2010 15:28:59 +0200 Subject: clarification: coordinates and volumelookup In-Reply-To: A<72E993C35FB11743B79FF9286E5B6D8B014A843D@Mail2-UKD.VMED.UKD> Message-ID: Sorry, 1 thing to clarify in the last question: By "labelling structures I recognize works fine" I meant setting power to 1 erverywhere and then defining a roi, e.g. 'Thalamus' in ft_sourceplot. What I see highlighted is the thalamus. Best, Jan ________________________________ Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag von Jan Hirschmann Gesendet: Freitag, 4. Juni 2010 15:21 An: FIELDTRIP at NIC.SURFNET.NL Betreff: [FIELDTRIP] coordinates and volumelookup Dear all, I am using the function ft_volumelookup with the AFNI atlas to find out the areas belonging to certain MNI coordinates. Regarding this I have 3 little questions: 1) If I create a grid from template brain T1 (spm2) and multiply the .pos entries by 10 to convert to mm, as described in the example matlab scripts on the fieldtrip homepage, the .pos entries are MNI coordinates, right? 2) When I use volumelookup to look up coordinates (I am giving a mask as input which really has only 1 nonzero entry) I often get the result: "no label found". Are there really that many places in the brain which do not have a label in the atlas? 3) When using the function I get the warning: "homogenous transformation might be incorrect for AFNI file". Should I worry about this? Labelling structures I recognize with the tool, e.g. thalamus, works fine, so I guess labels and cords match. Thanks for your help! Jan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ingrid.nieuwenhuis at FCDONDERS.RU.NL Fri Jun 4 16:46:51 2010 From: ingrid.nieuwenhuis at FCDONDERS.RU.NL (Ingrid Nieuwenhuis) Date: Fri, 4 Jun 2010 16:46:51 +0200 Subject: clarification: coordinates and volumelookup In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8B014A843E@Mail2-UKD.VMED.UKD> Message-ID: Dear Jan, 1) Yes, I think so. The template is in MNI coordinates. The *10 is necessary to go from cm to mm. I'm not totally sure if this step is still necessary, there is some improved handling of units. But it should be easy to spot if thing are a factor of 10 off. 2) Depends on the atlas. Some atlases have indeed many voxels (all white matter for instance) with no label. You can increase cfg.maxqueryrange, to find the closest label. 3) Where does the warning come from (file, line?). It sounds indeed if it's okay, but it's hard to judge without knowing which check in the code resulted in the warning. Do make sure that the cfg.inputcoordinates set to 'mni' and cfg.atlascoordinates is set to 'tal' (I think the last happens automatically in ft_prepare_atlas when you use the AFNI file). What helps to get a bit of insight is to prepare the atlas yourself with ft_prepare_atlas. You can subsequently plot atlas.brick0 or atlas.brick1 with ft_sourceplot, cfg.funparameter = 'brick0', cfg.interactive = 'yes', cfg.method = 'orthoplot'. The value is linked to the name in atlas.descr. Hope this helps, Ingrid ------------------------------------ Ingrid L.C. Nieuwenhuis PhD student Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging Radboud University Nijmegen, The Netherlands Email: ingrid.nieuwenhuis at donders.ru.nl Tel: 0031 (0)24 - 36 10887 _____ From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Jan Hirschmann Sent: Friday, June 04, 2010 3:29 PM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] clarification: coordinates and volumelookup Sorry, 1 thing to clarify in the last question: By "labelling structures I recognize works fine" I meant setting power to 1 erverywhere and then defining a roi, e.g. 'Thalamus' in ft_sourceplot. What I see highlighted is the thalamus. Best, Jan _____ Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag von Jan Hirschmann Gesendet: Freitag, 4. Juni 2010 15:21 An: FIELDTRIP at NIC.SURFNET.NL Betreff: [FIELDTRIP] coordinates and volumelookup Dear all, I am using the function ft_volumelookup with the AFNI atlas to find out the areas belonging to certain MNI coordinates. Regarding this I have 3 little questions: 1) If I create a grid from template brain T1 (spm2) and multiply the .pos entries by 10 to convert to mm, as described in the example matlab scripts on the fieldtrip homepage, the .pos entries are MNI coordinates, right? 2) When I use volumelookup to look up coordinates (I am giving a mask as input which really has only 1 nonzero entry) I often get the result: "no label found". Are there really that many places in the brain which do not have a label in the atlas? 3) When using the function I get the warning: "homogenous transformation might be incorrect for AFNI file". Should I worry about this? Labelling structures I recognize with the tool, e.g. thalamus, works fine, so I guess labels and cords match. Thanks for your help! Jan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.rotonda at GMAIL.COM Fri Jun 4 18:06:26 2010 From: marco.rotonda at GMAIL.COM (Marco Rotonda) Date: Fri, 4 Jun 2010 18:06:26 +0200 Subject: cohrefchannel In-Reply-To: Message-ID: Hi Jan... I got the point... but now I'm inside another problem that should be even easier... I give this script: cfg = []; cfg.xparam = 'time'; cfg.yparam = 'freq'; cfg.zparam = 'plvspctrm'; cfg.cohrefchannel = 'Cz'; cfg.layout = 'EEG1020.lay'; cfg.showlabels = 'yes'; cfg.colorbar = 'yes'; figure; ft_multiplotTFR(cfg, plvs001fnb1) but if I chage the cfg.cohrefchannel to 'Fz' or whatever the plot is always the same... the point is that the data I passed (plvs001fnb1) is <378x44x1000 double> (combinationXfreqXtime)... how can I plot the different combinations? I mean how could I plot the 378 combinations I have (of course I don't want to plot all at once:-)) and check the different plv for each couple of electrods? sorry for this trivial question but I can't get out from this easy problem... 2010/6/1 jan-mathijs schoffelen : > Hi Marco, > > Doesn't it just work if you specify cfg.cohrefchannel = > 'thenameofthereferencechannelyouthrewaway'? > As far as I know the plotting routine needs to know which rows from the > freq.labelcmb to select for plotting. For this it needs a channel name, but > it does not need the original channel to be present in the data. > > Cheers, > > Jan-Mathijs > > > On Jun 1, 2010, at 11:48 AM, Marco Rotonda wrote: > >> Hi again... >> I know that this could be quite a fool question but I still have this >> problem...  I don't know if this could be the solution but if I make a new >> channel that is the mean of all the others? >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG >> and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/neuroimaging/fieldtrip. >> > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3668063 > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From aostendorf at BESA.DE Mon Jun 7 08:54:21 2010 From: aostendorf at BESA.DE (Andrea Ostendorf) Date: Mon, 7 Jun 2010 08:54:21 +0200 Subject: SPM8 In-Reply-To: <4B96053B.1020306@donders.ru.nl> Message-ID: Dear Fieldtrip team, If I understand the notes on the development page right, you have switched from SPM2 to SPM8 and are currently working on the integration with Fieldtrip. Could you perhaps add an entry in the to-do list? I believe that if you allowed for the use of spm_bwlabel instead of bwlabeln if the latter is not available, one could use some of your statistics options even without the MATLAB Statistics toolbox. (For my purposes, for example, a few modifications in findcluster and clusterstat would be sufficient.) A nice day to all of you! All the best Andrea ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Jan.Hirschmann at MED.UNI-DUESSELDORF.DE Mon Jun 7 13:09:29 2010 From: Jan.Hirschmann at MED.UNI-DUESSELDORF.DE (Jan Hirschmann) Date: Mon, 7 Jun 2010 13:09:29 +0200 Subject: AW: [FIELDTRIP] clarification: coordinates and volumelookup In-Reply-To: A<20100604144650.C5E8716109B@smtp.ru.nl> Message-ID: Thanks Ingrid, your comments were of much help to me. I did not know that one can plot the atlas and about the function of cfg.maxqueryrange. So it means sth like: search in the x closest voxels for labels? The warning occurs in read_mri at line 105. There it says: % FIXME: this should be checked, but I only have a single BRIK file % construct the homogenous transformation matrix that defines the axes warning('homogenous transformation might be incorrect for AFNI file'); Thanks very much for your help! Jan ________________________________ Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag von Ingrid Nieuwenhuis Gesendet: Freitag, 4. Juni 2010 16:47 An: FIELDTRIP at NIC.SURFNET.NL Betreff: Re: [FIELDTRIP] clarification: coordinates and volumelookup Dear Jan, 1) Yes, I think so. The template is in MNI coordinates. The *10 is necessary to go from cm to mm. I'm not totally sure if this step is still necessary, there is some improved handling of units. But it should be easy to spot if thing are a factor of 10 off. 2) Depends on the atlas. Some atlases have indeed many voxels (all white matter for instance) with no label. You can increase cfg.maxqueryrange, to find the closest label. 3) Where does the warning come from (file, line?). It sounds indeed if it's okay, but it's hard to judge without knowing which check in the code resulted in the warning. Do make sure that the cfg.inputcoordinates set to 'mni' and cfg.atlascoordinates is set to 'tal' (I think the last happens automatically in ft_prepare_atlas when you use the AFNI file). What helps to get a bit of insight is to prepare the atlas yourself with ft_prepare_atlas. You can subsequently plot atlas.brick0 or atlas.brick1 with ft_sourceplot, cfg.funparameter = 'brick0', cfg.interactive = 'yes', cfg.method = 'orthoplot'. The value is linked to the name in atlas.descr. Hope this helps, Ingrid ------------------------------------ Ingrid L.C. Nieuwenhuis PhD student Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging Radboud University Nijmegen, The Netherlands Email: ingrid.nieuwenhuis at donders.ru.nl Tel: 0031 (0)24 - 36 10887 ________________________________ From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Jan Hirschmann Sent: Friday, June 04, 2010 3:29 PM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] clarification: coordinates and volumelookup Sorry, 1 thing to clarify in the last question: By "labelling structures I recognize works fine" I meant setting power to 1 erverywhere and then defining a roi, e.g. 'Thalamus' in ft_sourceplot. What I see highlighted is the thalamus. Best, Jan ________________________________ Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag von Jan Hirschmann Gesendet: Freitag, 4. Juni 2010 15:21 An: FIELDTRIP at NIC.SURFNET.NL Betreff: [FIELDTRIP] coordinates and volumelookup Dear all, I am using the function ft_volumelookup with the AFNI atlas to find out the areas belonging to certain MNI coordinates. Regarding this I have 3 little questions: 1) If I create a grid from template brain T1 (spm2) and multiply the .pos entries by 10 to convert to mm, as described in the example matlab scripts on the fieldtrip homepage, the .pos entries are MNI coordinates, right? 2) When I use volumelookup to look up coordinates (I am giving a mask as input which really has only 1 nonzero entry) I often get the result: "no label found". Are there really that many places in the brain which do not have a label in the atlas? 3) When using the function I get the warning: "homogenous transformation might be incorrect for AFNI file". Should I worry about this? Labelling structures I recognize with the tool, e.g. thalamus, works fine, so I guess labels and cords match. Thanks for your help! Jan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul_c at GMX.DE Tue Jun 8 12:09:19 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Tue, 8 Jun 2010 12:09:19 +0200 Subject: Dipoli issues Message-ID: Dear all, I'm trying to create a BEM model via prepare_bemmodel with the dipoli method for my diploma thesis, loosely based on the sample script on http://fieldtrip.fcdonders.nl/example/create_bem_headmodel_for_eeg . Unfortunately, if I try to create the BEM model with more than 1 compartment, dipoli crashes with the following error: Fatal error in dipoli: interface /tmp/tp331940.tri is not a single closed surface (totsolangle= -2.0000 from vertex 1 of /tmp/tp331943.tri ) I would be very grateful, if anybody was able to help me understanding and hopefully solving this error. Thanks in advance, Paul Czienskowski ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From dahliash at STANFORD.EDU Tue Jun 8 21:04:34 2010 From: dahliash at STANFORD.EDU (Dahlia Sharon) Date: Tue, 8 Jun 2010 12:04:34 -0700 Subject: freqstatistics with indepsamplesZcoh: incompatible dimensions? Message-ID: Hi, I'm trying to run cluster statistics on coherence between a single channel (actually 2) and a set of 516 channels. My code crashes when ft_freqstatistics reaches clusterstat [Error using ==> reshape; To RESHAPE the number of elements must not change. Error in ==> clusterstat at 182; posclusobs = findcluster(reshape(postailobs, [cfg.dim,1]),channeighbstructmat,cfg.minnbchan); ] At this point postailobs is much larger than multiplying the elements of cfg.dim. But digging into it the problem starts earlier, and as far as I can see is a result of incompatibility between the output of freqanalysis and the way indepsamplesZcoh treats the data: In freqanalysis I calculate csd between each of the two channels and all the rest, i.e. I have 2 * (516+1) = 1034 pairs. The dimension of the resulting freq.crssspctrm is 10 (trials) x 1034 (channel pairs) x 51 (frequencies) x 1 (times). In indepsamplesZcoh using the freqanalysis output, for each frequency I have a 1034x10 matrix multiplied by its transpose to get a dimension of 1034x1034. This is of-course much higher than the dimension of the data which should be something like 517x2. How should I transform the freqanalysis output so that it'll be used correctly by indepsamplesZcoh? Thanks! Dahlia. PS - here is part of the code that might be helpful, please let me know if any further information would help. +++++++++++++++++++++++++++++++++++++++++++++++++++++ % configuration for freqanalysis cfgfa = []; cfgfa.output = 'powandcsd'; % 'pow'; cfgfa.toi = -.25:.025:1.25; cfgfa.foi = 6:2:80; %% cfgfa.method = 'mtmfft'; % 'mtmconvol'; cfgfa.trials = 'all'; cfgfa.keeptrials = 'yes'; cfgfa.channel = {'all' }; cfgfa.channelcmb = { 'rh-Jz MT' 'all' ; 'lh-Jz MT' 'all' }; % compute csd between right MT and all % configuration for freqstatistics cfgfs = []; cfgfs.numrandomization = 100; cfgfs.method = 'montecarlo'; cfgfs.correctm = 'cluster'; cfgfs.clusteralpha = 0.05; % significance level for sample-level statistic, i.e. for being considered candidate for clustering cfgfs.clusterstatistic = 'maxsum'; % maxsize cfgfs.clusterthreshold = 'parametric'; % uses T distribution to calculate the sample-level statistic threshold - appropriate for cfg.statistic=indepsamplesT cfgfs.minnbchan = 0; % cfgfs.alpha = 0.05; % significance level for cluster-level statistic, i.e. for final result of significant cluster. cfgfs.tail = 0; % 0 for two-sided testing cfgfs.correcttail = 'alpha'; cfgfs.ivar = 1; cfgfs.latency = 'all'; cfgfs.frequency = 'all'; cfgfs.neighbours = []; cfgfs_coh = cfgfs; cfgfs_coh.statistic = 'indepsamplesZcoh'; cfgfs_coh.label = { 'all' }; %{ 'rh-Jz MT' 'all' ; 'lh-Jz MT' 'all' }; for trig = 100:100:200 trigstr = num2str( trig); disp([subj ' trig' trigstr]) invtrigfile = strcat( invtrigfile_base{1} , trigstr , invtrigfile_base{2}); load(invtrigfile) freq = ft_freqanalysis( cfgfa, data_ftrip); ntrl = size( freq.powspctrm, 1 ); eval(['ntrl' trigstr '=ntrl;']) end design = ones(1, ntrl100 + ntrl200); design(ntrl200+1:end)=2; ccfgfs_coh.design = design; % cfgfs_coh.label = freq.labelcmb; cfgfs_coh.channelcmb = freq.labelcmb; coh_stat = ft_freqstatistics( cfgfs_coh, freq200, freq100); ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.vandermeij at DONDERS.RU.NL Wed Jun 9 16:27:13 2010 From: r.vandermeij at DONDERS.RU.NL (Roemer van der Meij) Date: Wed, 9 Jun 2010 16:27:13 +0200 Subject: SPM8 In-Reply-To: <5E1E87335F0B4202BCE3C3463C40285C@LAT6500Andrea> Message-ID: Hi Andrea, Thanks for your suggestion! We've added it as a to-be-added feature in our bugzilla (it can also be used for that). If you're interested, you can find it at: http://bugzilla.fcdonders.nl/show_bug.cgi?id=89 Best, Roemer On 6/7/2010 8:54 AM, Andrea Ostendorf wrote: > Dear Fieldtrip team, > > If I understand the notes on the development page right, you have switched > from SPM2 to SPM8 and are currently working on the integration with > Fieldtrip. > Could you perhaps add an entry in the to-do list? I believe that if you > allowed for the use of spm_bwlabel instead of bwlabeln if the latter is not > available, one could use some of your statistics options even without the > MATLAB Statistics toolbox. (For my purposes, for example, a few > modifications in findcluster and clusterstat would be sufficient.) > > A nice day to all of you! > All the best > > Andrea > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > -- Roemer van der Meij MSc PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3612631 E-mail: r.vandermeij at donders.ru.nl ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From lhunt at FMRIB.OX.AC.UK Tue Jun 15 10:20:13 2010 From: lhunt at FMRIB.OX.AC.UK (Laurence Hunt) Date: Tue, 15 Jun 2010 09:20:13 +0100 Subject: ft_preproc_highpassfilter Message-ID: Hi folks, I'm trying to filter some MEG data sampled at 200Hz using ft_preproc_highpassfilter. It seems to be behaving slightly strangely. I'm calling it with Fs = 200; Fhp = 5; N = 6; and a stretch of single-channel data with ~50000 samples. However, the returned data doesn't seem to be filtered at 5Hz. When I go into the code and use fvtool to look at the frequency response of the filter, it doesn't have the shape I was expecting: I wondered whether this was because of the GNU public license version of butter that was being called by fieldtrip (in preproc/private), so I took this out of my matlab path and let it find the Mathworks' butter.m, from the signal processing toolbox. This seemed to give a more sensible looking filter design in fvtool: The Mathworks' butter.m also seemed to filter the data a bit more like I was expecting. Is this a problem with the GPL version, or am I calling the function wrong? Cheers, Laurence =========================================== Laurence Hunt, DPhil Student Centre for Functional MRI of the Brain (FMRIB), University of Oxford lhunt at fmrib.ox.ac.uk Phone: (+44)1865-(2)22738 =========================================== ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: GPLbutter.png Type: image/png Size: 8830 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MLbutter.png Type: image/png Size: 7196 bytes Desc: not available URL: From lhunt at FMRIB.OX.AC.UK Tue Jun 15 13:37:32 2010 From: lhunt at FMRIB.OX.AC.UK (Laurence Hunt) Date: Tue, 15 Jun 2010 12:37:32 +0100 Subject: Fwd: highpassfilter problems in fieldtrip Message-ID: Problems were already spotted by Jan-Mathijs... Begin forwarded message: > From: jan-mathijs schoffelen > Date: 15 June 2010 11:19:44 GMT+01:00 > To: Laurence Hunt > Subject: highpassfilter problems in fieldtrip > > Dear Laurence, > > Yes, you're absolutely right. I noticed the problem at some point, and it was caused by some typos in the octave-version of butter. This has been fixed recently, so that could mean that by updating to the most recent version may fix it. > > Cheers, > > Jan-Mathijs > > PS: I am not able to use my donders account for outgoing mails at the moment, so could you forward this reply to the mailing list, so that the rest of the community is aware of the issue? Thanks > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From aardesta at UCLA.EDU Fri Jun 18 00:40:38 2010 From: aardesta at UCLA.EDU (Allen Ardestani) Date: Thu, 17 Jun 2010 15:40:38 -0700 Subject: Connecivityanalysis ERROR Message-ID: Hi everyone, When I call connectivityanalysis using any of the methods that use frequency data, I get the following error: "??? Conversion to cell from double is not possible." I get it even when using the downloaded dataset and exact script from the tutorial: cfg = []; cfg.output = 'powandcsd'; cfg.method = 'mtmfft'; cfg.foilim = [5 100]; cfg.tapsmofrq = 5; cfg.keeptrials = 'yes'; cfg.channel = {'MEG' 'EMGlft' 'EMGrgt'}; cfg.channelcmb = {'MEG' 'EMGlft'; 'MEG' 'EMGrgt'}; freq = ft_freqanalysis(cfg, data); %% Plot %% cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'MEG' 'EMG'}; fd = ft_connectivityanalysis(cfg, freq); Any ideas what's wrong? Many thanks in advance. Best, Allen ____________________________________________________________________________ ______ Allen Ardestani Email: aardesta at ucla.edu Phone: (310) 825-5528 Medical Scientist Training Program David Geffen School of Medicine at UCLA Semel Institute for Neuroscience and Human Behavior 760 Westwood Plaza Los Angeles, CA 90095-1759 USA ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From saskia.haegens at DONDERS.RU.NL Fri Jun 18 11:08:27 2010 From: saskia.haegens at DONDERS.RU.NL (Saskia Haegens) Date: Fri, 18 Jun 2010 11:08:27 +0200 Subject: Connecivityanalysis ERROR In-Reply-To: <014301cb0e6e$1bf0abe0$53d203a0$@edu> Message-ID: Hi Allen, This sounds like a bug that was recently fixed, are you using the latest fieldtrip version? If you could copy/paste the exact error you are getting, would help in figuring out where this goes wrong. Best, Saskia _____ From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Allen Ardestani Sent: vrijdag 18 juni 2010 0:41 To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] Connecivityanalysis ERROR Hi everyone, When I call connectivityanalysis using any of the methods that use frequency data, I get the following error: "??? Conversion to cell from double is not possible." I get it even when using the downloaded dataset and exact script from the tutorial: cfg = []; cfg.output = 'powandcsd'; cfg.method = 'mtmfft'; cfg.foilim = [5 100]; cfg.tapsmofrq = 5; cfg.keeptrials = 'yes'; cfg.channel = {'MEG' 'EMGlft' 'EMGrgt'}; cfg.channelcmb = {'MEG' 'EMGlft'; 'MEG' 'EMGrgt'}; freq = ft_freqanalysis(cfg, data); %% Plot %% cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'MEG' 'EMG'}; fd = ft_connectivityanalysis(cfg, freq); Any ideas what's wrong? Many thanks in advance. Best, Allen ____________________________________________________________________________ ______ Allen Ardestani Email: aardesta at ucla.edu Phone: (310) 825-5528 Medical Scientist Training Program David Geffen School of Medicine at UCLA Semel Institute for Neuroscience and Human Behavior 760 Westwood Plaza Los Angeles, CA 90095-1759 USA ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From qi at BRAIN.K.U-TOKYO.AC.JP Fri Jun 18 11:36:38 2010 From: qi at BRAIN.K.U-TOKYO.AC.JP (=?SHIFT_JIS?Q?Liang_Qi?=) Date: Fri, 18 Jun 2010 11:36:38 +0200 Subject: How to use 'MNE' method in 'sourceanalysis' Message-ID: Hi everyone, I'm trying to do single trial source analysis on MEG data, and I think 'MNE' method in 'sourceanalysis' may accomplish this. However I have no idea how to set the parameters in 'cfg'. Would anyone tell me how to do this? Thanks in advance. Regards, Liang ----------------------- Liang Qi Biological Complex Systems Laboratory Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8561, Japan Tel : +81-4-7136-3899 E-mail : qi at brain.k.u-tokyo.ac.jp ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From bps231 at NYU.EDU Sat Jun 19 10:38:16 2010 From: bps231 at NYU.EDU (Bernhard Staresina) Date: Sat, 19 Jun 2010 10:38:16 +0200 Subject: preprocessing slowing down Message-ID: Dear FieldTrip users, A quick question on preprocessing. I noticed that as I preprocess my EEG data (no actual preprocessing settings, just getting the exportet raw data into FieldTrip format), the process dramatically slows down as it goes along. So by trial 100, MATLAB essentially stops. I don't think it's a working memory issue - I tried to preprocess only the last few trials with cleared working memory, and the process doesn't move on. I read in the trial information (beginsample, endsample and offset) via definetrial, and of my ~700 trials (with only 25 channels), the later trials have begin- and endsample values of eg. 4338002 and 4344000, respectively. But why is it that it takes longer to read in a trial as a function of its begin and end sample? Shouldn't the amount of preceding data points be irrelevant? I'm reading in BrainVision Analyser data, using FT version 'fieldtrip-20090120'. The segments are 5.9 sec long, with 1kHz sampling rate. Thanks, Bernhard ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From aostendorf at BESA.DE Mon Jun 21 08:21:27 2010 From: aostendorf at BESA.DE (Andrea Ostendorf) Date: Mon, 21 Jun 2010 08:21:27 +0200 Subject: SPM8 In-Reply-To: <4C0FA4C1.9050208@donders.ru.nl> Message-ID: Dear Roemer, Thanks a lot. I discussed this topic some months ago with Robert and he suggested that he/the Fieldtrip team could modify the code along the following lines (I copy this from his e-mail because I think he will not mind this) - - - - - I suggest to modify the low level code into two helper functions (findcluster_chanlevel and findcluster_sourcelevel), which both should check like this if hastoolbox('image', 1) % using image processing toolbox my_bwlabeln = @bwlabeln; elseif hastoolbox('spm8', 1) % using spm8 version my_bwlabeln = @spm8_bwlabeln; else error(...) end - - - - I have got SPM8 on my Matlab path and whenever I download a new Fieldtrip version, I have to edit clusterstat and findcluster because it is (or was) not sufficient to simply replace bwlabeln by spm_bwlabel. What I did is probably rather inelegant but I left it that way since it works: In findcluster: Before: % [labelmat(spatdimlev, :, :), num] = bwlabeln(reshape(onoff(spatdimlev, :, :), nfreq, ntime), 4); After: input_for_spm_bwlabel = reshape(onoff(spatdimlev, :, :), nfreq, ntime); input_for_spm_bwlabel = +input_for_spm_bwlabel; %convert from logical [labelmat(spatdimlev, :, :), num] = spm_bwlabel(input_for_spm_bwlabel , 6); In clusterstat: Before: %!!!posclusobs = bwlabeln(tmp, conndef(length(cfg.dim),'min')); After: [posclusobs,L] = spm_bwlabel(tmp, 6); Sorry for the late answer. By the way, I have got into trouble at work because we have a betting game going on and I predicted the Netherlands as the winner (not that I know anything about football but I chose the Netherlands because the Fieldtrip team is so nice)... All the best Andrea ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.vandermeij at DONDERS.RU.NL Tue Jun 22 12:09:07 2010 From: r.vandermeij at DONDERS.RU.NL (Roemer van der Meij) Date: Tue, 22 Jun 2010 12:09:07 +0200 Subject: SPM8 In-Reply-To: <72D3AA975E924FCFAD3FAA83DF7309E1@LAT6500Andrea> Message-ID: Hi Andrea, We are deeply honored by your betting choice! May good fortune come to both of us! Thanks for sharing your modifications. Right now most of my FieldTrip time is going in writing the low-level functions for the spectral estimation module (which eventually replace the current freqanalysis implementation), but an obvious project for me after that is rewriting the cluster-permutation code. It has evolved into its current from over the past years, and our new low-level - high-level function structure will clean it up and makes it easier to fix bugs. I hope I can find the time to work on the bwlabeln functions, I will keep you updated. I'll also add this e-mail to our bugzilla report on this, to keep track of the possibilities. Thanks again for sharing your suggestions, they are always welcome. Best, Roemer On 6/21/2010 8:21 AM, Andrea Ostendorf wrote: > Dear Roemer, > > Thanks a lot. I discussed this topic some months ago with Robert and he > suggested that he/the Fieldtrip team could modify the code along the > following lines (I copy this from his e-mail because I think he will not > mind this) > - - - - - > I suggest to modify the low level code into two helper functions > (findcluster_chanlevel and findcluster_sourcelevel), which both should check > like this > > > if hastoolbox('image', 1) > % using image processing toolbox > my_bwlabeln = @bwlabeln; > elseif hastoolbox('spm8', 1) > % using spm8 version > my_bwlabeln = @spm8_bwlabeln; > else > error(...) > end > - - - - > > I have got SPM8 on my Matlab path and whenever I download a new Fieldtrip > version, I have to edit clusterstat and findcluster because it is (or was) > not sufficient to simply replace bwlabeln by spm_bwlabel. What I did is > probably rather inelegant but I left it that way since it works: > > In findcluster: > Before: > % [labelmat(spatdimlev, :, :), num] = bwlabeln(reshape(onoff(spatdimlev, :, > :), nfreq, ntime), 4); > After: > input_for_spm_bwlabel = reshape(onoff(spatdimlev, :, :), nfreq, ntime); > input_for_spm_bwlabel = +input_for_spm_bwlabel; %convert from logical > [labelmat(spatdimlev, :, :), num] = spm_bwlabel(input_for_spm_bwlabel , 6); > > In clusterstat: > Before: > %!!!posclusobs = bwlabeln(tmp, conndef(length(cfg.dim),'min')); > After: > [posclusobs,L] = spm_bwlabel(tmp, 6); > > Sorry for the late answer. > By the way, I have got into trouble at work because we have a betting game > going on and I predicted the Netherlands as the winner (not that I know > anything about football but I chose the Netherlands because the Fieldtrip > team is so nice)... > > All the best > Andrea > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > -- Roemer van der Meij MSc PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From michael.wibral at WEB.DE Tue Jun 22 17:34:04 2010 From: michael.wibral at WEB.DE (Michael Wibral) Date: Tue, 22 Jun 2010 17:34:04 +0200 Subject: Importing FT data to SPM8 as "LFP" data Message-ID: Dear SPM and FT listusers, does anyone know by any chance which headerfield in FT data to set to which value so that spm_eeg_convert automatically recognizes these data as LFP data? I can't seem to spot the words lfp anywhere inside spm_eeg_convert.m so it all is a bit mysterious to me. Many thanks, Michael ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 628 bytes Desc: not available URL: From r.oostenveld at FCDONDERS.RU.NL Tue Jun 22 19:37:17 2010 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 22 Jun 2010 19:37:17 +0200 Subject: fieldtrip webserver will be down tomorrow evening Message-ID: Dear fieldtrip users Our technical group has to do some maintenance to the servers of the Donders Centre. The consequence is that the fieldtrip wiki (fieldtrip.fcdonders.nl) and the ftp server (ftp.fcdonders.nl) will be down. Hopefully the downtime will be only one evening, but it might extend into the next morning. See below for details. > Tomorrow Wednesday June 23rd, 18:00h CET we have planned a down-time window for central storage and all of the central storage dependent IT services! If everything goes smoothly, central storage and all services will be back up and running later in that evening. In case we encounter unforeseen problems down-time might last until the early next morning Thursday June 24th. best regards, Robert ----------------------------------------------------------- Robert Oostenveld, PhD Senior Researcher Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen tel.: +31 (0)24 3619695 e-mail: r.oostenveld at donders.ru.nl web: http://www.ru.nl/neuroimaging skype: r.oostenveld ----------------------------------------------------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From moratti at MED.UCM.ES Wed Jun 23 08:41:30 2010 From: moratti at MED.UCM.ES (Stephan Moratti) Date: Wed, 23 Jun 2010 08:41:30 +0200 Subject: How to use 'MNE' method in 'sourceanalysis' Message-ID: Hi Liang, I do not work with the most recent version of fieldtrip, but I think you hace to specify the mne parameters this way: cfg.mne.[parameter] = x; Hope that helps. Best, Stephan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From odidodi at HOTMAIL.COM Wed Jun 23 13:20:57 2010 From: odidodi at HOTMAIL.COM (Odelia Goldberg) Date: Wed, 23 Jun 2010 13:20:57 +0200 Subject: cfg.output error while running ft_componentanalysis Message-ID: Hello all, I run ft_artifact_muscle+jump functions, then reject artifacts and then ICA. After choosing the components for removal I've tried to run "comp_orig = ft_componentanalysis(cfg, datacln);", to identify the components on the original data and I get an error saying: ??? Reference to non-existent field 'outputfile'. Error in ==> ft_componentanalysis at 416 if ~isempty(cfg.outputfile) I work with fieldtrip-20100621, and if I put the last three lines in comment, it works (problem solved). (I've tried to add 'output' field but it did't help). Anything that I'm missing? Thanks in advance, Odelia. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Thu Jun 24 17:55:16 2010 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Thu, 24 Jun 2010 17:55:16 +0200 Subject: cfg.output error while running ft_componentanalysis In-Reply-To: Message-ID: Hi Odelia Sorry about that, it is a known bug recently introduced. It only happens in conjunction with cfg.trackconfig=yes. We will fix it asap. Robert On 23 Jun 2010, at 13:20, Odelia Goldberg wrote: > I get an error saying: > > ??? Reference to non-existent field 'outputfile'. > > Error in ==> ft_componentanalysis at 416 > if ~isempty(cfg.outputfile) > > I work with fieldtrip-20100621, and if I put the last three lines in > comment, it works (problem solved). (I've tried to add 'output' > field but it > did't help). > Anything that I'm missing? ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Matthias.Meyer at DONDERS.RU.NL Fri Jun 25 11:24:04 2010 From: Matthias.Meyer at DONDERS.RU.NL (Matthias C. Meyer) Date: Fri, 25 Jun 2010 11:24:04 +0200 Subject: Export EEG Data Message-ID: Dear ft_Community, I am quite new to Fieldtrip and hope that someone has solved my problem before. I recorded EEG data inside an MR Scanner with the BrainVision software and now I want to use Fieldtrip to run some error correction scripts - so far so god. But after that I need to write the corrected data back to the original EEG - data format. I use the ft_write_data function to do this. After some problems I manage to run the function, but the result is a double size datafile, a messed up header and a empty marker file. Probably the data is written in double precision. Giving the data to the function with "single(data_org.trial{1})" in the argument does not help. The command line I use to call the function is: ft_write_data('ScannerCor', data_org.trial{1}, 'dataformat', 'brainvision_eeg','header', data_org.hdr); (I copied the corrected data back to the read in matrix) I heard already, that I can tell Matlab to use only single precision, but it would be nice to tell that the function directly - Is there a way to do so? What do I need to do, to export the header and marker file correctly? The corrected data are exactly of the same size as the original data, if possible, I might also use the original marker file to get the trigger points. I hope some one can help me. Best regards, Matthias. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From h.holle at SUSSEX.AC.UK Fri Jun 25 14:19:53 2010 From: h.holle at SUSSEX.AC.UK (Henning Holle) Date: Fri, 25 Jun 2010 14:19:53 +0200 Subject: databrowser: change order in which channels appear? Message-ID: Dear all, when looking at data with the databrowser (vertical viewmode), the channels appear in the order in which they happen to be in the dataset. Is there a way to define another order (so that, for instance, more anterior channels appear more on top of the screen, and more posterior channels at the bottom of the screen). Kind regards, Henning ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From ingrid.nieuwenhuis at FCDONDERS.RU.NL Fri Jun 25 14:25:45 2010 From: ingrid.nieuwenhuis at FCDONDERS.RU.NL (Ingrid Nieuwenhuis) Date: Fri, 25 Jun 2010 14:25:45 +0200 Subject: databrowser: change order in which channels appear? In-Reply-To: Message-ID: Dear Henning, Are you using the latest version of FieldTrip? If I remember correctly, I changed this at some point into that the order of the channels is as you specify them in cfg.channel Best, Ingrid ------------------------------------ Ingrid L.C. Nieuwenhuis PhD student Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging Radboud University Nijmegen, The Netherlands Email: ingrid.nieuwenhuis at donders.ru.nl Tel: 0031 (0)24 - 36 10887 -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Henning Holle Sent: Friday, June 25, 2010 2:20 PM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] databrowser: change order in which channels appear? Dear all, when looking at data with the databrowser (vertical viewmode), the channels appear in the order in which they happen to be in the dataset. Is there a way to define another order (so that, for instance, more anterior channels appear more on top of the screen, and more posterior channels at the bottom of the screen). Kind regards, Henning ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From odidodi at HOTMAIL.COM Fri Jun 25 15:16:58 2010 From: odidodi at HOTMAIL.COM (odelia nakar) Date: Fri, 25 Jun 2010 13:16:58 +0000 Subject: cfg.output error while running ft_componentanalysis In-Reply-To: Message-ID: Hi Robert, Thank you for your answer. I think that on the 23rd of 6 version it was aready fixed. Good day! Odelia. > Date: Thu, 24 Jun 2010 17:55:16 +0200 > From: r.oostenveld at FCDONDERS.RU.NL > Subject: Re: [FIELDTRIP] cfg.output error while running ft_componentanalysis > To: FIELDTRIP at NIC.SURFNET.NL > > Hi Odelia > > Sorry about that, it is a known bug recently introduced. It only > happens in conjunction with cfg.trackconfig=yes. We will fix it asap. > > Robert > > > On 23 Jun 2010, at 13:20, Odelia Goldberg wrote: > > > I get an error saying: > > > > ??? Reference to non-existent field 'outputfile'. > > > > Error in ==> ft_componentanalysis at 416 > > if ~isempty(cfg.outputfile) > > > > I work with fieldtrip-20100621, and if I put the last three lines in > > comment, it works (problem solved). (I've tried to add 'output' > > field but it > > did't help). > > Anything that I'm missing? > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.rousselet at PSY.GLA.AC.UK Fri Jun 25 15:27:14 2010 From: g.rousselet at PSY.GLA.AC.UK (Guillaume Rousselet) Date: Fri, 25 Jun 2010 14:27:14 +0100 Subject: Frontiers in Perception Science: Call for participation in upcoming Special Topic Message-ID: Hosting Journal: Frontiers in Perception Science Topic Title: Single-trial analyses of behavioural and neuroimaging data in perception and decision-making. Host Editors: Guillaume A. Rousselet, Cyril R. Pernet, Paul Sajda Description: The cognitive psychology of perception and decision-making is at a cross-road. Most studies still employ categorical designs, a priori classified stimuli and perform statistical evaluations across subjects. However, a shift has been observed in recent years towards parametric designs in which the information content of stimuli is systematically manipulated to study the single-trial dynamics of behaviour (reaction times, eye movements) and brain activity (EEG, MEG, fMRI). By using the information contained in the variance of individual trials, the single-trial approach goes beyond the activity of the average brain: it reveals the specificity of information processing in individual subjects, across tasks and stimulus space, revealing both inter-individual commonalties and differences. This special issue provides theoretical and empirical support for the study of single-trial data. Topics of particular interest include: 1. description of the richness of information in single-trials and how it can be successfully extracted; 2. statistical issues related to measures of central tendency, control for multiple comparisons, multivariate approaches, hierarchical modelling and characterization of individual differences; 3. how manipulation of the stimulus space can allow for a direct mapping of stimulus properties onto brain activity to infer dynamics of information processing and information content of brain states; 4. how results from different brain imaging techniques can be integrated at the single-trial level. Abstract Submission Deadline: September 01, 2010 Article Submission Deadline: January 03, 2011 Link to Special Topic: http://www.frontiersin.org/psychology/perceptionscience/specialtopics/98/ The publishing fee for contributors amounts to €900, and a further reduction to €720 for Frontiers Associate Editors. Like all research published with Frontiers, the articles will be freely available to all of our readers on our website, and all Special Topic articles receive a DOI and are indexed in the National Institute of Health’s electronic depository of full text articles, PubMed Central, and many other international archives (Google Scholar, Directory of Open Access Journal, Psych INFO). Frontiers is also in the process of being archived in Thompson Scientific (ISI), and Web of Science. Frontiers has also announced that in the very near future, all published Special Topics will be available to view and download in an eBook format! For more information, you may refer to the Frontiers’ Special Topic page, where you can get further guidance and browse past Special Topics. << http://www.frontiersin.org/specialtopicspage/ >> With best regards, Guillaume Rousselet Associate Editor, Frontiers in Perception Science www.frontiersin.org ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sreenivasan.r.nadar at GMAIL.COM Sat Jun 26 21:04:25 2010 From: sreenivasan.r.nadar at GMAIL.COM (Dr. Sreenivasan Rajamoni Nadar, Ph.D.) Date: Sat, 26 Jun 2010 12:04:25 -0700 Subject: Dr. Sreenivasan Rajamoni Nadar, Ph.D. wants to stay in touch on LinkedIn Message-ID: LinkedIn ------------ FieldTrip, I'd like to add you to my professional network on LinkedIn. - Dr. Sreenivasan Rajamoni Nadar, Ph.D. Dr. Sreenivasan Rajamoni Nadar, Ph.D. Scientist at National Institute of Mental Health Washington D.C. Metro Area Confirm that you know Dr. Sreenivasan Rajamoni Nadar, Ph.D. https://www.linkedin.com/e/dwhirw-gawtl874-2e/isd/1418399407/pkkPy6v8/ ------ (c) 2010, LinkedIn Corporation ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.gomez at SCIENCE.RU.NL Mon Jun 28 13:35:57 2010 From: v.gomez at SCIENCE.RU.NL (=?ISO-8859-1?Q?Vicen=E7_G=F3mez?=) Date: Mon, 28 Jun 2010 13:35:57 +0200 Subject: fixtrialdef.m Message-ID: Dear fieldtripers, function fixtrialdef.m can't handle data with one trial only: K>> ??? Error using ==> cat CAT arguments dimensions are not consistent. Error in ==> fixtrialdef at 26 begsample = cat(1, 0, cumsum(nsmp(1:end-1))) + 1; I fixed it doing: if ntrial == 1 begsample = 1; else begsample = cat(1, 0, cumsum(nsmp(1:end-1))) + 1; end Is that right? thanks, -- Vicenç Gomez Cerda SNN Radboud University Nijmegen The Netherlands http://www.mbfys.ru.nl/staff/v.gomez/ tel: +31 (0)24 - 36 14230 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Mon Jun 28 17:09:29 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Mon, 28 Jun 2010 17:09:29 +0200 Subject: fixtrialdef.m In-Reply-To: <4C28891D.1030602@science.ru.nl> Message-ID: Dear Vicenç, Thanks for the suggestion. I will incorporate it into the ftp-version so that everybody can enjoy this improvement ;). It'll be available as of tomorrow. Cheers, Jan-Mathijs On Jun 28, 2010, at 1:35 PM, Vicenç Gómez wrote: > Dear fieldtripers, > > function fixtrialdef.m can't handle data with one trial only: > > K>> ??? Error using ==> cat > CAT arguments dimensions are not consistent. > > Error in ==> fixtrialdef at 26 > begsample = cat(1, 0, cumsum(nsmp(1:end-1))) + 1; > > I fixed it doing: > > if ntrial == 1 > begsample = 1; > else > begsample = cat(1, 0, cumsum(nsmp(1:end-1))) + 1; > end > > Is that right? > > thanks, > > > -- > Vicenç Gomez Cerda > SNN Radboud University Nijmegen > The Netherlands > http://www.mbfys.ru.nl/staff/v.gomez/ > tel: +31 (0)24 - 36 14230 > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From mcregar at UPO.ES Wed Jun 30 11:04:58 2010 From: mcregar at UPO.ES (Maite Crespo) Date: Wed, 30 Jun 2010 11:04:58 +0200 Subject: Matlab compiler for Windows XP 64-bit Message-ID: Hello, I had my first code errors with mex files. It seems I'll have to install a Matlab compiler for 64 bits (Windows XP). Does anybody knows a free compiler? Thank you very much. Best (first) regards, Maité ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From s.klanke at DONDERS.RU.NL Wed Jun 30 11:31:40 2010 From: s.klanke at DONDERS.RU.NL (Stefan Klanke) Date: Wed, 30 Jun 2010 11:31:40 +0200 Subject: Matlab compiler for Windows XP 64-bit In-Reply-To: Message-ID: Dear Maité, I do not have a 64-bit machine myself yet, but I know that you can produce 64 bit executables using the free "Express" version (both 2008 and 2010) of Microsoft Visual C++. You can get more information here: http://msdn.microsoft.com/en-us/library/9yb4317s.aspx Depending on how old your version of Matlab is, it might be easier to pick the 2008 version, so "mex -setup" can detect the compiler. With kind regards, Stefan On 30-6-2010 11:04, Maite Crespo wrote: > Hello, > > I had my first code errors with mex files. It seems I'll have to install a Matlab > compiler for 64 bits (Windows XP). Does anybody knows a free compiler? > > Thank you very much. > > Best (first) regards, > Maité > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Wed Jun 30 17:10:46 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Wed, 30 Jun 2010 17:10:46 +0200 Subject: Export EEG Data In-Reply-To: <4C2475B4.5030807@donders.ru.nl> Message-ID: Hi Mattias, > I am quite new to Fieldtrip and hope that someone has solved my > problem before. High expectations ;). > I recorded EEG data inside an MR Scanner with the BrainVision > software and now I want to use Fieldtrip to run some error > correction scripts - so far so god. > But after that I need to write the corrected data back to the > original EEG - data format. > I use the ft_write_data function to do this. After some problems I > manage to run the function, but the result is a double size > datafile, a messed up header and a empty marker file. > Probably the data is written in double precision. Giving the data to > the function with "single(data_org.trial{1})" in the argument does > not help. > The command line I use to call the function is: > ft_write_data('ScannerCor', data_org.trial{1}, 'dataformat', > 'brainvision_eeg','header', data_org.hdr); > > (I copied the corrected data back to the read in matrix) > > I heard already, that I can tell Matlab to use only single > precision, but it would be nice to tell that the function directly - > Is there a way to do so? > What do I need to do, to export the header and marker file correctly? I have not encountered this issue before, and I don't know whether anybody else has. This may mean that you need to do some digging yourself to get it solved. I never tried to export data to a different fileformat. The easy way out here would be to also do your subsequent analysis steps in matlab/fieldtrip. Did you already have a detailed look at ft_write_data, and in particular the part which deals with 'brainvision_eeg'. My suspicion is that there is a discrepancy between the information in data_org.hdr, and the exact data you try to export (data_org.trial{1}). Manually converting to single precision may not work if in data_org.hdr you need to specify the precision. (once again I don't know about the specifics of this function, or of the functions it relies on). Using the matlab debugger may help you to access the variables in the function's workspace and to see what's preventing it to work properly. Good luck, Jan-Mathijs Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcregar at UPO.ES Wed Jun 30 18:12:05 2010 From: mcregar at UPO.ES (Maite Crespo) Date: Wed, 30 Jun 2010 18:12:05 +0200 Subject: source analysis on time window and frequency range Message-ID: Hello again! I would like to apply the DICS and SAM methods to localize the source activity within a time window and a frequency range, but based on the CSD or covariance matrices obtained from a wavelet transformation to the time- frequency domain. At the moment I found only one possible frequency or latency as input to the ft_sourceanalysis function. I also read about applying the multitaper method for time-frequency analysis, but I worry about the non-stationarity of the signals. Could somebody give me a hint about how to proceed? Have a nice day. Best regards, Maité ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From marco.rotonda at GMAIL.COM Wed Jun 30 19:07:43 2010 From: marco.rotonda at GMAIL.COM (Marco Rotonda) Date: Wed, 30 Jun 2010 19:07:43 +0200 Subject: Nested analysis Message-ID: Hi Fieldtrippers! I have a question about an analysis that I would like to do. In this experiment I have the following design: 2 group X 2 stage X 2 stimulus X 278 electrodes combinations (plv) wherein group is a between factor and all the other factors are within factors. The electrodes combinations is nested in the stimulus factor and the stimulus is nested in the stage factor. How could I menage this situation? Regards, Marco ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From marco.rotonda at GMAIL.COM Tue Jun 1 11:48:44 2010 From: marco.rotonda at GMAIL.COM (Marco Rotonda) Date: Tue, 1 Jun 2010 11:48:44 +0200 Subject: cohrefchannel Message-ID: Hi again... I know that this could be quite a fool question but I still have this problem... I don't know if this could be the solution but if I make a new channel that is the mean of all the others? ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Tue Jun 1 12:22:26 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Tue, 1 Jun 2010 12:22:26 +0200 Subject: cohrefchannel In-Reply-To: Message-ID: Hi Marco, Doesn't it just work if you specify cfg.cohrefchannel = 'thenameofthereferencechannelyouthrewaway'? As far as I know the plotting routine needs to know which rows from the freq.labelcmb to select for plotting. For this it needs a channel name, but it does not need the original channel to be present in the data. Cheers, Jan-Mathijs On Jun 1, 2010, at 11:48 AM, Marco Rotonda wrote: > Hi again... > I know that this could be quite a fool question but I still have this > problem... I don't know if this could be the solution but if I make > a new > channel that is the mean of all the others? > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Matthias.Wacker at MTI.UNI-JENA.DE Tue Jun 1 15:00:15 2010 From: Matthias.Wacker at MTI.UNI-JENA.DE (Matthias Wacker) Date: Tue, 1 Jun 2010 15:00:15 +0200 Subject: Missing "subplots" in ft_multiplotER Message-ID: Dear Community, I have lasting problems with the ft_multiplotER routine. When I do a multiplot, the small plots themselves are missing (Snapshot.png). However, using the interactive mode, averaging over multiple channels with mouse interaction shows that the data is there (Snapshot2.png). What am I doing wrong? Or is it a known issue? %%%%%%% BEGIN CODE %%%%%%%% ... [data] = ft_preprocessing(cfg); ... %% time locked analysis cfg = []; avgData = ft_timelockanalysis(cfg, data); %% plot it % create layout lay = ft_prepare_layout([], data); % plot cfg = []; cfg.showlabels = 'yes'; cfg.fontsize = 6; cfg.layout = lay; cfg.interactive='yes'; ft_multiplotER(cfg, avgData); %%%%%%% END CODE %%%%%%%% Thanks for any help! Best regards, Matthias Wacker ____________________ Universitätsklinikum Jena Körperschaft des öffentlichen Rechts und Teilkörperschaft der Friedrich-Schiller-Universität Jena Bachstraße 18, 07743 Jena Verwaltungsratsvorsitzender: Prof. Dr. Thomas Deufel; Medizinischer Vorstand: Prof. Dr. Klaus Höffken; Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufmännischer Vorstand und Sprecher des Klinikumsvorstandes: Rudolf Kruse Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221; Gerichtsstand Jena Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Snapshot2.png Type: image/png Size: 41862 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Snapshot.png Type: image/png Size: 41348 bytes Desc: not available URL: From maglione.antongiulio at LIBERO.IT Tue Jun 1 15:39:33 2010 From: maglione.antongiulio at LIBERO.IT (Anton Giulio Maglione) Date: Tue, 1 Jun 2010 15:39:33 +0200 Subject: Make a leadfield from matlab structure Message-ID: Hi all! i have an MRI image in .img format. i made, with brainsuite software, tissue structure of the cortex, skull and skin (in matlab format). can i use some fieldtrip fuctions to make leadfield matrix?or should i make all the analysis only fieldtrip functions? best regards, giulio maglione -- " Un giorno, passeggiando nella foresta, ho visto una bestia. Quando mi sono avvicinato ho visto che era un uomo. Quando sono arrivato vicino a lui mi sono accorto che era mio fratello" (Proverbio tibetano) Vieni a trovarmi a quest'indirizzo: angima.blogspot.com oppure http://www.facebook.com/antongiulio.maglione?ref=name (Facebook) ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From gianpaolo.demarchi at UNITN.IT Tue Jun 1 16:01:14 2010 From: gianpaolo.demarchi at UNITN.IT (Gianpaolo Demarchi) Date: Tue, 1 Jun 2010 16:01:14 +0200 Subject: Missing "subplots" in ft_multiplotER In-Reply-To: <4C052081.CBF6.008E.0@mti.uni-jena.de> Message-ID: Dear Matthias, I encountered the same proble some time ago, and another user (Stephan Moratti) helped me a lot in solving it. You can look in the mailing list archives (i.e. use the "search" power ;-)), but for you convenience I repost here the link to the thread: https://listserv.surfnet.nl/scripts/wa.cgi?A2=ind1002&L=fieldtrip&T=0&F=&S=&P=4945 BTW, it's not a bug, but somehow a "feature", in the sense that forces you to select only one type of sensors to look at (with cfg.channel properly set for either magnetometers or gradiometers). Best, Gianpaolo ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From BelluscB at NINDS.NIH.GOV Thu Jun 3 18:00:29 2010 From: BelluscB at NINDS.NIH.GOV (Belluscio, Beth (NIH/NINDS) [E]) Date: Thu, 3 Jun 2010 12:00:29 -0400 Subject: evoked field amplitude Message-ID: I want to calculate the strength of the evoked fields in response to a series of stimuli. Initially, I tried doing this with the averaged data at sensors demonstrating an evoked field following the stimulus. However, I noticed that during the course of the response, the dipole of the source seemed to shift slightly, and that this dipole was not consistently oriented following successive stimuli. So I was concerned that by measuring only the response at the sensor, I would obtain a false sense of change in the underlying response. I decided to try looking at the response with the data converted into the corresponding planar gradient (I use a CTF MEG). However, I was unable to find a way to obtain values of the field within an ROI with this data set. Does anyone know how to do this? Lastly, it seems it might be best to compute the source and then evaluate the strength of the signal from an ROI in source-space. What are the pros/cons of using sensor space vs. source space to measure the amplitude of a response? Is there a convention within the field for the methodology for doing this? Beth Belluscio, MD-PhD Clinical Fellow Human Motor Control Section National Institute of Neurological Disorders and Stroke 301-402-3495 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sklein at BERKELEY.EDU Thu Jun 3 19:02:45 2010 From: sklein at BERKELEY.EDU (Stanley Klein) Date: Thu, 3 Jun 2010 10:02:45 -0700 Subject: evoked field amplitude In-Reply-To: <794DFDD3C128EF44AC49ADC58FD0090C02BA31C163@NIHMLBX10.nih.gov> Message-ID: Beth, you ask about going to source space. It's my understanding that people don't yet know how to reliably go from sensor space to source space. The problem is that neighboring cortical areas are often wired together and will fire together and since these neighboring areas will likely have different folding patterns and different time functions the inverse problem of going to sources has problems with both EEG and MEG because of how close these neighbors are to each other. There are two cases where there seem to be solutions, one is occipital cortex where V1, V2, V3, V3a have retinotopic organization that can be identified with fMRI/MRI. The idea here is that with tiny patches in a dartboard layout one can overwhelm the above ambiguity by making use of the topographic layout of cortex. Another area is in somatosensory and motor areas where the homunculus mapping also allows neighboring areas to be separated. Luckily fMRI can also identifying other regions that could be used in helping one go from sensors to sources. However, the above manipulations aren't easily carried out. In addition, there are many researchers who believe that ICA can help do the job. In summary it is healthy to be skeptical of some of the claims of success in going from sensors to sources. Stan On Thu, Jun 3, 2010 at 9:00 AM, Belluscio, Beth (NIH/NINDS) [E] < BelluscB at ninds.nih.gov> wrote: > I want to calculate the strength of the evoked fields in response to a > series of stimuli. Initially, I tried doing this with the averaged data at > sensors demonstrating an evoked field following the stimulus. However, I > noticed that during the course of the response, the dipole of the source > seemed to shift slightly, and that this dipole was not consistently oriented > following successive stimuli. So I was concerned that by measuring only the > response at the sensor, I would obtain a false sense of change in the > underlying response. > > I decided to try looking at the response with the data converted into the > corresponding planar gradient (I use a CTF MEG). However, I was unable to > find a way to obtain values of the field within an ROI with this data set. > Does anyone know how to do this? > > Lastly, it seems it might be best to compute the source and then evaluate > the strength of the signal from an ROI in source-space. What are the > pros/cons of using sensor space vs. source space to measure the amplitude of > a response? Is there a convention within the field for the methodology for > doing this? > > > > > > Beth Belluscio, MD-PhD > > Clinical Fellow > > Human Motor Control Section > > National Institute of Neurological Disorders and Stroke > > 301-402-3495 > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at MAC.COM Thu Jun 3 20:55:05 2010 From: nathanweisz at MAC.COM (Nathan Weisz) Date: Thu, 3 Jun 2010 20:55:05 +0200 Subject: evoked field amplitude In-Reply-To: <794DFDD3C128EF44AC49ADC58FD0090C02BA31C163@NIHMLBX10.nih.gov> Message-ID: > following the stimulus. However, I noticed that during the course of the response, the dipole of the source seemed to shift slightly, > it really depends what you mean by "shift slightly". small shifts shouldn't be a big deal (i hesitate to give a rule of thumb). your dipole doesn't just capture activity from that one spot. of course if the movement is huge then placing a single dipole somewhere to represent that activity does not make sense. > and that this dipole was not consistently oriented following successive stimuli. So I was concerned that by measuring only the response at the sensor, I would obtain a false sense of change in the underlying response. > the standard BESA approach e.g. would be to use a "regional source" i.e. a dipole with 3 orthogonal orientations. you can then calculate the vector magnitude (pythagoras). that should take care of a "rotating" dipole. this can also be done within fieldtrip if you don't have BESA. > the signal from an ROI in source-space. What are the pros/cons of using sensor space vs. source space to measure the amplitude of a response? > pro: - in case of "simple" activations (e.g. sensory evoked ERPs) you can reduce the information from >100 sensors to e.g. 2 sources. the dipole positions could also be standardized across subjects which may increase your power later when doing statistics (sensor positions are impossible to standardize without using offline tricks) - of course neighbouring sources capture almost identical activity (which is good regarding you issue of "slightly shifting" source; see above), however the mixing of diverse activities is far worse on a sensor level! cons: - some arbitrariness of placing sources in "cognitive" experiments. unless you have very good prior information where to expect activity to come from, doing sensor analysis first followed by some distributed sources solution seems more advisable. you could then still look at time courses of ROIs defined by your statistical contrast. in the end, there is no general cookbook-recipe and you should decide based on your experiment. the best situation is when your sensor and source data give converging results :-) best, nathan > > > > > Beth Belluscio, MD-PhD > > Clinical Fellow > > Human Motor Control Section > > National Institute of Neurological Disorders and Stroke > > 301-402-3495 > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Don.Rojas at UCDENVER.EDU Thu Jun 3 22:04:29 2010 From: Don.Rojas at UCDENVER.EDU (Rojas, Don) Date: Thu, 3 Jun 2010 14:04:29 -0600 Subject: evoked field amplitude In-Reply-To: Message-ID: I disagree somewhat with the idea that we don't know how to reliably go from sensor to source space. For datasets with large SNR sensory and motor evoked responses, constrained inverse solutions can be quite reliable and correspond very well in some cases with fMRI (whether evoked responses and fMRI "should" correspond to each other is a different question). The literature has many examples of this type of inverse. Some potential pros, depending on the validity of your source solution and your experiment: 1. Reduction of the number of comparisons made (e.g., 275 MEG sensors in the CTF system at NIMH can be reduced to several ECDs in some simple sensory experiments). 2. Independence of the source strength from the sensor-brain distance (signal amplitudes in MEG sensors in particular are highly dependent on how far away the head is from the sensory array and this can vary tremendously from subject to subject). 3. Higher signal to noise ratio, depending on the approach used. Some spatial filtering approaches such as SSP, beamforming, etc. can substantially reduce the impact of noise from non-brain source such as magnetic dental work artifacts in MEG, gamma-band range muscle activity in EEG, etc. Some potential cons: 1. Invalid source models can nullify any potential advantage. 2. In cognitive experiments, some potential sources may not have very large activity relative to the sensory evoked fields/potentials you measure, and depending on the preprocessing and inverse approaches, the source model may be biased towards the larger SNR responses. 3. Source modeling can be computationally and/or financially expensive, particularly when highly accurate individual anatomical MRI segmentations are needed to construct the conductor model. Best, Don __________________ Don Rojas, Ph.D. Director, Magnetoencephalography Laboratory University of Colorado Denver On 6/3/10 11:02 AM, "Stanley Klein" wrote: Beth, you ask about going to source space. It's my understanding that people don't yet know how to reliably go from sensor space to source space. The problem is that neighboring cortical areas are often wired together and will fire together and since these neighboring areas will likely have different folding patterns and different time functions the inverse problem of going to sources has problems with both EEG and MEG because of how close these neighbors are to each other. There are two cases where there seem to be solutions, one is occipital cortex where V1, V2, V3, V3a have retinotopic organization that can be identified with fMRI/MRI. The idea here is that with tiny patches in a dartboard layout one can overwhelm the above ambiguity by making use of the topographic layout of cortex. Another area is in somatosensory and motor areas where the homunculus mapping also allows neighboring areas to be separated. Luckily fMRI can also identifying other regions that could be used in helping one go from sensors to sources. However, the above manipulations aren't easily carried out. In addition, there are many researchers who believe that ICA can help do the job. In summary it is healthy to be skeptical of some of the claims of success in going from sensors to sources. Stan On Thu, Jun 3, 2010 at 9:00 AM, Belluscio, Beth (NIH/NINDS) [E] wrote: I want to calculate the strength of the evoked fields in response to a series of stimuli. Initially, I tried doing this with the averaged data at sensors demonstrating an evoked field following the stimulus. However, I noticed that during the course of the response, the dipole of the source seemed to shift slightly, and that this dipole was not consistently oriented following successive stimuli. So I was concerned that by measuring only the response at the sensor, I would obtain a false sense of change in the underlying response. I decided to try looking at the response with the data converted into the corresponding planar gradient (I use a CTF MEG). However, I was unable to find a way to obtain values of the field within an ROI with this data set. Does anyone know how to do this? Lastly, it seems it might be best to compute the source and then evaluate the strength of the signal from an ROI in source-space. What are the pros/cons of using sensor space vs. source space to measure the amplitude of a response? Is there a convention within the field for the methodology for doing this? Beth Belluscio, MD-PhD Clinical Fellow Human Motor Control Section National Institute of Neurological Disorders and Stroke 301-402-3495 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Jan.Hirschmann at MED.UNI-DUESSELDORF.DE Fri Jun 4 15:21:29 2010 From: Jan.Hirschmann at MED.UNI-DUESSELDORF.DE (Jan Hirschmann) Date: Fri, 4 Jun 2010 15:21:29 +0200 Subject: coordinates and volumelookup Message-ID: Dear all, I am using the function ft_volumelookup with the AFNI atlas to find out the areas belonging to certain MNI coordinates. Regarding this I have 3 little questions: 1) If I create a grid from template brain T1 (spm2) and multiply the .pos entries by 10 to convert to mm, as described in the example matlab scripts on the fieldtrip homepage, the .pos entries are MNI coordinates, right? 2) When I use volumelookup to look up coordinates (I am giving a mask as input which really has only 1 nonzero entry) I often get the result: "no label found". Are there really that many places in the brain which do not have a label in the atlas? 3) When using the function I get the warning: "homogenous transformation might be incorrect for AFNI file". Should I worry about this? Labelling structures I recognize with the tool, e.g. thalamus, works fine, so I guess labels and cords match. Thanks for your help! Jan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Jan.Hirschmann at MED.UNI-DUESSELDORF.DE Fri Jun 4 15:28:59 2010 From: Jan.Hirschmann at MED.UNI-DUESSELDORF.DE (Jan Hirschmann) Date: Fri, 4 Jun 2010 15:28:59 +0200 Subject: clarification: coordinates and volumelookup In-Reply-To: A<72E993C35FB11743B79FF9286E5B6D8B014A843D@Mail2-UKD.VMED.UKD> Message-ID: Sorry, 1 thing to clarify in the last question: By "labelling structures I recognize works fine" I meant setting power to 1 erverywhere and then defining a roi, e.g. 'Thalamus' in ft_sourceplot. What I see highlighted is the thalamus. Best, Jan ________________________________ Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag von Jan Hirschmann Gesendet: Freitag, 4. Juni 2010 15:21 An: FIELDTRIP at NIC.SURFNET.NL Betreff: [FIELDTRIP] coordinates and volumelookup Dear all, I am using the function ft_volumelookup with the AFNI atlas to find out the areas belonging to certain MNI coordinates. Regarding this I have 3 little questions: 1) If I create a grid from template brain T1 (spm2) and multiply the .pos entries by 10 to convert to mm, as described in the example matlab scripts on the fieldtrip homepage, the .pos entries are MNI coordinates, right? 2) When I use volumelookup to look up coordinates (I am giving a mask as input which really has only 1 nonzero entry) I often get the result: "no label found". Are there really that many places in the brain which do not have a label in the atlas? 3) When using the function I get the warning: "homogenous transformation might be incorrect for AFNI file". Should I worry about this? Labelling structures I recognize with the tool, e.g. thalamus, works fine, so I guess labels and cords match. Thanks for your help! Jan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ingrid.nieuwenhuis at FCDONDERS.RU.NL Fri Jun 4 16:46:51 2010 From: ingrid.nieuwenhuis at FCDONDERS.RU.NL (Ingrid Nieuwenhuis) Date: Fri, 4 Jun 2010 16:46:51 +0200 Subject: clarification: coordinates and volumelookup In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8B014A843E@Mail2-UKD.VMED.UKD> Message-ID: Dear Jan, 1) Yes, I think so. The template is in MNI coordinates. The *10 is necessary to go from cm to mm. I'm not totally sure if this step is still necessary, there is some improved handling of units. But it should be easy to spot if thing are a factor of 10 off. 2) Depends on the atlas. Some atlases have indeed many voxels (all white matter for instance) with no label. You can increase cfg.maxqueryrange, to find the closest label. 3) Where does the warning come from (file, line?). It sounds indeed if it's okay, but it's hard to judge without knowing which check in the code resulted in the warning. Do make sure that the cfg.inputcoordinates set to 'mni' and cfg.atlascoordinates is set to 'tal' (I think the last happens automatically in ft_prepare_atlas when you use the AFNI file). What helps to get a bit of insight is to prepare the atlas yourself with ft_prepare_atlas. You can subsequently plot atlas.brick0 or atlas.brick1 with ft_sourceplot, cfg.funparameter = 'brick0', cfg.interactive = 'yes', cfg.method = 'orthoplot'. The value is linked to the name in atlas.descr. Hope this helps, Ingrid ------------------------------------ Ingrid L.C. Nieuwenhuis PhD student Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging Radboud University Nijmegen, The Netherlands Email: ingrid.nieuwenhuis at donders.ru.nl Tel: 0031 (0)24 - 36 10887 _____ From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Jan Hirschmann Sent: Friday, June 04, 2010 3:29 PM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] clarification: coordinates and volumelookup Sorry, 1 thing to clarify in the last question: By "labelling structures I recognize works fine" I meant setting power to 1 erverywhere and then defining a roi, e.g. 'Thalamus' in ft_sourceplot. What I see highlighted is the thalamus. Best, Jan _____ Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag von Jan Hirschmann Gesendet: Freitag, 4. Juni 2010 15:21 An: FIELDTRIP at NIC.SURFNET.NL Betreff: [FIELDTRIP] coordinates and volumelookup Dear all, I am using the function ft_volumelookup with the AFNI atlas to find out the areas belonging to certain MNI coordinates. Regarding this I have 3 little questions: 1) If I create a grid from template brain T1 (spm2) and multiply the .pos entries by 10 to convert to mm, as described in the example matlab scripts on the fieldtrip homepage, the .pos entries are MNI coordinates, right? 2) When I use volumelookup to look up coordinates (I am giving a mask as input which really has only 1 nonzero entry) I often get the result: "no label found". Are there really that many places in the brain which do not have a label in the atlas? 3) When using the function I get the warning: "homogenous transformation might be incorrect for AFNI file". Should I worry about this? Labelling structures I recognize with the tool, e.g. thalamus, works fine, so I guess labels and cords match. Thanks for your help! Jan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.rotonda at GMAIL.COM Fri Jun 4 18:06:26 2010 From: marco.rotonda at GMAIL.COM (Marco Rotonda) Date: Fri, 4 Jun 2010 18:06:26 +0200 Subject: cohrefchannel In-Reply-To: Message-ID: Hi Jan... I got the point... but now I'm inside another problem that should be even easier... I give this script: cfg = []; cfg.xparam = 'time'; cfg.yparam = 'freq'; cfg.zparam = 'plvspctrm'; cfg.cohrefchannel = 'Cz'; cfg.layout = 'EEG1020.lay'; cfg.showlabels = 'yes'; cfg.colorbar = 'yes'; figure; ft_multiplotTFR(cfg, plvs001fnb1) but if I chage the cfg.cohrefchannel to 'Fz' or whatever the plot is always the same... the point is that the data I passed (plvs001fnb1) is <378x44x1000 double> (combinationXfreqXtime)... how can I plot the different combinations? I mean how could I plot the 378 combinations I have (of course I don't want to plot all at once:-)) and check the different plv for each couple of electrods? sorry for this trivial question but I can't get out from this easy problem... 2010/6/1 jan-mathijs schoffelen : > Hi Marco, > > Doesn't it just work if you specify cfg.cohrefchannel = > 'thenameofthereferencechannelyouthrewaway'? > As far as I know the plotting routine needs to know which rows from the > freq.labelcmb to select for plotting. For this it needs a channel name, but > it does not need the original channel to be present in the data. > > Cheers, > > Jan-Mathijs > > > On Jun 1, 2010, at 11:48 AM, Marco Rotonda wrote: > >> Hi again... >> I know that this could be quite a fool question but I still have this >> problem...  I don't know if this could be the solution but if I make a new >> channel that is the mean of all the others? >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG >> and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/neuroimaging/fieldtrip. >> > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3668063 > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From aostendorf at BESA.DE Mon Jun 7 08:54:21 2010 From: aostendorf at BESA.DE (Andrea Ostendorf) Date: Mon, 7 Jun 2010 08:54:21 +0200 Subject: SPM8 In-Reply-To: <4B96053B.1020306@donders.ru.nl> Message-ID: Dear Fieldtrip team, If I understand the notes on the development page right, you have switched from SPM2 to SPM8 and are currently working on the integration with Fieldtrip. Could you perhaps add an entry in the to-do list? I believe that if you allowed for the use of spm_bwlabel instead of bwlabeln if the latter is not available, one could use some of your statistics options even without the MATLAB Statistics toolbox. (For my purposes, for example, a few modifications in findcluster and clusterstat would be sufficient.) A nice day to all of you! All the best Andrea ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Jan.Hirschmann at MED.UNI-DUESSELDORF.DE Mon Jun 7 13:09:29 2010 From: Jan.Hirschmann at MED.UNI-DUESSELDORF.DE (Jan Hirschmann) Date: Mon, 7 Jun 2010 13:09:29 +0200 Subject: AW: [FIELDTRIP] clarification: coordinates and volumelookup In-Reply-To: A<20100604144650.C5E8716109B@smtp.ru.nl> Message-ID: Thanks Ingrid, your comments were of much help to me. I did not know that one can plot the atlas and about the function of cfg.maxqueryrange. So it means sth like: search in the x closest voxels for labels? The warning occurs in read_mri at line 105. There it says: % FIXME: this should be checked, but I only have a single BRIK file % construct the homogenous transformation matrix that defines the axes warning('homogenous transformation might be incorrect for AFNI file'); Thanks very much for your help! Jan ________________________________ Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag von Ingrid Nieuwenhuis Gesendet: Freitag, 4. Juni 2010 16:47 An: FIELDTRIP at NIC.SURFNET.NL Betreff: Re: [FIELDTRIP] clarification: coordinates and volumelookup Dear Jan, 1) Yes, I think so. The template is in MNI coordinates. The *10 is necessary to go from cm to mm. I'm not totally sure if this step is still necessary, there is some improved handling of units. But it should be easy to spot if thing are a factor of 10 off. 2) Depends on the atlas. Some atlases have indeed many voxels (all white matter for instance) with no label. You can increase cfg.maxqueryrange, to find the closest label. 3) Where does the warning come from (file, line?). It sounds indeed if it's okay, but it's hard to judge without knowing which check in the code resulted in the warning. Do make sure that the cfg.inputcoordinates set to 'mni' and cfg.atlascoordinates is set to 'tal' (I think the last happens automatically in ft_prepare_atlas when you use the AFNI file). What helps to get a bit of insight is to prepare the atlas yourself with ft_prepare_atlas. You can subsequently plot atlas.brick0 or atlas.brick1 with ft_sourceplot, cfg.funparameter = 'brick0', cfg.interactive = 'yes', cfg.method = 'orthoplot'. The value is linked to the name in atlas.descr. Hope this helps, Ingrid ------------------------------------ Ingrid L.C. Nieuwenhuis PhD student Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging Radboud University Nijmegen, The Netherlands Email: ingrid.nieuwenhuis at donders.ru.nl Tel: 0031 (0)24 - 36 10887 ________________________________ From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Jan Hirschmann Sent: Friday, June 04, 2010 3:29 PM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] clarification: coordinates and volumelookup Sorry, 1 thing to clarify in the last question: By "labelling structures I recognize works fine" I meant setting power to 1 erverywhere and then defining a roi, e.g. 'Thalamus' in ft_sourceplot. What I see highlighted is the thalamus. Best, Jan ________________________________ Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag von Jan Hirschmann Gesendet: Freitag, 4. Juni 2010 15:21 An: FIELDTRIP at NIC.SURFNET.NL Betreff: [FIELDTRIP] coordinates and volumelookup Dear all, I am using the function ft_volumelookup with the AFNI atlas to find out the areas belonging to certain MNI coordinates. Regarding this I have 3 little questions: 1) If I create a grid from template brain T1 (spm2) and multiply the .pos entries by 10 to convert to mm, as described in the example matlab scripts on the fieldtrip homepage, the .pos entries are MNI coordinates, right? 2) When I use volumelookup to look up coordinates (I am giving a mask as input which really has only 1 nonzero entry) I often get the result: "no label found". Are there really that many places in the brain which do not have a label in the atlas? 3) When using the function I get the warning: "homogenous transformation might be incorrect for AFNI file". Should I worry about this? Labelling structures I recognize with the tool, e.g. thalamus, works fine, so I guess labels and cords match. Thanks for your help! Jan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul_c at GMX.DE Tue Jun 8 12:09:19 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Tue, 8 Jun 2010 12:09:19 +0200 Subject: Dipoli issues Message-ID: Dear all, I'm trying to create a BEM model via prepare_bemmodel with the dipoli method for my diploma thesis, loosely based on the sample script on http://fieldtrip.fcdonders.nl/example/create_bem_headmodel_for_eeg . Unfortunately, if I try to create the BEM model with more than 1 compartment, dipoli crashes with the following error: Fatal error in dipoli: interface /tmp/tp331940.tri is not a single closed surface (totsolangle= -2.0000 from vertex 1 of /tmp/tp331943.tri ) I would be very grateful, if anybody was able to help me understanding and hopefully solving this error. Thanks in advance, Paul Czienskowski ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From dahliash at STANFORD.EDU Tue Jun 8 21:04:34 2010 From: dahliash at STANFORD.EDU (Dahlia Sharon) Date: Tue, 8 Jun 2010 12:04:34 -0700 Subject: freqstatistics with indepsamplesZcoh: incompatible dimensions? Message-ID: Hi, I'm trying to run cluster statistics on coherence between a single channel (actually 2) and a set of 516 channels. My code crashes when ft_freqstatistics reaches clusterstat [Error using ==> reshape; To RESHAPE the number of elements must not change. Error in ==> clusterstat at 182; posclusobs = findcluster(reshape(postailobs, [cfg.dim,1]),channeighbstructmat,cfg.minnbchan); ] At this point postailobs is much larger than multiplying the elements of cfg.dim. But digging into it the problem starts earlier, and as far as I can see is a result of incompatibility between the output of freqanalysis and the way indepsamplesZcoh treats the data: In freqanalysis I calculate csd between each of the two channels and all the rest, i.e. I have 2 * (516+1) = 1034 pairs. The dimension of the resulting freq.crssspctrm is 10 (trials) x 1034 (channel pairs) x 51 (frequencies) x 1 (times). In indepsamplesZcoh using the freqanalysis output, for each frequency I have a 1034x10 matrix multiplied by its transpose to get a dimension of 1034x1034. This is of-course much higher than the dimension of the data which should be something like 517x2. How should I transform the freqanalysis output so that it'll be used correctly by indepsamplesZcoh? Thanks! Dahlia. PS - here is part of the code that might be helpful, please let me know if any further information would help. +++++++++++++++++++++++++++++++++++++++++++++++++++++ % configuration for freqanalysis cfgfa = []; cfgfa.output = 'powandcsd'; % 'pow'; cfgfa.toi = -.25:.025:1.25; cfgfa.foi = 6:2:80; %% cfgfa.method = 'mtmfft'; % 'mtmconvol'; cfgfa.trials = 'all'; cfgfa.keeptrials = 'yes'; cfgfa.channel = {'all' }; cfgfa.channelcmb = { 'rh-Jz MT' 'all' ; 'lh-Jz MT' 'all' }; % compute csd between right MT and all % configuration for freqstatistics cfgfs = []; cfgfs.numrandomization = 100; cfgfs.method = 'montecarlo'; cfgfs.correctm = 'cluster'; cfgfs.clusteralpha = 0.05; % significance level for sample-level statistic, i.e. for being considered candidate for clustering cfgfs.clusterstatistic = 'maxsum'; % maxsize cfgfs.clusterthreshold = 'parametric'; % uses T distribution to calculate the sample-level statistic threshold - appropriate for cfg.statistic=indepsamplesT cfgfs.minnbchan = 0; % cfgfs.alpha = 0.05; % significance level for cluster-level statistic, i.e. for final result of significant cluster. cfgfs.tail = 0; % 0 for two-sided testing cfgfs.correcttail = 'alpha'; cfgfs.ivar = 1; cfgfs.latency = 'all'; cfgfs.frequency = 'all'; cfgfs.neighbours = []; cfgfs_coh = cfgfs; cfgfs_coh.statistic = 'indepsamplesZcoh'; cfgfs_coh.label = { 'all' }; %{ 'rh-Jz MT' 'all' ; 'lh-Jz MT' 'all' }; for trig = 100:100:200 trigstr = num2str( trig); disp([subj ' trig' trigstr]) invtrigfile = strcat( invtrigfile_base{1} , trigstr , invtrigfile_base{2}); load(invtrigfile) freq = ft_freqanalysis( cfgfa, data_ftrip); ntrl = size( freq.powspctrm, 1 ); eval(['ntrl' trigstr '=ntrl;']) end design = ones(1, ntrl100 + ntrl200); design(ntrl200+1:end)=2; ccfgfs_coh.design = design; % cfgfs_coh.label = freq.labelcmb; cfgfs_coh.channelcmb = freq.labelcmb; coh_stat = ft_freqstatistics( cfgfs_coh, freq200, freq100); ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.vandermeij at DONDERS.RU.NL Wed Jun 9 16:27:13 2010 From: r.vandermeij at DONDERS.RU.NL (Roemer van der Meij) Date: Wed, 9 Jun 2010 16:27:13 +0200 Subject: SPM8 In-Reply-To: <5E1E87335F0B4202BCE3C3463C40285C@LAT6500Andrea> Message-ID: Hi Andrea, Thanks for your suggestion! We've added it as a to-be-added feature in our bugzilla (it can also be used for that). If you're interested, you can find it at: http://bugzilla.fcdonders.nl/show_bug.cgi?id=89 Best, Roemer On 6/7/2010 8:54 AM, Andrea Ostendorf wrote: > Dear Fieldtrip team, > > If I understand the notes on the development page right, you have switched > from SPM2 to SPM8 and are currently working on the integration with > Fieldtrip. > Could you perhaps add an entry in the to-do list? I believe that if you > allowed for the use of spm_bwlabel instead of bwlabeln if the latter is not > available, one could use some of your statistics options even without the > MATLAB Statistics toolbox. (For my purposes, for example, a few > modifications in findcluster and clusterstat would be sufficient.) > > A nice day to all of you! > All the best > > Andrea > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > -- Roemer van der Meij MSc PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3612631 E-mail: r.vandermeij at donders.ru.nl ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From lhunt at FMRIB.OX.AC.UK Tue Jun 15 10:20:13 2010 From: lhunt at FMRIB.OX.AC.UK (Laurence Hunt) Date: Tue, 15 Jun 2010 09:20:13 +0100 Subject: ft_preproc_highpassfilter Message-ID: Hi folks, I'm trying to filter some MEG data sampled at 200Hz using ft_preproc_highpassfilter. It seems to be behaving slightly strangely. I'm calling it with Fs = 200; Fhp = 5; N = 6; and a stretch of single-channel data with ~50000 samples. However, the returned data doesn't seem to be filtered at 5Hz. When I go into the code and use fvtool to look at the frequency response of the filter, it doesn't have the shape I was expecting: I wondered whether this was because of the GNU public license version of butter that was being called by fieldtrip (in preproc/private), so I took this out of my matlab path and let it find the Mathworks' butter.m, from the signal processing toolbox. This seemed to give a more sensible looking filter design in fvtool: The Mathworks' butter.m also seemed to filter the data a bit more like I was expecting. Is this a problem with the GPL version, or am I calling the function wrong? Cheers, Laurence =========================================== Laurence Hunt, DPhil Student Centre for Functional MRI of the Brain (FMRIB), University of Oxford lhunt at fmrib.ox.ac.uk Phone: (+44)1865-(2)22738 =========================================== ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: GPLbutter.png Type: image/png Size: 8830 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MLbutter.png Type: image/png Size: 7196 bytes Desc: not available URL: From lhunt at FMRIB.OX.AC.UK Tue Jun 15 13:37:32 2010 From: lhunt at FMRIB.OX.AC.UK (Laurence Hunt) Date: Tue, 15 Jun 2010 12:37:32 +0100 Subject: Fwd: highpassfilter problems in fieldtrip Message-ID: Problems were already spotted by Jan-Mathijs... Begin forwarded message: > From: jan-mathijs schoffelen > Date: 15 June 2010 11:19:44 GMT+01:00 > To: Laurence Hunt > Subject: highpassfilter problems in fieldtrip > > Dear Laurence, > > Yes, you're absolutely right. I noticed the problem at some point, and it was caused by some typos in the octave-version of butter. This has been fixed recently, so that could mean that by updating to the most recent version may fix it. > > Cheers, > > Jan-Mathijs > > PS: I am not able to use my donders account for outgoing mails at the moment, so could you forward this reply to the mailing list, so that the rest of the community is aware of the issue? Thanks > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From aardesta at UCLA.EDU Fri Jun 18 00:40:38 2010 From: aardesta at UCLA.EDU (Allen Ardestani) Date: Thu, 17 Jun 2010 15:40:38 -0700 Subject: Connecivityanalysis ERROR Message-ID: Hi everyone, When I call connectivityanalysis using any of the methods that use frequency data, I get the following error: "??? Conversion to cell from double is not possible." I get it even when using the downloaded dataset and exact script from the tutorial: cfg = []; cfg.output = 'powandcsd'; cfg.method = 'mtmfft'; cfg.foilim = [5 100]; cfg.tapsmofrq = 5; cfg.keeptrials = 'yes'; cfg.channel = {'MEG' 'EMGlft' 'EMGrgt'}; cfg.channelcmb = {'MEG' 'EMGlft'; 'MEG' 'EMGrgt'}; freq = ft_freqanalysis(cfg, data); %% Plot %% cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'MEG' 'EMG'}; fd = ft_connectivityanalysis(cfg, freq); Any ideas what's wrong? Many thanks in advance. Best, Allen ____________________________________________________________________________ ______ Allen Ardestani Email: aardesta at ucla.edu Phone: (310) 825-5528 Medical Scientist Training Program David Geffen School of Medicine at UCLA Semel Institute for Neuroscience and Human Behavior 760 Westwood Plaza Los Angeles, CA 90095-1759 USA ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From saskia.haegens at DONDERS.RU.NL Fri Jun 18 11:08:27 2010 From: saskia.haegens at DONDERS.RU.NL (Saskia Haegens) Date: Fri, 18 Jun 2010 11:08:27 +0200 Subject: Connecivityanalysis ERROR In-Reply-To: <014301cb0e6e$1bf0abe0$53d203a0$@edu> Message-ID: Hi Allen, This sounds like a bug that was recently fixed, are you using the latest fieldtrip version? If you could copy/paste the exact error you are getting, would help in figuring out where this goes wrong. Best, Saskia _____ From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Allen Ardestani Sent: vrijdag 18 juni 2010 0:41 To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] Connecivityanalysis ERROR Hi everyone, When I call connectivityanalysis using any of the methods that use frequency data, I get the following error: "??? Conversion to cell from double is not possible." I get it even when using the downloaded dataset and exact script from the tutorial: cfg = []; cfg.output = 'powandcsd'; cfg.method = 'mtmfft'; cfg.foilim = [5 100]; cfg.tapsmofrq = 5; cfg.keeptrials = 'yes'; cfg.channel = {'MEG' 'EMGlft' 'EMGrgt'}; cfg.channelcmb = {'MEG' 'EMGlft'; 'MEG' 'EMGrgt'}; freq = ft_freqanalysis(cfg, data); %% Plot %% cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'MEG' 'EMG'}; fd = ft_connectivityanalysis(cfg, freq); Any ideas what's wrong? Many thanks in advance. Best, Allen ____________________________________________________________________________ ______ Allen Ardestani Email: aardesta at ucla.edu Phone: (310) 825-5528 Medical Scientist Training Program David Geffen School of Medicine at UCLA Semel Institute for Neuroscience and Human Behavior 760 Westwood Plaza Los Angeles, CA 90095-1759 USA ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From qi at BRAIN.K.U-TOKYO.AC.JP Fri Jun 18 11:36:38 2010 From: qi at BRAIN.K.U-TOKYO.AC.JP (=?SHIFT_JIS?Q?Liang_Qi?=) Date: Fri, 18 Jun 2010 11:36:38 +0200 Subject: How to use 'MNE' method in 'sourceanalysis' Message-ID: Hi everyone, I'm trying to do single trial source analysis on MEG data, and I think 'MNE' method in 'sourceanalysis' may accomplish this. However I have no idea how to set the parameters in 'cfg'. Would anyone tell me how to do this? Thanks in advance. Regards, Liang ----------------------- Liang Qi Biological Complex Systems Laboratory Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8561, Japan Tel : +81-4-7136-3899 E-mail : qi at brain.k.u-tokyo.ac.jp ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From bps231 at NYU.EDU Sat Jun 19 10:38:16 2010 From: bps231 at NYU.EDU (Bernhard Staresina) Date: Sat, 19 Jun 2010 10:38:16 +0200 Subject: preprocessing slowing down Message-ID: Dear FieldTrip users, A quick question on preprocessing. I noticed that as I preprocess my EEG data (no actual preprocessing settings, just getting the exportet raw data into FieldTrip format), the process dramatically slows down as it goes along. So by trial 100, MATLAB essentially stops. I don't think it's a working memory issue - I tried to preprocess only the last few trials with cleared working memory, and the process doesn't move on. I read in the trial information (beginsample, endsample and offset) via definetrial, and of my ~700 trials (with only 25 channels), the later trials have begin- and endsample values of eg. 4338002 and 4344000, respectively. But why is it that it takes longer to read in a trial as a function of its begin and end sample? Shouldn't the amount of preceding data points be irrelevant? I'm reading in BrainVision Analyser data, using FT version 'fieldtrip-20090120'. The segments are 5.9 sec long, with 1kHz sampling rate. Thanks, Bernhard ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From aostendorf at BESA.DE Mon Jun 21 08:21:27 2010 From: aostendorf at BESA.DE (Andrea Ostendorf) Date: Mon, 21 Jun 2010 08:21:27 +0200 Subject: SPM8 In-Reply-To: <4C0FA4C1.9050208@donders.ru.nl> Message-ID: Dear Roemer, Thanks a lot. I discussed this topic some months ago with Robert and he suggested that he/the Fieldtrip team could modify the code along the following lines (I copy this from his e-mail because I think he will not mind this) - - - - - I suggest to modify the low level code into two helper functions (findcluster_chanlevel and findcluster_sourcelevel), which both should check like this if hastoolbox('image', 1) % using image processing toolbox my_bwlabeln = @bwlabeln; elseif hastoolbox('spm8', 1) % using spm8 version my_bwlabeln = @spm8_bwlabeln; else error(...) end - - - - I have got SPM8 on my Matlab path and whenever I download a new Fieldtrip version, I have to edit clusterstat and findcluster because it is (or was) not sufficient to simply replace bwlabeln by spm_bwlabel. What I did is probably rather inelegant but I left it that way since it works: In findcluster: Before: % [labelmat(spatdimlev, :, :), num] = bwlabeln(reshape(onoff(spatdimlev, :, :), nfreq, ntime), 4); After: input_for_spm_bwlabel = reshape(onoff(spatdimlev, :, :), nfreq, ntime); input_for_spm_bwlabel = +input_for_spm_bwlabel; %convert from logical [labelmat(spatdimlev, :, :), num] = spm_bwlabel(input_for_spm_bwlabel , 6); In clusterstat: Before: %!!!posclusobs = bwlabeln(tmp, conndef(length(cfg.dim),'min')); After: [posclusobs,L] = spm_bwlabel(tmp, 6); Sorry for the late answer. By the way, I have got into trouble at work because we have a betting game going on and I predicted the Netherlands as the winner (not that I know anything about football but I chose the Netherlands because the Fieldtrip team is so nice)... All the best Andrea ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.vandermeij at DONDERS.RU.NL Tue Jun 22 12:09:07 2010 From: r.vandermeij at DONDERS.RU.NL (Roemer van der Meij) Date: Tue, 22 Jun 2010 12:09:07 +0200 Subject: SPM8 In-Reply-To: <72D3AA975E924FCFAD3FAA83DF7309E1@LAT6500Andrea> Message-ID: Hi Andrea, We are deeply honored by your betting choice! May good fortune come to both of us! Thanks for sharing your modifications. Right now most of my FieldTrip time is going in writing the low-level functions for the spectral estimation module (which eventually replace the current freqanalysis implementation), but an obvious project for me after that is rewriting the cluster-permutation code. It has evolved into its current from over the past years, and our new low-level - high-level function structure will clean it up and makes it easier to fix bugs. I hope I can find the time to work on the bwlabeln functions, I will keep you updated. I'll also add this e-mail to our bugzilla report on this, to keep track of the possibilities. Thanks again for sharing your suggestions, they are always welcome. Best, Roemer On 6/21/2010 8:21 AM, Andrea Ostendorf wrote: > Dear Roemer, > > Thanks a lot. I discussed this topic some months ago with Robert and he > suggested that he/the Fieldtrip team could modify the code along the > following lines (I copy this from his e-mail because I think he will not > mind this) > - - - - - > I suggest to modify the low level code into two helper functions > (findcluster_chanlevel and findcluster_sourcelevel), which both should check > like this > > > if hastoolbox('image', 1) > % using image processing toolbox > my_bwlabeln = @bwlabeln; > elseif hastoolbox('spm8', 1) > % using spm8 version > my_bwlabeln = @spm8_bwlabeln; > else > error(...) > end > - - - - > > I have got SPM8 on my Matlab path and whenever I download a new Fieldtrip > version, I have to edit clusterstat and findcluster because it is (or was) > not sufficient to simply replace bwlabeln by spm_bwlabel. What I did is > probably rather inelegant but I left it that way since it works: > > In findcluster: > Before: > % [labelmat(spatdimlev, :, :), num] = bwlabeln(reshape(onoff(spatdimlev, :, > :), nfreq, ntime), 4); > After: > input_for_spm_bwlabel = reshape(onoff(spatdimlev, :, :), nfreq, ntime); > input_for_spm_bwlabel = +input_for_spm_bwlabel; %convert from logical > [labelmat(spatdimlev, :, :), num] = spm_bwlabel(input_for_spm_bwlabel , 6); > > In clusterstat: > Before: > %!!!posclusobs = bwlabeln(tmp, conndef(length(cfg.dim),'min')); > After: > [posclusobs,L] = spm_bwlabel(tmp, 6); > > Sorry for the late answer. > By the way, I have got into trouble at work because we have a betting game > going on and I predicted the Netherlands as the winner (not that I know > anything about football but I chose the Netherlands because the Fieldtrip > team is so nice)... > > All the best > Andrea > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > -- Roemer van der Meij MSc PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From michael.wibral at WEB.DE Tue Jun 22 17:34:04 2010 From: michael.wibral at WEB.DE (Michael Wibral) Date: Tue, 22 Jun 2010 17:34:04 +0200 Subject: Importing FT data to SPM8 as "LFP" data Message-ID: Dear SPM and FT listusers, does anyone know by any chance which headerfield in FT data to set to which value so that spm_eeg_convert automatically recognizes these data as LFP data? I can't seem to spot the words lfp anywhere inside spm_eeg_convert.m so it all is a bit mysterious to me. Many thanks, Michael ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 628 bytes Desc: not available URL: From r.oostenveld at FCDONDERS.RU.NL Tue Jun 22 19:37:17 2010 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 22 Jun 2010 19:37:17 +0200 Subject: fieldtrip webserver will be down tomorrow evening Message-ID: Dear fieldtrip users Our technical group has to do some maintenance to the servers of the Donders Centre. The consequence is that the fieldtrip wiki (fieldtrip.fcdonders.nl) and the ftp server (ftp.fcdonders.nl) will be down. Hopefully the downtime will be only one evening, but it might extend into the next morning. See below for details. > Tomorrow Wednesday June 23rd, 18:00h CET we have planned a down-time window for central storage and all of the central storage dependent IT services! If everything goes smoothly, central storage and all services will be back up and running later in that evening. In case we encounter unforeseen problems down-time might last until the early next morning Thursday June 24th. best regards, Robert ----------------------------------------------------------- Robert Oostenveld, PhD Senior Researcher Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen tel.: +31 (0)24 3619695 e-mail: r.oostenveld at donders.ru.nl web: http://www.ru.nl/neuroimaging skype: r.oostenveld ----------------------------------------------------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From moratti at MED.UCM.ES Wed Jun 23 08:41:30 2010 From: moratti at MED.UCM.ES (Stephan Moratti) Date: Wed, 23 Jun 2010 08:41:30 +0200 Subject: How to use 'MNE' method in 'sourceanalysis' Message-ID: Hi Liang, I do not work with the most recent version of fieldtrip, but I think you hace to specify the mne parameters this way: cfg.mne.[parameter] = x; Hope that helps. Best, Stephan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From odidodi at HOTMAIL.COM Wed Jun 23 13:20:57 2010 From: odidodi at HOTMAIL.COM (Odelia Goldberg) Date: Wed, 23 Jun 2010 13:20:57 +0200 Subject: cfg.output error while running ft_componentanalysis Message-ID: Hello all, I run ft_artifact_muscle+jump functions, then reject artifacts and then ICA. After choosing the components for removal I've tried to run "comp_orig = ft_componentanalysis(cfg, datacln);", to identify the components on the original data and I get an error saying: ??? Reference to non-existent field 'outputfile'. Error in ==> ft_componentanalysis at 416 if ~isempty(cfg.outputfile) I work with fieldtrip-20100621, and if I put the last three lines in comment, it works (problem solved). (I've tried to add 'output' field but it did't help). Anything that I'm missing? Thanks in advance, Odelia. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Thu Jun 24 17:55:16 2010 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Thu, 24 Jun 2010 17:55:16 +0200 Subject: cfg.output error while running ft_componentanalysis In-Reply-To: Message-ID: Hi Odelia Sorry about that, it is a known bug recently introduced. It only happens in conjunction with cfg.trackconfig=yes. We will fix it asap. Robert On 23 Jun 2010, at 13:20, Odelia Goldberg wrote: > I get an error saying: > > ??? Reference to non-existent field 'outputfile'. > > Error in ==> ft_componentanalysis at 416 > if ~isempty(cfg.outputfile) > > I work with fieldtrip-20100621, and if I put the last three lines in > comment, it works (problem solved). (I've tried to add 'output' > field but it > did't help). > Anything that I'm missing? ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Matthias.Meyer at DONDERS.RU.NL Fri Jun 25 11:24:04 2010 From: Matthias.Meyer at DONDERS.RU.NL (Matthias C. Meyer) Date: Fri, 25 Jun 2010 11:24:04 +0200 Subject: Export EEG Data Message-ID: Dear ft_Community, I am quite new to Fieldtrip and hope that someone has solved my problem before. I recorded EEG data inside an MR Scanner with the BrainVision software and now I want to use Fieldtrip to run some error correction scripts - so far so god. But after that I need to write the corrected data back to the original EEG - data format. I use the ft_write_data function to do this. After some problems I manage to run the function, but the result is a double size datafile, a messed up header and a empty marker file. Probably the data is written in double precision. Giving the data to the function with "single(data_org.trial{1})" in the argument does not help. The command line I use to call the function is: ft_write_data('ScannerCor', data_org.trial{1}, 'dataformat', 'brainvision_eeg','header', data_org.hdr); (I copied the corrected data back to the read in matrix) I heard already, that I can tell Matlab to use only single precision, but it would be nice to tell that the function directly - Is there a way to do so? What do I need to do, to export the header and marker file correctly? The corrected data are exactly of the same size as the original data, if possible, I might also use the original marker file to get the trigger points. I hope some one can help me. Best regards, Matthias. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From h.holle at SUSSEX.AC.UK Fri Jun 25 14:19:53 2010 From: h.holle at SUSSEX.AC.UK (Henning Holle) Date: Fri, 25 Jun 2010 14:19:53 +0200 Subject: databrowser: change order in which channels appear? Message-ID: Dear all, when looking at data with the databrowser (vertical viewmode), the channels appear in the order in which they happen to be in the dataset. Is there a way to define another order (so that, for instance, more anterior channels appear more on top of the screen, and more posterior channels at the bottom of the screen). Kind regards, Henning ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From ingrid.nieuwenhuis at FCDONDERS.RU.NL Fri Jun 25 14:25:45 2010 From: ingrid.nieuwenhuis at FCDONDERS.RU.NL (Ingrid Nieuwenhuis) Date: Fri, 25 Jun 2010 14:25:45 +0200 Subject: databrowser: change order in which channels appear? In-Reply-To: Message-ID: Dear Henning, Are you using the latest version of FieldTrip? If I remember correctly, I changed this at some point into that the order of the channels is as you specify them in cfg.channel Best, Ingrid ------------------------------------ Ingrid L.C. Nieuwenhuis PhD student Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging Radboud University Nijmegen, The Netherlands Email: ingrid.nieuwenhuis at donders.ru.nl Tel: 0031 (0)24 - 36 10887 -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Henning Holle Sent: Friday, June 25, 2010 2:20 PM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] databrowser: change order in which channels appear? Dear all, when looking at data with the databrowser (vertical viewmode), the channels appear in the order in which they happen to be in the dataset. Is there a way to define another order (so that, for instance, more anterior channels appear more on top of the screen, and more posterior channels at the bottom of the screen). Kind regards, Henning ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From odidodi at HOTMAIL.COM Fri Jun 25 15:16:58 2010 From: odidodi at HOTMAIL.COM (odelia nakar) Date: Fri, 25 Jun 2010 13:16:58 +0000 Subject: cfg.output error while running ft_componentanalysis In-Reply-To: Message-ID: Hi Robert, Thank you for your answer. I think that on the 23rd of 6 version it was aready fixed. Good day! Odelia. > Date: Thu, 24 Jun 2010 17:55:16 +0200 > From: r.oostenveld at FCDONDERS.RU.NL > Subject: Re: [FIELDTRIP] cfg.output error while running ft_componentanalysis > To: FIELDTRIP at NIC.SURFNET.NL > > Hi Odelia > > Sorry about that, it is a known bug recently introduced. It only > happens in conjunction with cfg.trackconfig=yes. We will fix it asap. > > Robert > > > On 23 Jun 2010, at 13:20, Odelia Goldberg wrote: > > > I get an error saying: > > > > ??? Reference to non-existent field 'outputfile'. > > > > Error in ==> ft_componentanalysis at 416 > > if ~isempty(cfg.outputfile) > > > > I work with fieldtrip-20100621, and if I put the last three lines in > > comment, it works (problem solved). (I've tried to add 'output' > > field but it > > did't help). > > Anything that I'm missing? > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.rousselet at PSY.GLA.AC.UK Fri Jun 25 15:27:14 2010 From: g.rousselet at PSY.GLA.AC.UK (Guillaume Rousselet) Date: Fri, 25 Jun 2010 14:27:14 +0100 Subject: Frontiers in Perception Science: Call for participation in upcoming Special Topic Message-ID: Hosting Journal: Frontiers in Perception Science Topic Title: Single-trial analyses of behavioural and neuroimaging data in perception and decision-making. Host Editors: Guillaume A. Rousselet, Cyril R. Pernet, Paul Sajda Description: The cognitive psychology of perception and decision-making is at a cross-road. Most studies still employ categorical designs, a priori classified stimuli and perform statistical evaluations across subjects. However, a shift has been observed in recent years towards parametric designs in which the information content of stimuli is systematically manipulated to study the single-trial dynamics of behaviour (reaction times, eye movements) and brain activity (EEG, MEG, fMRI). By using the information contained in the variance of individual trials, the single-trial approach goes beyond the activity of the average brain: it reveals the specificity of information processing in individual subjects, across tasks and stimulus space, revealing both inter-individual commonalties and differences. This special issue provides theoretical and empirical support for the study of single-trial data. Topics of particular interest include: 1. description of the richness of information in single-trials and how it can be successfully extracted; 2. statistical issues related to measures of central tendency, control for multiple comparisons, multivariate approaches, hierarchical modelling and characterization of individual differences; 3. how manipulation of the stimulus space can allow for a direct mapping of stimulus properties onto brain activity to infer dynamics of information processing and information content of brain states; 4. how results from different brain imaging techniques can be integrated at the single-trial level. Abstract Submission Deadline: September 01, 2010 Article Submission Deadline: January 03, 2011 Link to Special Topic: http://www.frontiersin.org/psychology/perceptionscience/specialtopics/98/ The publishing fee for contributors amounts to €900, and a further reduction to €720 for Frontiers Associate Editors. Like all research published with Frontiers, the articles will be freely available to all of our readers on our website, and all Special Topic articles receive a DOI and are indexed in the National Institute of Health’s electronic depository of full text articles, PubMed Central, and many other international archives (Google Scholar, Directory of Open Access Journal, Psych INFO). Frontiers is also in the process of being archived in Thompson Scientific (ISI), and Web of Science. Frontiers has also announced that in the very near future, all published Special Topics will be available to view and download in an eBook format! For more information, you may refer to the Frontiers’ Special Topic page, where you can get further guidance and browse past Special Topics. << http://www.frontiersin.org/specialtopicspage/ >> With best regards, Guillaume Rousselet Associate Editor, Frontiers in Perception Science www.frontiersin.org ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sreenivasan.r.nadar at GMAIL.COM Sat Jun 26 21:04:25 2010 From: sreenivasan.r.nadar at GMAIL.COM (Dr. Sreenivasan Rajamoni Nadar, Ph.D.) Date: Sat, 26 Jun 2010 12:04:25 -0700 Subject: Dr. Sreenivasan Rajamoni Nadar, Ph.D. wants to stay in touch on LinkedIn Message-ID: LinkedIn ------------ FieldTrip, I'd like to add you to my professional network on LinkedIn. - Dr. Sreenivasan Rajamoni Nadar, Ph.D. Dr. Sreenivasan Rajamoni Nadar, Ph.D. Scientist at National Institute of Mental Health Washington D.C. Metro Area Confirm that you know Dr. Sreenivasan Rajamoni Nadar, Ph.D. https://www.linkedin.com/e/dwhirw-gawtl874-2e/isd/1418399407/pkkPy6v8/ ------ (c) 2010, LinkedIn Corporation ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.gomez at SCIENCE.RU.NL Mon Jun 28 13:35:57 2010 From: v.gomez at SCIENCE.RU.NL (=?ISO-8859-1?Q?Vicen=E7_G=F3mez?=) Date: Mon, 28 Jun 2010 13:35:57 +0200 Subject: fixtrialdef.m Message-ID: Dear fieldtripers, function fixtrialdef.m can't handle data with one trial only: K>> ??? Error using ==> cat CAT arguments dimensions are not consistent. Error in ==> fixtrialdef at 26 begsample = cat(1, 0, cumsum(nsmp(1:end-1))) + 1; I fixed it doing: if ntrial == 1 begsample = 1; else begsample = cat(1, 0, cumsum(nsmp(1:end-1))) + 1; end Is that right? thanks, -- Vicenç Gomez Cerda SNN Radboud University Nijmegen The Netherlands http://www.mbfys.ru.nl/staff/v.gomez/ tel: +31 (0)24 - 36 14230 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Mon Jun 28 17:09:29 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Mon, 28 Jun 2010 17:09:29 +0200 Subject: fixtrialdef.m In-Reply-To: <4C28891D.1030602@science.ru.nl> Message-ID: Dear Vicenç, Thanks for the suggestion. I will incorporate it into the ftp-version so that everybody can enjoy this improvement ;). It'll be available as of tomorrow. Cheers, Jan-Mathijs On Jun 28, 2010, at 1:35 PM, Vicenç Gómez wrote: > Dear fieldtripers, > > function fixtrialdef.m can't handle data with one trial only: > > K>> ??? Error using ==> cat > CAT arguments dimensions are not consistent. > > Error in ==> fixtrialdef at 26 > begsample = cat(1, 0, cumsum(nsmp(1:end-1))) + 1; > > I fixed it doing: > > if ntrial == 1 > begsample = 1; > else > begsample = cat(1, 0, cumsum(nsmp(1:end-1))) + 1; > end > > Is that right? > > thanks, > > > -- > Vicenç Gomez Cerda > SNN Radboud University Nijmegen > The Netherlands > http://www.mbfys.ru.nl/staff/v.gomez/ > tel: +31 (0)24 - 36 14230 > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From mcregar at UPO.ES Wed Jun 30 11:04:58 2010 From: mcregar at UPO.ES (Maite Crespo) Date: Wed, 30 Jun 2010 11:04:58 +0200 Subject: Matlab compiler for Windows XP 64-bit Message-ID: Hello, I had my first code errors with mex files. It seems I'll have to install a Matlab compiler for 64 bits (Windows XP). Does anybody knows a free compiler? Thank you very much. Best (first) regards, Maité ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From s.klanke at DONDERS.RU.NL Wed Jun 30 11:31:40 2010 From: s.klanke at DONDERS.RU.NL (Stefan Klanke) Date: Wed, 30 Jun 2010 11:31:40 +0200 Subject: Matlab compiler for Windows XP 64-bit In-Reply-To: Message-ID: Dear Maité, I do not have a 64-bit machine myself yet, but I know that you can produce 64 bit executables using the free "Express" version (both 2008 and 2010) of Microsoft Visual C++. You can get more information here: http://msdn.microsoft.com/en-us/library/9yb4317s.aspx Depending on how old your version of Matlab is, it might be easier to pick the 2008 version, so "mex -setup" can detect the compiler. With kind regards, Stefan On 30-6-2010 11:04, Maite Crespo wrote: > Hello, > > I had my first code errors with mex files. It seems I'll have to install a Matlab > compiler for 64 bits (Windows XP). Does anybody knows a free compiler? > > Thank you very much. > > Best (first) regards, > Maité > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Wed Jun 30 17:10:46 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Wed, 30 Jun 2010 17:10:46 +0200 Subject: Export EEG Data In-Reply-To: <4C2475B4.5030807@donders.ru.nl> Message-ID: Hi Mattias, > I am quite new to Fieldtrip and hope that someone has solved my > problem before. High expectations ;). > I recorded EEG data inside an MR Scanner with the BrainVision > software and now I want to use Fieldtrip to run some error > correction scripts - so far so god. > But after that I need to write the corrected data back to the > original EEG - data format. > I use the ft_write_data function to do this. After some problems I > manage to run the function, but the result is a double size > datafile, a messed up header and a empty marker file. > Probably the data is written in double precision. Giving the data to > the function with "single(data_org.trial{1})" in the argument does > not help. > The command line I use to call the function is: > ft_write_data('ScannerCor', data_org.trial{1}, 'dataformat', > 'brainvision_eeg','header', data_org.hdr); > > (I copied the corrected data back to the read in matrix) > > I heard already, that I can tell Matlab to use only single > precision, but it would be nice to tell that the function directly - > Is there a way to do so? > What do I need to do, to export the header and marker file correctly? I have not encountered this issue before, and I don't know whether anybody else has. This may mean that you need to do some digging yourself to get it solved. I never tried to export data to a different fileformat. The easy way out here would be to also do your subsequent analysis steps in matlab/fieldtrip. Did you already have a detailed look at ft_write_data, and in particular the part which deals with 'brainvision_eeg'. My suspicion is that there is a discrepancy between the information in data_org.hdr, and the exact data you try to export (data_org.trial{1}). Manually converting to single precision may not work if in data_org.hdr you need to specify the precision. (once again I don't know about the specifics of this function, or of the functions it relies on). Using the matlab debugger may help you to access the variables in the function's workspace and to see what's preventing it to work properly. Good luck, Jan-Mathijs Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcregar at UPO.ES Wed Jun 30 18:12:05 2010 From: mcregar at UPO.ES (Maite Crespo) Date: Wed, 30 Jun 2010 18:12:05 +0200 Subject: source analysis on time window and frequency range Message-ID: Hello again! I would like to apply the DICS and SAM methods to localize the source activity within a time window and a frequency range, but based on the CSD or covariance matrices obtained from a wavelet transformation to the time- frequency domain. At the moment I found only one possible frequency or latency as input to the ft_sourceanalysis function. I also read about applying the multitaper method for time-frequency analysis, but I worry about the non-stationarity of the signals. Could somebody give me a hint about how to proceed? Have a nice day. Best regards, Maité ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From marco.rotonda at GMAIL.COM Wed Jun 30 19:07:43 2010 From: marco.rotonda at GMAIL.COM (Marco Rotonda) Date: Wed, 30 Jun 2010 19:07:43 +0200 Subject: Nested analysis Message-ID: Hi Fieldtrippers! I have a question about an analysis that I would like to do. In this experiment I have the following design: 2 group X 2 stage X 2 stimulus X 278 electrodes combinations (plv) wherein group is a between factor and all the other factors are within factors. The electrodes combinations is nested in the stimulus factor and the stimulus is nested in the stage factor. How could I menage this situation? Regards, Marco ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From marco.rotonda at GMAIL.COM Tue Jun 1 11:48:44 2010 From: marco.rotonda at GMAIL.COM (Marco Rotonda) Date: Tue, 1 Jun 2010 11:48:44 +0200 Subject: cohrefchannel Message-ID: Hi again... I know that this could be quite a fool question but I still have this problem... I don't know if this could be the solution but if I make a new channel that is the mean of all the others? ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Tue Jun 1 12:22:26 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Tue, 1 Jun 2010 12:22:26 +0200 Subject: cohrefchannel In-Reply-To: Message-ID: Hi Marco, Doesn't it just work if you specify cfg.cohrefchannel = 'thenameofthereferencechannelyouthrewaway'? As far as I know the plotting routine needs to know which rows from the freq.labelcmb to select for plotting. For this it needs a channel name, but it does not need the original channel to be present in the data. Cheers, Jan-Mathijs On Jun 1, 2010, at 11:48 AM, Marco Rotonda wrote: > Hi again... > I know that this could be quite a fool question but I still have this > problem... I don't know if this could be the solution but if I make > a new > channel that is the mean of all the others? > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Matthias.Wacker at MTI.UNI-JENA.DE Tue Jun 1 15:00:15 2010 From: Matthias.Wacker at MTI.UNI-JENA.DE (Matthias Wacker) Date: Tue, 1 Jun 2010 15:00:15 +0200 Subject: Missing "subplots" in ft_multiplotER Message-ID: Dear Community, I have lasting problems with the ft_multiplotER routine. When I do a multiplot, the small plots themselves are missing (Snapshot.png). However, using the interactive mode, averaging over multiple channels with mouse interaction shows that the data is there (Snapshot2.png). What am I doing wrong? Or is it a known issue? %%%%%%% BEGIN CODE %%%%%%%% ... [data] = ft_preprocessing(cfg); ... %% time locked analysis cfg = []; avgData = ft_timelockanalysis(cfg, data); %% plot it % create layout lay = ft_prepare_layout([], data); % plot cfg = []; cfg.showlabels = 'yes'; cfg.fontsize = 6; cfg.layout = lay; cfg.interactive='yes'; ft_multiplotER(cfg, avgData); %%%%%%% END CODE %%%%%%%% Thanks for any help! Best regards, Matthias Wacker ____________________ Universitätsklinikum Jena Körperschaft des öffentlichen Rechts und Teilkörperschaft der Friedrich-Schiller-Universität Jena Bachstraße 18, 07743 Jena Verwaltungsratsvorsitzender: Prof. Dr. Thomas Deufel; Medizinischer Vorstand: Prof. Dr. Klaus Höffken; Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufmännischer Vorstand und Sprecher des Klinikumsvorstandes: Rudolf Kruse Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221; Gerichtsstand Jena Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Snapshot2.png Type: image/png Size: 41862 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Snapshot.png Type: image/png Size: 41348 bytes Desc: not available URL: From maglione.antongiulio at LIBERO.IT Tue Jun 1 15:39:33 2010 From: maglione.antongiulio at LIBERO.IT (Anton Giulio Maglione) Date: Tue, 1 Jun 2010 15:39:33 +0200 Subject: Make a leadfield from matlab structure Message-ID: Hi all! i have an MRI image in .img format. i made, with brainsuite software, tissue structure of the cortex, skull and skin (in matlab format). can i use some fieldtrip fuctions to make leadfield matrix?or should i make all the analysis only fieldtrip functions? best regards, giulio maglione -- " Un giorno, passeggiando nella foresta, ho visto una bestia. Quando mi sono avvicinato ho visto che era un uomo. Quando sono arrivato vicino a lui mi sono accorto che era mio fratello" (Proverbio tibetano) Vieni a trovarmi a quest'indirizzo: angima.blogspot.com oppure http://www.facebook.com/antongiulio.maglione?ref=name (Facebook) ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From gianpaolo.demarchi at UNITN.IT Tue Jun 1 16:01:14 2010 From: gianpaolo.demarchi at UNITN.IT (Gianpaolo Demarchi) Date: Tue, 1 Jun 2010 16:01:14 +0200 Subject: Missing "subplots" in ft_multiplotER In-Reply-To: <4C052081.CBF6.008E.0@mti.uni-jena.de> Message-ID: Dear Matthias, I encountered the same proble some time ago, and another user (Stephan Moratti) helped me a lot in solving it. You can look in the mailing list archives (i.e. use the "search" power ;-)), but for you convenience I repost here the link to the thread: https://listserv.surfnet.nl/scripts/wa.cgi?A2=ind1002&L=fieldtrip&T=0&F=&S=&P=4945 BTW, it's not a bug, but somehow a "feature", in the sense that forces you to select only one type of sensors to look at (with cfg.channel properly set for either magnetometers or gradiometers). Best, Gianpaolo ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From BelluscB at NINDS.NIH.GOV Thu Jun 3 18:00:29 2010 From: BelluscB at NINDS.NIH.GOV (Belluscio, Beth (NIH/NINDS) [E]) Date: Thu, 3 Jun 2010 12:00:29 -0400 Subject: evoked field amplitude Message-ID: I want to calculate the strength of the evoked fields in response to a series of stimuli. Initially, I tried doing this with the averaged data at sensors demonstrating an evoked field following the stimulus. However, I noticed that during the course of the response, the dipole of the source seemed to shift slightly, and that this dipole was not consistently oriented following successive stimuli. So I was concerned that by measuring only the response at the sensor, I would obtain a false sense of change in the underlying response. I decided to try looking at the response with the data converted into the corresponding planar gradient (I use a CTF MEG). However, I was unable to find a way to obtain values of the field within an ROI with this data set. Does anyone know how to do this? Lastly, it seems it might be best to compute the source and then evaluate the strength of the signal from an ROI in source-space. What are the pros/cons of using sensor space vs. source space to measure the amplitude of a response? Is there a convention within the field for the methodology for doing this? Beth Belluscio, MD-PhD Clinical Fellow Human Motor Control Section National Institute of Neurological Disorders and Stroke 301-402-3495 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sklein at BERKELEY.EDU Thu Jun 3 19:02:45 2010 From: sklein at BERKELEY.EDU (Stanley Klein) Date: Thu, 3 Jun 2010 10:02:45 -0700 Subject: evoked field amplitude In-Reply-To: <794DFDD3C128EF44AC49ADC58FD0090C02BA31C163@NIHMLBX10.nih.gov> Message-ID: Beth, you ask about going to source space. It's my understanding that people don't yet know how to reliably go from sensor space to source space. The problem is that neighboring cortical areas are often wired together and will fire together and since these neighboring areas will likely have different folding patterns and different time functions the inverse problem of going to sources has problems with both EEG and MEG because of how close these neighbors are to each other. There are two cases where there seem to be solutions, one is occipital cortex where V1, V2, V3, V3a have retinotopic organization that can be identified with fMRI/MRI. The idea here is that with tiny patches in a dartboard layout one can overwhelm the above ambiguity by making use of the topographic layout of cortex. Another area is in somatosensory and motor areas where the homunculus mapping also allows neighboring areas to be separated. Luckily fMRI can also identifying other regions that could be used in helping one go from sensors to sources. However, the above manipulations aren't easily carried out. In addition, there are many researchers who believe that ICA can help do the job. In summary it is healthy to be skeptical of some of the claims of success in going from sensors to sources. Stan On Thu, Jun 3, 2010 at 9:00 AM, Belluscio, Beth (NIH/NINDS) [E] < BelluscB at ninds.nih.gov> wrote: > I want to calculate the strength of the evoked fields in response to a > series of stimuli. Initially, I tried doing this with the averaged data at > sensors demonstrating an evoked field following the stimulus. However, I > noticed that during the course of the response, the dipole of the source > seemed to shift slightly, and that this dipole was not consistently oriented > following successive stimuli. So I was concerned that by measuring only the > response at the sensor, I would obtain a false sense of change in the > underlying response. > > I decided to try looking at the response with the data converted into the > corresponding planar gradient (I use a CTF MEG). However, I was unable to > find a way to obtain values of the field within an ROI with this data set. > Does anyone know how to do this? > > Lastly, it seems it might be best to compute the source and then evaluate > the strength of the signal from an ROI in source-space. What are the > pros/cons of using sensor space vs. source space to measure the amplitude of > a response? Is there a convention within the field for the methodology for > doing this? > > > > > > Beth Belluscio, MD-PhD > > Clinical Fellow > > Human Motor Control Section > > National Institute of Neurological Disorders and Stroke > > 301-402-3495 > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at MAC.COM Thu Jun 3 20:55:05 2010 From: nathanweisz at MAC.COM (Nathan Weisz) Date: Thu, 3 Jun 2010 20:55:05 +0200 Subject: evoked field amplitude In-Reply-To: <794DFDD3C128EF44AC49ADC58FD0090C02BA31C163@NIHMLBX10.nih.gov> Message-ID: > following the stimulus. However, I noticed that during the course of the response, the dipole of the source seemed to shift slightly, > it really depends what you mean by "shift slightly". small shifts shouldn't be a big deal (i hesitate to give a rule of thumb). your dipole doesn't just capture activity from that one spot. of course if the movement is huge then placing a single dipole somewhere to represent that activity does not make sense. > and that this dipole was not consistently oriented following successive stimuli. So I was concerned that by measuring only the response at the sensor, I would obtain a false sense of change in the underlying response. > the standard BESA approach e.g. would be to use a "regional source" i.e. a dipole with 3 orthogonal orientations. you can then calculate the vector magnitude (pythagoras). that should take care of a "rotating" dipole. this can also be done within fieldtrip if you don't have BESA. > the signal from an ROI in source-space. What are the pros/cons of using sensor space vs. source space to measure the amplitude of a response? > pro: - in case of "simple" activations (e.g. sensory evoked ERPs) you can reduce the information from >100 sensors to e.g. 2 sources. the dipole positions could also be standardized across subjects which may increase your power later when doing statistics (sensor positions are impossible to standardize without using offline tricks) - of course neighbouring sources capture almost identical activity (which is good regarding you issue of "slightly shifting" source; see above), however the mixing of diverse activities is far worse on a sensor level! cons: - some arbitrariness of placing sources in "cognitive" experiments. unless you have very good prior information where to expect activity to come from, doing sensor analysis first followed by some distributed sources solution seems more advisable. you could then still look at time courses of ROIs defined by your statistical contrast. in the end, there is no general cookbook-recipe and you should decide based on your experiment. the best situation is when your sensor and source data give converging results :-) best, nathan > > > > > Beth Belluscio, MD-PhD > > Clinical Fellow > > Human Motor Control Section > > National Institute of Neurological Disorders and Stroke > > 301-402-3495 > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Don.Rojas at UCDENVER.EDU Thu Jun 3 22:04:29 2010 From: Don.Rojas at UCDENVER.EDU (Rojas, Don) Date: Thu, 3 Jun 2010 14:04:29 -0600 Subject: evoked field amplitude In-Reply-To: Message-ID: I disagree somewhat with the idea that we don't know how to reliably go from sensor to source space. For datasets with large SNR sensory and motor evoked responses, constrained inverse solutions can be quite reliable and correspond very well in some cases with fMRI (whether evoked responses and fMRI "should" correspond to each other is a different question). The literature has many examples of this type of inverse. Some potential pros, depending on the validity of your source solution and your experiment: 1. Reduction of the number of comparisons made (e.g., 275 MEG sensors in the CTF system at NIMH can be reduced to several ECDs in some simple sensory experiments). 2. Independence of the source strength from the sensor-brain distance (signal amplitudes in MEG sensors in particular are highly dependent on how far away the head is from the sensory array and this can vary tremendously from subject to subject). 3. Higher signal to noise ratio, depending on the approach used. Some spatial filtering approaches such as SSP, beamforming, etc. can substantially reduce the impact of noise from non-brain source such as magnetic dental work artifacts in MEG, gamma-band range muscle activity in EEG, etc. Some potential cons: 1. Invalid source models can nullify any potential advantage. 2. In cognitive experiments, some potential sources may not have very large activity relative to the sensory evoked fields/potentials you measure, and depending on the preprocessing and inverse approaches, the source model may be biased towards the larger SNR responses. 3. Source modeling can be computationally and/or financially expensive, particularly when highly accurate individual anatomical MRI segmentations are needed to construct the conductor model. Best, Don __________________ Don Rojas, Ph.D. Director, Magnetoencephalography Laboratory University of Colorado Denver On 6/3/10 11:02 AM, "Stanley Klein" wrote: Beth, you ask about going to source space. It's my understanding that people don't yet know how to reliably go from sensor space to source space. The problem is that neighboring cortical areas are often wired together and will fire together and since these neighboring areas will likely have different folding patterns and different time functions the inverse problem of going to sources has problems with both EEG and MEG because of how close these neighbors are to each other. There are two cases where there seem to be solutions, one is occipital cortex where V1, V2, V3, V3a have retinotopic organization that can be identified with fMRI/MRI. The idea here is that with tiny patches in a dartboard layout one can overwhelm the above ambiguity by making use of the topographic layout of cortex. Another area is in somatosensory and motor areas where the homunculus mapping also allows neighboring areas to be separated. Luckily fMRI can also identifying other regions that could be used in helping one go from sensors to sources. However, the above manipulations aren't easily carried out. In addition, there are many researchers who believe that ICA can help do the job. In summary it is healthy to be skeptical of some of the claims of success in going from sensors to sources. Stan On Thu, Jun 3, 2010 at 9:00 AM, Belluscio, Beth (NIH/NINDS) [E] wrote: I want to calculate the strength of the evoked fields in response to a series of stimuli. Initially, I tried doing this with the averaged data at sensors demonstrating an evoked field following the stimulus. However, I noticed that during the course of the response, the dipole of the source seemed to shift slightly, and that this dipole was not consistently oriented following successive stimuli. So I was concerned that by measuring only the response at the sensor, I would obtain a false sense of change in the underlying response. I decided to try looking at the response with the data converted into the corresponding planar gradient (I use a CTF MEG). However, I was unable to find a way to obtain values of the field within an ROI with this data set. Does anyone know how to do this? Lastly, it seems it might be best to compute the source and then evaluate the strength of the signal from an ROI in source-space. What are the pros/cons of using sensor space vs. source space to measure the amplitude of a response? Is there a convention within the field for the methodology for doing this? Beth Belluscio, MD-PhD Clinical Fellow Human Motor Control Section National Institute of Neurological Disorders and Stroke 301-402-3495 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Jan.Hirschmann at MED.UNI-DUESSELDORF.DE Fri Jun 4 15:21:29 2010 From: Jan.Hirschmann at MED.UNI-DUESSELDORF.DE (Jan Hirschmann) Date: Fri, 4 Jun 2010 15:21:29 +0200 Subject: coordinates and volumelookup Message-ID: Dear all, I am using the function ft_volumelookup with the AFNI atlas to find out the areas belonging to certain MNI coordinates. Regarding this I have 3 little questions: 1) If I create a grid from template brain T1 (spm2) and multiply the .pos entries by 10 to convert to mm, as described in the example matlab scripts on the fieldtrip homepage, the .pos entries are MNI coordinates, right? 2) When I use volumelookup to look up coordinates (I am giving a mask as input which really has only 1 nonzero entry) I often get the result: "no label found". Are there really that many places in the brain which do not have a label in the atlas? 3) When using the function I get the warning: "homogenous transformation might be incorrect for AFNI file". Should I worry about this? Labelling structures I recognize with the tool, e.g. thalamus, works fine, so I guess labels and cords match. Thanks for your help! Jan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Jan.Hirschmann at MED.UNI-DUESSELDORF.DE Fri Jun 4 15:28:59 2010 From: Jan.Hirschmann at MED.UNI-DUESSELDORF.DE (Jan Hirschmann) Date: Fri, 4 Jun 2010 15:28:59 +0200 Subject: clarification: coordinates and volumelookup In-Reply-To: A<72E993C35FB11743B79FF9286E5B6D8B014A843D@Mail2-UKD.VMED.UKD> Message-ID: Sorry, 1 thing to clarify in the last question: By "labelling structures I recognize works fine" I meant setting power to 1 erverywhere and then defining a roi, e.g. 'Thalamus' in ft_sourceplot. What I see highlighted is the thalamus. Best, Jan ________________________________ Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag von Jan Hirschmann Gesendet: Freitag, 4. Juni 2010 15:21 An: FIELDTRIP at NIC.SURFNET.NL Betreff: [FIELDTRIP] coordinates and volumelookup Dear all, I am using the function ft_volumelookup with the AFNI atlas to find out the areas belonging to certain MNI coordinates. Regarding this I have 3 little questions: 1) If I create a grid from template brain T1 (spm2) and multiply the .pos entries by 10 to convert to mm, as described in the example matlab scripts on the fieldtrip homepage, the .pos entries are MNI coordinates, right? 2) When I use volumelookup to look up coordinates (I am giving a mask as input which really has only 1 nonzero entry) I often get the result: "no label found". Are there really that many places in the brain which do not have a label in the atlas? 3) When using the function I get the warning: "homogenous transformation might be incorrect for AFNI file". Should I worry about this? Labelling structures I recognize with the tool, e.g. thalamus, works fine, so I guess labels and cords match. Thanks for your help! Jan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ingrid.nieuwenhuis at FCDONDERS.RU.NL Fri Jun 4 16:46:51 2010 From: ingrid.nieuwenhuis at FCDONDERS.RU.NL (Ingrid Nieuwenhuis) Date: Fri, 4 Jun 2010 16:46:51 +0200 Subject: clarification: coordinates and volumelookup In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8B014A843E@Mail2-UKD.VMED.UKD> Message-ID: Dear Jan, 1) Yes, I think so. The template is in MNI coordinates. The *10 is necessary to go from cm to mm. I'm not totally sure if this step is still necessary, there is some improved handling of units. But it should be easy to spot if thing are a factor of 10 off. 2) Depends on the atlas. Some atlases have indeed many voxels (all white matter for instance) with no label. You can increase cfg.maxqueryrange, to find the closest label. 3) Where does the warning come from (file, line?). It sounds indeed if it's okay, but it's hard to judge without knowing which check in the code resulted in the warning. Do make sure that the cfg.inputcoordinates set to 'mni' and cfg.atlascoordinates is set to 'tal' (I think the last happens automatically in ft_prepare_atlas when you use the AFNI file). What helps to get a bit of insight is to prepare the atlas yourself with ft_prepare_atlas. You can subsequently plot atlas.brick0 or atlas.brick1 with ft_sourceplot, cfg.funparameter = 'brick0', cfg.interactive = 'yes', cfg.method = 'orthoplot'. The value is linked to the name in atlas.descr. Hope this helps, Ingrid ------------------------------------ Ingrid L.C. Nieuwenhuis PhD student Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging Radboud University Nijmegen, The Netherlands Email: ingrid.nieuwenhuis at donders.ru.nl Tel: 0031 (0)24 - 36 10887 _____ From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Jan Hirschmann Sent: Friday, June 04, 2010 3:29 PM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] clarification: coordinates and volumelookup Sorry, 1 thing to clarify in the last question: By "labelling structures I recognize works fine" I meant setting power to 1 erverywhere and then defining a roi, e.g. 'Thalamus' in ft_sourceplot. What I see highlighted is the thalamus. Best, Jan _____ Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag von Jan Hirschmann Gesendet: Freitag, 4. Juni 2010 15:21 An: FIELDTRIP at NIC.SURFNET.NL Betreff: [FIELDTRIP] coordinates and volumelookup Dear all, I am using the function ft_volumelookup with the AFNI atlas to find out the areas belonging to certain MNI coordinates. Regarding this I have 3 little questions: 1) If I create a grid from template brain T1 (spm2) and multiply the .pos entries by 10 to convert to mm, as described in the example matlab scripts on the fieldtrip homepage, the .pos entries are MNI coordinates, right? 2) When I use volumelookup to look up coordinates (I am giving a mask as input which really has only 1 nonzero entry) I often get the result: "no label found". Are there really that many places in the brain which do not have a label in the atlas? 3) When using the function I get the warning: "homogenous transformation might be incorrect for AFNI file". Should I worry about this? Labelling structures I recognize with the tool, e.g. thalamus, works fine, so I guess labels and cords match. Thanks for your help! Jan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.rotonda at GMAIL.COM Fri Jun 4 18:06:26 2010 From: marco.rotonda at GMAIL.COM (Marco Rotonda) Date: Fri, 4 Jun 2010 18:06:26 +0200 Subject: cohrefchannel In-Reply-To: Message-ID: Hi Jan... I got the point... but now I'm inside another problem that should be even easier... I give this script: cfg = []; cfg.xparam = 'time'; cfg.yparam = 'freq'; cfg.zparam = 'plvspctrm'; cfg.cohrefchannel = 'Cz'; cfg.layout = 'EEG1020.lay'; cfg.showlabels = 'yes'; cfg.colorbar = 'yes'; figure; ft_multiplotTFR(cfg, plvs001fnb1) but if I chage the cfg.cohrefchannel to 'Fz' or whatever the plot is always the same... the point is that the data I passed (plvs001fnb1) is <378x44x1000 double> (combinationXfreqXtime)... how can I plot the different combinations? I mean how could I plot the 378 combinations I have (of course I don't want to plot all at once:-)) and check the different plv for each couple of electrods? sorry for this trivial question but I can't get out from this easy problem... 2010/6/1 jan-mathijs schoffelen : > Hi Marco, > > Doesn't it just work if you specify cfg.cohrefchannel = > 'thenameofthereferencechannelyouthrewaway'? > As far as I know the plotting routine needs to know which rows from the > freq.labelcmb to select for plotting. For this it needs a channel name, but > it does not need the original channel to be present in the data. > > Cheers, > > Jan-Mathijs > > > On Jun 1, 2010, at 11:48 AM, Marco Rotonda wrote: > >> Hi again... >> I know that this could be quite a fool question but I still have this >> problem...  I don't know if this could be the solution but if I make a new >> channel that is the mean of all the others? >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG >> and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/neuroimaging/fieldtrip. >> > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3668063 > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From aostendorf at BESA.DE Mon Jun 7 08:54:21 2010 From: aostendorf at BESA.DE (Andrea Ostendorf) Date: Mon, 7 Jun 2010 08:54:21 +0200 Subject: SPM8 In-Reply-To: <4B96053B.1020306@donders.ru.nl> Message-ID: Dear Fieldtrip team, If I understand the notes on the development page right, you have switched from SPM2 to SPM8 and are currently working on the integration with Fieldtrip. Could you perhaps add an entry in the to-do list? I believe that if you allowed for the use of spm_bwlabel instead of bwlabeln if the latter is not available, one could use some of your statistics options even without the MATLAB Statistics toolbox. (For my purposes, for example, a few modifications in findcluster and clusterstat would be sufficient.) A nice day to all of you! All the best Andrea ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Jan.Hirschmann at MED.UNI-DUESSELDORF.DE Mon Jun 7 13:09:29 2010 From: Jan.Hirschmann at MED.UNI-DUESSELDORF.DE (Jan Hirschmann) Date: Mon, 7 Jun 2010 13:09:29 +0200 Subject: AW: [FIELDTRIP] clarification: coordinates and volumelookup In-Reply-To: A<20100604144650.C5E8716109B@smtp.ru.nl> Message-ID: Thanks Ingrid, your comments were of much help to me. I did not know that one can plot the atlas and about the function of cfg.maxqueryrange. So it means sth like: search in the x closest voxels for labels? The warning occurs in read_mri at line 105. There it says: % FIXME: this should be checked, but I only have a single BRIK file % construct the homogenous transformation matrix that defines the axes warning('homogenous transformation might be incorrect for AFNI file'); Thanks very much for your help! Jan ________________________________ Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag von Ingrid Nieuwenhuis Gesendet: Freitag, 4. Juni 2010 16:47 An: FIELDTRIP at NIC.SURFNET.NL Betreff: Re: [FIELDTRIP] clarification: coordinates and volumelookup Dear Jan, 1) Yes, I think so. The template is in MNI coordinates. The *10 is necessary to go from cm to mm. I'm not totally sure if this step is still necessary, there is some improved handling of units. But it should be easy to spot if thing are a factor of 10 off. 2) Depends on the atlas. Some atlases have indeed many voxels (all white matter for instance) with no label. You can increase cfg.maxqueryrange, to find the closest label. 3) Where does the warning come from (file, line?). It sounds indeed if it's okay, but it's hard to judge without knowing which check in the code resulted in the warning. Do make sure that the cfg.inputcoordinates set to 'mni' and cfg.atlascoordinates is set to 'tal' (I think the last happens automatically in ft_prepare_atlas when you use the AFNI file). What helps to get a bit of insight is to prepare the atlas yourself with ft_prepare_atlas. You can subsequently plot atlas.brick0 or atlas.brick1 with ft_sourceplot, cfg.funparameter = 'brick0', cfg.interactive = 'yes', cfg.method = 'orthoplot'. The value is linked to the name in atlas.descr. Hope this helps, Ingrid ------------------------------------ Ingrid L.C. Nieuwenhuis PhD student Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging Radboud University Nijmegen, The Netherlands Email: ingrid.nieuwenhuis at donders.ru.nl Tel: 0031 (0)24 - 36 10887 ________________________________ From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Jan Hirschmann Sent: Friday, June 04, 2010 3:29 PM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] clarification: coordinates and volumelookup Sorry, 1 thing to clarify in the last question: By "labelling structures I recognize works fine" I meant setting power to 1 erverywhere and then defining a roi, e.g. 'Thalamus' in ft_sourceplot. What I see highlighted is the thalamus. Best, Jan ________________________________ Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag von Jan Hirschmann Gesendet: Freitag, 4. Juni 2010 15:21 An: FIELDTRIP at NIC.SURFNET.NL Betreff: [FIELDTRIP] coordinates and volumelookup Dear all, I am using the function ft_volumelookup with the AFNI atlas to find out the areas belonging to certain MNI coordinates. Regarding this I have 3 little questions: 1) If I create a grid from template brain T1 (spm2) and multiply the .pos entries by 10 to convert to mm, as described in the example matlab scripts on the fieldtrip homepage, the .pos entries are MNI coordinates, right? 2) When I use volumelookup to look up coordinates (I am giving a mask as input which really has only 1 nonzero entry) I often get the result: "no label found". Are there really that many places in the brain which do not have a label in the atlas? 3) When using the function I get the warning: "homogenous transformation might be incorrect for AFNI file". Should I worry about this? Labelling structures I recognize with the tool, e.g. thalamus, works fine, so I guess labels and cords match. Thanks for your help! Jan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul_c at GMX.DE Tue Jun 8 12:09:19 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Tue, 8 Jun 2010 12:09:19 +0200 Subject: Dipoli issues Message-ID: Dear all, I'm trying to create a BEM model via prepare_bemmodel with the dipoli method for my diploma thesis, loosely based on the sample script on http://fieldtrip.fcdonders.nl/example/create_bem_headmodel_for_eeg . Unfortunately, if I try to create the BEM model with more than 1 compartment, dipoli crashes with the following error: Fatal error in dipoli: interface /tmp/tp331940.tri is not a single closed surface (totsolangle= -2.0000 from vertex 1 of /tmp/tp331943.tri ) I would be very grateful, if anybody was able to help me understanding and hopefully solving this error. Thanks in advance, Paul Czienskowski ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From dahliash at STANFORD.EDU Tue Jun 8 21:04:34 2010 From: dahliash at STANFORD.EDU (Dahlia Sharon) Date: Tue, 8 Jun 2010 12:04:34 -0700 Subject: freqstatistics with indepsamplesZcoh: incompatible dimensions? Message-ID: Hi, I'm trying to run cluster statistics on coherence between a single channel (actually 2) and a set of 516 channels. My code crashes when ft_freqstatistics reaches clusterstat [Error using ==> reshape; To RESHAPE the number of elements must not change. Error in ==> clusterstat at 182; posclusobs = findcluster(reshape(postailobs, [cfg.dim,1]),channeighbstructmat,cfg.minnbchan); ] At this point postailobs is much larger than multiplying the elements of cfg.dim. But digging into it the problem starts earlier, and as far as I can see is a result of incompatibility between the output of freqanalysis and the way indepsamplesZcoh treats the data: In freqanalysis I calculate csd between each of the two channels and all the rest, i.e. I have 2 * (516+1) = 1034 pairs. The dimension of the resulting freq.crssspctrm is 10 (trials) x 1034 (channel pairs) x 51 (frequencies) x 1 (times). In indepsamplesZcoh using the freqanalysis output, for each frequency I have a 1034x10 matrix multiplied by its transpose to get a dimension of 1034x1034. This is of-course much higher than the dimension of the data which should be something like 517x2. How should I transform the freqanalysis output so that it'll be used correctly by indepsamplesZcoh? Thanks! Dahlia. PS - here is part of the code that might be helpful, please let me know if any further information would help. +++++++++++++++++++++++++++++++++++++++++++++++++++++ % configuration for freqanalysis cfgfa = []; cfgfa.output = 'powandcsd'; % 'pow'; cfgfa.toi = -.25:.025:1.25; cfgfa.foi = 6:2:80; %% cfgfa.method = 'mtmfft'; % 'mtmconvol'; cfgfa.trials = 'all'; cfgfa.keeptrials = 'yes'; cfgfa.channel = {'all' }; cfgfa.channelcmb = { 'rh-Jz MT' 'all' ; 'lh-Jz MT' 'all' }; % compute csd between right MT and all % configuration for freqstatistics cfgfs = []; cfgfs.numrandomization = 100; cfgfs.method = 'montecarlo'; cfgfs.correctm = 'cluster'; cfgfs.clusteralpha = 0.05; % significance level for sample-level statistic, i.e. for being considered candidate for clustering cfgfs.clusterstatistic = 'maxsum'; % maxsize cfgfs.clusterthreshold = 'parametric'; % uses T distribution to calculate the sample-level statistic threshold - appropriate for cfg.statistic=indepsamplesT cfgfs.minnbchan = 0; % cfgfs.alpha = 0.05; % significance level for cluster-level statistic, i.e. for final result of significant cluster. cfgfs.tail = 0; % 0 for two-sided testing cfgfs.correcttail = 'alpha'; cfgfs.ivar = 1; cfgfs.latency = 'all'; cfgfs.frequency = 'all'; cfgfs.neighbours = []; cfgfs_coh = cfgfs; cfgfs_coh.statistic = 'indepsamplesZcoh'; cfgfs_coh.label = { 'all' }; %{ 'rh-Jz MT' 'all' ; 'lh-Jz MT' 'all' }; for trig = 100:100:200 trigstr = num2str( trig); disp([subj ' trig' trigstr]) invtrigfile = strcat( invtrigfile_base{1} , trigstr , invtrigfile_base{2}); load(invtrigfile) freq = ft_freqanalysis( cfgfa, data_ftrip); ntrl = size( freq.powspctrm, 1 ); eval(['ntrl' trigstr '=ntrl;']) end design = ones(1, ntrl100 + ntrl200); design(ntrl200+1:end)=2; ccfgfs_coh.design = design; % cfgfs_coh.label = freq.labelcmb; cfgfs_coh.channelcmb = freq.labelcmb; coh_stat = ft_freqstatistics( cfgfs_coh, freq200, freq100); ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.vandermeij at DONDERS.RU.NL Wed Jun 9 16:27:13 2010 From: r.vandermeij at DONDERS.RU.NL (Roemer van der Meij) Date: Wed, 9 Jun 2010 16:27:13 +0200 Subject: SPM8 In-Reply-To: <5E1E87335F0B4202BCE3C3463C40285C@LAT6500Andrea> Message-ID: Hi Andrea, Thanks for your suggestion! We've added it as a to-be-added feature in our bugzilla (it can also be used for that). If you're interested, you can find it at: http://bugzilla.fcdonders.nl/show_bug.cgi?id=89 Best, Roemer On 6/7/2010 8:54 AM, Andrea Ostendorf wrote: > Dear Fieldtrip team, > > If I understand the notes on the development page right, you have switched > from SPM2 to SPM8 and are currently working on the integration with > Fieldtrip. > Could you perhaps add an entry in the to-do list? I believe that if you > allowed for the use of spm_bwlabel instead of bwlabeln if the latter is not > available, one could use some of your statistics options even without the > MATLAB Statistics toolbox. (For my purposes, for example, a few > modifications in findcluster and clusterstat would be sufficient.) > > A nice day to all of you! > All the best > > Andrea > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > -- Roemer van der Meij MSc PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3612631 E-mail: r.vandermeij at donders.ru.nl ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From lhunt at FMRIB.OX.AC.UK Tue Jun 15 10:20:13 2010 From: lhunt at FMRIB.OX.AC.UK (Laurence Hunt) Date: Tue, 15 Jun 2010 09:20:13 +0100 Subject: ft_preproc_highpassfilter Message-ID: Hi folks, I'm trying to filter some MEG data sampled at 200Hz using ft_preproc_highpassfilter. It seems to be behaving slightly strangely. I'm calling it with Fs = 200; Fhp = 5; N = 6; and a stretch of single-channel data with ~50000 samples. However, the returned data doesn't seem to be filtered at 5Hz. When I go into the code and use fvtool to look at the frequency response of the filter, it doesn't have the shape I was expecting: I wondered whether this was because of the GNU public license version of butter that was being called by fieldtrip (in preproc/private), so I took this out of my matlab path and let it find the Mathworks' butter.m, from the signal processing toolbox. This seemed to give a more sensible looking filter design in fvtool: The Mathworks' butter.m also seemed to filter the data a bit more like I was expecting. Is this a problem with the GPL version, or am I calling the function wrong? Cheers, Laurence =========================================== Laurence Hunt, DPhil Student Centre for Functional MRI of the Brain (FMRIB), University of Oxford lhunt at fmrib.ox.ac.uk Phone: (+44)1865-(2)22738 =========================================== ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: GPLbutter.png Type: image/png Size: 8830 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MLbutter.png Type: image/png Size: 7196 bytes Desc: not available URL: From lhunt at FMRIB.OX.AC.UK Tue Jun 15 13:37:32 2010 From: lhunt at FMRIB.OX.AC.UK (Laurence Hunt) Date: Tue, 15 Jun 2010 12:37:32 +0100 Subject: Fwd: highpassfilter problems in fieldtrip Message-ID: Problems were already spotted by Jan-Mathijs... Begin forwarded message: > From: jan-mathijs schoffelen > Date: 15 June 2010 11:19:44 GMT+01:00 > To: Laurence Hunt > Subject: highpassfilter problems in fieldtrip > > Dear Laurence, > > Yes, you're absolutely right. I noticed the problem at some point, and it was caused by some typos in the octave-version of butter. This has been fixed recently, so that could mean that by updating to the most recent version may fix it. > > Cheers, > > Jan-Mathijs > > PS: I am not able to use my donders account for outgoing mails at the moment, so could you forward this reply to the mailing list, so that the rest of the community is aware of the issue? Thanks > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From aardesta at UCLA.EDU Fri Jun 18 00:40:38 2010 From: aardesta at UCLA.EDU (Allen Ardestani) Date: Thu, 17 Jun 2010 15:40:38 -0700 Subject: Connecivityanalysis ERROR Message-ID: Hi everyone, When I call connectivityanalysis using any of the methods that use frequency data, I get the following error: "??? Conversion to cell from double is not possible." I get it even when using the downloaded dataset and exact script from the tutorial: cfg = []; cfg.output = 'powandcsd'; cfg.method = 'mtmfft'; cfg.foilim = [5 100]; cfg.tapsmofrq = 5; cfg.keeptrials = 'yes'; cfg.channel = {'MEG' 'EMGlft' 'EMGrgt'}; cfg.channelcmb = {'MEG' 'EMGlft'; 'MEG' 'EMGrgt'}; freq = ft_freqanalysis(cfg, data); %% Plot %% cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'MEG' 'EMG'}; fd = ft_connectivityanalysis(cfg, freq); Any ideas what's wrong? Many thanks in advance. Best, Allen ____________________________________________________________________________ ______ Allen Ardestani Email: aardesta at ucla.edu Phone: (310) 825-5528 Medical Scientist Training Program David Geffen School of Medicine at UCLA Semel Institute for Neuroscience and Human Behavior 760 Westwood Plaza Los Angeles, CA 90095-1759 USA ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From saskia.haegens at DONDERS.RU.NL Fri Jun 18 11:08:27 2010 From: saskia.haegens at DONDERS.RU.NL (Saskia Haegens) Date: Fri, 18 Jun 2010 11:08:27 +0200 Subject: Connecivityanalysis ERROR In-Reply-To: <014301cb0e6e$1bf0abe0$53d203a0$@edu> Message-ID: Hi Allen, This sounds like a bug that was recently fixed, are you using the latest fieldtrip version? If you could copy/paste the exact error you are getting, would help in figuring out where this goes wrong. Best, Saskia _____ From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Allen Ardestani Sent: vrijdag 18 juni 2010 0:41 To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] Connecivityanalysis ERROR Hi everyone, When I call connectivityanalysis using any of the methods that use frequency data, I get the following error: "??? Conversion to cell from double is not possible." I get it even when using the downloaded dataset and exact script from the tutorial: cfg = []; cfg.output = 'powandcsd'; cfg.method = 'mtmfft'; cfg.foilim = [5 100]; cfg.tapsmofrq = 5; cfg.keeptrials = 'yes'; cfg.channel = {'MEG' 'EMGlft' 'EMGrgt'}; cfg.channelcmb = {'MEG' 'EMGlft'; 'MEG' 'EMGrgt'}; freq = ft_freqanalysis(cfg, data); %% Plot %% cfg = []; cfg.method = 'coh'; cfg.channelcmb = {'MEG' 'EMG'}; fd = ft_connectivityanalysis(cfg, freq); Any ideas what's wrong? Many thanks in advance. Best, Allen ____________________________________________________________________________ ______ Allen Ardestani Email: aardesta at ucla.edu Phone: (310) 825-5528 Medical Scientist Training Program David Geffen School of Medicine at UCLA Semel Institute for Neuroscience and Human Behavior 760 Westwood Plaza Los Angeles, CA 90095-1759 USA ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From qi at BRAIN.K.U-TOKYO.AC.JP Fri Jun 18 11:36:38 2010 From: qi at BRAIN.K.U-TOKYO.AC.JP (=?SHIFT_JIS?Q?Liang_Qi?=) Date: Fri, 18 Jun 2010 11:36:38 +0200 Subject: How to use 'MNE' method in 'sourceanalysis' Message-ID: Hi everyone, I'm trying to do single trial source analysis on MEG data, and I think 'MNE' method in 'sourceanalysis' may accomplish this. However I have no idea how to set the parameters in 'cfg'. Would anyone tell me how to do this? Thanks in advance. Regards, Liang ----------------------- Liang Qi Biological Complex Systems Laboratory Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8561, Japan Tel : +81-4-7136-3899 E-mail : qi at brain.k.u-tokyo.ac.jp ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From bps231 at NYU.EDU Sat Jun 19 10:38:16 2010 From: bps231 at NYU.EDU (Bernhard Staresina) Date: Sat, 19 Jun 2010 10:38:16 +0200 Subject: preprocessing slowing down Message-ID: Dear FieldTrip users, A quick question on preprocessing. I noticed that as I preprocess my EEG data (no actual preprocessing settings, just getting the exportet raw data into FieldTrip format), the process dramatically slows down as it goes along. So by trial 100, MATLAB essentially stops. I don't think it's a working memory issue - I tried to preprocess only the last few trials with cleared working memory, and the process doesn't move on. I read in the trial information (beginsample, endsample and offset) via definetrial, and of my ~700 trials (with only 25 channels), the later trials have begin- and endsample values of eg. 4338002 and 4344000, respectively. But why is it that it takes longer to read in a trial as a function of its begin and end sample? Shouldn't the amount of preceding data points be irrelevant? I'm reading in BrainVision Analyser data, using FT version 'fieldtrip-20090120'. The segments are 5.9 sec long, with 1kHz sampling rate. Thanks, Bernhard ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From aostendorf at BESA.DE Mon Jun 21 08:21:27 2010 From: aostendorf at BESA.DE (Andrea Ostendorf) Date: Mon, 21 Jun 2010 08:21:27 +0200 Subject: SPM8 In-Reply-To: <4C0FA4C1.9050208@donders.ru.nl> Message-ID: Dear Roemer, Thanks a lot. I discussed this topic some months ago with Robert and he suggested that he/the Fieldtrip team could modify the code along the following lines (I copy this from his e-mail because I think he will not mind this) - - - - - I suggest to modify the low level code into two helper functions (findcluster_chanlevel and findcluster_sourcelevel), which both should check like this if hastoolbox('image', 1) % using image processing toolbox my_bwlabeln = @bwlabeln; elseif hastoolbox('spm8', 1) % using spm8 version my_bwlabeln = @spm8_bwlabeln; else error(...) end - - - - I have got SPM8 on my Matlab path and whenever I download a new Fieldtrip version, I have to edit clusterstat and findcluster because it is (or was) not sufficient to simply replace bwlabeln by spm_bwlabel. What I did is probably rather inelegant but I left it that way since it works: In findcluster: Before: % [labelmat(spatdimlev, :, :), num] = bwlabeln(reshape(onoff(spatdimlev, :, :), nfreq, ntime), 4); After: input_for_spm_bwlabel = reshape(onoff(spatdimlev, :, :), nfreq, ntime); input_for_spm_bwlabel = +input_for_spm_bwlabel; %convert from logical [labelmat(spatdimlev, :, :), num] = spm_bwlabel(input_for_spm_bwlabel , 6); In clusterstat: Before: %!!!posclusobs = bwlabeln(tmp, conndef(length(cfg.dim),'min')); After: [posclusobs,L] = spm_bwlabel(tmp, 6); Sorry for the late answer. By the way, I have got into trouble at work because we have a betting game going on and I predicted the Netherlands as the winner (not that I know anything about football but I chose the Netherlands because the Fieldtrip team is so nice)... All the best Andrea ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.vandermeij at DONDERS.RU.NL Tue Jun 22 12:09:07 2010 From: r.vandermeij at DONDERS.RU.NL (Roemer van der Meij) Date: Tue, 22 Jun 2010 12:09:07 +0200 Subject: SPM8 In-Reply-To: <72D3AA975E924FCFAD3FAA83DF7309E1@LAT6500Andrea> Message-ID: Hi Andrea, We are deeply honored by your betting choice! May good fortune come to both of us! Thanks for sharing your modifications. Right now most of my FieldTrip time is going in writing the low-level functions for the spectral estimation module (which eventually replace the current freqanalysis implementation), but an obvious project for me after that is rewriting the cluster-permutation code. It has evolved into its current from over the past years, and our new low-level - high-level function structure will clean it up and makes it easier to fix bugs. I hope I can find the time to work on the bwlabeln functions, I will keep you updated. I'll also add this e-mail to our bugzilla report on this, to keep track of the possibilities. Thanks again for sharing your suggestions, they are always welcome. Best, Roemer On 6/21/2010 8:21 AM, Andrea Ostendorf wrote: > Dear Roemer, > > Thanks a lot. I discussed this topic some months ago with Robert and he > suggested that he/the Fieldtrip team could modify the code along the > following lines (I copy this from his e-mail because I think he will not > mind this) > - - - - - > I suggest to modify the low level code into two helper functions > (findcluster_chanlevel and findcluster_sourcelevel), which both should check > like this > > > if hastoolbox('image', 1) > % using image processing toolbox > my_bwlabeln = @bwlabeln; > elseif hastoolbox('spm8', 1) > % using spm8 version > my_bwlabeln = @spm8_bwlabeln; > else > error(...) > end > - - - - > > I have got SPM8 on my Matlab path and whenever I download a new Fieldtrip > version, I have to edit clusterstat and findcluster because it is (or was) > not sufficient to simply replace bwlabeln by spm_bwlabel. What I did is > probably rather inelegant but I left it that way since it works: > > In findcluster: > Before: > % [labelmat(spatdimlev, :, :), num] = bwlabeln(reshape(onoff(spatdimlev, :, > :), nfreq, ntime), 4); > After: > input_for_spm_bwlabel = reshape(onoff(spatdimlev, :, :), nfreq, ntime); > input_for_spm_bwlabel = +input_for_spm_bwlabel; %convert from logical > [labelmat(spatdimlev, :, :), num] = spm_bwlabel(input_for_spm_bwlabel , 6); > > In clusterstat: > Before: > %!!!posclusobs = bwlabeln(tmp, conndef(length(cfg.dim),'min')); > After: > [posclusobs,L] = spm_bwlabel(tmp, 6); > > Sorry for the late answer. > By the way, I have got into trouble at work because we have a betting game > going on and I predicted the Netherlands as the winner (not that I know > anything about football but I chose the Netherlands because the Fieldtrip > team is so nice)... > > All the best > Andrea > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > -- Roemer van der Meij MSc PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From michael.wibral at WEB.DE Tue Jun 22 17:34:04 2010 From: michael.wibral at WEB.DE (Michael Wibral) Date: Tue, 22 Jun 2010 17:34:04 +0200 Subject: Importing FT data to SPM8 as "LFP" data Message-ID: Dear SPM and FT listusers, does anyone know by any chance which headerfield in FT data to set to which value so that spm_eeg_convert automatically recognizes these data as LFP data? I can't seem to spot the words lfp anywhere inside spm_eeg_convert.m so it all is a bit mysterious to me. Many thanks, Michael ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 628 bytes Desc: not available URL: From r.oostenveld at FCDONDERS.RU.NL Tue Jun 22 19:37:17 2010 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 22 Jun 2010 19:37:17 +0200 Subject: fieldtrip webserver will be down tomorrow evening Message-ID: Dear fieldtrip users Our technical group has to do some maintenance to the servers of the Donders Centre. The consequence is that the fieldtrip wiki (fieldtrip.fcdonders.nl) and the ftp server (ftp.fcdonders.nl) will be down. Hopefully the downtime will be only one evening, but it might extend into the next morning. See below for details. > Tomorrow Wednesday June 23rd, 18:00h CET we have planned a down-time window for central storage and all of the central storage dependent IT services! If everything goes smoothly, central storage and all services will be back up and running later in that evening. In case we encounter unforeseen problems down-time might last until the early next morning Thursday June 24th. best regards, Robert ----------------------------------------------------------- Robert Oostenveld, PhD Senior Researcher Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen tel.: +31 (0)24 3619695 e-mail: r.oostenveld at donders.ru.nl web: http://www.ru.nl/neuroimaging skype: r.oostenveld ----------------------------------------------------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From moratti at MED.UCM.ES Wed Jun 23 08:41:30 2010 From: moratti at MED.UCM.ES (Stephan Moratti) Date: Wed, 23 Jun 2010 08:41:30 +0200 Subject: How to use 'MNE' method in 'sourceanalysis' Message-ID: Hi Liang, I do not work with the most recent version of fieldtrip, but I think you hace to specify the mne parameters this way: cfg.mne.[parameter] = x; Hope that helps. Best, Stephan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From odidodi at HOTMAIL.COM Wed Jun 23 13:20:57 2010 From: odidodi at HOTMAIL.COM (Odelia Goldberg) Date: Wed, 23 Jun 2010 13:20:57 +0200 Subject: cfg.output error while running ft_componentanalysis Message-ID: Hello all, I run ft_artifact_muscle+jump functions, then reject artifacts and then ICA. After choosing the components for removal I've tried to run "comp_orig = ft_componentanalysis(cfg, datacln);", to identify the components on the original data and I get an error saying: ??? Reference to non-existent field 'outputfile'. Error in ==> ft_componentanalysis at 416 if ~isempty(cfg.outputfile) I work with fieldtrip-20100621, and if I put the last three lines in comment, it works (problem solved). (I've tried to add 'output' field but it did't help). Anything that I'm missing? Thanks in advance, Odelia. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Thu Jun 24 17:55:16 2010 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Thu, 24 Jun 2010 17:55:16 +0200 Subject: cfg.output error while running ft_componentanalysis In-Reply-To: Message-ID: Hi Odelia Sorry about that, it is a known bug recently introduced. It only happens in conjunction with cfg.trackconfig=yes. We will fix it asap. Robert On 23 Jun 2010, at 13:20, Odelia Goldberg wrote: > I get an error saying: > > ??? Reference to non-existent field 'outputfile'. > > Error in ==> ft_componentanalysis at 416 > if ~isempty(cfg.outputfile) > > I work with fieldtrip-20100621, and if I put the last three lines in > comment, it works (problem solved). (I've tried to add 'output' > field but it > did't help). > Anything that I'm missing? ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Matthias.Meyer at DONDERS.RU.NL Fri Jun 25 11:24:04 2010 From: Matthias.Meyer at DONDERS.RU.NL (Matthias C. Meyer) Date: Fri, 25 Jun 2010 11:24:04 +0200 Subject: Export EEG Data Message-ID: Dear ft_Community, I am quite new to Fieldtrip and hope that someone has solved my problem before. I recorded EEG data inside an MR Scanner with the BrainVision software and now I want to use Fieldtrip to run some error correction scripts - so far so god. But after that I need to write the corrected data back to the original EEG - data format. I use the ft_write_data function to do this. After some problems I manage to run the function, but the result is a double size datafile, a messed up header and a empty marker file. Probably the data is written in double precision. Giving the data to the function with "single(data_org.trial{1})" in the argument does not help. The command line I use to call the function is: ft_write_data('ScannerCor', data_org.trial{1}, 'dataformat', 'brainvision_eeg','header', data_org.hdr); (I copied the corrected data back to the read in matrix) I heard already, that I can tell Matlab to use only single precision, but it would be nice to tell that the function directly - Is there a way to do so? What do I need to do, to export the header and marker file correctly? The corrected data are exactly of the same size as the original data, if possible, I might also use the original marker file to get the trigger points. I hope some one can help me. Best regards, Matthias. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From h.holle at SUSSEX.AC.UK Fri Jun 25 14:19:53 2010 From: h.holle at SUSSEX.AC.UK (Henning Holle) Date: Fri, 25 Jun 2010 14:19:53 +0200 Subject: databrowser: change order in which channels appear? Message-ID: Dear all, when looking at data with the databrowser (vertical viewmode), the channels appear in the order in which they happen to be in the dataset. Is there a way to define another order (so that, for instance, more anterior channels appear more on top of the screen, and more posterior channels at the bottom of the screen). Kind regards, Henning ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From ingrid.nieuwenhuis at FCDONDERS.RU.NL Fri Jun 25 14:25:45 2010 From: ingrid.nieuwenhuis at FCDONDERS.RU.NL (Ingrid Nieuwenhuis) Date: Fri, 25 Jun 2010 14:25:45 +0200 Subject: databrowser: change order in which channels appear? In-Reply-To: Message-ID: Dear Henning, Are you using the latest version of FieldTrip? If I remember correctly, I changed this at some point into that the order of the channels is as you specify them in cfg.channel Best, Ingrid ------------------------------------ Ingrid L.C. Nieuwenhuis PhD student Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging Radboud University Nijmegen, The Netherlands Email: ingrid.nieuwenhuis at donders.ru.nl Tel: 0031 (0)24 - 36 10887 -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Henning Holle Sent: Friday, June 25, 2010 2:20 PM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] databrowser: change order in which channels appear? Dear all, when looking at data with the databrowser (vertical viewmode), the channels appear in the order in which they happen to be in the dataset. Is there a way to define another order (so that, for instance, more anterior channels appear more on top of the screen, and more posterior channels at the bottom of the screen). Kind regards, Henning ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From odidodi at HOTMAIL.COM Fri Jun 25 15:16:58 2010 From: odidodi at HOTMAIL.COM (odelia nakar) Date: Fri, 25 Jun 2010 13:16:58 +0000 Subject: cfg.output error while running ft_componentanalysis In-Reply-To: Message-ID: Hi Robert, Thank you for your answer. I think that on the 23rd of 6 version it was aready fixed. Good day! Odelia. > Date: Thu, 24 Jun 2010 17:55:16 +0200 > From: r.oostenveld at FCDONDERS.RU.NL > Subject: Re: [FIELDTRIP] cfg.output error while running ft_componentanalysis > To: FIELDTRIP at NIC.SURFNET.NL > > Hi Odelia > > Sorry about that, it is a known bug recently introduced. It only > happens in conjunction with cfg.trackconfig=yes. We will fix it asap. > > Robert > > > On 23 Jun 2010, at 13:20, Odelia Goldberg wrote: > > > I get an error saying: > > > > ??? Reference to non-existent field 'outputfile'. > > > > Error in ==> ft_componentanalysis at 416 > > if ~isempty(cfg.outputfile) > > > > I work with fieldtrip-20100621, and if I put the last three lines in > > comment, it works (problem solved). (I've tried to add 'output' > > field but it > > did't help). > > Anything that I'm missing? > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.rousselet at PSY.GLA.AC.UK Fri Jun 25 15:27:14 2010 From: g.rousselet at PSY.GLA.AC.UK (Guillaume Rousselet) Date: Fri, 25 Jun 2010 14:27:14 +0100 Subject: Frontiers in Perception Science: Call for participation in upcoming Special Topic Message-ID: Hosting Journal: Frontiers in Perception Science Topic Title: Single-trial analyses of behavioural and neuroimaging data in perception and decision-making. Host Editors: Guillaume A. Rousselet, Cyril R. Pernet, Paul Sajda Description: The cognitive psychology of perception and decision-making is at a cross-road. Most studies still employ categorical designs, a priori classified stimuli and perform statistical evaluations across subjects. However, a shift has been observed in recent years towards parametric designs in which the information content of stimuli is systematically manipulated to study the single-trial dynamics of behaviour (reaction times, eye movements) and brain activity (EEG, MEG, fMRI). By using the information contained in the variance of individual trials, the single-trial approach goes beyond the activity of the average brain: it reveals the specificity of information processing in individual subjects, across tasks and stimulus space, revealing both inter-individual commonalties and differences. This special issue provides theoretical and empirical support for the study of single-trial data. Topics of particular interest include: 1. description of the richness of information in single-trials and how it can be successfully extracted; 2. statistical issues related to measures of central tendency, control for multiple comparisons, multivariate approaches, hierarchical modelling and characterization of individual differences; 3. how manipulation of the stimulus space can allow for a direct mapping of stimulus properties onto brain activity to infer dynamics of information processing and information content of brain states; 4. how results from different brain imaging techniques can be integrated at the single-trial level. Abstract Submission Deadline: September 01, 2010 Article Submission Deadline: January 03, 2011 Link to Special Topic: http://www.frontiersin.org/psychology/perceptionscience/specialtopics/98/ The publishing fee for contributors amounts to €900, and a further reduction to €720 for Frontiers Associate Editors. Like all research published with Frontiers, the articles will be freely available to all of our readers on our website, and all Special Topic articles receive a DOI and are indexed in the National Institute of Health’s electronic depository of full text articles, PubMed Central, and many other international archives (Google Scholar, Directory of Open Access Journal, Psych INFO). Frontiers is also in the process of being archived in Thompson Scientific (ISI), and Web of Science. Frontiers has also announced that in the very near future, all published Special Topics will be available to view and download in an eBook format! For more information, you may refer to the Frontiers’ Special Topic page, where you can get further guidance and browse past Special Topics. << http://www.frontiersin.org/specialtopicspage/ >> With best regards, Guillaume Rousselet Associate Editor, Frontiers in Perception Science www.frontiersin.org ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sreenivasan.r.nadar at GMAIL.COM Sat Jun 26 21:04:25 2010 From: sreenivasan.r.nadar at GMAIL.COM (Dr. Sreenivasan Rajamoni Nadar, Ph.D.) Date: Sat, 26 Jun 2010 12:04:25 -0700 Subject: Dr. Sreenivasan Rajamoni Nadar, Ph.D. wants to stay in touch on LinkedIn Message-ID: LinkedIn ------------ FieldTrip, I'd like to add you to my professional network on LinkedIn. - Dr. Sreenivasan Rajamoni Nadar, Ph.D. Dr. Sreenivasan Rajamoni Nadar, Ph.D. Scientist at National Institute of Mental Health Washington D.C. Metro Area Confirm that you know Dr. Sreenivasan Rajamoni Nadar, Ph.D. https://www.linkedin.com/e/dwhirw-gawtl874-2e/isd/1418399407/pkkPy6v8/ ------ (c) 2010, LinkedIn Corporation ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.gomez at SCIENCE.RU.NL Mon Jun 28 13:35:57 2010 From: v.gomez at SCIENCE.RU.NL (=?ISO-8859-1?Q?Vicen=E7_G=F3mez?=) Date: Mon, 28 Jun 2010 13:35:57 +0200 Subject: fixtrialdef.m Message-ID: Dear fieldtripers, function fixtrialdef.m can't handle data with one trial only: K>> ??? Error using ==> cat CAT arguments dimensions are not consistent. Error in ==> fixtrialdef at 26 begsample = cat(1, 0, cumsum(nsmp(1:end-1))) + 1; I fixed it doing: if ntrial == 1 begsample = 1; else begsample = cat(1, 0, cumsum(nsmp(1:end-1))) + 1; end Is that right? thanks, -- Vicenç Gomez Cerda SNN Radboud University Nijmegen The Netherlands http://www.mbfys.ru.nl/staff/v.gomez/ tel: +31 (0)24 - 36 14230 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Mon Jun 28 17:09:29 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Mon, 28 Jun 2010 17:09:29 +0200 Subject: fixtrialdef.m In-Reply-To: <4C28891D.1030602@science.ru.nl> Message-ID: Dear Vicenç, Thanks for the suggestion. I will incorporate it into the ftp-version so that everybody can enjoy this improvement ;). It'll be available as of tomorrow. Cheers, Jan-Mathijs On Jun 28, 2010, at 1:35 PM, Vicenç Gómez wrote: > Dear fieldtripers, > > function fixtrialdef.m can't handle data with one trial only: > > K>> ??? Error using ==> cat > CAT arguments dimensions are not consistent. > > Error in ==> fixtrialdef at 26 > begsample = cat(1, 0, cumsum(nsmp(1:end-1))) + 1; > > I fixed it doing: > > if ntrial == 1 > begsample = 1; > else > begsample = cat(1, 0, cumsum(nsmp(1:end-1))) + 1; > end > > Is that right? > > thanks, > > > -- > Vicenç Gomez Cerda > SNN Radboud University Nijmegen > The Netherlands > http://www.mbfys.ru.nl/staff/v.gomez/ > tel: +31 (0)24 - 36 14230 > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From mcregar at UPO.ES Wed Jun 30 11:04:58 2010 From: mcregar at UPO.ES (Maite Crespo) Date: Wed, 30 Jun 2010 11:04:58 +0200 Subject: Matlab compiler for Windows XP 64-bit Message-ID: Hello, I had my first code errors with mex files. It seems I'll have to install a Matlab compiler for 64 bits (Windows XP). Does anybody knows a free compiler? Thank you very much. Best (first) regards, Maité ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From s.klanke at DONDERS.RU.NL Wed Jun 30 11:31:40 2010 From: s.klanke at DONDERS.RU.NL (Stefan Klanke) Date: Wed, 30 Jun 2010 11:31:40 +0200 Subject: Matlab compiler for Windows XP 64-bit In-Reply-To: Message-ID: Dear Maité, I do not have a 64-bit machine myself yet, but I know that you can produce 64 bit executables using the free "Express" version (both 2008 and 2010) of Microsoft Visual C++. You can get more information here: http://msdn.microsoft.com/en-us/library/9yb4317s.aspx Depending on how old your version of Matlab is, it might be easier to pick the 2008 version, so "mex -setup" can detect the compiler. With kind regards, Stefan On 30-6-2010 11:04, Maite Crespo wrote: > Hello, > > I had my first code errors with mex files. It seems I'll have to install a Matlab > compiler for 64 bits (Windows XP). Does anybody knows a free compiler? > > Thank you very much. > > Best (first) regards, > Maité > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Wed Jun 30 17:10:46 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Wed, 30 Jun 2010 17:10:46 +0200 Subject: Export EEG Data In-Reply-To: <4C2475B4.5030807@donders.ru.nl> Message-ID: Hi Mattias, > I am quite new to Fieldtrip and hope that someone has solved my > problem before. High expectations ;). > I recorded EEG data inside an MR Scanner with the BrainVision > software and now I want to use Fieldtrip to run some error > correction scripts - so far so god. > But after that I need to write the corrected data back to the > original EEG - data format. > I use the ft_write_data function to do this. After some problems I > manage to run the function, but the result is a double size > datafile, a messed up header and a empty marker file. > Probably the data is written in double precision. Giving the data to > the function with "single(data_org.trial{1})" in the argument does > not help. > The command line I use to call the function is: > ft_write_data('ScannerCor', data_org.trial{1}, 'dataformat', > 'brainvision_eeg','header', data_org.hdr); > > (I copied the corrected data back to the read in matrix) > > I heard already, that I can tell Matlab to use only single > precision, but it would be nice to tell that the function directly - > Is there a way to do so? > What do I need to do, to export the header and marker file correctly? I have not encountered this issue before, and I don't know whether anybody else has. This may mean that you need to do some digging yourself to get it solved. I never tried to export data to a different fileformat. The easy way out here would be to also do your subsequent analysis steps in matlab/fieldtrip. Did you already have a detailed look at ft_write_data, and in particular the part which deals with 'brainvision_eeg'. My suspicion is that there is a discrepancy between the information in data_org.hdr, and the exact data you try to export (data_org.trial{1}). Manually converting to single precision may not work if in data_org.hdr you need to specify the precision. (once again I don't know about the specifics of this function, or of the functions it relies on). Using the matlab debugger may help you to access the variables in the function's workspace and to see what's preventing it to work properly. Good luck, Jan-Mathijs Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcregar at UPO.ES Wed Jun 30 18:12:05 2010 From: mcregar at UPO.ES (Maite Crespo) Date: Wed, 30 Jun 2010 18:12:05 +0200 Subject: source analysis on time window and frequency range Message-ID: Hello again! I would like to apply the DICS and SAM methods to localize the source activity within a time window and a frequency range, but based on the CSD or covariance matrices obtained from a wavelet transformation to the time- frequency domain. At the moment I found only one possible frequency or latency as input to the ft_sourceanalysis function. I also read about applying the multitaper method for time-frequency analysis, but I worry about the non-stationarity of the signals. Could somebody give me a hint about how to proceed? Have a nice day. Best regards, Maité ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From marco.rotonda at GMAIL.COM Wed Jun 30 19:07:43 2010 From: marco.rotonda at GMAIL.COM (Marco Rotonda) Date: Wed, 30 Jun 2010 19:07:43 +0200 Subject: Nested analysis Message-ID: Hi Fieldtrippers! I have a question about an analysis that I would like to do. In this experiment I have the following design: 2 group X 2 stage X 2 stimulus X 278 electrodes combinations (plv) wherein group is a between factor and all the other factors are within factors. The electrodes combinations is nested in the stimulus factor and the stimulus is nested in the stage factor. How could I menage this situation? Regards, Marco ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.