From wolpert at clipper.ens.fr Wed Nov 1 15:12:44 2017 From: wolpert at clipper.ens.fr (wolpert at clipper.ens.fr) Date: Wed, 1 Nov 2017 15:12:44 +0100 Subject: [FieldTrip] Create event structre from .mrk file Message-ID: <28f61ec01e3c4487dc3039704079e004.squirrel@squirrelmail.eleves.ens.fr> Dear all, I would like to read events from a .mrk file. Using ft_read_event does not work as it gives me the message that it's unsupported event format. By searching in the internet, I found the function "readmarkerfile" which is able to return the marker names and their samples, but in very inconvenient format. So is there any way of creating the classical event structure from files in .mrk format? Best regards, Nicolai From christian.merkel at med.ovgu.de Fri Nov 3 13:42:13 2017 From: christian.merkel at med.ovgu.de (christian.merkel at med.ovgu.de) Date: Fri, 3 Nov 2017 12:42:13 +0000 Subject: [FieldTrip] wMNE? Message-ID: <71D8A67A81D69A4CB5BE2B979021C26ECB016E51@ESEN4.imed.uni-magdeburg.de> Dear fieldtrip-community, Does the minimum-norm-estimate algorithm in ft_sourceanalysis support depth-weighting? Thank You, Christian From jan.schoffelen at donders.ru.nl Fri Nov 3 15:53:02 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 3 Nov 2017 14:53:02 +0000 Subject: [FieldTrip] wMNE? In-Reply-To: <71D8A67A81D69A4CB5BE2B979021C26ECB016E51@ESEN4.imed.uni-magdeburg.de> References: <71D8A67A81D69A4CB5BE2B979021C26ECB016E51@ESEN4.imed.uni-magdeburg.de> Message-ID: Hi Christian, Yes, depth weighting can be achieved by norm normalisation of the leadfields (using the normalize option in ft_prepare_leadfield), or by inclusion of a source-covariance matrix in the cfg to ft_sourceanalysis. Best wishes, Jan-Mathijs On 3 Nov 2017, at 13:42, christian.merkel at med.ovgu.de wrote: Dear fieldtrip-community, Does the minimum-norm-estimate algorithm in ft_sourceanalysis support depth-weighting? Thank You, Christian _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From fereshte.ramezani at gmail.com Sat Nov 4 07:53:09 2017 From: fereshte.ramezani at gmail.com (Fereshte) Date: Sat, 04 Nov 2017 06:53:09 +0000 Subject: [FieldTrip] Place Source Models in specific location Message-ID: Dear Experts, I'm so new to fieldtrip so I apologize if my question is very basic; How can I place source models in specific locations according to MRI image ( I've already made the head model based on FEM). Thanks for your attention. Regards, Fereshte -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Sat Nov 4 08:25:43 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Sat, 4 Nov 2017 07:25:43 +0000 Subject: [FieldTrip] Place Source Models in specific location In-Reply-To: References: Message-ID: Ferehste, Your question lacks specificity. I think the readers of this list need a bit more concrete input in order to think about answering your question. Is it about specific locations? Anatomical atlas based regions-of-interest? What inverse algorithm are you considering? Etc.? Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 4 Nov 2017, at 07:53, Fereshte > wrote: Dear Experts, I'm so new to fieldtrip so I apologize if my question is very basic; How can I place source models in specific locations according to MRI image ( I've already made the head model based on FEM). Thanks for your attention. Regards, Fereshte _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From fereshte.ramezani at gmail.com Sun Nov 5 12:05:58 2017 From: fereshte.ramezani at gmail.com (Fereshte) Date: Sun, 05 Nov 2017 11:05:58 +0000 Subject: [FieldTrip] Place Source Models in specific location In-Reply-To: References: Message-ID: I'm going to investigate the effect of segmentation on EEG forward problem( FreeSurfer segmentation and Filedtrip segmentation). I've already made the FE head model and placed the electrodes but I'm not really sure how to place the source models for such a comparison ( like to place source models where the two segmentations differ in GM). Thanks for your attention. On Sat, Nov 4, 2017 at 11:05 AM Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Ferehste, > > Your question lacks specificity. I think the readers of this list need a > bit more concrete input in order to think about answering your question. Is > it about specific locations? Anatomical atlas based regions-of-interest? > What inverse algorithm are you considering? Etc.? > > Best wishes, > > Jan-Mathijs > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > > On 4 Nov 2017, at 07:53, Fereshte wrote: > > Dear Experts, > I'm so new to fieldtrip so I apologize if my question is very basic; How > can I place source models in specific locations according to MRI image ( > I've already made the head model based on FEM). > Thanks for your attention. > Regards, > Fereshte > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsten.wolters at uni-muenster.de Mon Nov 6 09:01:59 2017 From: carsten.wolters at uni-muenster.de (Carsten Wolters) Date: Mon, 6 Nov 2017 09:01:59 +0100 Subject: [FieldTrip] Place Source Models in specific location In-Reply-To: References: Message-ID: <6def03a0-a71e-3a5d-981d-14bb921a9ea2@uni-muenster.de> Dear Ferehste, we have implemented the Venant approach for FEM source modeling in the Fieldtrip-SimBio pipeline. The Venant approach spreads monopolar sources around the dipole location in a way that the dipole location and moment is well approximated. You need to take care that all these monopoles are within the grey matter compartment. We call this the "Venant condition" that has to be fulfilled. You find detailed informations in http://www.sci.utah.edu/~wolters/PaperWolters/2014/VorwerkChoRamppHamerKnoescheWolters_NeuroImage_2014_Webversion.pdf or in Chapter 2.4.2 in http://www.sci.utah.edu/~wolters/PaperWolters/2016/PursiainenVorwerkWolters_PhysMedBiol_accepted2016_HDiv.pdf or very detailed in http://www.sci.utah.edu/~wolters/PaperWolters/2016/Vorwerk_Dissertation_2016.pdf BR      Carsten Am 05.11.2017 um 12:05 schrieb Fereshte: > I'm going to investigate the effect of segmentation on EEG forward > problem( FreeSurfer segmentation and Filedtrip segmentation). I've > already made the FE head model and placed the electrodes but I'm not > really sure how to place the source models for such a comparison ( > like to place source models where the two segmentations differ in GM). > Thanks for your attention. > > On Sat, Nov 4, 2017 at 11:05 AM Schoffelen, J.M. (Jan Mathijs) > > > wrote: > > Ferehste, > > Your question lacks specificity. I think the readers of this list > need a bit more concrete input in order to think about answering > your question. Is it about specific locations? Anatomical atlas > based regions-of-interest? What inverse algorithm are you > considering? Etc.? > > Best wishes, > > Jan-Mathijs > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > >> On 4 Nov 2017, at 07:53, Fereshte > > wrote: >> >> Dear Experts, >> I'm so new to fieldtrip so I apologize if my question is very >> basic; How can I place source models in specific locations >> according to MRI image ( I've already made the head model based >> on FEM). >> Thanks for your attention. >> Regards, >> Fereshte >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Prof. Dr.rer.nat. Carsten H. Wolters University of Münster Institute for Biomagnetism and Biosignalanalysis Malmedyweg 15 48149 Münster, Germany Phone: +49 (0)251 83 56904 +49 (0)251 83 56865 (secr.) Fax: +49 (0)251 83 56874 Email: carsten.wolters at uni-muenster.de Web: https://campus.uni-muenster.de/biomag/das-institut/mitarbeiter/carsten-wolters/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Mon Nov 6 17:41:21 2017 From: michelic72 at gmail.com (Cristiano Micheli) Date: Mon, 6 Nov 2017 17:41:21 +0100 Subject: [FieldTrip] reconstruction of EEG patterns on a 3D shape Message-ID: Dear Team I achieved a 3D reconstruction of a 64 electrodes Biosemi cap, as described in this tutorial: http://www.fieldtriptoolbox.org/tutorial/electrode Now I would like to visualise a [64x1] vector of EEG activity [64 electrodes x 1 time sample] as an interpolated overlay on top of the 3D electrodes reconstruction. Is there a quick way to obtain this by means of ft_sourceplot or other functions? All the best! Cris -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Nov 6 19:57:34 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 6 Nov 2017 18:57:34 +0000 Subject: [FieldTrip] reconstruction of EEG patterns on a 3D shape In-Reply-To: References: Message-ID: Ciao Cris, ft_plot_topo3d in the plotting module is your friend. Best wishes, JM J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 6 Nov 2017, at 17:41, Cristiano Micheli > wrote: Dear Team I achieved a 3D reconstruction of a 64 electrodes Biosemi cap, as described in this tutorial: http://www.fieldtriptoolbox.org/tutorial/electrode Now I would like to visualise a [64x1] vector of EEG activity [64 electrodes x 1 time sample] as an interpolated overlay on top of the 3D electrodes reconstruction. Is there a quick way to obtain this by means of ft_sourceplot or other functions? All the best! Cris _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From nadia.mueller at gmail.com Tue Nov 7 12:13:42 2017 From: nadia.mueller at gmail.com (Nadia Mueller) Date: Tue, 7 Nov 2017 12:13:42 +0100 Subject: [FieldTrip] Postdoc position and doctoral student position at the MEG in Erlangen Message-ID: Dear all, I'm offering one post-doc position and one position for a doctoral student in tinnitus research at the MEG Center in Erlangen (Germany) starting in February 2018. Please see the attached document for further information. It would be great if you could share this message with interested students, PhD students and postdocs around you. Thank you and best regards, Nadia Müller-Voggel -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Postdoc_Doctoral Student Position.pdf Type: application/pdf Size: 60316 bytes Desc: not available URL: From kirsten at carrot-village.de Tue Nov 7 12:16:51 2017 From: kirsten at carrot-village.de (Kirsten Herfurth) Date: Tue, 7 Nov 2017 12:16:51 +0100 (CET) Subject: [FieldTrip] Problem with ft_megrealign Message-ID: <1778422504.475907.1510053411840@communicator.strato.de> Dear all, I would like to apply the function ft_megrealign to my single subject meg data in order to do sensor level group analysis afterwards. I got stuck with the following error messages: Reference to non-existent field 'xgrid'. Error in ft_prepare_sourcemodel (line 709) xmin_indx = find(grid.xgrid==xmin); Error in ft_megrealign (line 249) grid = ft_prepare_sourcemodel(tmpcfg); I used the following configuration: cfg=[]; cfg.template = {MEGSubject1.grad; MEGSubject2.grad; MEGSubject3.grad, …}; cfg.headmodel = headmodel; cfg.headshape = strcat(Path2MEGData,'hs_file'); cfg.inwardshift = 0.025; % in meters cfg.vol.r=headmodel.r; cfg.vol.o=headmodel.o; cfg.vol.label=headmodel.label; [MEGSubject1_realigned] = ft_megrealign(cfg, MEGSubject1) The headmodel was built using the following configuration: cfg =[]; cfg.method = 'localspheres'; cfg.grad = MEGsingleSubjectData.grad; headmodel = ft_prepare_headmodel(cfg, headshape); There was a post with the same problem in the mailing list, with the suggestion to uncomment cfg.headshape: https://mailman.science.ru.nl/pipermail/fieldtrip/2015-September/009633.html When uncommenting cfg.headshape, it works until I get the following error message: Error using vertcat Dimensions of matrices being concatenated are not consistent. Error in ft_megrealign (line 391) interp.label = [interp.label; rest.label]; interpol.label is a 1x248 cell array, rest.label is 93x1 cell array. Did I miss something? Thanks a lot for your help in advance, Kirsten From xiew1202 at gmail.com Tue Nov 7 16:33:28 2017 From: xiew1202 at gmail.com (Xie Wanze) Date: Tue, 7 Nov 2017 10:33:28 -0500 Subject: [FieldTrip] Diagonal values for wpli in ft_connectivityanalysis Message-ID: Dear all, I have the diagonal values *unequal *to 0 or 1 in the output matrix from the ft_connectivityanalysis using 'wpli'. These diagonal values are even not equal to each other. The diagonal values are the same (0s or Infinite) by using 'coh' or 'coh' & cfg.complex = 'imag'. I never used the diagonal values in my later analysis, and I always changed them to 0s, but I am still curious and confused about why this happened to the method of 'wpli'. Does anyone ever meet this issue? Thanks. Wanze -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Tue Nov 7 16:33:28 2017 From: michelic72 at gmail.com (Cristiano Micheli) Date: Tue, 7 Nov 2017 16:33:28 +0100 Subject: [FieldTrip] reconstruction of EEG patterns on a 3D shape In-Reply-To: References: Message-ID: Thanks. That worked beautifully! Cris On Mon, Nov 6, 2017 at 7:57 PM, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Ciao Cris, > > ft_plot_topo3d in the plotting module is your friend. > > Best wishes, > > JM > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 <024%20361%204793> > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > > On 6 Nov 2017, at 17:41, Cristiano Micheli wrote: > > Dear Team > I achieved a 3D reconstruction of a 64 electrodes Biosemi cap, as > described in this tutorial: > http://www.fieldtriptoolbox.org/tutorial/electrode > Now I would like to visualise a [64x1] vector of EEG activity [64 > electrodes x 1 time sample] as an interpolated overlay on top of the 3D > electrodes reconstruction. > Is there a quick way to obtain this by means of ft_sourceplot or other > functions? > > All the best! > Cris > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Nov 7 21:46:49 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 7 Nov 2017 20:46:49 +0000 Subject: [FieldTrip] Problem with ft_megrealign In-Reply-To: <1778422504.475907.1510053411840@communicator.strato.de> References: <1778422504.475907.1510053411840@communicator.strato.de> Message-ID: <69C815C9-B6A5-4392-B06A-8FD34FB5DA71@donders.ru.nl> Dear Kirsten, These days I would not recommend the use of ft_megrealign to begin with. In our experience it often does more harm than that it improves results. In particular, if your subjects were relatively well-behaved, and well-positioned in the MEG. This might also be one of the reasons, why the code does not run through smoothly, because FieldTrip has evolved quite a bit over the past years. While we take the utmost care to keep the code internally consistent, rarely used functionality might have escaped our attention, which may have happened here. This being said, I am not sure whether I understand why the removal of the headshape option allows you to proceed deeper in the code. The second error you report is caused by a dimensionality mismatch, where matlab is asked to concatenate a row-vector (interp.label) with a column vector (rest.label). Given the code, it seems that the writer of the code assumed the interp.label to always be a column vector (which happens to be FieldTrip convention). I don’t know how interp.label ended up a row vector, but changing line 391 into interp.label = [interp.label(:);rest.label(:)]; should do the trick. You could try and fix this on your local copy of fieldtrip, but even better would be to contribute the fix to the release code-base, so that everyone can enjoy it. The way to do this is documented here: http://www.fieldtriptoolbox.org/development/git I am looking forward to your suggested fix. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 7 Nov 2017, at 12:16, Kirsten Herfurth > wrote: Dear all, I would like to apply the function ft_megrealign to my single subject meg data in order to do sensor level group analysis afterwards. I got stuck with the following error messages: Reference to non-existent field 'xgrid'. Error in ft_prepare_sourcemodel (line 709) xmin_indx = find(grid.xgrid==xmin); Error in ft_megrealign (line 249) grid = ft_prepare_sourcemodel(tmpcfg); I used the following configuration: cfg=[]; cfg.template = {MEGSubject1.grad; MEGSubject2.grad; MEGSubject3.grad, …}; cfg.headmodel = headmodel; cfg.headshape = strcat(Path2MEGData,'hs_file'); cfg.inwardshift = 0.025; % in meters cfg.vol.r=headmodel.r; cfg.vol.o=headmodel.o; cfg.vol.label=headmodel.label; [MEGSubject1_realigned] = ft_megrealign(cfg, MEGSubject1) The headmodel was built using the following configuration: cfg =[]; cfg.method = 'localspheres'; cfg.grad = MEGsingleSubjectData.grad; headmodel = ft_prepare_headmodel(cfg, headshape); There was a post with the same problem in the mailing list, with the suggestion to uncomment cfg.headshape: https://mailman.science.ru.nl/pipermail/fieldtrip/2015-September/009633.html When uncommenting cfg.headshape, it works until I get the following error message: Error using vertcat Dimensions of matrices being concatenated are not consistent. Error in ft_megrealign (line 391) interp.label = [interp.label; rest.label]; interpol.label is a 1x248 cell array, rest.label is 93x1 cell array. Did I miss something? Thanks a lot for your help in advance, Kirsten _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Nov 7 22:03:15 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 7 Nov 2017 21:03:15 +0000 Subject: [FieldTrip] Diagonal values for wpli in ft_connectivityanalysis In-Reply-To: References: Message-ID: <06BF6BE8-2170-4938-B3BE-74F25EFE89DE@donders.ru.nl> Dear Wanze, I don’t know what type of data you put into the algorithm, so it’s a bit ‘koffiedik’ kijken, as we say in Dutch. I’d suggest that you start by reading the code, and see whether you understand what causes your ‘issue’. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 7 Nov 2017, at 16:33, Xie Wanze > wrote: Dear all, I have the diagonal values unequal to 0 or 1 in the output matrix from the ft_connectivityanalysis using 'wpli'. These diagonal values are even not equal to each other. The diagonal values are the same (0s or Infinite) by using 'coh' or 'coh' & cfg.complex = 'imag'. I never used the diagonal values in my later analysis, and I always changed them to 0s, but I am still curious and confused about why this happened to the method of 'wpli'. Does anyone ever meet this issue? Thanks. Wanze _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.chettouf at vu.nl Wed Nov 8 11:14:42 2017 From: s.chettouf at vu.nl (Chettouf, S.) Date: Wed, 8 Nov 2017 10:14:42 +0000 Subject: [FieldTrip] Convert fieldtrip beamformers to SPM Message-ID: Dear fieldtrip community, I analysed my EEG data in fieldtrip and calculated beamformers. I would like to compare these source data with my fMRI sources and therefore do both statistical testings in SPM. But how can I export my beamformer data to SPM? Converting them with spm_ eeg _ ft2spm does not work with beamformer data. I also tried ft_volumewrite to convert the beamformer results to nifti, but without succes. Thanks in advance, Sabrina -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Nov 8 11:24:47 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 8 Nov 2017 10:24:47 +0000 Subject: [FieldTrip] Convert fieldtrip beamformers to SPM In-Reply-To: References: Message-ID: Dear Sabrina, I am not sure why your conversion to nifti does not work, but if you follow the recipe that is described in http://www.fieldtriptoolbox.org/tutorial/beamformer, in particular by using ft_sourceinterpolate to create a volumetric image of ther source-reconstructed activity, followed by an optional volumetric normalisation (using ft_volumenormalise), it should be relatively straightforward to save this to a nifti file. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 8 Nov 2017, at 11:14, Chettouf, S. > wrote: Dear fieldtrip community, I analysed my EEG data in fieldtrip and calculated beamformers. I would like to compare these source data with my fMRI sources and therefore do both statistical testings in SPM. But how can I export my beamformer data to SPM? Converting them with spm_ eeg _ ft2spm does not work with beamformer data. I also tried ft_volumewrite to convert the beamformer results to nifti, but without succes. Thanks in advance, Sabrina _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Nov 8 12:05:31 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 8 Nov 2017 11:05:31 +0000 Subject: [FieldTrip] Variance estimates for connectivity measures In-Reply-To: References: Message-ID: <2EBD91F4-1703-4F0E-A7D2-3DC6DC96E030@donders.ru.nl> Dear Matthew, I think it depends on the way that you compute these metrics. If you approach it parametrically (i.e. using MVAR-models) I think that the coefficients are computed across all observations by default. If you want a leave-one-out estimate of the coefficients, I think that you can use cfg.jackknife as an option to ft_mvaranalysis. How well this is supported throughout the rest of the analysis pipeline (i.e. ft_freqanalysis_mvar and ft_connectivityanalysis) I am not sure. I haven’t used this option for a long time, so the code may have become a bit rusty here and there. If you are using a non-parametric approach (i.e. using ft_freqanalysis, followed by ft_connectivity_csd2transfer, which is called on the fly by ft_connectivityanalysis), I think there used to be some functionality to compute leave-one-outs on the fly, and then essentially treat them as ‘single trials’. Also there, I assume that the code has become a bit rusty, because it hasn’t been used for quite a while. Either way, I guess that an definitive answer to your question would require you to inspect the code in some more detail. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 20 Oct 2017, at 16:16, MATTHEW I BANKS > wrote: Greetings. Is it possible to use jackknife to get variance estimates for Granger, partial directed coherence and directed transfer function? I use it for wPLI, but cannot figure out how to do it for these other measures. -Matt Banks ____________________________ Matthew I. Banks, Ph.D. Associate Professor Department of Anesthesiology University of Wisconsin 1300 University Avenue, Room 4605 Madison, WI 53706 office tel. (608)261-1143 lab tel. (608)263-6662 fax (608)263-2592 http://anesthesia.wisc.edu/index.php/Banks_Laboratory http://ntp.neuroscience.wisc.edu/banks.htm _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From SXM1085 at student.bham.ac.uk Wed Nov 8 12:07:43 2017 From: SXM1085 at student.bham.ac.uk (Sebastian Michelmann) Date: Wed, 8 Nov 2017 11:07:43 +0000 Subject: [FieldTrip] Convert fieldtrip beamformers to SPM In-Reply-To: References: Message-ID: <2D9C9145AF1E4D4799ADDB2C0F996AE8019EFD8425@EX13.adf.bham.ac.uk> Dear Sabrina, This code works for me on the interpolated volume: cfg = []; cfg.parameter = 'stat'; cfg.filename = 'stat_interp'; cfg.datatype = 'float'; cfg.filetype = 'nifti'; cfg.vmpversion = 2; cfg.coordsys = 'spm'; ft_volumewrite(cfg, sourceint); I use this to plot 'blobs' outside of fieldtrip. best, Sebastian From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of s.chettouf at vu.nl Sent: 08 November 2017 10:15 To: FieldTrip discussion list Subject: [FieldTrip] Convert fieldtrip beamformers to SPM Dear fieldtrip community, I analysed my EEG data in fieldtrip and calculated beamformers. I would like to compare these source data with my fMRI sources and therefore do both statistical testings in SPM. But how can I export my beamformer data to SPM? Converting them with spm_ eeg _ ft2spm does not work with beamformer data. I also tried ft_volumewrite to convert the beamformer results to nifti, but without succes. Thanks in advance, Sabrina -------------- next part -------------- An HTML attachment was scrubbed... URL: From joerg.hipp at googlemail.com Wed Nov 8 17:55:26 2017 From: joerg.hipp at googlemail.com (Joerg Hipp) Date: Wed, 8 Nov 2017 17:55:26 +0100 Subject: [FieldTrip] 9 month internship in EEG biomarker development at Roche in Basel, Switzerland Message-ID: Dear all, We are offering a 9 month internship (RiSE, Roche Internships for Scientific Exchange) in our biomarker group at Roche in Basel, Switzerland. We are looking for a motivated researcher to help us explore the utility of EEG as a biomarker for neurodevelopmental diseases. Besides the work on a specific project the intern will gain insights into research and development in the pharmaceutical industry. Our group supports neuroscience programs within the Roche portfolio, which covers a broad spectrum of neurological and psychiatric diseases and we apply various techniques including EEG/MEG, PET, MRI, and Neuropsychology to this end. I am responsible for electrophysiological biomarkers (EEG/MEG) and will supervise this project. Prerequisite for application to the RiSE program is enrollment in a university PhD or medical degree program at the time of application. Details on the RiSE program can be found here: http://www.roche.com/careers/ switzerland/ch_your_job/students_and_graduates/ch_ internships/rise_program.htm Details on the specific internship and how to apply can be found here: https://www.roche.com/careers/jobs/jobsearch/job.htm?id=E- 3425641919&locale=en&title=RiSE+-+Roche+internship+for+ Scientific+Exchange+-+in+Neuroscience+Biomarkers+%289+months%29 Best wishes, Joerg -- Joerg Hipp, PhD Biomarker and Experimental Medicine Leader F. Hoffmann-La Roche Ltd. Grenzacherstrasse 124 4070 Basel, Switzerland https://scholar.google.ch/citations?user=oxsJ6q4AAAAJ&hl=en -------------- next part -------------- An HTML attachment was scrubbed... URL: From kirsten at carrot-village.de Thu Nov 9 12:58:02 2017 From: kirsten at carrot-village.de (Kirsten Herfurth) Date: Thu, 9 Nov 2017 12:58:02 +0100 (CET) Subject: [FieldTrip] Problem with ft_megrealign Message-ID: <1899468378.586762.1510228682849@communicator.strato.de> Dear Jan-Mathijs, thank you very much for your answer! I will fix the bug and commit it to Github. Do you have any suggestions for an alternative approach for realigning data obtained with a non-CTF-system (we have a 4d-MEG-system)? Unfortunately we don’t have a head position time-series obtained online, just the position in the beginning and in the end of a run. I assume I cannot use the function ft_regressconfound or ft_headmovement. I’m sorry for this basic question, but I haven’t found a satisfying answer to my problem yet. The reason for accounting for head movement is that I would like to use the Machine Learning toolbox and do statistics using k-fold cross-validation, but have too few trials in one run per subject. So I thought to concatenate the trials of different runs with ft_appenddata using the realignment function first. Would it be ok to just go without the realignment in subjects that didn’t move that much, especially if it gives me the expected results? Thanks again and best wishes Kirsten From Bastiaansen4.M at nhtv.nl Fri Nov 10 12:04:37 2017 From: Bastiaansen4.M at nhtv.nl (Bastiaansen, Marcel) Date: Fri, 10 Nov 2017 11:04:37 +0000 Subject: [FieldTrip] multiclass svm In-Reply-To: References: Message-ID: Dear Fieldtrippers, As a relative novice to classification algorithms, I have been playing around with Fieldtrip's svm classifier (ft_statistics_crossvalidate). This seems to work pretty smoothly, but I have two questions related to that: 1. In the given contingency table one can see the actual classification of trials. However, I assume the actual classification is based on a classification probability for each trial. Is there a way of getting a list of classification probabilities for all trials from this function? Else, a quick hint at where in the code these probabilities are being computed / stored would help me build this functionality 2. I have EEG data that belong to 4 classes, but ft_statistics_crossvalidate does not afford multiclass approaches. Any tips or hints at what would be robust and well-validated approaches for multiclass models for EEG data would be much appreciated. Best, Marcel *** Dr Marcel C.M. Bastiaansen Senior lecturer and researcher in quantitative research methods Academy for Leisure & Academy for Tourism NHTV Breda University of Applied Sciences Visiting adress: Room C1.011, Academy for Leisure Archimedesstraat 17, 4816 BA, Breda Phone: +31 76 533 2869 Email: bastiaansen4.m at nhtv.nl And Department of Cognitive Neuropsychology Tilburg School of Social and Behavioral Sciences Tilburg University Visiting address: Room S217, Simon building Warandelaan 2 5000 LE Tilburg Email: M.C.M.Bastiaansen at uvt.nl publications linked-in *** -------------- next part -------------- An HTML attachment was scrubbed... URL: From ekenaykut at gmail.com Fri Nov 10 12:40:05 2017 From: ekenaykut at gmail.com (Aykut Eken) Date: Fri, 10 Nov 2017 14:40:05 +0300 Subject: [FieldTrip] multiclass svm In-Reply-To: References: Message-ID: <0A281A02-DB29-4F9D-BBBE-24078FA8B12F@gmail.com> Dear Marcel, Instead of using ft_statistics_crossvalidate, you can extract the features and use as input to fitcsvm in MATLAB that provides answers to your questions. After running the model, you can use fitSVMPosterior or fitPosterior to obtain classification probabilities. Best Aykut Eken, PhD Düzce University Faculty of Engineering Biomedical Engineering Department Düzce University, Konuralp Campus, 81620, Konuralp, Düzce, Turkey Tel: +905366777364 Office Tel: +90380542 11 00 /4546 Mail address1: aykuteken at duzce.edu.tr Mail address2: ekenaykut at gmail.com > On 10 Nov 2017, at 14:04, Bastiaansen, Marcel wrote: > > Dear Fieldtrippers, > > As a relative novice to classification algorithms, I have been playing around with Fieldtrip’s svm classifier (ft_statistics_crossvalidate). This seems to work pretty smoothly, but I have two questions related to that: > 1. In the given contingency table one can see the actual classification of trials. However, I assume the actual classification is based on a classification probability for each trial. Is there a way of getting a list of classification probabilities for all trials from this function? Else, a quick hint at where in the code these probabilities are being computed / stored would help me build this functionality > 2. I have EEG data that belong to 4 classes, but ft_statistics_crossvalidate does not afford multiclass approaches. Any tips or hints at what would be robust and well-validated approaches for multiclass models for EEG data would be much appreciated. > > Best, > Marcel > > *** > Dr Marcel C.M. Bastiaansen > Senior lecturer and researcher in quantitative research methods > Academy for Leisure & Academy for Tourism > NHTV Breda University of Applied Sciences > Visiting adress: > Room C1.011, Academy for Leisure > Archimedesstraat 17, > 4816 BA, Breda > Phone: +31 76 533 2869 > Email: bastiaansen4.m at nhtv.nl > > And > > Department of Cognitive Neuropsychology > Tilburg School of Social and Behavioral Sciences > Tilburg University > Visiting address: > Room S217, Simon building > Warandelaan 2 > 5000 LE Tilburg > Email: M.C.M.Bastiaansen at uvt.nl > > publications > linked-in > *** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From til.bergmann at uni-tuebingen.de Fri Nov 10 16:46:37 2017 From: til.bergmann at uni-tuebingen.de (Til Ole Bergmann) Date: Fri, 10 Nov 2017 16:46:37 +0100 Subject: [FieldTrip] PhD Position (3 years, 65% TV-L) on real-time EEG-TMS with Til Ole Bergmann, University of Tuebingen, Germany Message-ID: Dear FieldTrip community, I have a PhD position opening (3 years, salary accoording to 65% TV-L) in a DFG-funded project ("The sensorimotor µ-rhythm as cholinergically controlled pulsed inhibition"). We will use brain-state-dependent real-time EEG-triggered transcranial magnetic stimulation (EEG-TMS) to investigate the neurophysiology underlying mu-alpha (8-14 Hz) oscillations in the human sensorimotor cortex, their function for gating information flow and synaptic plasticity in the brain, and the cholinergic mechanisms mediating their prefrontal top-down control by attention. The ideal candidate has experience in Matlab (and preferrably FieldTrip) for EEG/MEG timeseries analyses. Please circulate this job opening amongst your peers and potential PhD candidates. For more information please see: http://tobergmann.de/downloads/PhD_position_Bergmann_Tuebingen.pdf Many thanks in advance! All the best, Til -- Dr. Til Ole Bergmann Department of Neurology & Stroke Hertie Institute for Clinical Brain Research Institute of Medical Psychology and Behavioral Neurobiology University of Tübingen Otfried-Müller-Straße 25, 72076 Tübingen, Germany til.bergmann at uni-tuebingen.de tel +49-7071-29-88795 fax +49 7071 29-25016 From springangel222 at gmail.com Sun Nov 12 06:37:12 2017 From: springangel222 at gmail.com (angel angel) Date: Sun, 12 Nov 2017 09:07:12 +0330 Subject: [FieldTrip] Equivalent parts in an image and a mesh Message-ID: Dear FieldTrip Experts, How you find the corresponding part of an image in a mesh? Looking forward to hearing from you. Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Sun Nov 12 12:58:42 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Sun, 12 Nov 2017 11:58:42 +0000 Subject: [FieldTrip] Equivalent parts in an image and a mesh In-Reply-To: References: Message-ID: Hi Angel Angel, I don’t understand the question. Can you please have a look at the following before trying again? http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002202 http://www.fieldtriptoolbox.org/faq/how_to_ask_good_questions_to_the_community?s[]=discussion&s[]=list Thanks very much, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 12 Nov 2017, at 06:37, angel angel > wrote: Dear FieldTrip Experts, How you find the corresponding part of an image in a mesh? Looking forward to hearing from you. Regards _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From springangel222 at gmail.com Mon Nov 13 17:57:37 2017 From: springangel222 at gmail.com (angel angel) Date: Mon, 13 Nov 2017 20:27:37 +0330 Subject: [FieldTrip] Equivalent parts in an image and a mesh In-Reply-To: References: Message-ID: Hi Dear All, I apologize for my unclear question. I want to figure out where does each voxel of an image stand in a mesh after the mesh generation pipeline? I mean on which face and between which vertices? I hope I asked the correct form of a question this time. Thanks for your attention. On Sun, Nov 12, 2017 at 3:28 PM, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Hi Angel Angel, > > I don’t understand the question. Can you please have a look at the > following before trying again? > > > http://journals.plos.org/ploscompbiol/article?id=10. > 1371/journal.pcbi.1002202 > > http://www.fieldtriptoolbox.org/faq/how_to_ask_good_ > questions_to_the_community?s[]=discussion&s[]=list > > Thanks very much, > > Jan-Mathijs > > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > On 12 Nov 2017, at 06:37, angel angel wrote: > > Dear FieldTrip Experts, > How you find the corresponding part of an image in a mesh? > Looking forward to hearing from you. > Regards > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From otobias at web.de Tue Nov 14 03:58:37 2017 From: otobias at web.de (Tobias Overath) Date: Mon, 13 Nov 2017 21:58:37 -0500 Subject: [FieldTrip] Phd position in the O-Lab at Duke University Message-ID: <05DB48BD-5388-4DAA-8AB1-99467DDC9B76@web.de> Dear all, We are looking for a highly motivated young scientist to join the O-Lab, led by Prof. Tobias Overath, in the Department of Psychology and Neuroscience at Duke University. Work in our lab investigates how sounds, from simple sinusoids to complex speech signals, are processed in the brain, using a combination of behavioral and neuroimaging methods (fMRI, EEG, ECoG) to track the underlying neural processes. Current projects investigate the transformation from acoustic to linguistic analysis of temporal speech structure, online measures of statistical learning, as well as optimization of cochlear implant coding strategies. Interested candidates should have received an undergraduate degree in psychology, neuroscience, biomedical engineering, or a related field by Summer 2018. Familiarity with signal processing, fMRI, M/EEG, or related experimental techniques is a plus, as is advanced knowledge of at least one programing language (preferably Matlab). Admission is possible via the Psychology and Neuroscience Graduate Program (https://psychandneuro.duke.edu/graduate ), or via the Cognitive Neuroscience Admitting Program (CNAP, https://dibs.duke.edu/centers/ccn/graduate-cnap ). The application deadline is December 1, 2017! Duke University provides a vibrant, highly connected scientific environment, with many associated departments and interdisciplinary initiatives (e.g. Departments of Neurobiology, Biomedical Engineering, Electrical and Computer Engineering; the Center for Cognitive Neuroscience, the Duke Institute for Brain Sciences, or the Brain Imaging and Analysis Center). Please contact Tobias Overath (t.overath at duke.edu ) for further information. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Nov 14 15:45:17 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 14 Nov 2017 14:45:17 +0000 Subject: [FieldTrip] Equivalent parts in an image and a mesh In-Reply-To: References: Message-ID: Why do you want this? JM J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 13 Nov 2017, at 17:57, angel angel > wrote: Hi Dear All, I apologize for my unclear question. I want to figure out where does each voxel of an image stand in a mesh after the mesh generation pipeline? I mean on which face and between which vertices? I hope I asked the correct form of a question this time. Thanks for your attention. On Sun, Nov 12, 2017 at 3:28 PM, Schoffelen, J.M. (Jan Mathijs) > wrote: Hi Angel Angel, I don’t understand the question. Can you please have a look at the following before trying again? http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002202 http://www.fieldtriptoolbox.org/faq/how_to_ask_good_questions_to_the_community?s[]=discussion&s[]=list Thanks very much, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 12 Nov 2017, at 06:37, angel angel > wrote: Dear FieldTrip Experts, How you find the corresponding part of an image in a mesh? Looking forward to hearing from you. Regards _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From springangel222 at gmail.com Wed Nov 15 09:33:56 2017 From: springangel222 at gmail.com (angel angel) Date: Wed, 15 Nov 2017 12:03:56 +0330 Subject: [FieldTrip] Equivalent parts in an image and a mesh In-Reply-To: References: Message-ID: I want to make a source model based on "regular 3D grid, based on segmented MRI, restricted to gray matter". Thanks in advance. On Tue, Nov 14, 2017 at 6:15 PM, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Why do you want this? > > JM > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > On 13 Nov 2017, at 17:57, angel angel wrote: > > Hi Dear All, > I apologize for my unclear question. I want to figure out where does each > voxel of an image stand in a mesh after the mesh generation pipeline? I > mean on which face and between which vertices? I hope I asked the correct > form of a question this time. > Thanks for your attention. > > On Sun, Nov 12, 2017 at 3:28 PM, Schoffelen, J.M. (Jan Mathijs) < > jan.schoffelen at donders.ru.nl> wrote: > >> Hi Angel Angel, >> >> I don’t understand the question. Can you please have a look at the >> following before trying again? >> >> >> http://journals.plos.org/ploscompbiol/article?id=10.1371/ >> journal.pcbi.1002202 >> >> http://www.fieldtriptoolbox.org/faq/how_to_ask_good_question >> s_to_the_community?s[]=discussion&s[]=list >> >> Thanks very much, >> >> Jan-Mathijs >> >> >> J.M.Schoffelen, MD PhD >> Senior Researcher, VIDI-fellow - PI, language in interaction >> Telephone: +31-24-3614793 >> Physical location: room 00.028 >> Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands >> >> On 12 Nov 2017, at 06:37, angel angel wrote: >> >> Dear FieldTrip Experts, >> How you find the corresponding part of an image in a mesh? >> Looking forward to hearing from you. >> Regards >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Nov 15 12:55:09 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 15 Nov 2017 11:55:09 +0000 Subject: [FieldTrip] Equivalent parts in an image and a mesh In-Reply-To: References: Message-ID: <7974CAAA-435E-46FC-8585-D60B49377B16@donders.ru.nl> Dear anonymous, If you want "a regular 3D grid, based on a segmented MRI, restricted to grey matter”, why do you need the cortical surface reconstruction? Best wishes, JAN-MATHIJS On 15 Nov 2017, at 09:33, angel angel > wrote: I want to make a source model based on "regular 3D grid, based on segmented MRI, restricted to gray matter". Thanks in advance. On Tue, Nov 14, 2017 at 6:15 PM, Schoffelen, J.M. (Jan Mathijs) > wrote: Why do you want this? JM J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 13 Nov 2017, at 17:57, angel angel > wrote: Hi Dear All, I apologize for my unclear question. I want to figure out where does each voxel of an image stand in a mesh after the mesh generation pipeline? I mean on which face and between which vertices? I hope I asked the correct form of a question this time. Thanks for your attention. On Sun, Nov 12, 2017 at 3:28 PM, Schoffelen, J.M. (Jan Mathijs) > wrote: Hi Angel Angel, I don’t understand the question. Can you please have a look at the following before trying again? http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002202 http://www.fieldtriptoolbox.org/faq/how_to_ask_good_questions_to_the_community?s[]=discussion&s[]=list Thanks very much, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 12 Nov 2017, at 06:37, angel angel > wrote: Dear FieldTrip Experts, How you find the corresponding part of an image in a mesh? Looking forward to hearing from you. Regards _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Nov 16 12:36:25 2017 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 16 Nov 2017 12:36:25 +0100 Subject: [FieldTrip] dimord single-trial source data Message-ID: Hi FieldTrippers, I was wondering is there is a recommend/most consistent way to represent trial x pos x time data from an LCMV beamformer, also considering the dimord. In other words: with: data.method = 'singletrial' should I use: data.trial{pos} = [rpt x time] data.dimord = '{pos}_rpt_time' or rather: data.trial = {pos x rpt x time} data.dimord = 'pos_rpt_time' or something else? The purpose is to then do a frequency analysis (with keeptrials = 'yes'). Best, Stephen -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Nov 16 14:31:53 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 16 Nov 2017 13:31:53 +0000 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: References: Message-ID: <59225E01-B07C-426B-96A4-9A669C82276C@donders.ru.nl> Hi Stephen, I think that it is currently not possible to pass the output of ft_sourceanalysis to ft_freqanalysis directly, since ft_freqanalysis expects channel-level type data in the input. The exact details of the computation depend a bit on the amount of RAM you have, and on what exactly you want to achieve. If it’s your intention to generate frequency spectra for many dipole locations (e.g. >1000 or so) I would consider the following: - compute spatial filters (cfg.keepfilter = ‘yes’); - use a for-loop across (chunks of) dipole locations to create ‘virtual channel data’, by premultiplying the sensor-level data.trial (loop across trials) with the location specific spatial filter. - stuff all this into a data-structure that looks like a raw data structure; - pass this to ft_freqanalysis Alternatively, you could consider using a parcellation approach, if you think it makes sense to reduce the number of spatial locations a bit, although theoretically it should be possible to create a parcellation that consists of just a single dipole per parcel. In this context, you could look into the inner workings of ft_sourceparcellate, which returns a data structure that ft_freqanalysis can work with. Whether ft_sourceparcellate can swallow single trial source data, I am not sure. Best wishes, JM > On 16 Nov 2017, at 12:36, Stephen Whitmarsh wrote: > > Hi FieldTrippers, > > I was wondering is there is a recommend/most consistent way to represent trial x pos x time data from an LCMV beamformer, also considering the dimord. In other words: > > with: > > data.method = 'singletrial' > > should I use: > > data.trial{pos} = [rpt x time] > data.dimord = '{pos}_rpt_time' > > or rather: > > data.trial = {pos x rpt x time} > data.dimord = 'pos_rpt_time' > > or something else? The purpose is to then do a frequency analysis (with keeptrials = 'yes'). > > Best, > Stephen > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Thu Nov 16 14:38:06 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 16 Nov 2017 13:38:06 +0000 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: References: Message-ID: Hi again Stephen, I forgot to mention a third approach: you can compute your spatial filter with cfg.method = ‘lcmv’ and cfg.lcmv.keepfilter = ‘yes’, and subsequently compute the source level spectra by applying these spatial filters to the sensor level fourier spectra. Best wishes, Jan-Mathijs > On 16 Nov 2017, at 12:36, Stephen Whitmarsh wrote: > > Hi FieldTrippers, > > I was wondering is there is a recommend/most consistent way to represent trial x pos x time data from an LCMV beamformer, also considering the dimord. In other words: > > with: > > data.method = 'singletrial' > > should I use: > > data.trial{pos} = [rpt x time] > data.dimord = '{pos}_rpt_time' > > or rather: > > data.trial = {pos x rpt x time} > data.dimord = 'pos_rpt_time' > > or something else? The purpose is to then do a frequency analysis (with keeptrials = 'yes'). > > Best, > Stephen > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From stephen.whitmarsh at gmail.com Thu Nov 16 14:40:41 2017 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 16 Nov 2017 14:40:41 +0100 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: <59225E01-B07C-426B-96A4-9A669C82276C@donders.ru.nl> References: <59225E01-B07C-426B-96A4-9A669C82276C@donders.ru.nl> Message-ID: Hi Jan-Mathijs, Thanks. In fact, I did what you suggest, but this entails a lot (nr. of positions) or creating and clearing a temporary variable. For a reason I do not understand (but which I encountered before), MATLAB seems not able to deal with this, and runs into memory problems. I suspect it is not able to create and clear many variables in a row, so that althought memory load does not seem to increase, it *will *break with an out-of-memory problem. I therefor started with this approach, but alas, I now understand that it was a wrong turn. So, I am in a pickle now, as neither option works... Best, Stephen On 16 November 2017 at 14:31, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Hi Stephen, > > I think that it is currently not possible to pass the output of > ft_sourceanalysis to ft_freqanalysis directly, since ft_freqanalysis > expects channel-level type data in the input. > The exact details of the computation depend a bit on the amount of RAM you > have, and on what exactly you want to achieve. > > If it’s your intention to generate frequency spectra for many dipole > locations (e.g. >1000 or so) I would consider the following: > > - compute spatial filters (cfg.keepfilter = ‘yes’); > - use a for-loop across (chunks of) dipole locations to create ‘virtual > channel data’, by premultiplying the sensor-level data.trial (loop across > trials) with the location specific spatial filter. > - stuff all this into a data-structure that looks like a raw data > structure; > - pass this to ft_freqanalysis > > > Alternatively, you could consider using a parcellation approach, if you > think it makes sense to reduce the number of spatial locations a bit, > although theoretically it should be possible to create a parcellation that > consists of just a single dipole per parcel. In this context, you could > look into the inner workings of ft_sourceparcellate, which returns a data > structure that ft_freqanalysis can work with. Whether ft_sourceparcellate > can swallow single trial source data, I am not sure. > > Best wishes, > > JM > > > > > On 16 Nov 2017, at 12:36, Stephen Whitmarsh > wrote: > > > > Hi FieldTrippers, > > > > I was wondering is there is a recommend/most consistent way to represent > trial x pos x time data from an LCMV beamformer, also considering the > dimord. In other words: > > > > with: > > > > data.method = 'singletrial' > > > > should I use: > > > > data.trial{pos} = [rpt x time] > > data.dimord = '{pos}_rpt_time' > > > > or rather: > > > > data.trial = {pos x rpt x time} > > data.dimord = 'pos_rpt_time' > > > > or something else? The purpose is to then do a frequency analysis (with > keeptrials = 'yes'). > > > > Best, > > Stephen > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Nov 16 14:44:36 2017 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 16 Nov 2017 14:44:36 +0100 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: References: <59225E01-B07C-426B-96A4-9A669C82276C@donders.ru.nl> Message-ID: For completeness, this is what I did in the way you suggest (I think). Note data is downsampled to 100Hz, and every trial is 1 second long. So I do not think that RAM should be a concern (I have about 128 Gig to work with): % load common filter [source_common, leadfield] = WANDER_common_filter_LCMV_MAG(isubject,rootpath,0); % prepare source datastructure source = rmfield(source_common,'avg'); source.pow = nan(size(source.pos,1),size(data_MEG_timebinned_append.trial,2),2); source.trialinfo = data_MEG_timebinned_append.trialinfo; for ivoxel = find(source.inside)' disp(['progress: ' round(num2str(ivoxel/size(find(source.inside),1)*100)) '%']); % make timecourse datastructure, clear first so that MATLAB does source_timecourse.trial{size(data_MEG_timebinned_append.trial,2)} = []; source_timecourse.label = {'voxel'}; source_timecourse.fsample = 100; source_timecourse.time = data_MEG_timebinned_append.time; for itrial = 1:size(data_MEG_timebinned_append.trial,2) source_timecourse.trial{itrial} = svdfft(source_common.avg.filter{ivoxel} * data_MEG_timebinned_append.trial{itrial}, 1); end % do mtmconvol on faux data structure cfg = []; cfg.channel = 'all'; cfg.method = 'mtmfft'; cfg.keeptrials = 'yes'; cfg.foilim = [10,11]; cfg.taper = 'hanning'; FFT = ft_freqanalysis(cfg, source_timecourse); clear source_timecourse source.pow(ivoxel,:,:) = squeeze(FFT.powspctrm); clear FFT memory end On 16 November 2017 at 14:40, Stephen Whitmarsh wrote: > Hi Jan-Mathijs, > > Thanks. In fact, I did what you suggest, but this entails a lot (nr. of > positions) or creating and clearing a temporary variable. For a reason I do > not understand (but which I encountered before), MATLAB seems not able to > deal with this, and runs into memory problems. I suspect it is not able to > create and clear many variables in a row, so that althought memory load > does not seem to increase, it *will *break with an out-of-memory problem. > I therefor started with this approach, but alas, I now understand that it > was a wrong turn. > > So, I am in a pickle now, as neither option works... > > Best, > Stephen > > On 16 November 2017 at 14:31, Schoffelen, J.M. (Jan Mathijs) < > jan.schoffelen at donders.ru.nl> wrote: > >> Hi Stephen, >> >> I think that it is currently not possible to pass the output of >> ft_sourceanalysis to ft_freqanalysis directly, since ft_freqanalysis >> expects channel-level type data in the input. >> The exact details of the computation depend a bit on the amount of RAM >> you have, and on what exactly you want to achieve. >> >> If it’s your intention to generate frequency spectra for many dipole >> locations (e.g. >1000 or so) I would consider the following: >> >> - compute spatial filters (cfg.keepfilter = ‘yes’); >> - use a for-loop across (chunks of) dipole locations to create ‘virtual >> channel data’, by premultiplying the sensor-level data.trial (loop across >> trials) with the location specific spatial filter. >> - stuff all this into a data-structure that looks like a raw data >> structure; >> - pass this to ft_freqanalysis >> >> >> Alternatively, you could consider using a parcellation approach, if you >> think it makes sense to reduce the number of spatial locations a bit, >> although theoretically it should be possible to create a parcellation that >> consists of just a single dipole per parcel. In this context, you could >> look into the inner workings of ft_sourceparcellate, which returns a data >> structure that ft_freqanalysis can work with. Whether ft_sourceparcellate >> can swallow single trial source data, I am not sure. >> >> Best wishes, >> >> JM >> >> >> >> > On 16 Nov 2017, at 12:36, Stephen Whitmarsh < >> stephen.whitmarsh at gmail.com> wrote: >> > >> > Hi FieldTrippers, >> > >> > I was wondering is there is a recommend/most consistent way to >> represent trial x pos x time data from an LCMV beamformer, also considering >> the dimord. In other words: >> > >> > with: >> > >> > data.method = 'singletrial' >> > >> > should I use: >> > >> > data.trial{pos} = [rpt x time] >> > data.dimord = '{pos}_rpt_time' >> > >> > or rather: >> > >> > data.trial = {pos x rpt x time} >> > data.dimord = 'pos_rpt_time' >> > >> > or something else? The purpose is to then do a frequency analysis (with >> keeptrials = 'yes'). >> > >> > Best, >> > Stephen >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Nov 16 15:43:21 2017 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 16 Nov 2017 15:43:21 +0100 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: References: Message-ID: Hi again again Jan-Mathijs, Ah yes, that does seem like the most elegant and memory-efficient approach! I will need to figure out how to apply spatial filters to Fourier (and redo my sensor level spectral analysis to Fourier). Shout-out to the list: anyone have an example of applying spatial filters to Fourier that I could use? Thanks again again, Stephen On 16 November 2017 at 14:38, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Hi again Stephen, > > I forgot to mention a third approach: you can compute your spatial filter > with cfg.method = ‘lcmv’ and cfg.lcmv.keepfilter = ‘yes’, and subsequently > compute the source level spectra by applying these spatial filters to the > sensor level fourier spectra. > > Best wishes, > Jan-Mathijs > > > > > > On 16 Nov 2017, at 12:36, Stephen Whitmarsh > wrote: > > > > Hi FieldTrippers, > > > > I was wondering is there is a recommend/most consistent way to represent > trial x pos x time data from an LCMV beamformer, also considering the > dimord. In other words: > > > > with: > > > > data.method = 'singletrial' > > > > should I use: > > > > data.trial{pos} = [rpt x time] > > data.dimord = '{pos}_rpt_time' > > > > or rather: > > > > data.trial = {pos x rpt x time} > > data.dimord = 'pos_rpt_time' > > > > or something else? The purpose is to then do a frequency analysis (with > keeptrials = 'yes'). > > > > Best, > > Stephen > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Nov 16 15:52:06 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 16 Nov 2017 14:52:06 +0000 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: References: Message-ID: <527ADD8B-D856-4355-9544-5AE785C5A9AD@donders.ru.nl> Hi Stephen, siz = size(freq.fourierspctrm); F = freq.fourierspctrm; F = permute(freq.fourierspctrm,[2 1 3]); F = reshape(F,siz(2),siz(1)*siz(3)); sourceF = svdfft(source.avg.filter{some_index}*F); % by the way, your use in the time domain per trial is dangerous, because it does a trial specific rotation, which you may or may not want sourceF = reshape(sourceF, siz(1), siz(3)); sourceP = abs(sourceF).^2; Of zoiets. Cheers, JM On 16 Nov 2017, at 15:43, Stephen Whitmarsh > wrote: Hi again again Jan-Mathijs, Ah yes, that does seem like the most elegant and memory-efficient approach! I will need to figure out how to apply spatial filters to Fourier (and redo my sensor level spectral analysis to Fourier). Shout-out to the list: anyone have an example of applying spatial filters to Fourier that I could use? Thanks again again, Stephen On 16 November 2017 at 14:38, Schoffelen, J.M. (Jan Mathijs) > wrote: Hi again Stephen, I forgot to mention a third approach: you can compute your spatial filter with cfg.method = ‘lcmv’ and cfg.lcmv.keepfilter = ‘yes’, and subsequently compute the source level spectra by applying these spatial filters to the sensor level fourier spectra. Best wishes, Jan-Mathijs > On 16 Nov 2017, at 12:36, Stephen Whitmarsh > wrote: > > Hi FieldTrippers, > > I was wondering is there is a recommend/most consistent way to represent trial x pos x time data from an LCMV beamformer, also considering the dimord. In other words: > > with: > > data.method = 'singletrial' > > should I use: > > data.trial{pos} = [rpt x time] > data.dimord = '{pos}_rpt_time' > > or rather: > > data.trial = {pos x rpt x time} > data.dimord = 'pos_rpt_time' > > or something else? The purpose is to then do a frequency analysis (with keeptrials = 'yes'). > > Best, > Stephen > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Nov 16 16:36:11 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 16 Nov 2017 15:36:11 +0000 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: References: Message-ID: Hi again Stephen, Just out of curiosity: why do you use a time-domain beamformer if you are interested in reconstructing a narrowband response? Best wishes, Jan-Mathijs On 16 Nov 2017, at 15:43, Stephen Whitmarsh > wrote: Hi again again Jan-Mathijs, Ah yes, that does seem like the most elegant and memory-efficient approach! I will need to figure out how to apply spatial filters to Fourier (and redo my sensor level spectral analysis to Fourier). Shout-out to the list: anyone have an example of applying spatial filters to Fourier that I could use? Thanks again again, Stephen On 16 November 2017 at 14:38, Schoffelen, J.M. (Jan Mathijs) > wrote: Hi again Stephen, I forgot to mention a third approach: you can compute your spatial filter with cfg.method = ‘lcmv’ and cfg.lcmv.keepfilter = ‘yes’, and subsequently compute the source level spectra by applying these spatial filters to the sensor level fourier spectra. Best wishes, Jan-Mathijs > On 16 Nov 2017, at 12:36, Stephen Whitmarsh > wrote: > > Hi FieldTrippers, > > I was wondering is there is a recommend/most consistent way to represent trial x pos x time data from an LCMV beamformer, also considering the dimord. In other words: > > with: > > data.method = 'singletrial' > > should I use: > > data.trial{pos} = [rpt x time] > data.dimord = '{pos}_rpt_time' > > or rather: > > data.trial = {pos x rpt x time} > data.dimord = 'pos_rpt_time' > > or something else? The purpose is to then do a frequency analysis (with keeptrials = 'yes'). > > Best, > Stephen > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Nov 16 17:42:41 2017 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 16 Nov 2017 17:42:41 +0100 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: References: Message-ID: Hi Mathijs, I know. Long story. Let's just say it's a check :-) I've done the same with DICS already. Cheers, Stephen On 16 November 2017 at 16:36, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Hi again Stephen, > > Just out of curiosity: why do you use a time-domain beamformer if you are > interested in reconstructing a narrowband response? > > Best wishes, > Jan-Mathijs > > On 16 Nov 2017, at 15:43, Stephen Whitmarsh > wrote: > > Hi again again Jan-Mathijs, > > Ah yes, that does seem like the most elegant and memory-efficient > approach! > I will need to figure out how to apply spatial filters to Fourier (and > redo my sensor level spectral analysis to Fourier). > > Shout-out to the list: anyone have an example of applying spatial filters > to Fourier that I could use? > > Thanks again again, > Stephen > > On 16 November 2017 at 14:38, Schoffelen, J.M. (Jan Mathijs) < > jan.schoffelen at donders.ru.nl> wrote: > >> Hi again Stephen, >> >> I forgot to mention a third approach: you can compute your spatial filter >> with cfg.method = ‘lcmv’ and cfg.lcmv.keepfilter = ‘yes’, and subsequently >> compute the source level spectra by applying these spatial filters to the >> sensor level fourier spectra. >> >> Best wishes, >> Jan-Mathijs >> >> >> >> >> > On 16 Nov 2017, at 12:36, Stephen Whitmarsh < >> stephen.whitmarsh at gmail.com> wrote: >> > >> > Hi FieldTrippers, >> > >> > I was wondering is there is a recommend/most consistent way to >> represent trial x pos x time data from an LCMV beamformer, also considering >> the dimord. In other words: >> > >> > with: >> > >> > data.method = 'singletrial' >> > >> > should I use: >> > >> > data.trial{pos} = [rpt x time] >> > data.dimord = '{pos}_rpt_time' >> > >> > or rather: >> > >> > data.trial = {pos x rpt x time} >> > data.dimord = 'pos_rpt_time' >> > >> > or something else? The purpose is to then do a frequency analysis (with >> keeptrials = 'yes'). >> > >> > Best, >> > Stephen >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mireia.torralba at upf.edu Wed Nov 22 10:41:51 2017 From: mireia.torralba at upf.edu (TORRALBA CUELLO, MIREIA) Date: Wed, 22 Nov 2017 10:41:51 +0100 Subject: [FieldTrip] Phd position in Cognitive Neuroscience in UPF (Barcelona) Message-ID: Please find attached information about a PhD position in Cognitive Neuroscience at Multisensory Research Group (UPF, Barcelona) Deadline: Feb 1st, 2018 Start date: May/June 2018 Gross salary: Approx 27.800€/year Research money (travel etc...): 3.500€/year Requirements*: Master's degree in the EU or equivalent (to be decided by the host university at application), and have not worked/resided in Spain for more than 12 months (within the last 3y). *Phd position in Cognitive Neuroscience: Neural predictors of Memory Perception and attention (Prof.Salvador Soto-Faraco)* *POSITION DESCRIPTION* *-Research Project / Research Group Description:* How “...the brain enables the mind...” is one of the core questions in neuroscience. Understanding this relationship will lead to improvements in the mitigation of brain disease. One of the major sources of evidence on how neurophysiological activity relates to mental phenomena comes from the realization that fluctuations in neural activity could be at the heart of cognitive processes. In fact, it is well known that ongoing brain activity itself is highly organized, so that neural communication (local, and long range) seems to capitalize on the fine temporal structure of neural activity. Consequently responses to sensory events depend strongly on the momentary state of the system. The overarching goal of the research project hosting the potential PhD candidate is to capitalize on the relationship between brain oscillations, brain states and cognitive processes to anticipate and be able to modulate the outcome of these processes via real-time neurodevices based on Brain Computer Interfaces. The research lines hosting the PhD candidate address the link between the pattern of oscillatory brain activity and three sets of concrete cognitive processes. (1) Memory encoding in healthy humans and/or patients with Mild Cognitive Impairment. (2) Attention and perception in real-life scenarios. And, (3) perceptual conflict and awareness. The overarching goal is to be able to find predictors (biomarkers) for these processes and be able to anticipate optimal brain states (windows of opportunity) for the success of these behaviours. To this end, we use psychophysics, human electroencephalography (EEG), and Transcranial Magnetic Stimulation (TMS). Psychophysics is essential to measure the behavioural expression of cognitive processes. EEG is sensitive to post-synaptic potentials of large neuron populations, and is an indirect index of neural activity. In order to infer brain states, we capitalize on a variety of measures from the EEG: spectral power, instantaneous phase, and temporal/spatial coherence of oscillatory activity. Neurostimulation (TMS) is used to probe causality. The MRG is part of the CBC master, has 3 postdoc researchers (specialized in signal processing, bioengineering, and neuropsychology) 3 Phds, and support staff. Our research is supported by EU and local funding. *-Job position description:* Role: The successful candidate will lead a research line which falls amongst the overall projects of the MRG laboratory (described above). It is expected that the candidate will have a prior motivation for cognitive neuroscience and will contribute in an active way to define the particular project from its inception, formulation of hypotheses, experimental designs, measurement and analysis, and interpretation of the data. In order to accomplish these tasks, the PhD candidate will of course count with the support of the MRG staff and knowledge base, and the guidance of Prof Soto-Faraco as well as senior members of the laboratory. Dissemination of the research output, and networking with other local, or external experts as well as advanced post-docs and phd students will be encouraged and fostered. Responsibilities: The candidate will be mainly responsible for the implementation of the assigned research tasks conducive toward the PhD project, the careful and systematic carrying out of the experimental work. Other responsibilities will be assigned commensurate with the PhD’s capacity and level of seniority. Amongst them, like other members of the team, the PhD student will contribute to the group activities (e.g., helping organize talks, group meetings, presenting the findings in conferences) , and to the training and support of other junior members of the laboratory (eventual supervision of master or degree students). Finally, the Phd candidate will also be responsible to provide timely responses to requests from the funding body, including progress reports, as well as to attend the meetings s/he might be called to, from the funding agency. Skills: Background in Biology, Bioengineering, Experimental Psychology or other fields related to Cognitive Neuroscience. Prior experience or background in Brain Computer Interfaces. Concrete experience with experimental work in the field of the cognitive neurosciences, preferably with psychophysics and/or electrophysiology (EEG, MEG). Knowledge of signal processing. Others: High motivation, proactivity and team work are very desirable. *RELATED LINK TO THE POSITION* http://www.mrg.upf.edu/node/112 *CENTER* Dept. of Information & Communication Technologies, DTIC-UPF https://portal.upf.edu/es/web/etic/inicio *CENTER DESCRIPTION* The Department of Information and Communication Technologies (DTIC) of Universitat Pompeu Fabra covers a broad range of research topics: Computation and Intelligent Systems; Multimedia Technologies; Networks and Communications; Computational Biology and Biomedical Systems; and the Center of Brain and Cognition (CBC). This broad spectrum of topics reflects the current interdisciplinary reality of cutting edge research in ICT. The DTIC is now running a Maria de Maeztu Strategic Research Program on data-driven knowledge extraction, boosting synergistic research initiatives across our different research areas. The DTIC consistently ranks among the top computer science departments in Spain (e.g. the only computer science department from an Spanish university that has even been included in the top 100 of the Shanghai Ranking). Its PhD program offers advanced training in this interdisciplinary field, becoming an innovative and unique program in Spain. The DTIC PhD program has been growing steadily and currently hosts about 140 PhD students and 40 supervisors. The program received a Mention of Excellence award from the Ministry of Science and Innovation in 2011. The UPF university was awarded in 2010 the distinction of International Excellence Campus by the Spanish Ministry of Education and it is widely considered to be one of the best universities in Spain (e.g. is the top Spanish university according to 2013 Times Higher Education Ranking). The UPF is located in Barcelona. Its excellent location on the shores of the Mediterranean, its gentle climate, its open, cosmopolitan character, its gastronomy and architecture make Barcelona an extraordinary place to live. The DTIC is sited in UPF's Communication Campus, which was opened in 2009 and is located within the vibrant 22@ technological district of Barcelona. *Indicators: * - Research incomes: 15.6 M€ / year - 67 FP7 projects participated and coordinated by 26 staff members (> 60% UPF EU funds) including 13 prestigious ERC Grants, the Human Brain Project - Leader in Spain with > 5% of all the competitive funds obtained by Spanish Universities, Maria de Maeztu Strategic Program. - Consolidated scientific productivity ~200 articles/year, > 75% Q1 international journals - 50% scientific papers and articles with at least one international collaborator *ADDRESS* Roc Boronat, 138 - edifici Tànger, 08018 Barcelona, Barcelona *GROUP DISCIPLINES* Life Science Panel *GROUP LEADER* Prof.Salvador Soto-Faraco salvador.soto at upf.edu www.mrg.upf.edu Mireia Torralba Cuello Multisensory Research Group Center for Brain and Cognition, Universitat Pompeu Fabra Address: Edifici Mercè Rodoreda 24.313 c\ Ramon Trias Fargas, 25-27 08005 Barcelona http://www.mrg.upf.edu Tel +34 935422745 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonas at obleser.de Wed Nov 22 19:00:13 2017 From: jonas at obleser.de (Jonas Obleser) Date: Wed, 22 Nov 2017 19:00:13 +0100 Subject: [FieldTrip] =?utf-8?q?Postdoc_opportunity=2C_modelling/EEG/MRI_Ob?= =?utf-8?q?leser_lab_in_L=C3=BCbeck?= Message-ID: Dear colleagues around the globe, On somewhat shot notice, we have another postdoc Position in my lab available. Funded through the ERC Project «AUDADAPT», starting asap. Deadline for electronic, simple applications per email is Nov 30. Thanks for spreading the word! Best wishes, Jonas https://www.uni-luebeck.de/fileadmin/uzl_personal/stellenausschreibungen/1060_17_Ausschreibung_Obleser_Postdoc2018_ERC_EN.pdf Jonas Obleser Professor University of Lübeck Department of Psychology MFC 8, Maria-Goeppert-Straße 9a 23562 Lübeck, Germany Phone +49 (0)451 3101 3620 Mobile +49 (0)171 6993337 jonas.obleser at uni-luebeck.de http://auditorycognition.com From liyy90 at 163.com Thu Nov 23 15:44:10 2017 From: liyy90 at 163.com (liyy90) Date: Thu, 23 Nov 2017 22:44:10 +0800 (CST) Subject: [FieldTrip] Phd position in Cognitive Neuroscience in UPF (Barcelona) In-Reply-To: References: Message-ID: I am interested in this program. How to apply? At 2017-11-22 17:41:51, "TORRALBA CUELLO, MIREIA" wrote: Please find attached information about a PhD position in Cognitive Neuroscience at Multisensory Research Group (UPF, Barcelona) Deadline: Feb 1st, 2018 Start date: May/June 2018 Gross salary: Approx 27.800€/year Research money (travel etc...): 3.500€/year Requirements*: Master's degree in the EU or equivalent (to be decided by the host university at application), and have not worked/resided in Spain for more than 12 months (within the last 3y). Phd position in Cognitive Neuroscience: Neural predictors of Memory Perception and attention (Prof.Salvador Soto-Faraco) POSITION DESCRIPTION -Research Project / Research Group Description: How “...the brain enables the mind...” is one of the core questions in neuroscience. Understanding this relationship will lead to improvements in the mitigation of brain disease. One of the major sources of evidence on how neurophysiological activity relates to mental phenomena comes from the realization that fluctuations in neural activity could be at the heart of cognitive processes. In fact, it is well known that ongoing brain activity itself is highly organized, so that neural communication (local, and long range) seems to capitalize on the fine temporal structure of neural activity. Consequently responses to sensory events depend strongly on the momentary state of the system. The overarching goal of the research project hosting the potential PhD candidate is to capitalize on the relationship between brain oscillations, brain states and cognitive processes to anticipate and be able to modulate the outcome of these processes via real-time neurodevices based on Brain Computer Interfaces. The research lines hosting the PhD candidate address the link between the pattern of oscillatory brain activity and three sets of concrete cognitive processes. (1) Memory encoding in healthy humans and/or patients with Mild Cognitive Impairment. (2) Attention and perception in real-life scenarios. And, (3) perceptual conflict and awareness. The overarching goal is to be able to find predictors (biomarkers) for these processes and be able to anticipate optimal brain states (windows of opportunity) for the success of these behaviours. To this end, we use psychophysics, human electroencephalography (EEG), and Transcranial Magnetic Stimulation (TMS). Psychophysics is essential to measure the behavioural expression of cognitive processes. EEG is sensitive to post-synaptic potentials of large neuron populations, and is an indirect index of neural activity. In order to infer brain states, we capitalize on a variety of measures from the EEG: spectral power, instantaneous phase, and temporal/spatial coherence of oscillatory activity. Neurostimulation (TMS) is used to probe causality. The MRG is part of the CBC master, has 3 postdoc researchers (specialized in signal processing, bioengineering, and neuropsychology) 3 Phds, and support staff. Our research is supported by EU and local funding. -Job position description: Role: The successful candidate will lead a research line which falls amongst the overall projects of the MRG laboratory (described above). It is expected that the candidate will have a prior motivation for cognitive neuroscience and will contribute in an active way to define the particular project from its inception, formulation of hypotheses, experimental designs, measurement and analysis, and interpretation of the data. In order to accomplish these tasks, the PhD candidate will of course count with the support of the MRG staff and knowledge base, and the guidance of Prof Soto-Faraco as well as senior members of the laboratory. Dissemination of the research output, and networking with other local, or external experts as well as advanced post-docs and phd students will be encouraged and fostered. Responsibilities: The candidate will be mainly responsible for the implementation of the assigned research tasks conducive toward the PhD project, the careful and systematic carrying out of the experimental work. Other responsibilities will be assigned commensurate with the PhD’s capacity and level of seniority. Amongst them, like other members of the team, the PhD student will contribute to the group activities (e.g., helping organize talks, group meetings, presenting the findings in conferences) , and to the training and support of other junior members of the laboratory (eventual supervision of master or degree students). Finally, the Phd candidate will also be responsible to provide timely responses to requests from the funding body, including progress reports, as well as to attend the meetings s/he might be called to, from the funding agency. Skills: Background in Biology, Bioengineering, Experimental Psychology or other fields related to Cognitive Neuroscience. Prior experience or background in Brain Computer Interfaces. Concrete experience with experimental work in the field of the cognitive neurosciences, preferably with psychophysics and/or electrophysiology (EEG, MEG). Knowledge of signal processing. Others: High motivation, proactivity and team work are very desirable. RELATED LINK TO THE POSITION http://www.mrg.upf.edu/node/112 CENTER Dept. of Information & Communication Technologies, DTIC-UPF https://portal.upf.edu/es/web/etic/inicio CENTER DESCRIPTION The Department of Information and Communication Technologies (DTIC) of Universitat Pompeu Fabra covers a broad range of research topics: Computation and Intelligent Systems; Multimedia Technologies; Networks and Communications; Computational Biology and Biomedical Systems; and the Center of Brain and Cognition (CBC). This broad spectrum of topics reflects the current interdisciplinary reality of cutting edge research in ICT. The DTIC is now running a Maria de Maeztu Strategic Research Program on data-driven knowledge extraction, boosting synergistic research initiatives across our different research areas. The DTIC consistently ranks among the top computer science departments in Spain (e.g. the only computer science department from an Spanish university that has even been included in the top 100 of the Shanghai Ranking). Its PhD program offers advanced training in this interdisciplinary field, becoming an innovative and unique program in Spain. The DTIC PhD program has been growing steadily and currently hosts about 140 PhD students and 40 supervisors. The program received a Mention of Excellence award from the Ministry of Science and Innovation in 2011. The UPF university was awarded in 2010 the distinction of International Excellence Campus by the Spanish Ministry of Education and it is widely considered to be one of the best universities in Spain (e.g. is the top Spanish university according to 2013 Times Higher Education Ranking). The UPF is located in Barcelona. Its excellent location on the shores of the Mediterranean, its gentle climate, its open, cosmopolitan character, its gastronomy and architecture make Barcelona an extraordinary place to live. The DTIC is sited in UPF's Communication Campus, which was opened in 2009 and is located within the vibrant 22@ technological district of Barcelona. Indicators: Research incomes: 15.6 M€ / year 67 FP7 projects participated and coordinated by 26 staff members (> 60% UPF EU funds) including 13 prestigious ERC Grants, the Human Brain Project Leader in Spain with > 5% of all the competitive funds obtained by Spanish Universities, Maria de Maeztu Strategic Program. Consolidated scientific productivity ~200 articles/year, > 75% Q1 international journals 50% scientific papers and articles with at least one international collaborator ADDRESS Roc Boronat, 138 - edifici Tànger, 08018 Barcelona, Barcelona GROUP DISCIPLINES Life Science Panel GROUP LEADER Prof.Salvador Soto-Faraco salvador.soto at upf.edu www.mrg.upf.edu Mireia Torralba Cuello Multisensory Research Group Center for Brain and Cognition, Universitat Pompeu Fabra Address: Edifici Mercè Rodoreda 24.313 c\ Ramon Trias Fargas, 25-27 08005 Barcelona http://www.mrg.upf.edu Tel +34 935422745 -------------- next part -------------- An HTML attachment was scrubbed... URL: From changa5 at mcmaster.ca Thu Nov 23 21:44:19 2017 From: changa5 at mcmaster.ca (Andrew Chang) Date: Thu, 23 Nov 2017 15:44:19 -0500 Subject: [FieldTrip] Grad Student Positions in Auditory Neuroscience, Human Interaction & Music Message-ID: *Graduate Student Positions in Auditory Neuroscience, Human Interaction & Music* *McMaster University* Two graduate student positions are available to work with *Dr. Laurel Trainor* who directs both the Infant Auditory Lab ( https://trainorlab.mcmaster.ca) and the LIVELab (https://LIVELab.mcmaster.ca) at McMaster University. Projects include understanding human interaction in musical ensembles using behaviour, motion capture and EEG measures; studying brain oscillations involved in predictive timing and predictive coding; musical development in infants and children; and applications using non-verbal measures to understand auditory perception and communicative processes in special populations such adults with dementia or hearing loss and children with Developmental Coordination Disorder. The research group is multidisciplinary with ties to Engineering, Health Science and Music. In addition to infant and adult behavioural and EEG labs, students will have access to the internationally acclaimed LIVELab, a research-concert hall capable of simulating almost any acoustical environment and equipped with multiperson EEG, physiology, motion capture and more (https://LIVELab.mcmaster.ca). Applicants should have a Bachelor’s degree in Psychology, Neuroscience, Cognitive Science, Engineering, Computer Science or other affiliated disciplines. General information on the graduate program can be found here: https://science.mcmaster.ca/pnb/graduate-studies. Initial inquiries can be directed to Dr. Trainor at LJT at mcmaster.ca. Please include a CV and unofficial transcript with your inquiry. Papers from the lab can be accessed at https://trainorlab.mcmaster.ca/publications -- Andrew Chang, Ph.D. Candidate Vanier Canada Graduate Scholar http://changa5.wordpress.com/ Auditory Development Lab Department of Psychology, Neuroscience & Behaviour McMaster University -------------- next part -------------- An HTML attachment was scrubbed... URL: From clh at pku.edu.cn Fri Nov 24 00:57:47 2017 From: clh at pku.edu.cn (=?UTF-8?Q?=E9=99=88=E7=AB=8B=E7=BF=B0_=28Lihan_Chen=29?=) Date: Fri, 24 Nov 2017 07:57:47 +0800 (GMT+08:00) Subject: [FieldTrip] About a demo prog in fieldtrip- ERP analysis Message-ID: <1816d6b8.15bae.15feb50e32d.Coremail.clh@pku.edu.cn> Dear colleagues I am learning to use fieldtrip to analysis eyetracking data. And i found this demo very helpful. http://www.fieldtriptoolbox.org/example/use_simulated_erps_to_explore_cluster_statistics However, when i run this command: difference = ft_math(cfg, timelock1, timelock2); it generated the following and i can not go through the whole demo "Warning: timelock structure contains field with and without repetitions selecting these fields that have repetitions: trial removing these fields that do not have repetitions: avg, dof, var Warning: timelock structure contains field with and without repetitions selecting these fields that have repetitions: trial removing these fields that do not have repetitions: avg, dof, var Error using ft_notification (line 340) the requested parameter is not present in the data Error in ft_error (line 39) ft_notification(varargin{:}); Error in ft_math (line 151) ft_error('the requested parameter is not present in the data');" Would you please kindly find time to instruct how to make it run so that i can how a look how the final results look like? By the way, if i have 12 subjects, with two conditions ('congruent', 'incongruent'). Each condition has 1000 data points (1 second), so that how is the cfg.design i should make? Thank you very much in advance! Best, Lihan chen Peking Uiversity -------------- next part -------------- An HTML attachment was scrubbed... URL: From holmgren.jostein at gmail.com Tue Nov 28 21:29:07 2017 From: holmgren.jostein at gmail.com (Jostein Holmgren) Date: Tue, 28 Nov 2017 20:29:07 +0000 Subject: [FieldTrip] Trouble writing data from TMSi to FieldTrip buffer (Error message: "Cannot initiate device") Message-ID: <5066A2DB-146C-4BB2-8BAB-E9C19A0A6D63@gmail.com> Dear all, I am having trouble writing data from my TMSi Porti 7 system to the FieldTrip buffer. I have tried both the tmsidriver.exe and tmsi2ft.exe tools, but I’ve focused my efforts on the latter. I have the TMSi system connected to my PC via USB and have tested the connection by recording some data in Polybench without issue. When I attempt to run tmsi2ft nothing happens until I terminate the process, at which point the error message “Cannot initiate device” is displayed. The exact syntax I run in the cmd is tmsi2ft config.txt - where config.txt file contains the following (misc commented lines excluded) [select] 25=Blip25 samplerate=2048 For testing purposes I’ve only got a bipolar electrode connected to the TMSi system, which is the channel listed in the config file. For tmsidriver.exe I changed the sampling rate in parameter file to match my system to attempt to get it to work, but no success there either. I also have the buffer open when running tmsidriver.exe. The contents of preferences.txt is sampleRate(milliHz) BufSizeFactor savedata(0/1) 2048000 5 1 The TMSi Porti 7 system has a sampling rate of 2048Hz. The PC is running Windows 8.1 64-bit. I’m using fieldtrip-20171106. Any advice or suggestions is greatly appreciated. Best regards, Jostein Holmgren ---------------------- Jostein Holmgren DPhil Student (PRS) Nuffield Department of Clinical Neurosciences Wellcome Centre for Integrative Neuroimaging, FMRIB Building University of Oxford -------------- next part -------------- An HTML attachment was scrubbed... URL: From C.Mazzetti at donders.ru.nl Wed Nov 29 11:20:53 2017 From: C.Mazzetti at donders.ru.nl (Mazzetti, C. (Cecilia)) Date: Wed, 29 Nov 2017 10:20:53 +0000 Subject: [FieldTrip] problems plotting source grandaverage - no anatomy fied (ft_sourcegrandaverage) Message-ID: <389DA1293690C94C93E3A53201F6C91E59226B5C@EXPRD98.hosting.ru.nl> Hi Everyone, I am struggling with the source analysis and especially when averaging across subjects' source reconstruction. The analysis for every subject was done according to the tutorial (creating MNI aligned grids in individual head space). The point is when I try to plot the source grandaverage I get an error saying there is no 'anatomy' field in my data. I tried to use both sourceinterpolate or add the anatomy field manually to the gsource_grandaverage structure but nothing works. Here is what my source_grandaverage contains: ga_sources pow: [6×902629 double] dim: [91 109 91] freq: 9.9723 inside: [902629×1 logical] pos: [902629×3 double] unit: 'mm' cfg: [1×1 struct] Any help is appreciated! Thanks! Best, Cecilia -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Nov 29 12:53:36 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 29 Nov 2017 11:53:36 +0000 Subject: [FieldTrip] problems plotting source grandaverage - no anatomy fied (ft_sourcegrandaverage) In-Reply-To: <389DA1293690C94C93E3A53201F6C91E59226B5C@EXPRD98.hosting.ru.nl> References: <389DA1293690C94C93E3A53201F6C91E59226B5C@EXPRD98.hosting.ru.nl> Message-ID: Hi Cecilia, Have you tried to compute the average on the low-resolution solutions, and only do the interpolation on the average? This should be possible, because you use the ‘mni-aligned grids’. Also, ft_sourcegrandaverage is a dinosaur of a function, and it looks as if it hasn’t grown along with the rest of the code. The pasted matlab-structure looks a bit strange, and I can imagine that FieldTrip chokes on it. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 29 Nov 2017, at 11:20, Mazzetti, C. (Cecilia) > wrote: Hi Everyone, I am struggling with the source analysis and especially when averaging across subjects' source reconstruction. The analysis for every subject was done according to the tutorial (creating MNI aligned grids in individual head space). The point is when I try to plot the source grandaverage I get an error saying there is no 'anatomy' field in my data. I tried to use both sourceinterpolate or add the anatomy field manually to the gsource_grandaverage structure but nothing works. Here is what my source_grandaverage contains: ga_sources pow: [6×902629 double] dim: [91 109 91] freq: 9.9723 inside: [902629×1 logical] pos: [902629×3 double] unit: 'mm' cfg: [1×1 struct] Any help is appreciated! Thanks! Best, Cecilia _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From C.Mazzetti at donders.ru.nl Thu Nov 30 12:05:33 2017 From: C.Mazzetti at donders.ru.nl (Mazzetti, C. (Cecilia)) Date: Thu, 30 Nov 2017 11:05:33 +0000 Subject: [FieldTrip] fieldtrip Digest, Vol 84, Issue 18 In-Reply-To: References: Message-ID: <389DA1293690C94C93E3A53201F6C91E59227015@EXPRD98.hosting.ru.nl> Thanks Jan Mathijs! I don't know whether that's supposed to be the case, but the problem is 'solved' by choosing cfg.keepindividual='no' when computing sourcegrandaverage, before the interpolation. then everything is fine! Might be helpful for others maybe! Thanks! Best, Cecilia Cecilia Mazzetti - Ph.D. Candidate Donders Centre for Cognitive Neuroimaging, room 0.068 Kapittelweg 29 | 6525 EN Nijmegen ________________________________________ Da: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] per conto di fieldtrip-request at science.ru.nl [fieldtrip-request at science.ru.nl] Inviato: giovedì 30 novembre 2017 12.00 A: fieldtrip at science.ru.nl Oggetto: fieldtrip Digest, Vol 84, Issue 18 Send fieldtrip mailing list submissions to fieldtrip at science.ru.nl To subscribe or unsubscribe via the World Wide Web, visit https://mailman.science.ru.nl/mailman/listinfo/fieldtrip or, via email, send a message with subject or body 'help' to fieldtrip-request at science.ru.nl You can reach the person managing the list at fieldtrip-owner at science.ru.nl When replying, please edit your Subject line so it is more specific than "Re: Contents of fieldtrip digest..." Today's Topics: 1. Re: problems plotting source grandaverage - no anatomy fied (ft_sourcegrandaverage) (Schoffelen, J.M. (Jan Mathijs)) ---------------------------------------------------------------------- Message: 1 Date: Wed, 29 Nov 2017 11:53:36 +0000 From: "Schoffelen, J.M. (Jan Mathijs)" To: FieldTrip discussion list Subject: Re: [FieldTrip] problems plotting source grandaverage - no anatomy fied (ft_sourcegrandaverage) Message-ID: Content-Type: text/plain; charset="utf-8" Hi Cecilia, Have you tried to compute the average on the low-resolution solutions, and only do the interpolation on the average? This should be possible, because you use the ?mni-aligned grids?. Also, ft_sourcegrandaverage is a dinosaur of a function, and it looks as if it hasn?t grown along with the rest of the code. The pasted matlab-structure looks a bit strange, and I can imagine that FieldTrip chokes on it. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 29 Nov 2017, at 11:20, Mazzetti, C. (Cecilia) > wrote: Hi Everyone, I am struggling with the source analysis and especially when averaging across subjects' source reconstruction. The analysis for every subject was done according to the tutorial (creating MNI aligned grids in individual head space). The point is when I try to plot the source grandaverage I get an error saying there is no 'anatomy' field in my data. I tried to use both sourceinterpolate or add the anatomy field manually to the gsource_grandaverage structure but nothing works. Here is what my source_grandaverage contains: ga_sources pow: [6?902629 double] dim: [91 109 91] freq: 9.9723 inside: [902629?1 logical] pos: [902629?3 double] unit: 'mm' cfg: [1?1 struct] Any help is appreciated! Thanks! Best, Cecilia _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip End of fieldtrip Digest, Vol 84, Issue 18 ***************************************** From jan.schoffelen at donders.ru.nl Thu Nov 30 12:28:39 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 30 Nov 2017 11:28:39 +0000 Subject: [FieldTrip] problems plotting source grandaverage - no anatomy fied (ft_sourcegrandaverage) In-Reply-To: <389DA1293690C94C93E3A53201F6C91E59227015@EXPRD98.hosting.ru.nl> References: <389DA1293690C94C93E3A53201F6C91E59227015@EXPRD98.hosting.ru.nl> Message-ID: Hi Cecilia, I am glad that you have resolved it. Best wishes, Jan-Mathijs > On 30 Nov 2017, at 12:05, Mazzetti, C. (Cecilia) wrote: > > Thanks Jan Mathijs! > I don't know whether that's supposed to be the case, but the problem is 'solved' by choosing cfg.keepindividual='no' when computing sourcegrandaverage, before the interpolation. then everything is fine! > Might be helpful for others maybe! > > Thanks! > > Best, > Cecilia > > > Cecilia Mazzetti - Ph.D. Candidate > Donders Centre for Cognitive Neuroimaging, room 0.068 > Kapittelweg 29 | 6525 EN Nijmegen > > > ________________________________________ > Da: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] per conto di fieldtrip-request at science.ru.nl [fieldtrip-request at science.ru.nl] > Inviato: giovedì 30 novembre 2017 12.00 > A: fieldtrip at science.ru.nl > Oggetto: fieldtrip Digest, Vol 84, Issue 18 > > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Re: problems plotting source grandaverage - no anatomy fied > (ft_sourcegrandaverage) (Schoffelen, J.M. (Jan Mathijs)) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 29 Nov 2017 11:53:36 +0000 > From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] problems plotting source grandaverage - no > anatomy fied (ft_sourcegrandaverage) > Message-ID: > Content-Type: text/plain; charset="utf-8" > > Hi Cecilia, > > Have you tried to compute the average on the low-resolution solutions, and only do the interpolation on the average? > > This should be possible, because you use the ?mni-aligned grids?. > > Also, ft_sourcegrandaverage is a dinosaur of a function, and it looks as if it hasn?t grown along with the rest of the code. The pasted matlab-structure looks a bit strange, and I can imagine that FieldTrip chokes on it. > > Best wishes, > Jan-Mathijs > > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > On 29 Nov 2017, at 11:20, Mazzetti, C. (Cecilia) > wrote: > > Hi Everyone, > I am struggling with the source analysis and especially when averaging across subjects' source reconstruction. > The analysis for every subject was done according to the tutorial (creating MNI aligned grids in individual head space). > The point is when I try to plot the source grandaverage I get an error saying there is no 'anatomy' field in my data. > I tried to use both sourceinterpolate or add the anatomy field manually to the gsource_grandaverage structure but nothing works. > Here is what my source_grandaverage contains: > ga_sources > > pow: [6?902629 double] > dim: [91 109 91] > freq: 9.9723 > inside: [902629?1 logical] > pos: [902629?3 double] > unit: 'mm' > cfg: [1?1 struct] > > > > Any help is appreciated! Thanks! > > Best, > Cecilia > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 84, Issue 18 > ***************************************** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From wolpert at clipper.ens.fr Wed Nov 1 15:12:44 2017 From: wolpert at clipper.ens.fr (wolpert at clipper.ens.fr) Date: Wed, 1 Nov 2017 15:12:44 +0100 Subject: [FieldTrip] Create event structre from .mrk file Message-ID: <28f61ec01e3c4487dc3039704079e004.squirrel@squirrelmail.eleves.ens.fr> Dear all, I would like to read events from a .mrk file. Using ft_read_event does not work as it gives me the message that it's unsupported event format. By searching in the internet, I found the function "readmarkerfile" which is able to return the marker names and their samples, but in very inconvenient format. So is there any way of creating the classical event structure from files in .mrk format? Best regards, Nicolai From christian.merkel at med.ovgu.de Fri Nov 3 13:42:13 2017 From: christian.merkel at med.ovgu.de (christian.merkel at med.ovgu.de) Date: Fri, 3 Nov 2017 12:42:13 +0000 Subject: [FieldTrip] wMNE? Message-ID: <71D8A67A81D69A4CB5BE2B979021C26ECB016E51@ESEN4.imed.uni-magdeburg.de> Dear fieldtrip-community, Does the minimum-norm-estimate algorithm in ft_sourceanalysis support depth-weighting? Thank You, Christian From jan.schoffelen at donders.ru.nl Fri Nov 3 15:53:02 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 3 Nov 2017 14:53:02 +0000 Subject: [FieldTrip] wMNE? In-Reply-To: <71D8A67A81D69A4CB5BE2B979021C26ECB016E51@ESEN4.imed.uni-magdeburg.de> References: <71D8A67A81D69A4CB5BE2B979021C26ECB016E51@ESEN4.imed.uni-magdeburg.de> Message-ID: Hi Christian, Yes, depth weighting can be achieved by norm normalisation of the leadfields (using the normalize option in ft_prepare_leadfield), or by inclusion of a source-covariance matrix in the cfg to ft_sourceanalysis. Best wishes, Jan-Mathijs On 3 Nov 2017, at 13:42, christian.merkel at med.ovgu.de wrote: Dear fieldtrip-community, Does the minimum-norm-estimate algorithm in ft_sourceanalysis support depth-weighting? Thank You, Christian _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From fereshte.ramezani at gmail.com Sat Nov 4 07:53:09 2017 From: fereshte.ramezani at gmail.com (Fereshte) Date: Sat, 04 Nov 2017 06:53:09 +0000 Subject: [FieldTrip] Place Source Models in specific location Message-ID: Dear Experts, I'm so new to fieldtrip so I apologize if my question is very basic; How can I place source models in specific locations according to MRI image ( I've already made the head model based on FEM). Thanks for your attention. Regards, Fereshte -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Sat Nov 4 08:25:43 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Sat, 4 Nov 2017 07:25:43 +0000 Subject: [FieldTrip] Place Source Models in specific location In-Reply-To: References: Message-ID: Ferehste, Your question lacks specificity. I think the readers of this list need a bit more concrete input in order to think about answering your question. Is it about specific locations? Anatomical atlas based regions-of-interest? What inverse algorithm are you considering? Etc.? Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 4 Nov 2017, at 07:53, Fereshte > wrote: Dear Experts, I'm so new to fieldtrip so I apologize if my question is very basic; How can I place source models in specific locations according to MRI image ( I've already made the head model based on FEM). Thanks for your attention. Regards, Fereshte _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From fereshte.ramezani at gmail.com Sun Nov 5 12:05:58 2017 From: fereshte.ramezani at gmail.com (Fereshte) Date: Sun, 05 Nov 2017 11:05:58 +0000 Subject: [FieldTrip] Place Source Models in specific location In-Reply-To: References: Message-ID: I'm going to investigate the effect of segmentation on EEG forward problem( FreeSurfer segmentation and Filedtrip segmentation). I've already made the FE head model and placed the electrodes but I'm not really sure how to place the source models for such a comparison ( like to place source models where the two segmentations differ in GM). Thanks for your attention. On Sat, Nov 4, 2017 at 11:05 AM Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Ferehste, > > Your question lacks specificity. I think the readers of this list need a > bit more concrete input in order to think about answering your question. Is > it about specific locations? Anatomical atlas based regions-of-interest? > What inverse algorithm are you considering? Etc.? > > Best wishes, > > Jan-Mathijs > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > > On 4 Nov 2017, at 07:53, Fereshte wrote: > > Dear Experts, > I'm so new to fieldtrip so I apologize if my question is very basic; How > can I place source models in specific locations according to MRI image ( > I've already made the head model based on FEM). > Thanks for your attention. > Regards, > Fereshte > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsten.wolters at uni-muenster.de Mon Nov 6 09:01:59 2017 From: carsten.wolters at uni-muenster.de (Carsten Wolters) Date: Mon, 6 Nov 2017 09:01:59 +0100 Subject: [FieldTrip] Place Source Models in specific location In-Reply-To: References: Message-ID: <6def03a0-a71e-3a5d-981d-14bb921a9ea2@uni-muenster.de> Dear Ferehste, we have implemented the Venant approach for FEM source modeling in the Fieldtrip-SimBio pipeline. The Venant approach spreads monopolar sources around the dipole location in a way that the dipole location and moment is well approximated. You need to take care that all these monopoles are within the grey matter compartment. We call this the "Venant condition" that has to be fulfilled. You find detailed informations in http://www.sci.utah.edu/~wolters/PaperWolters/2014/VorwerkChoRamppHamerKnoescheWolters_NeuroImage_2014_Webversion.pdf or in Chapter 2.4.2 in http://www.sci.utah.edu/~wolters/PaperWolters/2016/PursiainenVorwerkWolters_PhysMedBiol_accepted2016_HDiv.pdf or very detailed in http://www.sci.utah.edu/~wolters/PaperWolters/2016/Vorwerk_Dissertation_2016.pdf BR      Carsten Am 05.11.2017 um 12:05 schrieb Fereshte: > I'm going to investigate the effect of segmentation on EEG forward > problem( FreeSurfer segmentation and Filedtrip segmentation). I've > already made the FE head model and placed the electrodes but I'm not > really sure how to place the source models for such a comparison ( > like to place source models where the two segmentations differ in GM). > Thanks for your attention. > > On Sat, Nov 4, 2017 at 11:05 AM Schoffelen, J.M. (Jan Mathijs) > > > wrote: > > Ferehste, > > Your question lacks specificity. I think the readers of this list > need a bit more concrete input in order to think about answering > your question. Is it about specific locations? Anatomical atlas > based regions-of-interest? What inverse algorithm are you > considering? Etc.? > > Best wishes, > > Jan-Mathijs > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > >> On 4 Nov 2017, at 07:53, Fereshte > > wrote: >> >> Dear Experts, >> I'm so new to fieldtrip so I apologize if my question is very >> basic; How can I place source models in specific locations >> according to MRI image ( I've already made the head model based >> on FEM). >> Thanks for your attention. >> Regards, >> Fereshte >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Prof. Dr.rer.nat. Carsten H. Wolters University of Münster Institute for Biomagnetism and Biosignalanalysis Malmedyweg 15 48149 Münster, Germany Phone: +49 (0)251 83 56904 +49 (0)251 83 56865 (secr.) Fax: +49 (0)251 83 56874 Email: carsten.wolters at uni-muenster.de Web: https://campus.uni-muenster.de/biomag/das-institut/mitarbeiter/carsten-wolters/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Mon Nov 6 17:41:21 2017 From: michelic72 at gmail.com (Cristiano Micheli) Date: Mon, 6 Nov 2017 17:41:21 +0100 Subject: [FieldTrip] reconstruction of EEG patterns on a 3D shape Message-ID: Dear Team I achieved a 3D reconstruction of a 64 electrodes Biosemi cap, as described in this tutorial: http://www.fieldtriptoolbox.org/tutorial/electrode Now I would like to visualise a [64x1] vector of EEG activity [64 electrodes x 1 time sample] as an interpolated overlay on top of the 3D electrodes reconstruction. Is there a quick way to obtain this by means of ft_sourceplot or other functions? All the best! Cris -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Nov 6 19:57:34 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 6 Nov 2017 18:57:34 +0000 Subject: [FieldTrip] reconstruction of EEG patterns on a 3D shape In-Reply-To: References: Message-ID: Ciao Cris, ft_plot_topo3d in the plotting module is your friend. Best wishes, JM J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 6 Nov 2017, at 17:41, Cristiano Micheli > wrote: Dear Team I achieved a 3D reconstruction of a 64 electrodes Biosemi cap, as described in this tutorial: http://www.fieldtriptoolbox.org/tutorial/electrode Now I would like to visualise a [64x1] vector of EEG activity [64 electrodes x 1 time sample] as an interpolated overlay on top of the 3D electrodes reconstruction. Is there a quick way to obtain this by means of ft_sourceplot or other functions? All the best! Cris _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From nadia.mueller at gmail.com Tue Nov 7 12:13:42 2017 From: nadia.mueller at gmail.com (Nadia Mueller) Date: Tue, 7 Nov 2017 12:13:42 +0100 Subject: [FieldTrip] Postdoc position and doctoral student position at the MEG in Erlangen Message-ID: Dear all, I'm offering one post-doc position and one position for a doctoral student in tinnitus research at the MEG Center in Erlangen (Germany) starting in February 2018. Please see the attached document for further information. It would be great if you could share this message with interested students, PhD students and postdocs around you. Thank you and best regards, Nadia Müller-Voggel -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Postdoc_Doctoral Student Position.pdf Type: application/pdf Size: 60316 bytes Desc: not available URL: From kirsten at carrot-village.de Tue Nov 7 12:16:51 2017 From: kirsten at carrot-village.de (Kirsten Herfurth) Date: Tue, 7 Nov 2017 12:16:51 +0100 (CET) Subject: [FieldTrip] Problem with ft_megrealign Message-ID: <1778422504.475907.1510053411840@communicator.strato.de> Dear all, I would like to apply the function ft_megrealign to my single subject meg data in order to do sensor level group analysis afterwards. I got stuck with the following error messages: Reference to non-existent field 'xgrid'. Error in ft_prepare_sourcemodel (line 709) xmin_indx = find(grid.xgrid==xmin); Error in ft_megrealign (line 249) grid = ft_prepare_sourcemodel(tmpcfg); I used the following configuration: cfg=[]; cfg.template = {MEGSubject1.grad; MEGSubject2.grad; MEGSubject3.grad, …}; cfg.headmodel = headmodel; cfg.headshape = strcat(Path2MEGData,'hs_file'); cfg.inwardshift = 0.025; % in meters cfg.vol.r=headmodel.r; cfg.vol.o=headmodel.o; cfg.vol.label=headmodel.label; [MEGSubject1_realigned] = ft_megrealign(cfg, MEGSubject1) The headmodel was built using the following configuration: cfg =[]; cfg.method = 'localspheres'; cfg.grad = MEGsingleSubjectData.grad; headmodel = ft_prepare_headmodel(cfg, headshape); There was a post with the same problem in the mailing list, with the suggestion to uncomment cfg.headshape: https://mailman.science.ru.nl/pipermail/fieldtrip/2015-September/009633.html When uncommenting cfg.headshape, it works until I get the following error message: Error using vertcat Dimensions of matrices being concatenated are not consistent. Error in ft_megrealign (line 391) interp.label = [interp.label; rest.label]; interpol.label is a 1x248 cell array, rest.label is 93x1 cell array. Did I miss something? Thanks a lot for your help in advance, Kirsten From xiew1202 at gmail.com Tue Nov 7 16:33:28 2017 From: xiew1202 at gmail.com (Xie Wanze) Date: Tue, 7 Nov 2017 10:33:28 -0500 Subject: [FieldTrip] Diagonal values for wpli in ft_connectivityanalysis Message-ID: Dear all, I have the diagonal values *unequal *to 0 or 1 in the output matrix from the ft_connectivityanalysis using 'wpli'. These diagonal values are even not equal to each other. The diagonal values are the same (0s or Infinite) by using 'coh' or 'coh' & cfg.complex = 'imag'. I never used the diagonal values in my later analysis, and I always changed them to 0s, but I am still curious and confused about why this happened to the method of 'wpli'. Does anyone ever meet this issue? Thanks. Wanze -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Tue Nov 7 16:33:28 2017 From: michelic72 at gmail.com (Cristiano Micheli) Date: Tue, 7 Nov 2017 16:33:28 +0100 Subject: [FieldTrip] reconstruction of EEG patterns on a 3D shape In-Reply-To: References: Message-ID: Thanks. That worked beautifully! Cris On Mon, Nov 6, 2017 at 7:57 PM, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Ciao Cris, > > ft_plot_topo3d in the plotting module is your friend. > > Best wishes, > > JM > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 <024%20361%204793> > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > > On 6 Nov 2017, at 17:41, Cristiano Micheli wrote: > > Dear Team > I achieved a 3D reconstruction of a 64 electrodes Biosemi cap, as > described in this tutorial: > http://www.fieldtriptoolbox.org/tutorial/electrode > Now I would like to visualise a [64x1] vector of EEG activity [64 > electrodes x 1 time sample] as an interpolated overlay on top of the 3D > electrodes reconstruction. > Is there a quick way to obtain this by means of ft_sourceplot or other > functions? > > All the best! > Cris > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Nov 7 21:46:49 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 7 Nov 2017 20:46:49 +0000 Subject: [FieldTrip] Problem with ft_megrealign In-Reply-To: <1778422504.475907.1510053411840@communicator.strato.de> References: <1778422504.475907.1510053411840@communicator.strato.de> Message-ID: <69C815C9-B6A5-4392-B06A-8FD34FB5DA71@donders.ru.nl> Dear Kirsten, These days I would not recommend the use of ft_megrealign to begin with. In our experience it often does more harm than that it improves results. In particular, if your subjects were relatively well-behaved, and well-positioned in the MEG. This might also be one of the reasons, why the code does not run through smoothly, because FieldTrip has evolved quite a bit over the past years. While we take the utmost care to keep the code internally consistent, rarely used functionality might have escaped our attention, which may have happened here. This being said, I am not sure whether I understand why the removal of the headshape option allows you to proceed deeper in the code. The second error you report is caused by a dimensionality mismatch, where matlab is asked to concatenate a row-vector (interp.label) with a column vector (rest.label). Given the code, it seems that the writer of the code assumed the interp.label to always be a column vector (which happens to be FieldTrip convention). I don’t know how interp.label ended up a row vector, but changing line 391 into interp.label = [interp.label(:);rest.label(:)]; should do the trick. You could try and fix this on your local copy of fieldtrip, but even better would be to contribute the fix to the release code-base, so that everyone can enjoy it. The way to do this is documented here: http://www.fieldtriptoolbox.org/development/git I am looking forward to your suggested fix. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 7 Nov 2017, at 12:16, Kirsten Herfurth > wrote: Dear all, I would like to apply the function ft_megrealign to my single subject meg data in order to do sensor level group analysis afterwards. I got stuck with the following error messages: Reference to non-existent field 'xgrid'. Error in ft_prepare_sourcemodel (line 709) xmin_indx = find(grid.xgrid==xmin); Error in ft_megrealign (line 249) grid = ft_prepare_sourcemodel(tmpcfg); I used the following configuration: cfg=[]; cfg.template = {MEGSubject1.grad; MEGSubject2.grad; MEGSubject3.grad, …}; cfg.headmodel = headmodel; cfg.headshape = strcat(Path2MEGData,'hs_file'); cfg.inwardshift = 0.025; % in meters cfg.vol.r=headmodel.r; cfg.vol.o=headmodel.o; cfg.vol.label=headmodel.label; [MEGSubject1_realigned] = ft_megrealign(cfg, MEGSubject1) The headmodel was built using the following configuration: cfg =[]; cfg.method = 'localspheres'; cfg.grad = MEGsingleSubjectData.grad; headmodel = ft_prepare_headmodel(cfg, headshape); There was a post with the same problem in the mailing list, with the suggestion to uncomment cfg.headshape: https://mailman.science.ru.nl/pipermail/fieldtrip/2015-September/009633.html When uncommenting cfg.headshape, it works until I get the following error message: Error using vertcat Dimensions of matrices being concatenated are not consistent. Error in ft_megrealign (line 391) interp.label = [interp.label; rest.label]; interpol.label is a 1x248 cell array, rest.label is 93x1 cell array. Did I miss something? Thanks a lot for your help in advance, Kirsten _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Nov 7 22:03:15 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 7 Nov 2017 21:03:15 +0000 Subject: [FieldTrip] Diagonal values for wpli in ft_connectivityanalysis In-Reply-To: References: Message-ID: <06BF6BE8-2170-4938-B3BE-74F25EFE89DE@donders.ru.nl> Dear Wanze, I don’t know what type of data you put into the algorithm, so it’s a bit ‘koffiedik’ kijken, as we say in Dutch. I’d suggest that you start by reading the code, and see whether you understand what causes your ‘issue’. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 7 Nov 2017, at 16:33, Xie Wanze > wrote: Dear all, I have the diagonal values unequal to 0 or 1 in the output matrix from the ft_connectivityanalysis using 'wpli'. These diagonal values are even not equal to each other. The diagonal values are the same (0s or Infinite) by using 'coh' or 'coh' & cfg.complex = 'imag'. I never used the diagonal values in my later analysis, and I always changed them to 0s, but I am still curious and confused about why this happened to the method of 'wpli'. Does anyone ever meet this issue? Thanks. Wanze _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.chettouf at vu.nl Wed Nov 8 11:14:42 2017 From: s.chettouf at vu.nl (Chettouf, S.) Date: Wed, 8 Nov 2017 10:14:42 +0000 Subject: [FieldTrip] Convert fieldtrip beamformers to SPM Message-ID: Dear fieldtrip community, I analysed my EEG data in fieldtrip and calculated beamformers. I would like to compare these source data with my fMRI sources and therefore do both statistical testings in SPM. But how can I export my beamformer data to SPM? Converting them with spm_ eeg _ ft2spm does not work with beamformer data. I also tried ft_volumewrite to convert the beamformer results to nifti, but without succes. Thanks in advance, Sabrina -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Nov 8 11:24:47 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 8 Nov 2017 10:24:47 +0000 Subject: [FieldTrip] Convert fieldtrip beamformers to SPM In-Reply-To: References: Message-ID: Dear Sabrina, I am not sure why your conversion to nifti does not work, but if you follow the recipe that is described in http://www.fieldtriptoolbox.org/tutorial/beamformer, in particular by using ft_sourceinterpolate to create a volumetric image of ther source-reconstructed activity, followed by an optional volumetric normalisation (using ft_volumenormalise), it should be relatively straightforward to save this to a nifti file. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 8 Nov 2017, at 11:14, Chettouf, S. > wrote: Dear fieldtrip community, I analysed my EEG data in fieldtrip and calculated beamformers. I would like to compare these source data with my fMRI sources and therefore do both statistical testings in SPM. But how can I export my beamformer data to SPM? Converting them with spm_ eeg _ ft2spm does not work with beamformer data. I also tried ft_volumewrite to convert the beamformer results to nifti, but without succes. Thanks in advance, Sabrina _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Nov 8 12:05:31 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 8 Nov 2017 11:05:31 +0000 Subject: [FieldTrip] Variance estimates for connectivity measures In-Reply-To: References: Message-ID: <2EBD91F4-1703-4F0E-A7D2-3DC6DC96E030@donders.ru.nl> Dear Matthew, I think it depends on the way that you compute these metrics. If you approach it parametrically (i.e. using MVAR-models) I think that the coefficients are computed across all observations by default. If you want a leave-one-out estimate of the coefficients, I think that you can use cfg.jackknife as an option to ft_mvaranalysis. How well this is supported throughout the rest of the analysis pipeline (i.e. ft_freqanalysis_mvar and ft_connectivityanalysis) I am not sure. I haven’t used this option for a long time, so the code may have become a bit rusty here and there. If you are using a non-parametric approach (i.e. using ft_freqanalysis, followed by ft_connectivity_csd2transfer, which is called on the fly by ft_connectivityanalysis), I think there used to be some functionality to compute leave-one-outs on the fly, and then essentially treat them as ‘single trials’. Also there, I assume that the code has become a bit rusty, because it hasn’t been used for quite a while. Either way, I guess that an definitive answer to your question would require you to inspect the code in some more detail. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 20 Oct 2017, at 16:16, MATTHEW I BANKS > wrote: Greetings. Is it possible to use jackknife to get variance estimates for Granger, partial directed coherence and directed transfer function? I use it for wPLI, but cannot figure out how to do it for these other measures. -Matt Banks ____________________________ Matthew I. Banks, Ph.D. Associate Professor Department of Anesthesiology University of Wisconsin 1300 University Avenue, Room 4605 Madison, WI 53706 office tel. (608)261-1143 lab tel. (608)263-6662 fax (608)263-2592 http://anesthesia.wisc.edu/index.php/Banks_Laboratory http://ntp.neuroscience.wisc.edu/banks.htm _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From SXM1085 at student.bham.ac.uk Wed Nov 8 12:07:43 2017 From: SXM1085 at student.bham.ac.uk (Sebastian Michelmann) Date: Wed, 8 Nov 2017 11:07:43 +0000 Subject: [FieldTrip] Convert fieldtrip beamformers to SPM In-Reply-To: References: Message-ID: <2D9C9145AF1E4D4799ADDB2C0F996AE8019EFD8425@EX13.adf.bham.ac.uk> Dear Sabrina, This code works for me on the interpolated volume: cfg = []; cfg.parameter = 'stat'; cfg.filename = 'stat_interp'; cfg.datatype = 'float'; cfg.filetype = 'nifti'; cfg.vmpversion = 2; cfg.coordsys = 'spm'; ft_volumewrite(cfg, sourceint); I use this to plot 'blobs' outside of fieldtrip. best, Sebastian From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of s.chettouf at vu.nl Sent: 08 November 2017 10:15 To: FieldTrip discussion list Subject: [FieldTrip] Convert fieldtrip beamformers to SPM Dear fieldtrip community, I analysed my EEG data in fieldtrip and calculated beamformers. I would like to compare these source data with my fMRI sources and therefore do both statistical testings in SPM. But how can I export my beamformer data to SPM? Converting them with spm_ eeg _ ft2spm does not work with beamformer data. I also tried ft_volumewrite to convert the beamformer results to nifti, but without succes. Thanks in advance, Sabrina -------------- next part -------------- An HTML attachment was scrubbed... URL: From joerg.hipp at googlemail.com Wed Nov 8 17:55:26 2017 From: joerg.hipp at googlemail.com (Joerg Hipp) Date: Wed, 8 Nov 2017 17:55:26 +0100 Subject: [FieldTrip] 9 month internship in EEG biomarker development at Roche in Basel, Switzerland Message-ID: Dear all, We are offering a 9 month internship (RiSE, Roche Internships for Scientific Exchange) in our biomarker group at Roche in Basel, Switzerland. We are looking for a motivated researcher to help us explore the utility of EEG as a biomarker for neurodevelopmental diseases. Besides the work on a specific project the intern will gain insights into research and development in the pharmaceutical industry. Our group supports neuroscience programs within the Roche portfolio, which covers a broad spectrum of neurological and psychiatric diseases and we apply various techniques including EEG/MEG, PET, MRI, and Neuropsychology to this end. I am responsible for electrophysiological biomarkers (EEG/MEG) and will supervise this project. Prerequisite for application to the RiSE program is enrollment in a university PhD or medical degree program at the time of application. Details on the RiSE program can be found here: http://www.roche.com/careers/ switzerland/ch_your_job/students_and_graduates/ch_ internships/rise_program.htm Details on the specific internship and how to apply can be found here: https://www.roche.com/careers/jobs/jobsearch/job.htm?id=E- 3425641919&locale=en&title=RiSE+-+Roche+internship+for+ Scientific+Exchange+-+in+Neuroscience+Biomarkers+%289+months%29 Best wishes, Joerg -- Joerg Hipp, PhD Biomarker and Experimental Medicine Leader F. Hoffmann-La Roche Ltd. Grenzacherstrasse 124 4070 Basel, Switzerland https://scholar.google.ch/citations?user=oxsJ6q4AAAAJ&hl=en -------------- next part -------------- An HTML attachment was scrubbed... URL: From kirsten at carrot-village.de Thu Nov 9 12:58:02 2017 From: kirsten at carrot-village.de (Kirsten Herfurth) Date: Thu, 9 Nov 2017 12:58:02 +0100 (CET) Subject: [FieldTrip] Problem with ft_megrealign Message-ID: <1899468378.586762.1510228682849@communicator.strato.de> Dear Jan-Mathijs, thank you very much for your answer! I will fix the bug and commit it to Github. Do you have any suggestions for an alternative approach for realigning data obtained with a non-CTF-system (we have a 4d-MEG-system)? Unfortunately we don’t have a head position time-series obtained online, just the position in the beginning and in the end of a run. I assume I cannot use the function ft_regressconfound or ft_headmovement. I’m sorry for this basic question, but I haven’t found a satisfying answer to my problem yet. The reason for accounting for head movement is that I would like to use the Machine Learning toolbox and do statistics using k-fold cross-validation, but have too few trials in one run per subject. So I thought to concatenate the trials of different runs with ft_appenddata using the realignment function first. Would it be ok to just go without the realignment in subjects that didn’t move that much, especially if it gives me the expected results? Thanks again and best wishes Kirsten From Bastiaansen4.M at nhtv.nl Fri Nov 10 12:04:37 2017 From: Bastiaansen4.M at nhtv.nl (Bastiaansen, Marcel) Date: Fri, 10 Nov 2017 11:04:37 +0000 Subject: [FieldTrip] multiclass svm In-Reply-To: References: Message-ID: Dear Fieldtrippers, As a relative novice to classification algorithms, I have been playing around with Fieldtrip's svm classifier (ft_statistics_crossvalidate). This seems to work pretty smoothly, but I have two questions related to that: 1. In the given contingency table one can see the actual classification of trials. However, I assume the actual classification is based on a classification probability for each trial. Is there a way of getting a list of classification probabilities for all trials from this function? Else, a quick hint at where in the code these probabilities are being computed / stored would help me build this functionality 2. I have EEG data that belong to 4 classes, but ft_statistics_crossvalidate does not afford multiclass approaches. Any tips or hints at what would be robust and well-validated approaches for multiclass models for EEG data would be much appreciated. Best, Marcel *** Dr Marcel C.M. Bastiaansen Senior lecturer and researcher in quantitative research methods Academy for Leisure & Academy for Tourism NHTV Breda University of Applied Sciences Visiting adress: Room C1.011, Academy for Leisure Archimedesstraat 17, 4816 BA, Breda Phone: +31 76 533 2869 Email: bastiaansen4.m at nhtv.nl And Department of Cognitive Neuropsychology Tilburg School of Social and Behavioral Sciences Tilburg University Visiting address: Room S217, Simon building Warandelaan 2 5000 LE Tilburg Email: M.C.M.Bastiaansen at uvt.nl publications linked-in *** -------------- next part -------------- An HTML attachment was scrubbed... URL: From ekenaykut at gmail.com Fri Nov 10 12:40:05 2017 From: ekenaykut at gmail.com (Aykut Eken) Date: Fri, 10 Nov 2017 14:40:05 +0300 Subject: [FieldTrip] multiclass svm In-Reply-To: References: Message-ID: <0A281A02-DB29-4F9D-BBBE-24078FA8B12F@gmail.com> Dear Marcel, Instead of using ft_statistics_crossvalidate, you can extract the features and use as input to fitcsvm in MATLAB that provides answers to your questions. After running the model, you can use fitSVMPosterior or fitPosterior to obtain classification probabilities. Best Aykut Eken, PhD Düzce University Faculty of Engineering Biomedical Engineering Department Düzce University, Konuralp Campus, 81620, Konuralp, Düzce, Turkey Tel: +905366777364 Office Tel: +90380542 11 00 /4546 Mail address1: aykuteken at duzce.edu.tr Mail address2: ekenaykut at gmail.com > On 10 Nov 2017, at 14:04, Bastiaansen, Marcel wrote: > > Dear Fieldtrippers, > > As a relative novice to classification algorithms, I have been playing around with Fieldtrip’s svm classifier (ft_statistics_crossvalidate). This seems to work pretty smoothly, but I have two questions related to that: > 1. In the given contingency table one can see the actual classification of trials. However, I assume the actual classification is based on a classification probability for each trial. Is there a way of getting a list of classification probabilities for all trials from this function? Else, a quick hint at where in the code these probabilities are being computed / stored would help me build this functionality > 2. I have EEG data that belong to 4 classes, but ft_statistics_crossvalidate does not afford multiclass approaches. Any tips or hints at what would be robust and well-validated approaches for multiclass models for EEG data would be much appreciated. > > Best, > Marcel > > *** > Dr Marcel C.M. Bastiaansen > Senior lecturer and researcher in quantitative research methods > Academy for Leisure & Academy for Tourism > NHTV Breda University of Applied Sciences > Visiting adress: > Room C1.011, Academy for Leisure > Archimedesstraat 17, > 4816 BA, Breda > Phone: +31 76 533 2869 > Email: bastiaansen4.m at nhtv.nl > > And > > Department of Cognitive Neuropsychology > Tilburg School of Social and Behavioral Sciences > Tilburg University > Visiting address: > Room S217, Simon building > Warandelaan 2 > 5000 LE Tilburg > Email: M.C.M.Bastiaansen at uvt.nl > > publications > linked-in > *** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From til.bergmann at uni-tuebingen.de Fri Nov 10 16:46:37 2017 From: til.bergmann at uni-tuebingen.de (Til Ole Bergmann) Date: Fri, 10 Nov 2017 16:46:37 +0100 Subject: [FieldTrip] PhD Position (3 years, 65% TV-L) on real-time EEG-TMS with Til Ole Bergmann, University of Tuebingen, Germany Message-ID: Dear FieldTrip community, I have a PhD position opening (3 years, salary accoording to 65% TV-L) in a DFG-funded project ("The sensorimotor µ-rhythm as cholinergically controlled pulsed inhibition"). We will use brain-state-dependent real-time EEG-triggered transcranial magnetic stimulation (EEG-TMS) to investigate the neurophysiology underlying mu-alpha (8-14 Hz) oscillations in the human sensorimotor cortex, their function for gating information flow and synaptic plasticity in the brain, and the cholinergic mechanisms mediating their prefrontal top-down control by attention. The ideal candidate has experience in Matlab (and preferrably FieldTrip) for EEG/MEG timeseries analyses. Please circulate this job opening amongst your peers and potential PhD candidates. For more information please see: http://tobergmann.de/downloads/PhD_position_Bergmann_Tuebingen.pdf Many thanks in advance! All the best, Til -- Dr. Til Ole Bergmann Department of Neurology & Stroke Hertie Institute for Clinical Brain Research Institute of Medical Psychology and Behavioral Neurobiology University of Tübingen Otfried-Müller-Straße 25, 72076 Tübingen, Germany til.bergmann at uni-tuebingen.de tel +49-7071-29-88795 fax +49 7071 29-25016 From springangel222 at gmail.com Sun Nov 12 06:37:12 2017 From: springangel222 at gmail.com (angel angel) Date: Sun, 12 Nov 2017 09:07:12 +0330 Subject: [FieldTrip] Equivalent parts in an image and a mesh Message-ID: Dear FieldTrip Experts, How you find the corresponding part of an image in a mesh? Looking forward to hearing from you. Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Sun Nov 12 12:58:42 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Sun, 12 Nov 2017 11:58:42 +0000 Subject: [FieldTrip] Equivalent parts in an image and a mesh In-Reply-To: References: Message-ID: Hi Angel Angel, I don’t understand the question. Can you please have a look at the following before trying again? http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002202 http://www.fieldtriptoolbox.org/faq/how_to_ask_good_questions_to_the_community?s[]=discussion&s[]=list Thanks very much, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 12 Nov 2017, at 06:37, angel angel > wrote: Dear FieldTrip Experts, How you find the corresponding part of an image in a mesh? Looking forward to hearing from you. Regards _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From springangel222 at gmail.com Mon Nov 13 17:57:37 2017 From: springangel222 at gmail.com (angel angel) Date: Mon, 13 Nov 2017 20:27:37 +0330 Subject: [FieldTrip] Equivalent parts in an image and a mesh In-Reply-To: References: Message-ID: Hi Dear All, I apologize for my unclear question. I want to figure out where does each voxel of an image stand in a mesh after the mesh generation pipeline? I mean on which face and between which vertices? I hope I asked the correct form of a question this time. Thanks for your attention. On Sun, Nov 12, 2017 at 3:28 PM, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Hi Angel Angel, > > I don’t understand the question. Can you please have a look at the > following before trying again? > > > http://journals.plos.org/ploscompbiol/article?id=10. > 1371/journal.pcbi.1002202 > > http://www.fieldtriptoolbox.org/faq/how_to_ask_good_ > questions_to_the_community?s[]=discussion&s[]=list > > Thanks very much, > > Jan-Mathijs > > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > On 12 Nov 2017, at 06:37, angel angel wrote: > > Dear FieldTrip Experts, > How you find the corresponding part of an image in a mesh? > Looking forward to hearing from you. > Regards > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From otobias at web.de Tue Nov 14 03:58:37 2017 From: otobias at web.de (Tobias Overath) Date: Mon, 13 Nov 2017 21:58:37 -0500 Subject: [FieldTrip] Phd position in the O-Lab at Duke University Message-ID: <05DB48BD-5388-4DAA-8AB1-99467DDC9B76@web.de> Dear all, We are looking for a highly motivated young scientist to join the O-Lab, led by Prof. Tobias Overath, in the Department of Psychology and Neuroscience at Duke University. Work in our lab investigates how sounds, from simple sinusoids to complex speech signals, are processed in the brain, using a combination of behavioral and neuroimaging methods (fMRI, EEG, ECoG) to track the underlying neural processes. Current projects investigate the transformation from acoustic to linguistic analysis of temporal speech structure, online measures of statistical learning, as well as optimization of cochlear implant coding strategies. Interested candidates should have received an undergraduate degree in psychology, neuroscience, biomedical engineering, or a related field by Summer 2018. Familiarity with signal processing, fMRI, M/EEG, or related experimental techniques is a plus, as is advanced knowledge of at least one programing language (preferably Matlab). Admission is possible via the Psychology and Neuroscience Graduate Program (https://psychandneuro.duke.edu/graduate ), or via the Cognitive Neuroscience Admitting Program (CNAP, https://dibs.duke.edu/centers/ccn/graduate-cnap ). The application deadline is December 1, 2017! Duke University provides a vibrant, highly connected scientific environment, with many associated departments and interdisciplinary initiatives (e.g. Departments of Neurobiology, Biomedical Engineering, Electrical and Computer Engineering; the Center for Cognitive Neuroscience, the Duke Institute for Brain Sciences, or the Brain Imaging and Analysis Center). Please contact Tobias Overath (t.overath at duke.edu ) for further information. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Nov 14 15:45:17 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 14 Nov 2017 14:45:17 +0000 Subject: [FieldTrip] Equivalent parts in an image and a mesh In-Reply-To: References: Message-ID: Why do you want this? JM J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 13 Nov 2017, at 17:57, angel angel > wrote: Hi Dear All, I apologize for my unclear question. I want to figure out where does each voxel of an image stand in a mesh after the mesh generation pipeline? I mean on which face and between which vertices? I hope I asked the correct form of a question this time. Thanks for your attention. On Sun, Nov 12, 2017 at 3:28 PM, Schoffelen, J.M. (Jan Mathijs) > wrote: Hi Angel Angel, I don’t understand the question. Can you please have a look at the following before trying again? http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002202 http://www.fieldtriptoolbox.org/faq/how_to_ask_good_questions_to_the_community?s[]=discussion&s[]=list Thanks very much, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 12 Nov 2017, at 06:37, angel angel > wrote: Dear FieldTrip Experts, How you find the corresponding part of an image in a mesh? Looking forward to hearing from you. Regards _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From springangel222 at gmail.com Wed Nov 15 09:33:56 2017 From: springangel222 at gmail.com (angel angel) Date: Wed, 15 Nov 2017 12:03:56 +0330 Subject: [FieldTrip] Equivalent parts in an image and a mesh In-Reply-To: References: Message-ID: I want to make a source model based on "regular 3D grid, based on segmented MRI, restricted to gray matter". Thanks in advance. On Tue, Nov 14, 2017 at 6:15 PM, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Why do you want this? > > JM > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > On 13 Nov 2017, at 17:57, angel angel wrote: > > Hi Dear All, > I apologize for my unclear question. I want to figure out where does each > voxel of an image stand in a mesh after the mesh generation pipeline? I > mean on which face and between which vertices? I hope I asked the correct > form of a question this time. > Thanks for your attention. > > On Sun, Nov 12, 2017 at 3:28 PM, Schoffelen, J.M. (Jan Mathijs) < > jan.schoffelen at donders.ru.nl> wrote: > >> Hi Angel Angel, >> >> I don’t understand the question. Can you please have a look at the >> following before trying again? >> >> >> http://journals.plos.org/ploscompbiol/article?id=10.1371/ >> journal.pcbi.1002202 >> >> http://www.fieldtriptoolbox.org/faq/how_to_ask_good_question >> s_to_the_community?s[]=discussion&s[]=list >> >> Thanks very much, >> >> Jan-Mathijs >> >> >> J.M.Schoffelen, MD PhD >> Senior Researcher, VIDI-fellow - PI, language in interaction >> Telephone: +31-24-3614793 >> Physical location: room 00.028 >> Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands >> >> On 12 Nov 2017, at 06:37, angel angel wrote: >> >> Dear FieldTrip Experts, >> How you find the corresponding part of an image in a mesh? >> Looking forward to hearing from you. >> Regards >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Nov 15 12:55:09 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 15 Nov 2017 11:55:09 +0000 Subject: [FieldTrip] Equivalent parts in an image and a mesh In-Reply-To: References: Message-ID: <7974CAAA-435E-46FC-8585-D60B49377B16@donders.ru.nl> Dear anonymous, If you want "a regular 3D grid, based on a segmented MRI, restricted to grey matter”, why do you need the cortical surface reconstruction? Best wishes, JAN-MATHIJS On 15 Nov 2017, at 09:33, angel angel > wrote: I want to make a source model based on "regular 3D grid, based on segmented MRI, restricted to gray matter". Thanks in advance. On Tue, Nov 14, 2017 at 6:15 PM, Schoffelen, J.M. (Jan Mathijs) > wrote: Why do you want this? JM J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 13 Nov 2017, at 17:57, angel angel > wrote: Hi Dear All, I apologize for my unclear question. I want to figure out where does each voxel of an image stand in a mesh after the mesh generation pipeline? I mean on which face and between which vertices? I hope I asked the correct form of a question this time. Thanks for your attention. On Sun, Nov 12, 2017 at 3:28 PM, Schoffelen, J.M. (Jan Mathijs) > wrote: Hi Angel Angel, I don’t understand the question. Can you please have a look at the following before trying again? http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002202 http://www.fieldtriptoolbox.org/faq/how_to_ask_good_questions_to_the_community?s[]=discussion&s[]=list Thanks very much, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 12 Nov 2017, at 06:37, angel angel > wrote: Dear FieldTrip Experts, How you find the corresponding part of an image in a mesh? Looking forward to hearing from you. Regards _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Nov 16 12:36:25 2017 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 16 Nov 2017 12:36:25 +0100 Subject: [FieldTrip] dimord single-trial source data Message-ID: Hi FieldTrippers, I was wondering is there is a recommend/most consistent way to represent trial x pos x time data from an LCMV beamformer, also considering the dimord. In other words: with: data.method = 'singletrial' should I use: data.trial{pos} = [rpt x time] data.dimord = '{pos}_rpt_time' or rather: data.trial = {pos x rpt x time} data.dimord = 'pos_rpt_time' or something else? The purpose is to then do a frequency analysis (with keeptrials = 'yes'). Best, Stephen -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Nov 16 14:31:53 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 16 Nov 2017 13:31:53 +0000 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: References: Message-ID: <59225E01-B07C-426B-96A4-9A669C82276C@donders.ru.nl> Hi Stephen, I think that it is currently not possible to pass the output of ft_sourceanalysis to ft_freqanalysis directly, since ft_freqanalysis expects channel-level type data in the input. The exact details of the computation depend a bit on the amount of RAM you have, and on what exactly you want to achieve. If it’s your intention to generate frequency spectra for many dipole locations (e.g. >1000 or so) I would consider the following: - compute spatial filters (cfg.keepfilter = ‘yes’); - use a for-loop across (chunks of) dipole locations to create ‘virtual channel data’, by premultiplying the sensor-level data.trial (loop across trials) with the location specific spatial filter. - stuff all this into a data-structure that looks like a raw data structure; - pass this to ft_freqanalysis Alternatively, you could consider using a parcellation approach, if you think it makes sense to reduce the number of spatial locations a bit, although theoretically it should be possible to create a parcellation that consists of just a single dipole per parcel. In this context, you could look into the inner workings of ft_sourceparcellate, which returns a data structure that ft_freqanalysis can work with. Whether ft_sourceparcellate can swallow single trial source data, I am not sure. Best wishes, JM > On 16 Nov 2017, at 12:36, Stephen Whitmarsh wrote: > > Hi FieldTrippers, > > I was wondering is there is a recommend/most consistent way to represent trial x pos x time data from an LCMV beamformer, also considering the dimord. In other words: > > with: > > data.method = 'singletrial' > > should I use: > > data.trial{pos} = [rpt x time] > data.dimord = '{pos}_rpt_time' > > or rather: > > data.trial = {pos x rpt x time} > data.dimord = 'pos_rpt_time' > > or something else? The purpose is to then do a frequency analysis (with keeptrials = 'yes'). > > Best, > Stephen > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Thu Nov 16 14:38:06 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 16 Nov 2017 13:38:06 +0000 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: References: Message-ID: Hi again Stephen, I forgot to mention a third approach: you can compute your spatial filter with cfg.method = ‘lcmv’ and cfg.lcmv.keepfilter = ‘yes’, and subsequently compute the source level spectra by applying these spatial filters to the sensor level fourier spectra. Best wishes, Jan-Mathijs > On 16 Nov 2017, at 12:36, Stephen Whitmarsh wrote: > > Hi FieldTrippers, > > I was wondering is there is a recommend/most consistent way to represent trial x pos x time data from an LCMV beamformer, also considering the dimord. In other words: > > with: > > data.method = 'singletrial' > > should I use: > > data.trial{pos} = [rpt x time] > data.dimord = '{pos}_rpt_time' > > or rather: > > data.trial = {pos x rpt x time} > data.dimord = 'pos_rpt_time' > > or something else? The purpose is to then do a frequency analysis (with keeptrials = 'yes'). > > Best, > Stephen > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From stephen.whitmarsh at gmail.com Thu Nov 16 14:40:41 2017 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 16 Nov 2017 14:40:41 +0100 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: <59225E01-B07C-426B-96A4-9A669C82276C@donders.ru.nl> References: <59225E01-B07C-426B-96A4-9A669C82276C@donders.ru.nl> Message-ID: Hi Jan-Mathijs, Thanks. In fact, I did what you suggest, but this entails a lot (nr. of positions) or creating and clearing a temporary variable. For a reason I do not understand (but which I encountered before), MATLAB seems not able to deal with this, and runs into memory problems. I suspect it is not able to create and clear many variables in a row, so that althought memory load does not seem to increase, it *will *break with an out-of-memory problem. I therefor started with this approach, but alas, I now understand that it was a wrong turn. So, I am in a pickle now, as neither option works... Best, Stephen On 16 November 2017 at 14:31, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Hi Stephen, > > I think that it is currently not possible to pass the output of > ft_sourceanalysis to ft_freqanalysis directly, since ft_freqanalysis > expects channel-level type data in the input. > The exact details of the computation depend a bit on the amount of RAM you > have, and on what exactly you want to achieve. > > If it’s your intention to generate frequency spectra for many dipole > locations (e.g. >1000 or so) I would consider the following: > > - compute spatial filters (cfg.keepfilter = ‘yes’); > - use a for-loop across (chunks of) dipole locations to create ‘virtual > channel data’, by premultiplying the sensor-level data.trial (loop across > trials) with the location specific spatial filter. > - stuff all this into a data-structure that looks like a raw data > structure; > - pass this to ft_freqanalysis > > > Alternatively, you could consider using a parcellation approach, if you > think it makes sense to reduce the number of spatial locations a bit, > although theoretically it should be possible to create a parcellation that > consists of just a single dipole per parcel. In this context, you could > look into the inner workings of ft_sourceparcellate, which returns a data > structure that ft_freqanalysis can work with. Whether ft_sourceparcellate > can swallow single trial source data, I am not sure. > > Best wishes, > > JM > > > > > On 16 Nov 2017, at 12:36, Stephen Whitmarsh > wrote: > > > > Hi FieldTrippers, > > > > I was wondering is there is a recommend/most consistent way to represent > trial x pos x time data from an LCMV beamformer, also considering the > dimord. In other words: > > > > with: > > > > data.method = 'singletrial' > > > > should I use: > > > > data.trial{pos} = [rpt x time] > > data.dimord = '{pos}_rpt_time' > > > > or rather: > > > > data.trial = {pos x rpt x time} > > data.dimord = 'pos_rpt_time' > > > > or something else? The purpose is to then do a frequency analysis (with > keeptrials = 'yes'). > > > > Best, > > Stephen > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Nov 16 14:44:36 2017 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 16 Nov 2017 14:44:36 +0100 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: References: <59225E01-B07C-426B-96A4-9A669C82276C@donders.ru.nl> Message-ID: For completeness, this is what I did in the way you suggest (I think). Note data is downsampled to 100Hz, and every trial is 1 second long. So I do not think that RAM should be a concern (I have about 128 Gig to work with): % load common filter [source_common, leadfield] = WANDER_common_filter_LCMV_MAG(isubject,rootpath,0); % prepare source datastructure source = rmfield(source_common,'avg'); source.pow = nan(size(source.pos,1),size(data_MEG_timebinned_append.trial,2),2); source.trialinfo = data_MEG_timebinned_append.trialinfo; for ivoxel = find(source.inside)' disp(['progress: ' round(num2str(ivoxel/size(find(source.inside),1)*100)) '%']); % make timecourse datastructure, clear first so that MATLAB does source_timecourse.trial{size(data_MEG_timebinned_append.trial,2)} = []; source_timecourse.label = {'voxel'}; source_timecourse.fsample = 100; source_timecourse.time = data_MEG_timebinned_append.time; for itrial = 1:size(data_MEG_timebinned_append.trial,2) source_timecourse.trial{itrial} = svdfft(source_common.avg.filter{ivoxel} * data_MEG_timebinned_append.trial{itrial}, 1); end % do mtmconvol on faux data structure cfg = []; cfg.channel = 'all'; cfg.method = 'mtmfft'; cfg.keeptrials = 'yes'; cfg.foilim = [10,11]; cfg.taper = 'hanning'; FFT = ft_freqanalysis(cfg, source_timecourse); clear source_timecourse source.pow(ivoxel,:,:) = squeeze(FFT.powspctrm); clear FFT memory end On 16 November 2017 at 14:40, Stephen Whitmarsh wrote: > Hi Jan-Mathijs, > > Thanks. In fact, I did what you suggest, but this entails a lot (nr. of > positions) or creating and clearing a temporary variable. For a reason I do > not understand (but which I encountered before), MATLAB seems not able to > deal with this, and runs into memory problems. I suspect it is not able to > create and clear many variables in a row, so that althought memory load > does not seem to increase, it *will *break with an out-of-memory problem. > I therefor started with this approach, but alas, I now understand that it > was a wrong turn. > > So, I am in a pickle now, as neither option works... > > Best, > Stephen > > On 16 November 2017 at 14:31, Schoffelen, J.M. (Jan Mathijs) < > jan.schoffelen at donders.ru.nl> wrote: > >> Hi Stephen, >> >> I think that it is currently not possible to pass the output of >> ft_sourceanalysis to ft_freqanalysis directly, since ft_freqanalysis >> expects channel-level type data in the input. >> The exact details of the computation depend a bit on the amount of RAM >> you have, and on what exactly you want to achieve. >> >> If it’s your intention to generate frequency spectra for many dipole >> locations (e.g. >1000 or so) I would consider the following: >> >> - compute spatial filters (cfg.keepfilter = ‘yes’); >> - use a for-loop across (chunks of) dipole locations to create ‘virtual >> channel data’, by premultiplying the sensor-level data.trial (loop across >> trials) with the location specific spatial filter. >> - stuff all this into a data-structure that looks like a raw data >> structure; >> - pass this to ft_freqanalysis >> >> >> Alternatively, you could consider using a parcellation approach, if you >> think it makes sense to reduce the number of spatial locations a bit, >> although theoretically it should be possible to create a parcellation that >> consists of just a single dipole per parcel. In this context, you could >> look into the inner workings of ft_sourceparcellate, which returns a data >> structure that ft_freqanalysis can work with. Whether ft_sourceparcellate >> can swallow single trial source data, I am not sure. >> >> Best wishes, >> >> JM >> >> >> >> > On 16 Nov 2017, at 12:36, Stephen Whitmarsh < >> stephen.whitmarsh at gmail.com> wrote: >> > >> > Hi FieldTrippers, >> > >> > I was wondering is there is a recommend/most consistent way to >> represent trial x pos x time data from an LCMV beamformer, also considering >> the dimord. In other words: >> > >> > with: >> > >> > data.method = 'singletrial' >> > >> > should I use: >> > >> > data.trial{pos} = [rpt x time] >> > data.dimord = '{pos}_rpt_time' >> > >> > or rather: >> > >> > data.trial = {pos x rpt x time} >> > data.dimord = 'pos_rpt_time' >> > >> > or something else? The purpose is to then do a frequency analysis (with >> keeptrials = 'yes'). >> > >> > Best, >> > Stephen >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Nov 16 15:43:21 2017 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 16 Nov 2017 15:43:21 +0100 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: References: Message-ID: Hi again again Jan-Mathijs, Ah yes, that does seem like the most elegant and memory-efficient approach! I will need to figure out how to apply spatial filters to Fourier (and redo my sensor level spectral analysis to Fourier). Shout-out to the list: anyone have an example of applying spatial filters to Fourier that I could use? Thanks again again, Stephen On 16 November 2017 at 14:38, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Hi again Stephen, > > I forgot to mention a third approach: you can compute your spatial filter > with cfg.method = ‘lcmv’ and cfg.lcmv.keepfilter = ‘yes’, and subsequently > compute the source level spectra by applying these spatial filters to the > sensor level fourier spectra. > > Best wishes, > Jan-Mathijs > > > > > > On 16 Nov 2017, at 12:36, Stephen Whitmarsh > wrote: > > > > Hi FieldTrippers, > > > > I was wondering is there is a recommend/most consistent way to represent > trial x pos x time data from an LCMV beamformer, also considering the > dimord. In other words: > > > > with: > > > > data.method = 'singletrial' > > > > should I use: > > > > data.trial{pos} = [rpt x time] > > data.dimord = '{pos}_rpt_time' > > > > or rather: > > > > data.trial = {pos x rpt x time} > > data.dimord = 'pos_rpt_time' > > > > or something else? The purpose is to then do a frequency analysis (with > keeptrials = 'yes'). > > > > Best, > > Stephen > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Nov 16 15:52:06 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 16 Nov 2017 14:52:06 +0000 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: References: Message-ID: <527ADD8B-D856-4355-9544-5AE785C5A9AD@donders.ru.nl> Hi Stephen, siz = size(freq.fourierspctrm); F = freq.fourierspctrm; F = permute(freq.fourierspctrm,[2 1 3]); F = reshape(F,siz(2),siz(1)*siz(3)); sourceF = svdfft(source.avg.filter{some_index}*F); % by the way, your use in the time domain per trial is dangerous, because it does a trial specific rotation, which you may or may not want sourceF = reshape(sourceF, siz(1), siz(3)); sourceP = abs(sourceF).^2; Of zoiets. Cheers, JM On 16 Nov 2017, at 15:43, Stephen Whitmarsh > wrote: Hi again again Jan-Mathijs, Ah yes, that does seem like the most elegant and memory-efficient approach! I will need to figure out how to apply spatial filters to Fourier (and redo my sensor level spectral analysis to Fourier). Shout-out to the list: anyone have an example of applying spatial filters to Fourier that I could use? Thanks again again, Stephen On 16 November 2017 at 14:38, Schoffelen, J.M. (Jan Mathijs) > wrote: Hi again Stephen, I forgot to mention a third approach: you can compute your spatial filter with cfg.method = ‘lcmv’ and cfg.lcmv.keepfilter = ‘yes’, and subsequently compute the source level spectra by applying these spatial filters to the sensor level fourier spectra. Best wishes, Jan-Mathijs > On 16 Nov 2017, at 12:36, Stephen Whitmarsh > wrote: > > Hi FieldTrippers, > > I was wondering is there is a recommend/most consistent way to represent trial x pos x time data from an LCMV beamformer, also considering the dimord. In other words: > > with: > > data.method = 'singletrial' > > should I use: > > data.trial{pos} = [rpt x time] > data.dimord = '{pos}_rpt_time' > > or rather: > > data.trial = {pos x rpt x time} > data.dimord = 'pos_rpt_time' > > or something else? The purpose is to then do a frequency analysis (with keeptrials = 'yes'). > > Best, > Stephen > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Nov 16 16:36:11 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 16 Nov 2017 15:36:11 +0000 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: References: Message-ID: Hi again Stephen, Just out of curiosity: why do you use a time-domain beamformer if you are interested in reconstructing a narrowband response? Best wishes, Jan-Mathijs On 16 Nov 2017, at 15:43, Stephen Whitmarsh > wrote: Hi again again Jan-Mathijs, Ah yes, that does seem like the most elegant and memory-efficient approach! I will need to figure out how to apply spatial filters to Fourier (and redo my sensor level spectral analysis to Fourier). Shout-out to the list: anyone have an example of applying spatial filters to Fourier that I could use? Thanks again again, Stephen On 16 November 2017 at 14:38, Schoffelen, J.M. (Jan Mathijs) > wrote: Hi again Stephen, I forgot to mention a third approach: you can compute your spatial filter with cfg.method = ‘lcmv’ and cfg.lcmv.keepfilter = ‘yes’, and subsequently compute the source level spectra by applying these spatial filters to the sensor level fourier spectra. Best wishes, Jan-Mathijs > On 16 Nov 2017, at 12:36, Stephen Whitmarsh > wrote: > > Hi FieldTrippers, > > I was wondering is there is a recommend/most consistent way to represent trial x pos x time data from an LCMV beamformer, also considering the dimord. In other words: > > with: > > data.method = 'singletrial' > > should I use: > > data.trial{pos} = [rpt x time] > data.dimord = '{pos}_rpt_time' > > or rather: > > data.trial = {pos x rpt x time} > data.dimord = 'pos_rpt_time' > > or something else? The purpose is to then do a frequency analysis (with keeptrials = 'yes'). > > Best, > Stephen > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Nov 16 17:42:41 2017 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 16 Nov 2017 17:42:41 +0100 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: References: Message-ID: Hi Mathijs, I know. Long story. Let's just say it's a check :-) I've done the same with DICS already. Cheers, Stephen On 16 November 2017 at 16:36, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Hi again Stephen, > > Just out of curiosity: why do you use a time-domain beamformer if you are > interested in reconstructing a narrowband response? > > Best wishes, > Jan-Mathijs > > On 16 Nov 2017, at 15:43, Stephen Whitmarsh > wrote: > > Hi again again Jan-Mathijs, > > Ah yes, that does seem like the most elegant and memory-efficient > approach! > I will need to figure out how to apply spatial filters to Fourier (and > redo my sensor level spectral analysis to Fourier). > > Shout-out to the list: anyone have an example of applying spatial filters > to Fourier that I could use? > > Thanks again again, > Stephen > > On 16 November 2017 at 14:38, Schoffelen, J.M. (Jan Mathijs) < > jan.schoffelen at donders.ru.nl> wrote: > >> Hi again Stephen, >> >> I forgot to mention a third approach: you can compute your spatial filter >> with cfg.method = ‘lcmv’ and cfg.lcmv.keepfilter = ‘yes’, and subsequently >> compute the source level spectra by applying these spatial filters to the >> sensor level fourier spectra. >> >> Best wishes, >> Jan-Mathijs >> >> >> >> >> > On 16 Nov 2017, at 12:36, Stephen Whitmarsh < >> stephen.whitmarsh at gmail.com> wrote: >> > >> > Hi FieldTrippers, >> > >> > I was wondering is there is a recommend/most consistent way to >> represent trial x pos x time data from an LCMV beamformer, also considering >> the dimord. In other words: >> > >> > with: >> > >> > data.method = 'singletrial' >> > >> > should I use: >> > >> > data.trial{pos} = [rpt x time] >> > data.dimord = '{pos}_rpt_time' >> > >> > or rather: >> > >> > data.trial = {pos x rpt x time} >> > data.dimord = 'pos_rpt_time' >> > >> > or something else? The purpose is to then do a frequency analysis (with >> keeptrials = 'yes'). >> > >> > Best, >> > Stephen >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mireia.torralba at upf.edu Wed Nov 22 10:41:51 2017 From: mireia.torralba at upf.edu (TORRALBA CUELLO, MIREIA) Date: Wed, 22 Nov 2017 10:41:51 +0100 Subject: [FieldTrip] Phd position in Cognitive Neuroscience in UPF (Barcelona) Message-ID: Please find attached information about a PhD position in Cognitive Neuroscience at Multisensory Research Group (UPF, Barcelona) Deadline: Feb 1st, 2018 Start date: May/June 2018 Gross salary: Approx 27.800€/year Research money (travel etc...): 3.500€/year Requirements*: Master's degree in the EU or equivalent (to be decided by the host university at application), and have not worked/resided in Spain for more than 12 months (within the last 3y). *Phd position in Cognitive Neuroscience: Neural predictors of Memory Perception and attention (Prof.Salvador Soto-Faraco)* *POSITION DESCRIPTION* *-Research Project / Research Group Description:* How “...the brain enables the mind...” is one of the core questions in neuroscience. Understanding this relationship will lead to improvements in the mitigation of brain disease. One of the major sources of evidence on how neurophysiological activity relates to mental phenomena comes from the realization that fluctuations in neural activity could be at the heart of cognitive processes. In fact, it is well known that ongoing brain activity itself is highly organized, so that neural communication (local, and long range) seems to capitalize on the fine temporal structure of neural activity. Consequently responses to sensory events depend strongly on the momentary state of the system. The overarching goal of the research project hosting the potential PhD candidate is to capitalize on the relationship between brain oscillations, brain states and cognitive processes to anticipate and be able to modulate the outcome of these processes via real-time neurodevices based on Brain Computer Interfaces. The research lines hosting the PhD candidate address the link between the pattern of oscillatory brain activity and three sets of concrete cognitive processes. (1) Memory encoding in healthy humans and/or patients with Mild Cognitive Impairment. (2) Attention and perception in real-life scenarios. And, (3) perceptual conflict and awareness. The overarching goal is to be able to find predictors (biomarkers) for these processes and be able to anticipate optimal brain states (windows of opportunity) for the success of these behaviours. To this end, we use psychophysics, human electroencephalography (EEG), and Transcranial Magnetic Stimulation (TMS). Psychophysics is essential to measure the behavioural expression of cognitive processes. EEG is sensitive to post-synaptic potentials of large neuron populations, and is an indirect index of neural activity. In order to infer brain states, we capitalize on a variety of measures from the EEG: spectral power, instantaneous phase, and temporal/spatial coherence of oscillatory activity. Neurostimulation (TMS) is used to probe causality. The MRG is part of the CBC master, has 3 postdoc researchers (specialized in signal processing, bioengineering, and neuropsychology) 3 Phds, and support staff. Our research is supported by EU and local funding. *-Job position description:* Role: The successful candidate will lead a research line which falls amongst the overall projects of the MRG laboratory (described above). It is expected that the candidate will have a prior motivation for cognitive neuroscience and will contribute in an active way to define the particular project from its inception, formulation of hypotheses, experimental designs, measurement and analysis, and interpretation of the data. In order to accomplish these tasks, the PhD candidate will of course count with the support of the MRG staff and knowledge base, and the guidance of Prof Soto-Faraco as well as senior members of the laboratory. Dissemination of the research output, and networking with other local, or external experts as well as advanced post-docs and phd students will be encouraged and fostered. Responsibilities: The candidate will be mainly responsible for the implementation of the assigned research tasks conducive toward the PhD project, the careful and systematic carrying out of the experimental work. Other responsibilities will be assigned commensurate with the PhD’s capacity and level of seniority. Amongst them, like other members of the team, the PhD student will contribute to the group activities (e.g., helping organize talks, group meetings, presenting the findings in conferences) , and to the training and support of other junior members of the laboratory (eventual supervision of master or degree students). Finally, the Phd candidate will also be responsible to provide timely responses to requests from the funding body, including progress reports, as well as to attend the meetings s/he might be called to, from the funding agency. Skills: Background in Biology, Bioengineering, Experimental Psychology or other fields related to Cognitive Neuroscience. Prior experience or background in Brain Computer Interfaces. Concrete experience with experimental work in the field of the cognitive neurosciences, preferably with psychophysics and/or electrophysiology (EEG, MEG). Knowledge of signal processing. Others: High motivation, proactivity and team work are very desirable. *RELATED LINK TO THE POSITION* http://www.mrg.upf.edu/node/112 *CENTER* Dept. of Information & Communication Technologies, DTIC-UPF https://portal.upf.edu/es/web/etic/inicio *CENTER DESCRIPTION* The Department of Information and Communication Technologies (DTIC) of Universitat Pompeu Fabra covers a broad range of research topics: Computation and Intelligent Systems; Multimedia Technologies; Networks and Communications; Computational Biology and Biomedical Systems; and the Center of Brain and Cognition (CBC). This broad spectrum of topics reflects the current interdisciplinary reality of cutting edge research in ICT. The DTIC is now running a Maria de Maeztu Strategic Research Program on data-driven knowledge extraction, boosting synergistic research initiatives across our different research areas. The DTIC consistently ranks among the top computer science departments in Spain (e.g. the only computer science department from an Spanish university that has even been included in the top 100 of the Shanghai Ranking). Its PhD program offers advanced training in this interdisciplinary field, becoming an innovative and unique program in Spain. The DTIC PhD program has been growing steadily and currently hosts about 140 PhD students and 40 supervisors. The program received a Mention of Excellence award from the Ministry of Science and Innovation in 2011. The UPF university was awarded in 2010 the distinction of International Excellence Campus by the Spanish Ministry of Education and it is widely considered to be one of the best universities in Spain (e.g. is the top Spanish university according to 2013 Times Higher Education Ranking). The UPF is located in Barcelona. Its excellent location on the shores of the Mediterranean, its gentle climate, its open, cosmopolitan character, its gastronomy and architecture make Barcelona an extraordinary place to live. The DTIC is sited in UPF's Communication Campus, which was opened in 2009 and is located within the vibrant 22@ technological district of Barcelona. *Indicators: * - Research incomes: 15.6 M€ / year - 67 FP7 projects participated and coordinated by 26 staff members (> 60% UPF EU funds) including 13 prestigious ERC Grants, the Human Brain Project - Leader in Spain with > 5% of all the competitive funds obtained by Spanish Universities, Maria de Maeztu Strategic Program. - Consolidated scientific productivity ~200 articles/year, > 75% Q1 international journals - 50% scientific papers and articles with at least one international collaborator *ADDRESS* Roc Boronat, 138 - edifici Tànger, 08018 Barcelona, Barcelona *GROUP DISCIPLINES* Life Science Panel *GROUP LEADER* Prof.Salvador Soto-Faraco salvador.soto at upf.edu www.mrg.upf.edu Mireia Torralba Cuello Multisensory Research Group Center for Brain and Cognition, Universitat Pompeu Fabra Address: Edifici Mercè Rodoreda 24.313 c\ Ramon Trias Fargas, 25-27 08005 Barcelona http://www.mrg.upf.edu Tel +34 935422745 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonas at obleser.de Wed Nov 22 19:00:13 2017 From: jonas at obleser.de (Jonas Obleser) Date: Wed, 22 Nov 2017 19:00:13 +0100 Subject: [FieldTrip] =?utf-8?q?Postdoc_opportunity=2C_modelling/EEG/MRI_Ob?= =?utf-8?q?leser_lab_in_L=C3=BCbeck?= Message-ID: Dear colleagues around the globe, On somewhat shot notice, we have another postdoc Position in my lab available. Funded through the ERC Project «AUDADAPT», starting asap. Deadline for electronic, simple applications per email is Nov 30. Thanks for spreading the word! Best wishes, Jonas https://www.uni-luebeck.de/fileadmin/uzl_personal/stellenausschreibungen/1060_17_Ausschreibung_Obleser_Postdoc2018_ERC_EN.pdf Jonas Obleser Professor University of Lübeck Department of Psychology MFC 8, Maria-Goeppert-Straße 9a 23562 Lübeck, Germany Phone +49 (0)451 3101 3620 Mobile +49 (0)171 6993337 jonas.obleser at uni-luebeck.de http://auditorycognition.com From liyy90 at 163.com Thu Nov 23 15:44:10 2017 From: liyy90 at 163.com (liyy90) Date: Thu, 23 Nov 2017 22:44:10 +0800 (CST) Subject: [FieldTrip] Phd position in Cognitive Neuroscience in UPF (Barcelona) In-Reply-To: References: Message-ID: I am interested in this program. How to apply? At 2017-11-22 17:41:51, "TORRALBA CUELLO, MIREIA" wrote: Please find attached information about a PhD position in Cognitive Neuroscience at Multisensory Research Group (UPF, Barcelona) Deadline: Feb 1st, 2018 Start date: May/June 2018 Gross salary: Approx 27.800€/year Research money (travel etc...): 3.500€/year Requirements*: Master's degree in the EU or equivalent (to be decided by the host university at application), and have not worked/resided in Spain for more than 12 months (within the last 3y). Phd position in Cognitive Neuroscience: Neural predictors of Memory Perception and attention (Prof.Salvador Soto-Faraco) POSITION DESCRIPTION -Research Project / Research Group Description: How “...the brain enables the mind...” is one of the core questions in neuroscience. Understanding this relationship will lead to improvements in the mitigation of brain disease. One of the major sources of evidence on how neurophysiological activity relates to mental phenomena comes from the realization that fluctuations in neural activity could be at the heart of cognitive processes. In fact, it is well known that ongoing brain activity itself is highly organized, so that neural communication (local, and long range) seems to capitalize on the fine temporal structure of neural activity. Consequently responses to sensory events depend strongly on the momentary state of the system. The overarching goal of the research project hosting the potential PhD candidate is to capitalize on the relationship between brain oscillations, brain states and cognitive processes to anticipate and be able to modulate the outcome of these processes via real-time neurodevices based on Brain Computer Interfaces. The research lines hosting the PhD candidate address the link between the pattern of oscillatory brain activity and three sets of concrete cognitive processes. (1) Memory encoding in healthy humans and/or patients with Mild Cognitive Impairment. (2) Attention and perception in real-life scenarios. And, (3) perceptual conflict and awareness. The overarching goal is to be able to find predictors (biomarkers) for these processes and be able to anticipate optimal brain states (windows of opportunity) for the success of these behaviours. To this end, we use psychophysics, human electroencephalography (EEG), and Transcranial Magnetic Stimulation (TMS). Psychophysics is essential to measure the behavioural expression of cognitive processes. EEG is sensitive to post-synaptic potentials of large neuron populations, and is an indirect index of neural activity. In order to infer brain states, we capitalize on a variety of measures from the EEG: spectral power, instantaneous phase, and temporal/spatial coherence of oscillatory activity. Neurostimulation (TMS) is used to probe causality. The MRG is part of the CBC master, has 3 postdoc researchers (specialized in signal processing, bioengineering, and neuropsychology) 3 Phds, and support staff. Our research is supported by EU and local funding. -Job position description: Role: The successful candidate will lead a research line which falls amongst the overall projects of the MRG laboratory (described above). It is expected that the candidate will have a prior motivation for cognitive neuroscience and will contribute in an active way to define the particular project from its inception, formulation of hypotheses, experimental designs, measurement and analysis, and interpretation of the data. In order to accomplish these tasks, the PhD candidate will of course count with the support of the MRG staff and knowledge base, and the guidance of Prof Soto-Faraco as well as senior members of the laboratory. Dissemination of the research output, and networking with other local, or external experts as well as advanced post-docs and phd students will be encouraged and fostered. Responsibilities: The candidate will be mainly responsible for the implementation of the assigned research tasks conducive toward the PhD project, the careful and systematic carrying out of the experimental work. Other responsibilities will be assigned commensurate with the PhD’s capacity and level of seniority. Amongst them, like other members of the team, the PhD student will contribute to the group activities (e.g., helping organize talks, group meetings, presenting the findings in conferences) , and to the training and support of other junior members of the laboratory (eventual supervision of master or degree students). Finally, the Phd candidate will also be responsible to provide timely responses to requests from the funding body, including progress reports, as well as to attend the meetings s/he might be called to, from the funding agency. Skills: Background in Biology, Bioengineering, Experimental Psychology or other fields related to Cognitive Neuroscience. Prior experience or background in Brain Computer Interfaces. Concrete experience with experimental work in the field of the cognitive neurosciences, preferably with psychophysics and/or electrophysiology (EEG, MEG). Knowledge of signal processing. Others: High motivation, proactivity and team work are very desirable. RELATED LINK TO THE POSITION http://www.mrg.upf.edu/node/112 CENTER Dept. of Information & Communication Technologies, DTIC-UPF https://portal.upf.edu/es/web/etic/inicio CENTER DESCRIPTION The Department of Information and Communication Technologies (DTIC) of Universitat Pompeu Fabra covers a broad range of research topics: Computation and Intelligent Systems; Multimedia Technologies; Networks and Communications; Computational Biology and Biomedical Systems; and the Center of Brain and Cognition (CBC). This broad spectrum of topics reflects the current interdisciplinary reality of cutting edge research in ICT. The DTIC is now running a Maria de Maeztu Strategic Research Program on data-driven knowledge extraction, boosting synergistic research initiatives across our different research areas. The DTIC consistently ranks among the top computer science departments in Spain (e.g. the only computer science department from an Spanish university that has even been included in the top 100 of the Shanghai Ranking). Its PhD program offers advanced training in this interdisciplinary field, becoming an innovative and unique program in Spain. The DTIC PhD program has been growing steadily and currently hosts about 140 PhD students and 40 supervisors. The program received a Mention of Excellence award from the Ministry of Science and Innovation in 2011. The UPF university was awarded in 2010 the distinction of International Excellence Campus by the Spanish Ministry of Education and it is widely considered to be one of the best universities in Spain (e.g. is the top Spanish university according to 2013 Times Higher Education Ranking). The UPF is located in Barcelona. Its excellent location on the shores of the Mediterranean, its gentle climate, its open, cosmopolitan character, its gastronomy and architecture make Barcelona an extraordinary place to live. The DTIC is sited in UPF's Communication Campus, which was opened in 2009 and is located within the vibrant 22@ technological district of Barcelona. Indicators: Research incomes: 15.6 M€ / year 67 FP7 projects participated and coordinated by 26 staff members (> 60% UPF EU funds) including 13 prestigious ERC Grants, the Human Brain Project Leader in Spain with > 5% of all the competitive funds obtained by Spanish Universities, Maria de Maeztu Strategic Program. Consolidated scientific productivity ~200 articles/year, > 75% Q1 international journals 50% scientific papers and articles with at least one international collaborator ADDRESS Roc Boronat, 138 - edifici Tànger, 08018 Barcelona, Barcelona GROUP DISCIPLINES Life Science Panel GROUP LEADER Prof.Salvador Soto-Faraco salvador.soto at upf.edu www.mrg.upf.edu Mireia Torralba Cuello Multisensory Research Group Center for Brain and Cognition, Universitat Pompeu Fabra Address: Edifici Mercè Rodoreda 24.313 c\ Ramon Trias Fargas, 25-27 08005 Barcelona http://www.mrg.upf.edu Tel +34 935422745 -------------- next part -------------- An HTML attachment was scrubbed... URL: From changa5 at mcmaster.ca Thu Nov 23 21:44:19 2017 From: changa5 at mcmaster.ca (Andrew Chang) Date: Thu, 23 Nov 2017 15:44:19 -0500 Subject: [FieldTrip] Grad Student Positions in Auditory Neuroscience, Human Interaction & Music Message-ID: *Graduate Student Positions in Auditory Neuroscience, Human Interaction & Music* *McMaster University* Two graduate student positions are available to work with *Dr. Laurel Trainor* who directs both the Infant Auditory Lab ( https://trainorlab.mcmaster.ca) and the LIVELab (https://LIVELab.mcmaster.ca) at McMaster University. Projects include understanding human interaction in musical ensembles using behaviour, motion capture and EEG measures; studying brain oscillations involved in predictive timing and predictive coding; musical development in infants and children; and applications using non-verbal measures to understand auditory perception and communicative processes in special populations such adults with dementia or hearing loss and children with Developmental Coordination Disorder. The research group is multidisciplinary with ties to Engineering, Health Science and Music. In addition to infant and adult behavioural and EEG labs, students will have access to the internationally acclaimed LIVELab, a research-concert hall capable of simulating almost any acoustical environment and equipped with multiperson EEG, physiology, motion capture and more (https://LIVELab.mcmaster.ca). Applicants should have a Bachelor’s degree in Psychology, Neuroscience, Cognitive Science, Engineering, Computer Science or other affiliated disciplines. General information on the graduate program can be found here: https://science.mcmaster.ca/pnb/graduate-studies. Initial inquiries can be directed to Dr. Trainor at LJT at mcmaster.ca. Please include a CV and unofficial transcript with your inquiry. Papers from the lab can be accessed at https://trainorlab.mcmaster.ca/publications -- Andrew Chang, Ph.D. Candidate Vanier Canada Graduate Scholar http://changa5.wordpress.com/ Auditory Development Lab Department of Psychology, Neuroscience & Behaviour McMaster University -------------- next part -------------- An HTML attachment was scrubbed... URL: From clh at pku.edu.cn Fri Nov 24 00:57:47 2017 From: clh at pku.edu.cn (=?UTF-8?Q?=E9=99=88=E7=AB=8B=E7=BF=B0_=28Lihan_Chen=29?=) Date: Fri, 24 Nov 2017 07:57:47 +0800 (GMT+08:00) Subject: [FieldTrip] About a demo prog in fieldtrip- ERP analysis Message-ID: <1816d6b8.15bae.15feb50e32d.Coremail.clh@pku.edu.cn> Dear colleagues I am learning to use fieldtrip to analysis eyetracking data. And i found this demo very helpful. http://www.fieldtriptoolbox.org/example/use_simulated_erps_to_explore_cluster_statistics However, when i run this command: difference = ft_math(cfg, timelock1, timelock2); it generated the following and i can not go through the whole demo "Warning: timelock structure contains field with and without repetitions selecting these fields that have repetitions: trial removing these fields that do not have repetitions: avg, dof, var Warning: timelock structure contains field with and without repetitions selecting these fields that have repetitions: trial removing these fields that do not have repetitions: avg, dof, var Error using ft_notification (line 340) the requested parameter is not present in the data Error in ft_error (line 39) ft_notification(varargin{:}); Error in ft_math (line 151) ft_error('the requested parameter is not present in the data');" Would you please kindly find time to instruct how to make it run so that i can how a look how the final results look like? By the way, if i have 12 subjects, with two conditions ('congruent', 'incongruent'). Each condition has 1000 data points (1 second), so that how is the cfg.design i should make? Thank you very much in advance! Best, Lihan chen Peking Uiversity -------------- next part -------------- An HTML attachment was scrubbed... URL: From holmgren.jostein at gmail.com Tue Nov 28 21:29:07 2017 From: holmgren.jostein at gmail.com (Jostein Holmgren) Date: Tue, 28 Nov 2017 20:29:07 +0000 Subject: [FieldTrip] Trouble writing data from TMSi to FieldTrip buffer (Error message: "Cannot initiate device") Message-ID: <5066A2DB-146C-4BB2-8BAB-E9C19A0A6D63@gmail.com> Dear all, I am having trouble writing data from my TMSi Porti 7 system to the FieldTrip buffer. I have tried both the tmsidriver.exe and tmsi2ft.exe tools, but I’ve focused my efforts on the latter. I have the TMSi system connected to my PC via USB and have tested the connection by recording some data in Polybench without issue. When I attempt to run tmsi2ft nothing happens until I terminate the process, at which point the error message “Cannot initiate device” is displayed. The exact syntax I run in the cmd is tmsi2ft config.txt - where config.txt file contains the following (misc commented lines excluded) [select] 25=Blip25 samplerate=2048 For testing purposes I’ve only got a bipolar electrode connected to the TMSi system, which is the channel listed in the config file. For tmsidriver.exe I changed the sampling rate in parameter file to match my system to attempt to get it to work, but no success there either. I also have the buffer open when running tmsidriver.exe. The contents of preferences.txt is sampleRate(milliHz) BufSizeFactor savedata(0/1) 2048000 5 1 The TMSi Porti 7 system has a sampling rate of 2048Hz. The PC is running Windows 8.1 64-bit. I’m using fieldtrip-20171106. Any advice or suggestions is greatly appreciated. Best regards, Jostein Holmgren ---------------------- Jostein Holmgren DPhil Student (PRS) Nuffield Department of Clinical Neurosciences Wellcome Centre for Integrative Neuroimaging, FMRIB Building University of Oxford -------------- next part -------------- An HTML attachment was scrubbed... URL: From C.Mazzetti at donders.ru.nl Wed Nov 29 11:20:53 2017 From: C.Mazzetti at donders.ru.nl (Mazzetti, C. (Cecilia)) Date: Wed, 29 Nov 2017 10:20:53 +0000 Subject: [FieldTrip] problems plotting source grandaverage - no anatomy fied (ft_sourcegrandaverage) Message-ID: <389DA1293690C94C93E3A53201F6C91E59226B5C@EXPRD98.hosting.ru.nl> Hi Everyone, I am struggling with the source analysis and especially when averaging across subjects' source reconstruction. The analysis for every subject was done according to the tutorial (creating MNI aligned grids in individual head space). The point is when I try to plot the source grandaverage I get an error saying there is no 'anatomy' field in my data. I tried to use both sourceinterpolate or add the anatomy field manually to the gsource_grandaverage structure but nothing works. Here is what my source_grandaverage contains: ga_sources pow: [6×902629 double] dim: [91 109 91] freq: 9.9723 inside: [902629×1 logical] pos: [902629×3 double] unit: 'mm' cfg: [1×1 struct] Any help is appreciated! Thanks! Best, Cecilia -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Nov 29 12:53:36 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 29 Nov 2017 11:53:36 +0000 Subject: [FieldTrip] problems plotting source grandaverage - no anatomy fied (ft_sourcegrandaverage) In-Reply-To: <389DA1293690C94C93E3A53201F6C91E59226B5C@EXPRD98.hosting.ru.nl> References: <389DA1293690C94C93E3A53201F6C91E59226B5C@EXPRD98.hosting.ru.nl> Message-ID: Hi Cecilia, Have you tried to compute the average on the low-resolution solutions, and only do the interpolation on the average? This should be possible, because you use the ‘mni-aligned grids’. Also, ft_sourcegrandaverage is a dinosaur of a function, and it looks as if it hasn’t grown along with the rest of the code. The pasted matlab-structure looks a bit strange, and I can imagine that FieldTrip chokes on it. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 29 Nov 2017, at 11:20, Mazzetti, C. (Cecilia) > wrote: Hi Everyone, I am struggling with the source analysis and especially when averaging across subjects' source reconstruction. The analysis for every subject was done according to the tutorial (creating MNI aligned grids in individual head space). The point is when I try to plot the source grandaverage I get an error saying there is no 'anatomy' field in my data. I tried to use both sourceinterpolate or add the anatomy field manually to the gsource_grandaverage structure but nothing works. Here is what my source_grandaverage contains: ga_sources pow: [6×902629 double] dim: [91 109 91] freq: 9.9723 inside: [902629×1 logical] pos: [902629×3 double] unit: 'mm' cfg: [1×1 struct] Any help is appreciated! Thanks! Best, Cecilia _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From C.Mazzetti at donders.ru.nl Thu Nov 30 12:05:33 2017 From: C.Mazzetti at donders.ru.nl (Mazzetti, C. (Cecilia)) Date: Thu, 30 Nov 2017 11:05:33 +0000 Subject: [FieldTrip] fieldtrip Digest, Vol 84, Issue 18 In-Reply-To: References: Message-ID: <389DA1293690C94C93E3A53201F6C91E59227015@EXPRD98.hosting.ru.nl> Thanks Jan Mathijs! I don't know whether that's supposed to be the case, but the problem is 'solved' by choosing cfg.keepindividual='no' when computing sourcegrandaverage, before the interpolation. then everything is fine! Might be helpful for others maybe! Thanks! Best, Cecilia Cecilia Mazzetti - Ph.D. Candidate Donders Centre for Cognitive Neuroimaging, room 0.068 Kapittelweg 29 | 6525 EN Nijmegen ________________________________________ Da: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] per conto di fieldtrip-request at science.ru.nl [fieldtrip-request at science.ru.nl] Inviato: giovedì 30 novembre 2017 12.00 A: fieldtrip at science.ru.nl Oggetto: fieldtrip Digest, Vol 84, Issue 18 Send fieldtrip mailing list submissions to fieldtrip at science.ru.nl To subscribe or unsubscribe via the World Wide Web, visit https://mailman.science.ru.nl/mailman/listinfo/fieldtrip or, via email, send a message with subject or body 'help' to fieldtrip-request at science.ru.nl You can reach the person managing the list at fieldtrip-owner at science.ru.nl When replying, please edit your Subject line so it is more specific than "Re: Contents of fieldtrip digest..." Today's Topics: 1. Re: problems plotting source grandaverage - no anatomy fied (ft_sourcegrandaverage) (Schoffelen, J.M. (Jan Mathijs)) ---------------------------------------------------------------------- Message: 1 Date: Wed, 29 Nov 2017 11:53:36 +0000 From: "Schoffelen, J.M. (Jan Mathijs)" To: FieldTrip discussion list Subject: Re: [FieldTrip] problems plotting source grandaverage - no anatomy fied (ft_sourcegrandaverage) Message-ID: Content-Type: text/plain; charset="utf-8" Hi Cecilia, Have you tried to compute the average on the low-resolution solutions, and only do the interpolation on the average? This should be possible, because you use the ?mni-aligned grids?. Also, ft_sourcegrandaverage is a dinosaur of a function, and it looks as if it hasn?t grown along with the rest of the code. The pasted matlab-structure looks a bit strange, and I can imagine that FieldTrip chokes on it. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 29 Nov 2017, at 11:20, Mazzetti, C. (Cecilia) > wrote: Hi Everyone, I am struggling with the source analysis and especially when averaging across subjects' source reconstruction. The analysis for every subject was done according to the tutorial (creating MNI aligned grids in individual head space). The point is when I try to plot the source grandaverage I get an error saying there is no 'anatomy' field in my data. I tried to use both sourceinterpolate or add the anatomy field manually to the gsource_grandaverage structure but nothing works. Here is what my source_grandaverage contains: ga_sources pow: [6?902629 double] dim: [91 109 91] freq: 9.9723 inside: [902629?1 logical] pos: [902629?3 double] unit: 'mm' cfg: [1?1 struct] Any help is appreciated! Thanks! Best, Cecilia _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip End of fieldtrip Digest, Vol 84, Issue 18 ***************************************** From jan.schoffelen at donders.ru.nl Thu Nov 30 12:28:39 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 30 Nov 2017 11:28:39 +0000 Subject: [FieldTrip] problems plotting source grandaverage - no anatomy fied (ft_sourcegrandaverage) In-Reply-To: <389DA1293690C94C93E3A53201F6C91E59227015@EXPRD98.hosting.ru.nl> References: <389DA1293690C94C93E3A53201F6C91E59227015@EXPRD98.hosting.ru.nl> Message-ID: Hi Cecilia, I am glad that you have resolved it. Best wishes, Jan-Mathijs > On 30 Nov 2017, at 12:05, Mazzetti, C. (Cecilia) wrote: > > Thanks Jan Mathijs! > I don't know whether that's supposed to be the case, but the problem is 'solved' by choosing cfg.keepindividual='no' when computing sourcegrandaverage, before the interpolation. then everything is fine! > Might be helpful for others maybe! > > Thanks! > > Best, > Cecilia > > > Cecilia Mazzetti - Ph.D. Candidate > Donders Centre for Cognitive Neuroimaging, room 0.068 > Kapittelweg 29 | 6525 EN Nijmegen > > > ________________________________________ > Da: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] per conto di fieldtrip-request at science.ru.nl [fieldtrip-request at science.ru.nl] > Inviato: giovedì 30 novembre 2017 12.00 > A: fieldtrip at science.ru.nl > Oggetto: fieldtrip Digest, Vol 84, Issue 18 > > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Re: problems plotting source grandaverage - no anatomy fied > (ft_sourcegrandaverage) (Schoffelen, J.M. (Jan Mathijs)) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 29 Nov 2017 11:53:36 +0000 > From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] problems plotting source grandaverage - no > anatomy fied (ft_sourcegrandaverage) > Message-ID: > Content-Type: text/plain; charset="utf-8" > > Hi Cecilia, > > Have you tried to compute the average on the low-resolution solutions, and only do the interpolation on the average? > > This should be possible, because you use the ?mni-aligned grids?. > > Also, ft_sourcegrandaverage is a dinosaur of a function, and it looks as if it hasn?t grown along with the rest of the code. The pasted matlab-structure looks a bit strange, and I can imagine that FieldTrip chokes on it. > > Best wishes, > Jan-Mathijs > > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > On 29 Nov 2017, at 11:20, Mazzetti, C. (Cecilia) > wrote: > > Hi Everyone, > I am struggling with the source analysis and especially when averaging across subjects' source reconstruction. > The analysis for every subject was done according to the tutorial (creating MNI aligned grids in individual head space). > The point is when I try to plot the source grandaverage I get an error saying there is no 'anatomy' field in my data. > I tried to use both sourceinterpolate or add the anatomy field manually to the gsource_grandaverage structure but nothing works. > Here is what my source_grandaverage contains: > ga_sources > > pow: [6?902629 double] > dim: [91 109 91] > freq: 9.9723 > inside: [902629?1 logical] > pos: [902629?3 double] > unit: 'mm' > cfg: [1?1 struct] > > > > Any help is appreciated! Thanks! > > Best, > Cecilia > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 84, Issue 18 > ***************************************** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From wolpert at clipper.ens.fr Wed Nov 1 15:12:44 2017 From: wolpert at clipper.ens.fr (wolpert at clipper.ens.fr) Date: Wed, 1 Nov 2017 15:12:44 +0100 Subject: [FieldTrip] Create event structre from .mrk file Message-ID: <28f61ec01e3c4487dc3039704079e004.squirrel@squirrelmail.eleves.ens.fr> Dear all, I would like to read events from a .mrk file. Using ft_read_event does not work as it gives me the message that it's unsupported event format. By searching in the internet, I found the function "readmarkerfile" which is able to return the marker names and their samples, but in very inconvenient format. So is there any way of creating the classical event structure from files in .mrk format? Best regards, Nicolai From christian.merkel at med.ovgu.de Fri Nov 3 13:42:13 2017 From: christian.merkel at med.ovgu.de (christian.merkel at med.ovgu.de) Date: Fri, 3 Nov 2017 12:42:13 +0000 Subject: [FieldTrip] wMNE? Message-ID: <71D8A67A81D69A4CB5BE2B979021C26ECB016E51@ESEN4.imed.uni-magdeburg.de> Dear fieldtrip-community, Does the minimum-norm-estimate algorithm in ft_sourceanalysis support depth-weighting? Thank You, Christian From jan.schoffelen at donders.ru.nl Fri Nov 3 15:53:02 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 3 Nov 2017 14:53:02 +0000 Subject: [FieldTrip] wMNE? In-Reply-To: <71D8A67A81D69A4CB5BE2B979021C26ECB016E51@ESEN4.imed.uni-magdeburg.de> References: <71D8A67A81D69A4CB5BE2B979021C26ECB016E51@ESEN4.imed.uni-magdeburg.de> Message-ID: Hi Christian, Yes, depth weighting can be achieved by norm normalisation of the leadfields (using the normalize option in ft_prepare_leadfield), or by inclusion of a source-covariance matrix in the cfg to ft_sourceanalysis. Best wishes, Jan-Mathijs On 3 Nov 2017, at 13:42, christian.merkel at med.ovgu.de wrote: Dear fieldtrip-community, Does the minimum-norm-estimate algorithm in ft_sourceanalysis support depth-weighting? Thank You, Christian _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From fereshte.ramezani at gmail.com Sat Nov 4 07:53:09 2017 From: fereshte.ramezani at gmail.com (Fereshte) Date: Sat, 04 Nov 2017 06:53:09 +0000 Subject: [FieldTrip] Place Source Models in specific location Message-ID: Dear Experts, I'm so new to fieldtrip so I apologize if my question is very basic; How can I place source models in specific locations according to MRI image ( I've already made the head model based on FEM). Thanks for your attention. Regards, Fereshte -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Sat Nov 4 08:25:43 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Sat, 4 Nov 2017 07:25:43 +0000 Subject: [FieldTrip] Place Source Models in specific location In-Reply-To: References: Message-ID: Ferehste, Your question lacks specificity. I think the readers of this list need a bit more concrete input in order to think about answering your question. Is it about specific locations? Anatomical atlas based regions-of-interest? What inverse algorithm are you considering? Etc.? Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 4 Nov 2017, at 07:53, Fereshte > wrote: Dear Experts, I'm so new to fieldtrip so I apologize if my question is very basic; How can I place source models in specific locations according to MRI image ( I've already made the head model based on FEM). Thanks for your attention. Regards, Fereshte _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From fereshte.ramezani at gmail.com Sun Nov 5 12:05:58 2017 From: fereshte.ramezani at gmail.com (Fereshte) Date: Sun, 05 Nov 2017 11:05:58 +0000 Subject: [FieldTrip] Place Source Models in specific location In-Reply-To: References: Message-ID: I'm going to investigate the effect of segmentation on EEG forward problem( FreeSurfer segmentation and Filedtrip segmentation). I've already made the FE head model and placed the electrodes but I'm not really sure how to place the source models for such a comparison ( like to place source models where the two segmentations differ in GM). Thanks for your attention. On Sat, Nov 4, 2017 at 11:05 AM Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Ferehste, > > Your question lacks specificity. I think the readers of this list need a > bit more concrete input in order to think about answering your question. Is > it about specific locations? Anatomical atlas based regions-of-interest? > What inverse algorithm are you considering? Etc.? > > Best wishes, > > Jan-Mathijs > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > > On 4 Nov 2017, at 07:53, Fereshte wrote: > > Dear Experts, > I'm so new to fieldtrip so I apologize if my question is very basic; How > can I place source models in specific locations according to MRI image ( > I've already made the head model based on FEM). > Thanks for your attention. > Regards, > Fereshte > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsten.wolters at uni-muenster.de Mon Nov 6 09:01:59 2017 From: carsten.wolters at uni-muenster.de (Carsten Wolters) Date: Mon, 6 Nov 2017 09:01:59 +0100 Subject: [FieldTrip] Place Source Models in specific location In-Reply-To: References: Message-ID: <6def03a0-a71e-3a5d-981d-14bb921a9ea2@uni-muenster.de> Dear Ferehste, we have implemented the Venant approach for FEM source modeling in the Fieldtrip-SimBio pipeline. The Venant approach spreads monopolar sources around the dipole location in a way that the dipole location and moment is well approximated. You need to take care that all these monopoles are within the grey matter compartment. We call this the "Venant condition" that has to be fulfilled. You find detailed informations in http://www.sci.utah.edu/~wolters/PaperWolters/2014/VorwerkChoRamppHamerKnoescheWolters_NeuroImage_2014_Webversion.pdf or in Chapter 2.4.2 in http://www.sci.utah.edu/~wolters/PaperWolters/2016/PursiainenVorwerkWolters_PhysMedBiol_accepted2016_HDiv.pdf or very detailed in http://www.sci.utah.edu/~wolters/PaperWolters/2016/Vorwerk_Dissertation_2016.pdf BR      Carsten Am 05.11.2017 um 12:05 schrieb Fereshte: > I'm going to investigate the effect of segmentation on EEG forward > problem( FreeSurfer segmentation and Filedtrip segmentation). I've > already made the FE head model and placed the electrodes but I'm not > really sure how to place the source models for such a comparison ( > like to place source models where the two segmentations differ in GM). > Thanks for your attention. > > On Sat, Nov 4, 2017 at 11:05 AM Schoffelen, J.M. (Jan Mathijs) > > > wrote: > > Ferehste, > > Your question lacks specificity. I think the readers of this list > need a bit more concrete input in order to think about answering > your question. Is it about specific locations? Anatomical atlas > based regions-of-interest? What inverse algorithm are you > considering? Etc.? > > Best wishes, > > Jan-Mathijs > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > >> On 4 Nov 2017, at 07:53, Fereshte > > wrote: >> >> Dear Experts, >> I'm so new to fieldtrip so I apologize if my question is very >> basic; How can I place source models in specific locations >> according to MRI image ( I've already made the head model based >> on FEM). >> Thanks for your attention. >> Regards, >> Fereshte >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Prof. Dr.rer.nat. Carsten H. Wolters University of Münster Institute for Biomagnetism and Biosignalanalysis Malmedyweg 15 48149 Münster, Germany Phone: +49 (0)251 83 56904 +49 (0)251 83 56865 (secr.) Fax: +49 (0)251 83 56874 Email: carsten.wolters at uni-muenster.de Web: https://campus.uni-muenster.de/biomag/das-institut/mitarbeiter/carsten-wolters/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Mon Nov 6 17:41:21 2017 From: michelic72 at gmail.com (Cristiano Micheli) Date: Mon, 6 Nov 2017 17:41:21 +0100 Subject: [FieldTrip] reconstruction of EEG patterns on a 3D shape Message-ID: Dear Team I achieved a 3D reconstruction of a 64 electrodes Biosemi cap, as described in this tutorial: http://www.fieldtriptoolbox.org/tutorial/electrode Now I would like to visualise a [64x1] vector of EEG activity [64 electrodes x 1 time sample] as an interpolated overlay on top of the 3D electrodes reconstruction. Is there a quick way to obtain this by means of ft_sourceplot or other functions? All the best! Cris -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Nov 6 19:57:34 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 6 Nov 2017 18:57:34 +0000 Subject: [FieldTrip] reconstruction of EEG patterns on a 3D shape In-Reply-To: References: Message-ID: Ciao Cris, ft_plot_topo3d in the plotting module is your friend. Best wishes, JM J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 6 Nov 2017, at 17:41, Cristiano Micheli > wrote: Dear Team I achieved a 3D reconstruction of a 64 electrodes Biosemi cap, as described in this tutorial: http://www.fieldtriptoolbox.org/tutorial/electrode Now I would like to visualise a [64x1] vector of EEG activity [64 electrodes x 1 time sample] as an interpolated overlay on top of the 3D electrodes reconstruction. Is there a quick way to obtain this by means of ft_sourceplot or other functions? All the best! Cris _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From nadia.mueller at gmail.com Tue Nov 7 12:13:42 2017 From: nadia.mueller at gmail.com (Nadia Mueller) Date: Tue, 7 Nov 2017 12:13:42 +0100 Subject: [FieldTrip] Postdoc position and doctoral student position at the MEG in Erlangen Message-ID: Dear all, I'm offering one post-doc position and one position for a doctoral student in tinnitus research at the MEG Center in Erlangen (Germany) starting in February 2018. Please see the attached document for further information. It would be great if you could share this message with interested students, PhD students and postdocs around you. Thank you and best regards, Nadia Müller-Voggel -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Postdoc_Doctoral Student Position.pdf Type: application/pdf Size: 60316 bytes Desc: not available URL: From kirsten at carrot-village.de Tue Nov 7 12:16:51 2017 From: kirsten at carrot-village.de (Kirsten Herfurth) Date: Tue, 7 Nov 2017 12:16:51 +0100 (CET) Subject: [FieldTrip] Problem with ft_megrealign Message-ID: <1778422504.475907.1510053411840@communicator.strato.de> Dear all, I would like to apply the function ft_megrealign to my single subject meg data in order to do sensor level group analysis afterwards. I got stuck with the following error messages: Reference to non-existent field 'xgrid'. Error in ft_prepare_sourcemodel (line 709) xmin_indx = find(grid.xgrid==xmin); Error in ft_megrealign (line 249) grid = ft_prepare_sourcemodel(tmpcfg); I used the following configuration: cfg=[]; cfg.template = {MEGSubject1.grad; MEGSubject2.grad; MEGSubject3.grad, …}; cfg.headmodel = headmodel; cfg.headshape = strcat(Path2MEGData,'hs_file'); cfg.inwardshift = 0.025; % in meters cfg.vol.r=headmodel.r; cfg.vol.o=headmodel.o; cfg.vol.label=headmodel.label; [MEGSubject1_realigned] = ft_megrealign(cfg, MEGSubject1) The headmodel was built using the following configuration: cfg =[]; cfg.method = 'localspheres'; cfg.grad = MEGsingleSubjectData.grad; headmodel = ft_prepare_headmodel(cfg, headshape); There was a post with the same problem in the mailing list, with the suggestion to uncomment cfg.headshape: https://mailman.science.ru.nl/pipermail/fieldtrip/2015-September/009633.html When uncommenting cfg.headshape, it works until I get the following error message: Error using vertcat Dimensions of matrices being concatenated are not consistent. Error in ft_megrealign (line 391) interp.label = [interp.label; rest.label]; interpol.label is a 1x248 cell array, rest.label is 93x1 cell array. Did I miss something? Thanks a lot for your help in advance, Kirsten From xiew1202 at gmail.com Tue Nov 7 16:33:28 2017 From: xiew1202 at gmail.com (Xie Wanze) Date: Tue, 7 Nov 2017 10:33:28 -0500 Subject: [FieldTrip] Diagonal values for wpli in ft_connectivityanalysis Message-ID: Dear all, I have the diagonal values *unequal *to 0 or 1 in the output matrix from the ft_connectivityanalysis using 'wpli'. These diagonal values are even not equal to each other. The diagonal values are the same (0s or Infinite) by using 'coh' or 'coh' & cfg.complex = 'imag'. I never used the diagonal values in my later analysis, and I always changed them to 0s, but I am still curious and confused about why this happened to the method of 'wpli'. Does anyone ever meet this issue? Thanks. Wanze -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Tue Nov 7 16:33:28 2017 From: michelic72 at gmail.com (Cristiano Micheli) Date: Tue, 7 Nov 2017 16:33:28 +0100 Subject: [FieldTrip] reconstruction of EEG patterns on a 3D shape In-Reply-To: References: Message-ID: Thanks. That worked beautifully! Cris On Mon, Nov 6, 2017 at 7:57 PM, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Ciao Cris, > > ft_plot_topo3d in the plotting module is your friend. > > Best wishes, > > JM > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 <024%20361%204793> > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > > On 6 Nov 2017, at 17:41, Cristiano Micheli wrote: > > Dear Team > I achieved a 3D reconstruction of a 64 electrodes Biosemi cap, as > described in this tutorial: > http://www.fieldtriptoolbox.org/tutorial/electrode > Now I would like to visualise a [64x1] vector of EEG activity [64 > electrodes x 1 time sample] as an interpolated overlay on top of the 3D > electrodes reconstruction. > Is there a quick way to obtain this by means of ft_sourceplot or other > functions? > > All the best! > Cris > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Nov 7 21:46:49 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 7 Nov 2017 20:46:49 +0000 Subject: [FieldTrip] Problem with ft_megrealign In-Reply-To: <1778422504.475907.1510053411840@communicator.strato.de> References: <1778422504.475907.1510053411840@communicator.strato.de> Message-ID: <69C815C9-B6A5-4392-B06A-8FD34FB5DA71@donders.ru.nl> Dear Kirsten, These days I would not recommend the use of ft_megrealign to begin with. In our experience it often does more harm than that it improves results. In particular, if your subjects were relatively well-behaved, and well-positioned in the MEG. This might also be one of the reasons, why the code does not run through smoothly, because FieldTrip has evolved quite a bit over the past years. While we take the utmost care to keep the code internally consistent, rarely used functionality might have escaped our attention, which may have happened here. This being said, I am not sure whether I understand why the removal of the headshape option allows you to proceed deeper in the code. The second error you report is caused by a dimensionality mismatch, where matlab is asked to concatenate a row-vector (interp.label) with a column vector (rest.label). Given the code, it seems that the writer of the code assumed the interp.label to always be a column vector (which happens to be FieldTrip convention). I don’t know how interp.label ended up a row vector, but changing line 391 into interp.label = [interp.label(:);rest.label(:)]; should do the trick. You could try and fix this on your local copy of fieldtrip, but even better would be to contribute the fix to the release code-base, so that everyone can enjoy it. The way to do this is documented here: http://www.fieldtriptoolbox.org/development/git I am looking forward to your suggested fix. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 7 Nov 2017, at 12:16, Kirsten Herfurth > wrote: Dear all, I would like to apply the function ft_megrealign to my single subject meg data in order to do sensor level group analysis afterwards. I got stuck with the following error messages: Reference to non-existent field 'xgrid'. Error in ft_prepare_sourcemodel (line 709) xmin_indx = find(grid.xgrid==xmin); Error in ft_megrealign (line 249) grid = ft_prepare_sourcemodel(tmpcfg); I used the following configuration: cfg=[]; cfg.template = {MEGSubject1.grad; MEGSubject2.grad; MEGSubject3.grad, …}; cfg.headmodel = headmodel; cfg.headshape = strcat(Path2MEGData,'hs_file'); cfg.inwardshift = 0.025; % in meters cfg.vol.r=headmodel.r; cfg.vol.o=headmodel.o; cfg.vol.label=headmodel.label; [MEGSubject1_realigned] = ft_megrealign(cfg, MEGSubject1) The headmodel was built using the following configuration: cfg =[]; cfg.method = 'localspheres'; cfg.grad = MEGsingleSubjectData.grad; headmodel = ft_prepare_headmodel(cfg, headshape); There was a post with the same problem in the mailing list, with the suggestion to uncomment cfg.headshape: https://mailman.science.ru.nl/pipermail/fieldtrip/2015-September/009633.html When uncommenting cfg.headshape, it works until I get the following error message: Error using vertcat Dimensions of matrices being concatenated are not consistent. Error in ft_megrealign (line 391) interp.label = [interp.label; rest.label]; interpol.label is a 1x248 cell array, rest.label is 93x1 cell array. Did I miss something? Thanks a lot for your help in advance, Kirsten _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Nov 7 22:03:15 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 7 Nov 2017 21:03:15 +0000 Subject: [FieldTrip] Diagonal values for wpli in ft_connectivityanalysis In-Reply-To: References: Message-ID: <06BF6BE8-2170-4938-B3BE-74F25EFE89DE@donders.ru.nl> Dear Wanze, I don’t know what type of data you put into the algorithm, so it’s a bit ‘koffiedik’ kijken, as we say in Dutch. I’d suggest that you start by reading the code, and see whether you understand what causes your ‘issue’. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 7 Nov 2017, at 16:33, Xie Wanze > wrote: Dear all, I have the diagonal values unequal to 0 or 1 in the output matrix from the ft_connectivityanalysis using 'wpli'. These diagonal values are even not equal to each other. The diagonal values are the same (0s or Infinite) by using 'coh' or 'coh' & cfg.complex = 'imag'. I never used the diagonal values in my later analysis, and I always changed them to 0s, but I am still curious and confused about why this happened to the method of 'wpli'. Does anyone ever meet this issue? Thanks. Wanze _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.chettouf at vu.nl Wed Nov 8 11:14:42 2017 From: s.chettouf at vu.nl (Chettouf, S.) Date: Wed, 8 Nov 2017 10:14:42 +0000 Subject: [FieldTrip] Convert fieldtrip beamformers to SPM Message-ID: Dear fieldtrip community, I analysed my EEG data in fieldtrip and calculated beamformers. I would like to compare these source data with my fMRI sources and therefore do both statistical testings in SPM. But how can I export my beamformer data to SPM? Converting them with spm_ eeg _ ft2spm does not work with beamformer data. I also tried ft_volumewrite to convert the beamformer results to nifti, but without succes. Thanks in advance, Sabrina -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Nov 8 11:24:47 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 8 Nov 2017 10:24:47 +0000 Subject: [FieldTrip] Convert fieldtrip beamformers to SPM In-Reply-To: References: Message-ID: Dear Sabrina, I am not sure why your conversion to nifti does not work, but if you follow the recipe that is described in http://www.fieldtriptoolbox.org/tutorial/beamformer, in particular by using ft_sourceinterpolate to create a volumetric image of ther source-reconstructed activity, followed by an optional volumetric normalisation (using ft_volumenormalise), it should be relatively straightforward to save this to a nifti file. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 8 Nov 2017, at 11:14, Chettouf, S. > wrote: Dear fieldtrip community, I analysed my EEG data in fieldtrip and calculated beamformers. I would like to compare these source data with my fMRI sources and therefore do both statistical testings in SPM. But how can I export my beamformer data to SPM? Converting them with spm_ eeg _ ft2spm does not work with beamformer data. I also tried ft_volumewrite to convert the beamformer results to nifti, but without succes. Thanks in advance, Sabrina _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Nov 8 12:05:31 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 8 Nov 2017 11:05:31 +0000 Subject: [FieldTrip] Variance estimates for connectivity measures In-Reply-To: References: Message-ID: <2EBD91F4-1703-4F0E-A7D2-3DC6DC96E030@donders.ru.nl> Dear Matthew, I think it depends on the way that you compute these metrics. If you approach it parametrically (i.e. using MVAR-models) I think that the coefficients are computed across all observations by default. If you want a leave-one-out estimate of the coefficients, I think that you can use cfg.jackknife as an option to ft_mvaranalysis. How well this is supported throughout the rest of the analysis pipeline (i.e. ft_freqanalysis_mvar and ft_connectivityanalysis) I am not sure. I haven’t used this option for a long time, so the code may have become a bit rusty here and there. If you are using a non-parametric approach (i.e. using ft_freqanalysis, followed by ft_connectivity_csd2transfer, which is called on the fly by ft_connectivityanalysis), I think there used to be some functionality to compute leave-one-outs on the fly, and then essentially treat them as ‘single trials’. Also there, I assume that the code has become a bit rusty, because it hasn’t been used for quite a while. Either way, I guess that an definitive answer to your question would require you to inspect the code in some more detail. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 20 Oct 2017, at 16:16, MATTHEW I BANKS > wrote: Greetings. Is it possible to use jackknife to get variance estimates for Granger, partial directed coherence and directed transfer function? I use it for wPLI, but cannot figure out how to do it for these other measures. -Matt Banks ____________________________ Matthew I. Banks, Ph.D. Associate Professor Department of Anesthesiology University of Wisconsin 1300 University Avenue, Room 4605 Madison, WI 53706 office tel. (608)261-1143 lab tel. (608)263-6662 fax (608)263-2592 http://anesthesia.wisc.edu/index.php/Banks_Laboratory http://ntp.neuroscience.wisc.edu/banks.htm _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From SXM1085 at student.bham.ac.uk Wed Nov 8 12:07:43 2017 From: SXM1085 at student.bham.ac.uk (Sebastian Michelmann) Date: Wed, 8 Nov 2017 11:07:43 +0000 Subject: [FieldTrip] Convert fieldtrip beamformers to SPM In-Reply-To: References: Message-ID: <2D9C9145AF1E4D4799ADDB2C0F996AE8019EFD8425@EX13.adf.bham.ac.uk> Dear Sabrina, This code works for me on the interpolated volume: cfg = []; cfg.parameter = 'stat'; cfg.filename = 'stat_interp'; cfg.datatype = 'float'; cfg.filetype = 'nifti'; cfg.vmpversion = 2; cfg.coordsys = 'spm'; ft_volumewrite(cfg, sourceint); I use this to plot 'blobs' outside of fieldtrip. best, Sebastian From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of s.chettouf at vu.nl Sent: 08 November 2017 10:15 To: FieldTrip discussion list Subject: [FieldTrip] Convert fieldtrip beamformers to SPM Dear fieldtrip community, I analysed my EEG data in fieldtrip and calculated beamformers. I would like to compare these source data with my fMRI sources and therefore do both statistical testings in SPM. But how can I export my beamformer data to SPM? Converting them with spm_ eeg _ ft2spm does not work with beamformer data. I also tried ft_volumewrite to convert the beamformer results to nifti, but without succes. Thanks in advance, Sabrina -------------- next part -------------- An HTML attachment was scrubbed... URL: From joerg.hipp at googlemail.com Wed Nov 8 17:55:26 2017 From: joerg.hipp at googlemail.com (Joerg Hipp) Date: Wed, 8 Nov 2017 17:55:26 +0100 Subject: [FieldTrip] 9 month internship in EEG biomarker development at Roche in Basel, Switzerland Message-ID: Dear all, We are offering a 9 month internship (RiSE, Roche Internships for Scientific Exchange) in our biomarker group at Roche in Basel, Switzerland. We are looking for a motivated researcher to help us explore the utility of EEG as a biomarker for neurodevelopmental diseases. Besides the work on a specific project the intern will gain insights into research and development in the pharmaceutical industry. Our group supports neuroscience programs within the Roche portfolio, which covers a broad spectrum of neurological and psychiatric diseases and we apply various techniques including EEG/MEG, PET, MRI, and Neuropsychology to this end. I am responsible for electrophysiological biomarkers (EEG/MEG) and will supervise this project. Prerequisite for application to the RiSE program is enrollment in a university PhD or medical degree program at the time of application. Details on the RiSE program can be found here: http://www.roche.com/careers/ switzerland/ch_your_job/students_and_graduates/ch_ internships/rise_program.htm Details on the specific internship and how to apply can be found here: https://www.roche.com/careers/jobs/jobsearch/job.htm?id=E- 3425641919&locale=en&title=RiSE+-+Roche+internship+for+ Scientific+Exchange+-+in+Neuroscience+Biomarkers+%289+months%29 Best wishes, Joerg -- Joerg Hipp, PhD Biomarker and Experimental Medicine Leader F. Hoffmann-La Roche Ltd. Grenzacherstrasse 124 4070 Basel, Switzerland https://scholar.google.ch/citations?user=oxsJ6q4AAAAJ&hl=en -------------- next part -------------- An HTML attachment was scrubbed... URL: From kirsten at carrot-village.de Thu Nov 9 12:58:02 2017 From: kirsten at carrot-village.de (Kirsten Herfurth) Date: Thu, 9 Nov 2017 12:58:02 +0100 (CET) Subject: [FieldTrip] Problem with ft_megrealign Message-ID: <1899468378.586762.1510228682849@communicator.strato.de> Dear Jan-Mathijs, thank you very much for your answer! I will fix the bug and commit it to Github. Do you have any suggestions for an alternative approach for realigning data obtained with a non-CTF-system (we have a 4d-MEG-system)? Unfortunately we don’t have a head position time-series obtained online, just the position in the beginning and in the end of a run. I assume I cannot use the function ft_regressconfound or ft_headmovement. I’m sorry for this basic question, but I haven’t found a satisfying answer to my problem yet. The reason for accounting for head movement is that I would like to use the Machine Learning toolbox and do statistics using k-fold cross-validation, but have too few trials in one run per subject. So I thought to concatenate the trials of different runs with ft_appenddata using the realignment function first. Would it be ok to just go without the realignment in subjects that didn’t move that much, especially if it gives me the expected results? Thanks again and best wishes Kirsten From Bastiaansen4.M at nhtv.nl Fri Nov 10 12:04:37 2017 From: Bastiaansen4.M at nhtv.nl (Bastiaansen, Marcel) Date: Fri, 10 Nov 2017 11:04:37 +0000 Subject: [FieldTrip] multiclass svm In-Reply-To: References: Message-ID: Dear Fieldtrippers, As a relative novice to classification algorithms, I have been playing around with Fieldtrip's svm classifier (ft_statistics_crossvalidate). This seems to work pretty smoothly, but I have two questions related to that: 1. In the given contingency table one can see the actual classification of trials. However, I assume the actual classification is based on a classification probability for each trial. Is there a way of getting a list of classification probabilities for all trials from this function? Else, a quick hint at where in the code these probabilities are being computed / stored would help me build this functionality 2. I have EEG data that belong to 4 classes, but ft_statistics_crossvalidate does not afford multiclass approaches. Any tips or hints at what would be robust and well-validated approaches for multiclass models for EEG data would be much appreciated. Best, Marcel *** Dr Marcel C.M. Bastiaansen Senior lecturer and researcher in quantitative research methods Academy for Leisure & Academy for Tourism NHTV Breda University of Applied Sciences Visiting adress: Room C1.011, Academy for Leisure Archimedesstraat 17, 4816 BA, Breda Phone: +31 76 533 2869 Email: bastiaansen4.m at nhtv.nl And Department of Cognitive Neuropsychology Tilburg School of Social and Behavioral Sciences Tilburg University Visiting address: Room S217, Simon building Warandelaan 2 5000 LE Tilburg Email: M.C.M.Bastiaansen at uvt.nl publications linked-in *** -------------- next part -------------- An HTML attachment was scrubbed... URL: From ekenaykut at gmail.com Fri Nov 10 12:40:05 2017 From: ekenaykut at gmail.com (Aykut Eken) Date: Fri, 10 Nov 2017 14:40:05 +0300 Subject: [FieldTrip] multiclass svm In-Reply-To: References: Message-ID: <0A281A02-DB29-4F9D-BBBE-24078FA8B12F@gmail.com> Dear Marcel, Instead of using ft_statistics_crossvalidate, you can extract the features and use as input to fitcsvm in MATLAB that provides answers to your questions. After running the model, you can use fitSVMPosterior or fitPosterior to obtain classification probabilities. Best Aykut Eken, PhD Düzce University Faculty of Engineering Biomedical Engineering Department Düzce University, Konuralp Campus, 81620, Konuralp, Düzce, Turkey Tel: +905366777364 Office Tel: +90380542 11 00 /4546 Mail address1: aykuteken at duzce.edu.tr Mail address2: ekenaykut at gmail.com > On 10 Nov 2017, at 14:04, Bastiaansen, Marcel wrote: > > Dear Fieldtrippers, > > As a relative novice to classification algorithms, I have been playing around with Fieldtrip’s svm classifier (ft_statistics_crossvalidate). This seems to work pretty smoothly, but I have two questions related to that: > 1. In the given contingency table one can see the actual classification of trials. However, I assume the actual classification is based on a classification probability for each trial. Is there a way of getting a list of classification probabilities for all trials from this function? Else, a quick hint at where in the code these probabilities are being computed / stored would help me build this functionality > 2. I have EEG data that belong to 4 classes, but ft_statistics_crossvalidate does not afford multiclass approaches. Any tips or hints at what would be robust and well-validated approaches for multiclass models for EEG data would be much appreciated. > > Best, > Marcel > > *** > Dr Marcel C.M. Bastiaansen > Senior lecturer and researcher in quantitative research methods > Academy for Leisure & Academy for Tourism > NHTV Breda University of Applied Sciences > Visiting adress: > Room C1.011, Academy for Leisure > Archimedesstraat 17, > 4816 BA, Breda > Phone: +31 76 533 2869 > Email: bastiaansen4.m at nhtv.nl > > And > > Department of Cognitive Neuropsychology > Tilburg School of Social and Behavioral Sciences > Tilburg University > Visiting address: > Room S217, Simon building > Warandelaan 2 > 5000 LE Tilburg > Email: M.C.M.Bastiaansen at uvt.nl > > publications > linked-in > *** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From til.bergmann at uni-tuebingen.de Fri Nov 10 16:46:37 2017 From: til.bergmann at uni-tuebingen.de (Til Ole Bergmann) Date: Fri, 10 Nov 2017 16:46:37 +0100 Subject: [FieldTrip] PhD Position (3 years, 65% TV-L) on real-time EEG-TMS with Til Ole Bergmann, University of Tuebingen, Germany Message-ID: Dear FieldTrip community, I have a PhD position opening (3 years, salary accoording to 65% TV-L) in a DFG-funded project ("The sensorimotor µ-rhythm as cholinergically controlled pulsed inhibition"). We will use brain-state-dependent real-time EEG-triggered transcranial magnetic stimulation (EEG-TMS) to investigate the neurophysiology underlying mu-alpha (8-14 Hz) oscillations in the human sensorimotor cortex, their function for gating information flow and synaptic plasticity in the brain, and the cholinergic mechanisms mediating their prefrontal top-down control by attention. The ideal candidate has experience in Matlab (and preferrably FieldTrip) for EEG/MEG timeseries analyses. Please circulate this job opening amongst your peers and potential PhD candidates. For more information please see: http://tobergmann.de/downloads/PhD_position_Bergmann_Tuebingen.pdf Many thanks in advance! All the best, Til -- Dr. Til Ole Bergmann Department of Neurology & Stroke Hertie Institute for Clinical Brain Research Institute of Medical Psychology and Behavioral Neurobiology University of Tübingen Otfried-Müller-Straße 25, 72076 Tübingen, Germany til.bergmann at uni-tuebingen.de tel +49-7071-29-88795 fax +49 7071 29-25016 From springangel222 at gmail.com Sun Nov 12 06:37:12 2017 From: springangel222 at gmail.com (angel angel) Date: Sun, 12 Nov 2017 09:07:12 +0330 Subject: [FieldTrip] Equivalent parts in an image and a mesh Message-ID: Dear FieldTrip Experts, How you find the corresponding part of an image in a mesh? Looking forward to hearing from you. Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Sun Nov 12 12:58:42 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Sun, 12 Nov 2017 11:58:42 +0000 Subject: [FieldTrip] Equivalent parts in an image and a mesh In-Reply-To: References: Message-ID: Hi Angel Angel, I don’t understand the question. Can you please have a look at the following before trying again? http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002202 http://www.fieldtriptoolbox.org/faq/how_to_ask_good_questions_to_the_community?s[]=discussion&s[]=list Thanks very much, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 12 Nov 2017, at 06:37, angel angel > wrote: Dear FieldTrip Experts, How you find the corresponding part of an image in a mesh? Looking forward to hearing from you. Regards _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From springangel222 at gmail.com Mon Nov 13 17:57:37 2017 From: springangel222 at gmail.com (angel angel) Date: Mon, 13 Nov 2017 20:27:37 +0330 Subject: [FieldTrip] Equivalent parts in an image and a mesh In-Reply-To: References: Message-ID: Hi Dear All, I apologize for my unclear question. I want to figure out where does each voxel of an image stand in a mesh after the mesh generation pipeline? I mean on which face and between which vertices? I hope I asked the correct form of a question this time. Thanks for your attention. On Sun, Nov 12, 2017 at 3:28 PM, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Hi Angel Angel, > > I don’t understand the question. Can you please have a look at the > following before trying again? > > > http://journals.plos.org/ploscompbiol/article?id=10. > 1371/journal.pcbi.1002202 > > http://www.fieldtriptoolbox.org/faq/how_to_ask_good_ > questions_to_the_community?s[]=discussion&s[]=list > > Thanks very much, > > Jan-Mathijs > > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > On 12 Nov 2017, at 06:37, angel angel wrote: > > Dear FieldTrip Experts, > How you find the corresponding part of an image in a mesh? > Looking forward to hearing from you. > Regards > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From otobias at web.de Tue Nov 14 03:58:37 2017 From: otobias at web.de (Tobias Overath) Date: Mon, 13 Nov 2017 21:58:37 -0500 Subject: [FieldTrip] Phd position in the O-Lab at Duke University Message-ID: <05DB48BD-5388-4DAA-8AB1-99467DDC9B76@web.de> Dear all, We are looking for a highly motivated young scientist to join the O-Lab, led by Prof. Tobias Overath, in the Department of Psychology and Neuroscience at Duke University. Work in our lab investigates how sounds, from simple sinusoids to complex speech signals, are processed in the brain, using a combination of behavioral and neuroimaging methods (fMRI, EEG, ECoG) to track the underlying neural processes. Current projects investigate the transformation from acoustic to linguistic analysis of temporal speech structure, online measures of statistical learning, as well as optimization of cochlear implant coding strategies. Interested candidates should have received an undergraduate degree in psychology, neuroscience, biomedical engineering, or a related field by Summer 2018. Familiarity with signal processing, fMRI, M/EEG, or related experimental techniques is a plus, as is advanced knowledge of at least one programing language (preferably Matlab). Admission is possible via the Psychology and Neuroscience Graduate Program (https://psychandneuro.duke.edu/graduate ), or via the Cognitive Neuroscience Admitting Program (CNAP, https://dibs.duke.edu/centers/ccn/graduate-cnap ). The application deadline is December 1, 2017! Duke University provides a vibrant, highly connected scientific environment, with many associated departments and interdisciplinary initiatives (e.g. Departments of Neurobiology, Biomedical Engineering, Electrical and Computer Engineering; the Center for Cognitive Neuroscience, the Duke Institute for Brain Sciences, or the Brain Imaging and Analysis Center). Please contact Tobias Overath (t.overath at duke.edu ) for further information. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Nov 14 15:45:17 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 14 Nov 2017 14:45:17 +0000 Subject: [FieldTrip] Equivalent parts in an image and a mesh In-Reply-To: References: Message-ID: Why do you want this? JM J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 13 Nov 2017, at 17:57, angel angel > wrote: Hi Dear All, I apologize for my unclear question. I want to figure out where does each voxel of an image stand in a mesh after the mesh generation pipeline? I mean on which face and between which vertices? I hope I asked the correct form of a question this time. Thanks for your attention. On Sun, Nov 12, 2017 at 3:28 PM, Schoffelen, J.M. (Jan Mathijs) > wrote: Hi Angel Angel, I don’t understand the question. Can you please have a look at the following before trying again? http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002202 http://www.fieldtriptoolbox.org/faq/how_to_ask_good_questions_to_the_community?s[]=discussion&s[]=list Thanks very much, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 12 Nov 2017, at 06:37, angel angel > wrote: Dear FieldTrip Experts, How you find the corresponding part of an image in a mesh? Looking forward to hearing from you. Regards _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From springangel222 at gmail.com Wed Nov 15 09:33:56 2017 From: springangel222 at gmail.com (angel angel) Date: Wed, 15 Nov 2017 12:03:56 +0330 Subject: [FieldTrip] Equivalent parts in an image and a mesh In-Reply-To: References: Message-ID: I want to make a source model based on "regular 3D grid, based on segmented MRI, restricted to gray matter". Thanks in advance. On Tue, Nov 14, 2017 at 6:15 PM, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Why do you want this? > > JM > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > On 13 Nov 2017, at 17:57, angel angel wrote: > > Hi Dear All, > I apologize for my unclear question. I want to figure out where does each > voxel of an image stand in a mesh after the mesh generation pipeline? I > mean on which face and between which vertices? I hope I asked the correct > form of a question this time. > Thanks for your attention. > > On Sun, Nov 12, 2017 at 3:28 PM, Schoffelen, J.M. (Jan Mathijs) < > jan.schoffelen at donders.ru.nl> wrote: > >> Hi Angel Angel, >> >> I don’t understand the question. Can you please have a look at the >> following before trying again? >> >> >> http://journals.plos.org/ploscompbiol/article?id=10.1371/ >> journal.pcbi.1002202 >> >> http://www.fieldtriptoolbox.org/faq/how_to_ask_good_question >> s_to_the_community?s[]=discussion&s[]=list >> >> Thanks very much, >> >> Jan-Mathijs >> >> >> J.M.Schoffelen, MD PhD >> Senior Researcher, VIDI-fellow - PI, language in interaction >> Telephone: +31-24-3614793 >> Physical location: room 00.028 >> Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands >> >> On 12 Nov 2017, at 06:37, angel angel wrote: >> >> Dear FieldTrip Experts, >> How you find the corresponding part of an image in a mesh? >> Looking forward to hearing from you. >> Regards >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Nov 15 12:55:09 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 15 Nov 2017 11:55:09 +0000 Subject: [FieldTrip] Equivalent parts in an image and a mesh In-Reply-To: References: Message-ID: <7974CAAA-435E-46FC-8585-D60B49377B16@donders.ru.nl> Dear anonymous, If you want "a regular 3D grid, based on a segmented MRI, restricted to grey matter”, why do you need the cortical surface reconstruction? Best wishes, JAN-MATHIJS On 15 Nov 2017, at 09:33, angel angel > wrote: I want to make a source model based on "regular 3D grid, based on segmented MRI, restricted to gray matter". Thanks in advance. On Tue, Nov 14, 2017 at 6:15 PM, Schoffelen, J.M. (Jan Mathijs) > wrote: Why do you want this? JM J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 13 Nov 2017, at 17:57, angel angel > wrote: Hi Dear All, I apologize for my unclear question. I want to figure out where does each voxel of an image stand in a mesh after the mesh generation pipeline? I mean on which face and between which vertices? I hope I asked the correct form of a question this time. Thanks for your attention. On Sun, Nov 12, 2017 at 3:28 PM, Schoffelen, J.M. (Jan Mathijs) > wrote: Hi Angel Angel, I don’t understand the question. Can you please have a look at the following before trying again? http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002202 http://www.fieldtriptoolbox.org/faq/how_to_ask_good_questions_to_the_community?s[]=discussion&s[]=list Thanks very much, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 12 Nov 2017, at 06:37, angel angel > wrote: Dear FieldTrip Experts, How you find the corresponding part of an image in a mesh? Looking forward to hearing from you. Regards _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Nov 16 12:36:25 2017 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 16 Nov 2017 12:36:25 +0100 Subject: [FieldTrip] dimord single-trial source data Message-ID: Hi FieldTrippers, I was wondering is there is a recommend/most consistent way to represent trial x pos x time data from an LCMV beamformer, also considering the dimord. In other words: with: data.method = 'singletrial' should I use: data.trial{pos} = [rpt x time] data.dimord = '{pos}_rpt_time' or rather: data.trial = {pos x rpt x time} data.dimord = 'pos_rpt_time' or something else? The purpose is to then do a frequency analysis (with keeptrials = 'yes'). Best, Stephen -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Nov 16 14:31:53 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 16 Nov 2017 13:31:53 +0000 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: References: Message-ID: <59225E01-B07C-426B-96A4-9A669C82276C@donders.ru.nl> Hi Stephen, I think that it is currently not possible to pass the output of ft_sourceanalysis to ft_freqanalysis directly, since ft_freqanalysis expects channel-level type data in the input. The exact details of the computation depend a bit on the amount of RAM you have, and on what exactly you want to achieve. If it’s your intention to generate frequency spectra for many dipole locations (e.g. >1000 or so) I would consider the following: - compute spatial filters (cfg.keepfilter = ‘yes’); - use a for-loop across (chunks of) dipole locations to create ‘virtual channel data’, by premultiplying the sensor-level data.trial (loop across trials) with the location specific spatial filter. - stuff all this into a data-structure that looks like a raw data structure; - pass this to ft_freqanalysis Alternatively, you could consider using a parcellation approach, if you think it makes sense to reduce the number of spatial locations a bit, although theoretically it should be possible to create a parcellation that consists of just a single dipole per parcel. In this context, you could look into the inner workings of ft_sourceparcellate, which returns a data structure that ft_freqanalysis can work with. Whether ft_sourceparcellate can swallow single trial source data, I am not sure. Best wishes, JM > On 16 Nov 2017, at 12:36, Stephen Whitmarsh wrote: > > Hi FieldTrippers, > > I was wondering is there is a recommend/most consistent way to represent trial x pos x time data from an LCMV beamformer, also considering the dimord. In other words: > > with: > > data.method = 'singletrial' > > should I use: > > data.trial{pos} = [rpt x time] > data.dimord = '{pos}_rpt_time' > > or rather: > > data.trial = {pos x rpt x time} > data.dimord = 'pos_rpt_time' > > or something else? The purpose is to then do a frequency analysis (with keeptrials = 'yes'). > > Best, > Stephen > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Thu Nov 16 14:38:06 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 16 Nov 2017 13:38:06 +0000 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: References: Message-ID: Hi again Stephen, I forgot to mention a third approach: you can compute your spatial filter with cfg.method = ‘lcmv’ and cfg.lcmv.keepfilter = ‘yes’, and subsequently compute the source level spectra by applying these spatial filters to the sensor level fourier spectra. Best wishes, Jan-Mathijs > On 16 Nov 2017, at 12:36, Stephen Whitmarsh wrote: > > Hi FieldTrippers, > > I was wondering is there is a recommend/most consistent way to represent trial x pos x time data from an LCMV beamformer, also considering the dimord. In other words: > > with: > > data.method = 'singletrial' > > should I use: > > data.trial{pos} = [rpt x time] > data.dimord = '{pos}_rpt_time' > > or rather: > > data.trial = {pos x rpt x time} > data.dimord = 'pos_rpt_time' > > or something else? The purpose is to then do a frequency analysis (with keeptrials = 'yes'). > > Best, > Stephen > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From stephen.whitmarsh at gmail.com Thu Nov 16 14:40:41 2017 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 16 Nov 2017 14:40:41 +0100 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: <59225E01-B07C-426B-96A4-9A669C82276C@donders.ru.nl> References: <59225E01-B07C-426B-96A4-9A669C82276C@donders.ru.nl> Message-ID: Hi Jan-Mathijs, Thanks. In fact, I did what you suggest, but this entails a lot (nr. of positions) or creating and clearing a temporary variable. For a reason I do not understand (but which I encountered before), MATLAB seems not able to deal with this, and runs into memory problems. I suspect it is not able to create and clear many variables in a row, so that althought memory load does not seem to increase, it *will *break with an out-of-memory problem. I therefor started with this approach, but alas, I now understand that it was a wrong turn. So, I am in a pickle now, as neither option works... Best, Stephen On 16 November 2017 at 14:31, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Hi Stephen, > > I think that it is currently not possible to pass the output of > ft_sourceanalysis to ft_freqanalysis directly, since ft_freqanalysis > expects channel-level type data in the input. > The exact details of the computation depend a bit on the amount of RAM you > have, and on what exactly you want to achieve. > > If it’s your intention to generate frequency spectra for many dipole > locations (e.g. >1000 or so) I would consider the following: > > - compute spatial filters (cfg.keepfilter = ‘yes’); > - use a for-loop across (chunks of) dipole locations to create ‘virtual > channel data’, by premultiplying the sensor-level data.trial (loop across > trials) with the location specific spatial filter. > - stuff all this into a data-structure that looks like a raw data > structure; > - pass this to ft_freqanalysis > > > Alternatively, you could consider using a parcellation approach, if you > think it makes sense to reduce the number of spatial locations a bit, > although theoretically it should be possible to create a parcellation that > consists of just a single dipole per parcel. In this context, you could > look into the inner workings of ft_sourceparcellate, which returns a data > structure that ft_freqanalysis can work with. Whether ft_sourceparcellate > can swallow single trial source data, I am not sure. > > Best wishes, > > JM > > > > > On 16 Nov 2017, at 12:36, Stephen Whitmarsh > wrote: > > > > Hi FieldTrippers, > > > > I was wondering is there is a recommend/most consistent way to represent > trial x pos x time data from an LCMV beamformer, also considering the > dimord. In other words: > > > > with: > > > > data.method = 'singletrial' > > > > should I use: > > > > data.trial{pos} = [rpt x time] > > data.dimord = '{pos}_rpt_time' > > > > or rather: > > > > data.trial = {pos x rpt x time} > > data.dimord = 'pos_rpt_time' > > > > or something else? The purpose is to then do a frequency analysis (with > keeptrials = 'yes'). > > > > Best, > > Stephen > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Nov 16 14:44:36 2017 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 16 Nov 2017 14:44:36 +0100 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: References: <59225E01-B07C-426B-96A4-9A669C82276C@donders.ru.nl> Message-ID: For completeness, this is what I did in the way you suggest (I think). Note data is downsampled to 100Hz, and every trial is 1 second long. So I do not think that RAM should be a concern (I have about 128 Gig to work with): % load common filter [source_common, leadfield] = WANDER_common_filter_LCMV_MAG(isubject,rootpath,0); % prepare source datastructure source = rmfield(source_common,'avg'); source.pow = nan(size(source.pos,1),size(data_MEG_timebinned_append.trial,2),2); source.trialinfo = data_MEG_timebinned_append.trialinfo; for ivoxel = find(source.inside)' disp(['progress: ' round(num2str(ivoxel/size(find(source.inside),1)*100)) '%']); % make timecourse datastructure, clear first so that MATLAB does source_timecourse.trial{size(data_MEG_timebinned_append.trial,2)} = []; source_timecourse.label = {'voxel'}; source_timecourse.fsample = 100; source_timecourse.time = data_MEG_timebinned_append.time; for itrial = 1:size(data_MEG_timebinned_append.trial,2) source_timecourse.trial{itrial} = svdfft(source_common.avg.filter{ivoxel} * data_MEG_timebinned_append.trial{itrial}, 1); end % do mtmconvol on faux data structure cfg = []; cfg.channel = 'all'; cfg.method = 'mtmfft'; cfg.keeptrials = 'yes'; cfg.foilim = [10,11]; cfg.taper = 'hanning'; FFT = ft_freqanalysis(cfg, source_timecourse); clear source_timecourse source.pow(ivoxel,:,:) = squeeze(FFT.powspctrm); clear FFT memory end On 16 November 2017 at 14:40, Stephen Whitmarsh wrote: > Hi Jan-Mathijs, > > Thanks. In fact, I did what you suggest, but this entails a lot (nr. of > positions) or creating and clearing a temporary variable. For a reason I do > not understand (but which I encountered before), MATLAB seems not able to > deal with this, and runs into memory problems. I suspect it is not able to > create and clear many variables in a row, so that althought memory load > does not seem to increase, it *will *break with an out-of-memory problem. > I therefor started with this approach, but alas, I now understand that it > was a wrong turn. > > So, I am in a pickle now, as neither option works... > > Best, > Stephen > > On 16 November 2017 at 14:31, Schoffelen, J.M. (Jan Mathijs) < > jan.schoffelen at donders.ru.nl> wrote: > >> Hi Stephen, >> >> I think that it is currently not possible to pass the output of >> ft_sourceanalysis to ft_freqanalysis directly, since ft_freqanalysis >> expects channel-level type data in the input. >> The exact details of the computation depend a bit on the amount of RAM >> you have, and on what exactly you want to achieve. >> >> If it’s your intention to generate frequency spectra for many dipole >> locations (e.g. >1000 or so) I would consider the following: >> >> - compute spatial filters (cfg.keepfilter = ‘yes’); >> - use a for-loop across (chunks of) dipole locations to create ‘virtual >> channel data’, by premultiplying the sensor-level data.trial (loop across >> trials) with the location specific spatial filter. >> - stuff all this into a data-structure that looks like a raw data >> structure; >> - pass this to ft_freqanalysis >> >> >> Alternatively, you could consider using a parcellation approach, if you >> think it makes sense to reduce the number of spatial locations a bit, >> although theoretically it should be possible to create a parcellation that >> consists of just a single dipole per parcel. In this context, you could >> look into the inner workings of ft_sourceparcellate, which returns a data >> structure that ft_freqanalysis can work with. Whether ft_sourceparcellate >> can swallow single trial source data, I am not sure. >> >> Best wishes, >> >> JM >> >> >> >> > On 16 Nov 2017, at 12:36, Stephen Whitmarsh < >> stephen.whitmarsh at gmail.com> wrote: >> > >> > Hi FieldTrippers, >> > >> > I was wondering is there is a recommend/most consistent way to >> represent trial x pos x time data from an LCMV beamformer, also considering >> the dimord. In other words: >> > >> > with: >> > >> > data.method = 'singletrial' >> > >> > should I use: >> > >> > data.trial{pos} = [rpt x time] >> > data.dimord = '{pos}_rpt_time' >> > >> > or rather: >> > >> > data.trial = {pos x rpt x time} >> > data.dimord = 'pos_rpt_time' >> > >> > or something else? The purpose is to then do a frequency analysis (with >> keeptrials = 'yes'). >> > >> > Best, >> > Stephen >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Nov 16 15:43:21 2017 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 16 Nov 2017 15:43:21 +0100 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: References: Message-ID: Hi again again Jan-Mathijs, Ah yes, that does seem like the most elegant and memory-efficient approach! I will need to figure out how to apply spatial filters to Fourier (and redo my sensor level spectral analysis to Fourier). Shout-out to the list: anyone have an example of applying spatial filters to Fourier that I could use? Thanks again again, Stephen On 16 November 2017 at 14:38, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Hi again Stephen, > > I forgot to mention a third approach: you can compute your spatial filter > with cfg.method = ‘lcmv’ and cfg.lcmv.keepfilter = ‘yes’, and subsequently > compute the source level spectra by applying these spatial filters to the > sensor level fourier spectra. > > Best wishes, > Jan-Mathijs > > > > > > On 16 Nov 2017, at 12:36, Stephen Whitmarsh > wrote: > > > > Hi FieldTrippers, > > > > I was wondering is there is a recommend/most consistent way to represent > trial x pos x time data from an LCMV beamformer, also considering the > dimord. In other words: > > > > with: > > > > data.method = 'singletrial' > > > > should I use: > > > > data.trial{pos} = [rpt x time] > > data.dimord = '{pos}_rpt_time' > > > > or rather: > > > > data.trial = {pos x rpt x time} > > data.dimord = 'pos_rpt_time' > > > > or something else? The purpose is to then do a frequency analysis (with > keeptrials = 'yes'). > > > > Best, > > Stephen > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Nov 16 15:52:06 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 16 Nov 2017 14:52:06 +0000 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: References: Message-ID: <527ADD8B-D856-4355-9544-5AE785C5A9AD@donders.ru.nl> Hi Stephen, siz = size(freq.fourierspctrm); F = freq.fourierspctrm; F = permute(freq.fourierspctrm,[2 1 3]); F = reshape(F,siz(2),siz(1)*siz(3)); sourceF = svdfft(source.avg.filter{some_index}*F); % by the way, your use in the time domain per trial is dangerous, because it does a trial specific rotation, which you may or may not want sourceF = reshape(sourceF, siz(1), siz(3)); sourceP = abs(sourceF).^2; Of zoiets. Cheers, JM On 16 Nov 2017, at 15:43, Stephen Whitmarsh > wrote: Hi again again Jan-Mathijs, Ah yes, that does seem like the most elegant and memory-efficient approach! I will need to figure out how to apply spatial filters to Fourier (and redo my sensor level spectral analysis to Fourier). Shout-out to the list: anyone have an example of applying spatial filters to Fourier that I could use? Thanks again again, Stephen On 16 November 2017 at 14:38, Schoffelen, J.M. (Jan Mathijs) > wrote: Hi again Stephen, I forgot to mention a third approach: you can compute your spatial filter with cfg.method = ‘lcmv’ and cfg.lcmv.keepfilter = ‘yes’, and subsequently compute the source level spectra by applying these spatial filters to the sensor level fourier spectra. Best wishes, Jan-Mathijs > On 16 Nov 2017, at 12:36, Stephen Whitmarsh > wrote: > > Hi FieldTrippers, > > I was wondering is there is a recommend/most consistent way to represent trial x pos x time data from an LCMV beamformer, also considering the dimord. In other words: > > with: > > data.method = 'singletrial' > > should I use: > > data.trial{pos} = [rpt x time] > data.dimord = '{pos}_rpt_time' > > or rather: > > data.trial = {pos x rpt x time} > data.dimord = 'pos_rpt_time' > > or something else? The purpose is to then do a frequency analysis (with keeptrials = 'yes'). > > Best, > Stephen > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Nov 16 16:36:11 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 16 Nov 2017 15:36:11 +0000 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: References: Message-ID: Hi again Stephen, Just out of curiosity: why do you use a time-domain beamformer if you are interested in reconstructing a narrowband response? Best wishes, Jan-Mathijs On 16 Nov 2017, at 15:43, Stephen Whitmarsh > wrote: Hi again again Jan-Mathijs, Ah yes, that does seem like the most elegant and memory-efficient approach! I will need to figure out how to apply spatial filters to Fourier (and redo my sensor level spectral analysis to Fourier). Shout-out to the list: anyone have an example of applying spatial filters to Fourier that I could use? Thanks again again, Stephen On 16 November 2017 at 14:38, Schoffelen, J.M. (Jan Mathijs) > wrote: Hi again Stephen, I forgot to mention a third approach: you can compute your spatial filter with cfg.method = ‘lcmv’ and cfg.lcmv.keepfilter = ‘yes’, and subsequently compute the source level spectra by applying these spatial filters to the sensor level fourier spectra. Best wishes, Jan-Mathijs > On 16 Nov 2017, at 12:36, Stephen Whitmarsh > wrote: > > Hi FieldTrippers, > > I was wondering is there is a recommend/most consistent way to represent trial x pos x time data from an LCMV beamformer, also considering the dimord. In other words: > > with: > > data.method = 'singletrial' > > should I use: > > data.trial{pos} = [rpt x time] > data.dimord = '{pos}_rpt_time' > > or rather: > > data.trial = {pos x rpt x time} > data.dimord = 'pos_rpt_time' > > or something else? The purpose is to then do a frequency analysis (with keeptrials = 'yes'). > > Best, > Stephen > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Nov 16 17:42:41 2017 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 16 Nov 2017 17:42:41 +0100 Subject: [FieldTrip] dimord single-trial source data In-Reply-To: References: Message-ID: Hi Mathijs, I know. Long story. Let's just say it's a check :-) I've done the same with DICS already. Cheers, Stephen On 16 November 2017 at 16:36, Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Hi again Stephen, > > Just out of curiosity: why do you use a time-domain beamformer if you are > interested in reconstructing a narrowband response? > > Best wishes, > Jan-Mathijs > > On 16 Nov 2017, at 15:43, Stephen Whitmarsh > wrote: > > Hi again again Jan-Mathijs, > > Ah yes, that does seem like the most elegant and memory-efficient > approach! > I will need to figure out how to apply spatial filters to Fourier (and > redo my sensor level spectral analysis to Fourier). > > Shout-out to the list: anyone have an example of applying spatial filters > to Fourier that I could use? > > Thanks again again, > Stephen > > On 16 November 2017 at 14:38, Schoffelen, J.M. (Jan Mathijs) < > jan.schoffelen at donders.ru.nl> wrote: > >> Hi again Stephen, >> >> I forgot to mention a third approach: you can compute your spatial filter >> with cfg.method = ‘lcmv’ and cfg.lcmv.keepfilter = ‘yes’, and subsequently >> compute the source level spectra by applying these spatial filters to the >> sensor level fourier spectra. >> >> Best wishes, >> Jan-Mathijs >> >> >> >> >> > On 16 Nov 2017, at 12:36, Stephen Whitmarsh < >> stephen.whitmarsh at gmail.com> wrote: >> > >> > Hi FieldTrippers, >> > >> > I was wondering is there is a recommend/most consistent way to >> represent trial x pos x time data from an LCMV beamformer, also considering >> the dimord. In other words: >> > >> > with: >> > >> > data.method = 'singletrial' >> > >> > should I use: >> > >> > data.trial{pos} = [rpt x time] >> > data.dimord = '{pos}_rpt_time' >> > >> > or rather: >> > >> > data.trial = {pos x rpt x time} >> > data.dimord = 'pos_rpt_time' >> > >> > or something else? The purpose is to then do a frequency analysis (with >> keeptrials = 'yes'). >> > >> > Best, >> > Stephen >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mireia.torralba at upf.edu Wed Nov 22 10:41:51 2017 From: mireia.torralba at upf.edu (TORRALBA CUELLO, MIREIA) Date: Wed, 22 Nov 2017 10:41:51 +0100 Subject: [FieldTrip] Phd position in Cognitive Neuroscience in UPF (Barcelona) Message-ID: Please find attached information about a PhD position in Cognitive Neuroscience at Multisensory Research Group (UPF, Barcelona) Deadline: Feb 1st, 2018 Start date: May/June 2018 Gross salary: Approx 27.800€/year Research money (travel etc...): 3.500€/year Requirements*: Master's degree in the EU or equivalent (to be decided by the host university at application), and have not worked/resided in Spain for more than 12 months (within the last 3y). *Phd position in Cognitive Neuroscience: Neural predictors of Memory Perception and attention (Prof.Salvador Soto-Faraco)* *POSITION DESCRIPTION* *-Research Project / Research Group Description:* How “...the brain enables the mind...” is one of the core questions in neuroscience. Understanding this relationship will lead to improvements in the mitigation of brain disease. One of the major sources of evidence on how neurophysiological activity relates to mental phenomena comes from the realization that fluctuations in neural activity could be at the heart of cognitive processes. In fact, it is well known that ongoing brain activity itself is highly organized, so that neural communication (local, and long range) seems to capitalize on the fine temporal structure of neural activity. Consequently responses to sensory events depend strongly on the momentary state of the system. The overarching goal of the research project hosting the potential PhD candidate is to capitalize on the relationship between brain oscillations, brain states and cognitive processes to anticipate and be able to modulate the outcome of these processes via real-time neurodevices based on Brain Computer Interfaces. The research lines hosting the PhD candidate address the link between the pattern of oscillatory brain activity and three sets of concrete cognitive processes. (1) Memory encoding in healthy humans and/or patients with Mild Cognitive Impairment. (2) Attention and perception in real-life scenarios. And, (3) perceptual conflict and awareness. The overarching goal is to be able to find predictors (biomarkers) for these processes and be able to anticipate optimal brain states (windows of opportunity) for the success of these behaviours. To this end, we use psychophysics, human electroencephalography (EEG), and Transcranial Magnetic Stimulation (TMS). Psychophysics is essential to measure the behavioural expression of cognitive processes. EEG is sensitive to post-synaptic potentials of large neuron populations, and is an indirect index of neural activity. In order to infer brain states, we capitalize on a variety of measures from the EEG: spectral power, instantaneous phase, and temporal/spatial coherence of oscillatory activity. Neurostimulation (TMS) is used to probe causality. The MRG is part of the CBC master, has 3 postdoc researchers (specialized in signal processing, bioengineering, and neuropsychology) 3 Phds, and support staff. Our research is supported by EU and local funding. *-Job position description:* Role: The successful candidate will lead a research line which falls amongst the overall projects of the MRG laboratory (described above). It is expected that the candidate will have a prior motivation for cognitive neuroscience and will contribute in an active way to define the particular project from its inception, formulation of hypotheses, experimental designs, measurement and analysis, and interpretation of the data. In order to accomplish these tasks, the PhD candidate will of course count with the support of the MRG staff and knowledge base, and the guidance of Prof Soto-Faraco as well as senior members of the laboratory. Dissemination of the research output, and networking with other local, or external experts as well as advanced post-docs and phd students will be encouraged and fostered. Responsibilities: The candidate will be mainly responsible for the implementation of the assigned research tasks conducive toward the PhD project, the careful and systematic carrying out of the experimental work. Other responsibilities will be assigned commensurate with the PhD’s capacity and level of seniority. Amongst them, like other members of the team, the PhD student will contribute to the group activities (e.g., helping organize talks, group meetings, presenting the findings in conferences) , and to the training and support of other junior members of the laboratory (eventual supervision of master or degree students). Finally, the Phd candidate will also be responsible to provide timely responses to requests from the funding body, including progress reports, as well as to attend the meetings s/he might be called to, from the funding agency. Skills: Background in Biology, Bioengineering, Experimental Psychology or other fields related to Cognitive Neuroscience. Prior experience or background in Brain Computer Interfaces. Concrete experience with experimental work in the field of the cognitive neurosciences, preferably with psychophysics and/or electrophysiology (EEG, MEG). Knowledge of signal processing. Others: High motivation, proactivity and team work are very desirable. *RELATED LINK TO THE POSITION* http://www.mrg.upf.edu/node/112 *CENTER* Dept. of Information & Communication Technologies, DTIC-UPF https://portal.upf.edu/es/web/etic/inicio *CENTER DESCRIPTION* The Department of Information and Communication Technologies (DTIC) of Universitat Pompeu Fabra covers a broad range of research topics: Computation and Intelligent Systems; Multimedia Technologies; Networks and Communications; Computational Biology and Biomedical Systems; and the Center of Brain and Cognition (CBC). This broad spectrum of topics reflects the current interdisciplinary reality of cutting edge research in ICT. The DTIC is now running a Maria de Maeztu Strategic Research Program on data-driven knowledge extraction, boosting synergistic research initiatives across our different research areas. The DTIC consistently ranks among the top computer science departments in Spain (e.g. the only computer science department from an Spanish university that has even been included in the top 100 of the Shanghai Ranking). Its PhD program offers advanced training in this interdisciplinary field, becoming an innovative and unique program in Spain. The DTIC PhD program has been growing steadily and currently hosts about 140 PhD students and 40 supervisors. The program received a Mention of Excellence award from the Ministry of Science and Innovation in 2011. The UPF university was awarded in 2010 the distinction of International Excellence Campus by the Spanish Ministry of Education and it is widely considered to be one of the best universities in Spain (e.g. is the top Spanish university according to 2013 Times Higher Education Ranking). The UPF is located in Barcelona. Its excellent location on the shores of the Mediterranean, its gentle climate, its open, cosmopolitan character, its gastronomy and architecture make Barcelona an extraordinary place to live. The DTIC is sited in UPF's Communication Campus, which was opened in 2009 and is located within the vibrant 22@ technological district of Barcelona. *Indicators: * - Research incomes: 15.6 M€ / year - 67 FP7 projects participated and coordinated by 26 staff members (> 60% UPF EU funds) including 13 prestigious ERC Grants, the Human Brain Project - Leader in Spain with > 5% of all the competitive funds obtained by Spanish Universities, Maria de Maeztu Strategic Program. - Consolidated scientific productivity ~200 articles/year, > 75% Q1 international journals - 50% scientific papers and articles with at least one international collaborator *ADDRESS* Roc Boronat, 138 - edifici Tànger, 08018 Barcelona, Barcelona *GROUP DISCIPLINES* Life Science Panel *GROUP LEADER* Prof.Salvador Soto-Faraco salvador.soto at upf.edu www.mrg.upf.edu Mireia Torralba Cuello Multisensory Research Group Center for Brain and Cognition, Universitat Pompeu Fabra Address: Edifici Mercè Rodoreda 24.313 c\ Ramon Trias Fargas, 25-27 08005 Barcelona http://www.mrg.upf.edu Tel +34 935422745 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonas at obleser.de Wed Nov 22 19:00:13 2017 From: jonas at obleser.de (Jonas Obleser) Date: Wed, 22 Nov 2017 19:00:13 +0100 Subject: [FieldTrip] =?utf-8?q?Postdoc_opportunity=2C_modelling/EEG/MRI_Ob?= =?utf-8?q?leser_lab_in_L=C3=BCbeck?= Message-ID: Dear colleagues around the globe, On somewhat shot notice, we have another postdoc Position in my lab available. Funded through the ERC Project «AUDADAPT», starting asap. Deadline for electronic, simple applications per email is Nov 30. Thanks for spreading the word! Best wishes, Jonas https://www.uni-luebeck.de/fileadmin/uzl_personal/stellenausschreibungen/1060_17_Ausschreibung_Obleser_Postdoc2018_ERC_EN.pdf Jonas Obleser Professor University of Lübeck Department of Psychology MFC 8, Maria-Goeppert-Straße 9a 23562 Lübeck, Germany Phone +49 (0)451 3101 3620 Mobile +49 (0)171 6993337 jonas.obleser at uni-luebeck.de http://auditorycognition.com From liyy90 at 163.com Thu Nov 23 15:44:10 2017 From: liyy90 at 163.com (liyy90) Date: Thu, 23 Nov 2017 22:44:10 +0800 (CST) Subject: [FieldTrip] Phd position in Cognitive Neuroscience in UPF (Barcelona) In-Reply-To: References: Message-ID: I am interested in this program. How to apply? At 2017-11-22 17:41:51, "TORRALBA CUELLO, MIREIA" wrote: Please find attached information about a PhD position in Cognitive Neuroscience at Multisensory Research Group (UPF, Barcelona) Deadline: Feb 1st, 2018 Start date: May/June 2018 Gross salary: Approx 27.800€/year Research money (travel etc...): 3.500€/year Requirements*: Master's degree in the EU or equivalent (to be decided by the host university at application), and have not worked/resided in Spain for more than 12 months (within the last 3y). Phd position in Cognitive Neuroscience: Neural predictors of Memory Perception and attention (Prof.Salvador Soto-Faraco) POSITION DESCRIPTION -Research Project / Research Group Description: How “...the brain enables the mind...” is one of the core questions in neuroscience. Understanding this relationship will lead to improvements in the mitigation of brain disease. One of the major sources of evidence on how neurophysiological activity relates to mental phenomena comes from the realization that fluctuations in neural activity could be at the heart of cognitive processes. In fact, it is well known that ongoing brain activity itself is highly organized, so that neural communication (local, and long range) seems to capitalize on the fine temporal structure of neural activity. Consequently responses to sensory events depend strongly on the momentary state of the system. The overarching goal of the research project hosting the potential PhD candidate is to capitalize on the relationship between brain oscillations, brain states and cognitive processes to anticipate and be able to modulate the outcome of these processes via real-time neurodevices based on Brain Computer Interfaces. The research lines hosting the PhD candidate address the link between the pattern of oscillatory brain activity and three sets of concrete cognitive processes. (1) Memory encoding in healthy humans and/or patients with Mild Cognitive Impairment. (2) Attention and perception in real-life scenarios. And, (3) perceptual conflict and awareness. The overarching goal is to be able to find predictors (biomarkers) for these processes and be able to anticipate optimal brain states (windows of opportunity) for the success of these behaviours. To this end, we use psychophysics, human electroencephalography (EEG), and Transcranial Magnetic Stimulation (TMS). Psychophysics is essential to measure the behavioural expression of cognitive processes. EEG is sensitive to post-synaptic potentials of large neuron populations, and is an indirect index of neural activity. In order to infer brain states, we capitalize on a variety of measures from the EEG: spectral power, instantaneous phase, and temporal/spatial coherence of oscillatory activity. Neurostimulation (TMS) is used to probe causality. The MRG is part of the CBC master, has 3 postdoc researchers (specialized in signal processing, bioengineering, and neuropsychology) 3 Phds, and support staff. Our research is supported by EU and local funding. -Job position description: Role: The successful candidate will lead a research line which falls amongst the overall projects of the MRG laboratory (described above). It is expected that the candidate will have a prior motivation for cognitive neuroscience and will contribute in an active way to define the particular project from its inception, formulation of hypotheses, experimental designs, measurement and analysis, and interpretation of the data. In order to accomplish these tasks, the PhD candidate will of course count with the support of the MRG staff and knowledge base, and the guidance of Prof Soto-Faraco as well as senior members of the laboratory. Dissemination of the research output, and networking with other local, or external experts as well as advanced post-docs and phd students will be encouraged and fostered. Responsibilities: The candidate will be mainly responsible for the implementation of the assigned research tasks conducive toward the PhD project, the careful and systematic carrying out of the experimental work. Other responsibilities will be assigned commensurate with the PhD’s capacity and level of seniority. Amongst them, like other members of the team, the PhD student will contribute to the group activities (e.g., helping organize talks, group meetings, presenting the findings in conferences) , and to the training and support of other junior members of the laboratory (eventual supervision of master or degree students). Finally, the Phd candidate will also be responsible to provide timely responses to requests from the funding body, including progress reports, as well as to attend the meetings s/he might be called to, from the funding agency. Skills: Background in Biology, Bioengineering, Experimental Psychology or other fields related to Cognitive Neuroscience. Prior experience or background in Brain Computer Interfaces. Concrete experience with experimental work in the field of the cognitive neurosciences, preferably with psychophysics and/or electrophysiology (EEG, MEG). Knowledge of signal processing. Others: High motivation, proactivity and team work are very desirable. RELATED LINK TO THE POSITION http://www.mrg.upf.edu/node/112 CENTER Dept. of Information & Communication Technologies, DTIC-UPF https://portal.upf.edu/es/web/etic/inicio CENTER DESCRIPTION The Department of Information and Communication Technologies (DTIC) of Universitat Pompeu Fabra covers a broad range of research topics: Computation and Intelligent Systems; Multimedia Technologies; Networks and Communications; Computational Biology and Biomedical Systems; and the Center of Brain and Cognition (CBC). This broad spectrum of topics reflects the current interdisciplinary reality of cutting edge research in ICT. The DTIC is now running a Maria de Maeztu Strategic Research Program on data-driven knowledge extraction, boosting synergistic research initiatives across our different research areas. The DTIC consistently ranks among the top computer science departments in Spain (e.g. the only computer science department from an Spanish university that has even been included in the top 100 of the Shanghai Ranking). Its PhD program offers advanced training in this interdisciplinary field, becoming an innovative and unique program in Spain. The DTIC PhD program has been growing steadily and currently hosts about 140 PhD students and 40 supervisors. The program received a Mention of Excellence award from the Ministry of Science and Innovation in 2011. The UPF university was awarded in 2010 the distinction of International Excellence Campus by the Spanish Ministry of Education and it is widely considered to be one of the best universities in Spain (e.g. is the top Spanish university according to 2013 Times Higher Education Ranking). The UPF is located in Barcelona. Its excellent location on the shores of the Mediterranean, its gentle climate, its open, cosmopolitan character, its gastronomy and architecture make Barcelona an extraordinary place to live. The DTIC is sited in UPF's Communication Campus, which was opened in 2009 and is located within the vibrant 22@ technological district of Barcelona. Indicators: Research incomes: 15.6 M€ / year 67 FP7 projects participated and coordinated by 26 staff members (> 60% UPF EU funds) including 13 prestigious ERC Grants, the Human Brain Project Leader in Spain with > 5% of all the competitive funds obtained by Spanish Universities, Maria de Maeztu Strategic Program. Consolidated scientific productivity ~200 articles/year, > 75% Q1 international journals 50% scientific papers and articles with at least one international collaborator ADDRESS Roc Boronat, 138 - edifici Tànger, 08018 Barcelona, Barcelona GROUP DISCIPLINES Life Science Panel GROUP LEADER Prof.Salvador Soto-Faraco salvador.soto at upf.edu www.mrg.upf.edu Mireia Torralba Cuello Multisensory Research Group Center for Brain and Cognition, Universitat Pompeu Fabra Address: Edifici Mercè Rodoreda 24.313 c\ Ramon Trias Fargas, 25-27 08005 Barcelona http://www.mrg.upf.edu Tel +34 935422745 -------------- next part -------------- An HTML attachment was scrubbed... URL: From changa5 at mcmaster.ca Thu Nov 23 21:44:19 2017 From: changa5 at mcmaster.ca (Andrew Chang) Date: Thu, 23 Nov 2017 15:44:19 -0500 Subject: [FieldTrip] Grad Student Positions in Auditory Neuroscience, Human Interaction & Music Message-ID: *Graduate Student Positions in Auditory Neuroscience, Human Interaction & Music* *McMaster University* Two graduate student positions are available to work with *Dr. Laurel Trainor* who directs both the Infant Auditory Lab ( https://trainorlab.mcmaster.ca) and the LIVELab (https://LIVELab.mcmaster.ca) at McMaster University. Projects include understanding human interaction in musical ensembles using behaviour, motion capture and EEG measures; studying brain oscillations involved in predictive timing and predictive coding; musical development in infants and children; and applications using non-verbal measures to understand auditory perception and communicative processes in special populations such adults with dementia or hearing loss and children with Developmental Coordination Disorder. The research group is multidisciplinary with ties to Engineering, Health Science and Music. In addition to infant and adult behavioural and EEG labs, students will have access to the internationally acclaimed LIVELab, a research-concert hall capable of simulating almost any acoustical environment and equipped with multiperson EEG, physiology, motion capture and more (https://LIVELab.mcmaster.ca). Applicants should have a Bachelor’s degree in Psychology, Neuroscience, Cognitive Science, Engineering, Computer Science or other affiliated disciplines. General information on the graduate program can be found here: https://science.mcmaster.ca/pnb/graduate-studies. Initial inquiries can be directed to Dr. Trainor at LJT at mcmaster.ca. Please include a CV and unofficial transcript with your inquiry. Papers from the lab can be accessed at https://trainorlab.mcmaster.ca/publications -- Andrew Chang, Ph.D. Candidate Vanier Canada Graduate Scholar http://changa5.wordpress.com/ Auditory Development Lab Department of Psychology, Neuroscience & Behaviour McMaster University -------------- next part -------------- An HTML attachment was scrubbed... URL: From clh at pku.edu.cn Fri Nov 24 00:57:47 2017 From: clh at pku.edu.cn (=?UTF-8?Q?=E9=99=88=E7=AB=8B=E7=BF=B0_=28Lihan_Chen=29?=) Date: Fri, 24 Nov 2017 07:57:47 +0800 (GMT+08:00) Subject: [FieldTrip] About a demo prog in fieldtrip- ERP analysis Message-ID: <1816d6b8.15bae.15feb50e32d.Coremail.clh@pku.edu.cn> Dear colleagues I am learning to use fieldtrip to analysis eyetracking data. And i found this demo very helpful. http://www.fieldtriptoolbox.org/example/use_simulated_erps_to_explore_cluster_statistics However, when i run this command: difference = ft_math(cfg, timelock1, timelock2); it generated the following and i can not go through the whole demo "Warning: timelock structure contains field with and without repetitions selecting these fields that have repetitions: trial removing these fields that do not have repetitions: avg, dof, var Warning: timelock structure contains field with and without repetitions selecting these fields that have repetitions: trial removing these fields that do not have repetitions: avg, dof, var Error using ft_notification (line 340) the requested parameter is not present in the data Error in ft_error (line 39) ft_notification(varargin{:}); Error in ft_math (line 151) ft_error('the requested parameter is not present in the data');" Would you please kindly find time to instruct how to make it run so that i can how a look how the final results look like? By the way, if i have 12 subjects, with two conditions ('congruent', 'incongruent'). Each condition has 1000 data points (1 second), so that how is the cfg.design i should make? Thank you very much in advance! Best, Lihan chen Peking Uiversity -------------- next part -------------- An HTML attachment was scrubbed... URL: From holmgren.jostein at gmail.com Tue Nov 28 21:29:07 2017 From: holmgren.jostein at gmail.com (Jostein Holmgren) Date: Tue, 28 Nov 2017 20:29:07 +0000 Subject: [FieldTrip] Trouble writing data from TMSi to FieldTrip buffer (Error message: "Cannot initiate device") Message-ID: <5066A2DB-146C-4BB2-8BAB-E9C19A0A6D63@gmail.com> Dear all, I am having trouble writing data from my TMSi Porti 7 system to the FieldTrip buffer. I have tried both the tmsidriver.exe and tmsi2ft.exe tools, but I’ve focused my efforts on the latter. I have the TMSi system connected to my PC via USB and have tested the connection by recording some data in Polybench without issue. When I attempt to run tmsi2ft nothing happens until I terminate the process, at which point the error message “Cannot initiate device” is displayed. The exact syntax I run in the cmd is tmsi2ft config.txt - where config.txt file contains the following (misc commented lines excluded) [select] 25=Blip25 samplerate=2048 For testing purposes I’ve only got a bipolar electrode connected to the TMSi system, which is the channel listed in the config file. For tmsidriver.exe I changed the sampling rate in parameter file to match my system to attempt to get it to work, but no success there either. I also have the buffer open when running tmsidriver.exe. The contents of preferences.txt is sampleRate(milliHz) BufSizeFactor savedata(0/1) 2048000 5 1 The TMSi Porti 7 system has a sampling rate of 2048Hz. The PC is running Windows 8.1 64-bit. I’m using fieldtrip-20171106. Any advice or suggestions is greatly appreciated. Best regards, Jostein Holmgren ---------------------- Jostein Holmgren DPhil Student (PRS) Nuffield Department of Clinical Neurosciences Wellcome Centre for Integrative Neuroimaging, FMRIB Building University of Oxford -------------- next part -------------- An HTML attachment was scrubbed... URL: From C.Mazzetti at donders.ru.nl Wed Nov 29 11:20:53 2017 From: C.Mazzetti at donders.ru.nl (Mazzetti, C. (Cecilia)) Date: Wed, 29 Nov 2017 10:20:53 +0000 Subject: [FieldTrip] problems plotting source grandaverage - no anatomy fied (ft_sourcegrandaverage) Message-ID: <389DA1293690C94C93E3A53201F6C91E59226B5C@EXPRD98.hosting.ru.nl> Hi Everyone, I am struggling with the source analysis and especially when averaging across subjects' source reconstruction. The analysis for every subject was done according to the tutorial (creating MNI aligned grids in individual head space). The point is when I try to plot the source grandaverage I get an error saying there is no 'anatomy' field in my data. I tried to use both sourceinterpolate or add the anatomy field manually to the gsource_grandaverage structure but nothing works. Here is what my source_grandaverage contains: ga_sources pow: [6×902629 double] dim: [91 109 91] freq: 9.9723 inside: [902629×1 logical] pos: [902629×3 double] unit: 'mm' cfg: [1×1 struct] Any help is appreciated! Thanks! Best, Cecilia -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Nov 29 12:53:36 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 29 Nov 2017 11:53:36 +0000 Subject: [FieldTrip] problems plotting source grandaverage - no anatomy fied (ft_sourcegrandaverage) In-Reply-To: <389DA1293690C94C93E3A53201F6C91E59226B5C@EXPRD98.hosting.ru.nl> References: <389DA1293690C94C93E3A53201F6C91E59226B5C@EXPRD98.hosting.ru.nl> Message-ID: Hi Cecilia, Have you tried to compute the average on the low-resolution solutions, and only do the interpolation on the average? This should be possible, because you use the ‘mni-aligned grids’. Also, ft_sourcegrandaverage is a dinosaur of a function, and it looks as if it hasn’t grown along with the rest of the code. The pasted matlab-structure looks a bit strange, and I can imagine that FieldTrip chokes on it. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 29 Nov 2017, at 11:20, Mazzetti, C. (Cecilia) > wrote: Hi Everyone, I am struggling with the source analysis and especially when averaging across subjects' source reconstruction. The analysis for every subject was done according to the tutorial (creating MNI aligned grids in individual head space). The point is when I try to plot the source grandaverage I get an error saying there is no 'anatomy' field in my data. I tried to use both sourceinterpolate or add the anatomy field manually to the gsource_grandaverage structure but nothing works. Here is what my source_grandaverage contains: ga_sources pow: [6×902629 double] dim: [91 109 91] freq: 9.9723 inside: [902629×1 logical] pos: [902629×3 double] unit: 'mm' cfg: [1×1 struct] Any help is appreciated! Thanks! Best, Cecilia _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From C.Mazzetti at donders.ru.nl Thu Nov 30 12:05:33 2017 From: C.Mazzetti at donders.ru.nl (Mazzetti, C. (Cecilia)) Date: Thu, 30 Nov 2017 11:05:33 +0000 Subject: [FieldTrip] fieldtrip Digest, Vol 84, Issue 18 In-Reply-To: References: Message-ID: <389DA1293690C94C93E3A53201F6C91E59227015@EXPRD98.hosting.ru.nl> Thanks Jan Mathijs! I don't know whether that's supposed to be the case, but the problem is 'solved' by choosing cfg.keepindividual='no' when computing sourcegrandaverage, before the interpolation. then everything is fine! Might be helpful for others maybe! Thanks! Best, Cecilia Cecilia Mazzetti - Ph.D. Candidate Donders Centre for Cognitive Neuroimaging, room 0.068 Kapittelweg 29 | 6525 EN Nijmegen ________________________________________ Da: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] per conto di fieldtrip-request at science.ru.nl [fieldtrip-request at science.ru.nl] Inviato: giovedì 30 novembre 2017 12.00 A: fieldtrip at science.ru.nl Oggetto: fieldtrip Digest, Vol 84, Issue 18 Send fieldtrip mailing list submissions to fieldtrip at science.ru.nl To subscribe or unsubscribe via the World Wide Web, visit https://mailman.science.ru.nl/mailman/listinfo/fieldtrip or, via email, send a message with subject or body 'help' to fieldtrip-request at science.ru.nl You can reach the person managing the list at fieldtrip-owner at science.ru.nl When replying, please edit your Subject line so it is more specific than "Re: Contents of fieldtrip digest..." Today's Topics: 1. Re: problems plotting source grandaverage - no anatomy fied (ft_sourcegrandaverage) (Schoffelen, J.M. (Jan Mathijs)) ---------------------------------------------------------------------- Message: 1 Date: Wed, 29 Nov 2017 11:53:36 +0000 From: "Schoffelen, J.M. (Jan Mathijs)" To: FieldTrip discussion list Subject: Re: [FieldTrip] problems plotting source grandaverage - no anatomy fied (ft_sourcegrandaverage) Message-ID: Content-Type: text/plain; charset="utf-8" Hi Cecilia, Have you tried to compute the average on the low-resolution solutions, and only do the interpolation on the average? This should be possible, because you use the ?mni-aligned grids?. Also, ft_sourcegrandaverage is a dinosaur of a function, and it looks as if it hasn?t grown along with the rest of the code. The pasted matlab-structure looks a bit strange, and I can imagine that FieldTrip chokes on it. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 29 Nov 2017, at 11:20, Mazzetti, C. (Cecilia) > wrote: Hi Everyone, I am struggling with the source analysis and especially when averaging across subjects' source reconstruction. The analysis for every subject was done according to the tutorial (creating MNI aligned grids in individual head space). The point is when I try to plot the source grandaverage I get an error saying there is no 'anatomy' field in my data. I tried to use both sourceinterpolate or add the anatomy field manually to the gsource_grandaverage structure but nothing works. Here is what my source_grandaverage contains: ga_sources pow: [6?902629 double] dim: [91 109 91] freq: 9.9723 inside: [902629?1 logical] pos: [902629?3 double] unit: 'mm' cfg: [1?1 struct] Any help is appreciated! Thanks! Best, Cecilia _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip End of fieldtrip Digest, Vol 84, Issue 18 ***************************************** From jan.schoffelen at donders.ru.nl Thu Nov 30 12:28:39 2017 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 30 Nov 2017 11:28:39 +0000 Subject: [FieldTrip] problems plotting source grandaverage - no anatomy fied (ft_sourcegrandaverage) In-Reply-To: <389DA1293690C94C93E3A53201F6C91E59227015@EXPRD98.hosting.ru.nl> References: <389DA1293690C94C93E3A53201F6C91E59227015@EXPRD98.hosting.ru.nl> Message-ID: Hi Cecilia, I am glad that you have resolved it. Best wishes, Jan-Mathijs > On 30 Nov 2017, at 12:05, Mazzetti, C. (Cecilia) wrote: > > Thanks Jan Mathijs! > I don't know whether that's supposed to be the case, but the problem is 'solved' by choosing cfg.keepindividual='no' when computing sourcegrandaverage, before the interpolation. then everything is fine! > Might be helpful for others maybe! > > Thanks! > > Best, > Cecilia > > > Cecilia Mazzetti - Ph.D. Candidate > Donders Centre for Cognitive Neuroimaging, room 0.068 > Kapittelweg 29 | 6525 EN Nijmegen > > > ________________________________________ > Da: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] per conto di fieldtrip-request at science.ru.nl [fieldtrip-request at science.ru.nl] > Inviato: giovedì 30 novembre 2017 12.00 > A: fieldtrip at science.ru.nl > Oggetto: fieldtrip Digest, Vol 84, Issue 18 > > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Re: problems plotting source grandaverage - no anatomy fied > (ft_sourcegrandaverage) (Schoffelen, J.M. (Jan Mathijs)) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 29 Nov 2017 11:53:36 +0000 > From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] problems plotting source grandaverage - no > anatomy fied (ft_sourcegrandaverage) > Message-ID: > Content-Type: text/plain; charset="utf-8" > > Hi Cecilia, > > Have you tried to compute the average on the low-resolution solutions, and only do the interpolation on the average? > > This should be possible, because you use the ?mni-aligned grids?. > > Also, ft_sourcegrandaverage is a dinosaur of a function, and it looks as if it hasn?t grown along with the rest of the code. The pasted matlab-structure looks a bit strange, and I can imagine that FieldTrip chokes on it. > > Best wishes, > Jan-Mathijs > > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > On 29 Nov 2017, at 11:20, Mazzetti, C. (Cecilia) > wrote: > > Hi Everyone, > I am struggling with the source analysis and especially when averaging across subjects' source reconstruction. > The analysis for every subject was done according to the tutorial (creating MNI aligned grids in individual head space). > The point is when I try to plot the source grandaverage I get an error saying there is no 'anatomy' field in my data. > I tried to use both sourceinterpolate or add the anatomy field manually to the gsource_grandaverage structure but nothing works. > Here is what my source_grandaverage contains: > ga_sources > > pow: [6?902629 double] > dim: [91 109 91] > freq: 9.9723 > inside: [902629?1 logical] > pos: [902629?3 double] > unit: 'mm' > cfg: [1?1 struct] > > > > Any help is appreciated! Thanks! > > Best, > Cecilia > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 84, Issue 18 > ***************************************** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip