From jdien07 at mac.com Sat Dec 1 00:08:26 2018 From: jdien07 at mac.com (Joseph Dien) Date: Fri, 30 Nov 2018 18:08:26 -0500 Subject: [FieldTrip] automatic IC rejection In-Reply-To: <48E6E95C4AB29E4BAD7908051F5C17EF016E1E3CBD@MBXP07.ds.man.ac.uk> References: <5e257bfd-121e-d151-08d0-3c31ff0ada5a@uzh.ch> <9b277ef4-067a-9a61-a11b-da7d504b9717@uni-konstanz.de> <48E6E95C4AB29E4BAD7908051F5C17EF016E1E31BC@MBXP07.ds.man.ac.uk> <6630afcc-003d-3ecf-2d53-d0174a75ea09@uzh.ch> <48E6E95C4AB29E4BAD7908051F5C17EF016E1E3CBD@MBXP07.ds.man.ac.uk> Message-ID: <78BF4010-FCE8-4A86-BE5C-E7E1B0295736@mac.com> I have a comprehensive automated artifact correction routine (MAAC) implemented in my EP Toolkit, which you may find helpful. It follows the principle that different artifacts have different characteristics and so different algorithms will be most effective for each one. I’m in the middle of writing it up. https://sourceforge.net/projects/erppcatoolkit/ Joe > On Nov 30, 2018, at 12:08, Jason Taylor wrote: > > Hi Aitor, > > No, not that I know of. I generally use a hacky combination of SPM, fieldtrip, and EEGLAB functions, but if you've already run ICA, you could accomplish what I suggested with some standard matlab functions. > > Best wishes, > Jason > > -----Original Message----- > From: Aitor Egurtzegi [mailto:aitor.martinezegurcegui at uzh.ch] > Sent: 30 November 2018 13:43 > To: Jason Taylor; FieldTrip discussion list > Subject: Re: [FieldTrip] automatic IC rejection > > Dear Jason, > > Thanks a lot for your reply. Is there a Fieldtrip method already > implemented to run such temporal correlation? or would I have to do the > implementation in raw Matlab? > > Thanks in advance, > Aitor > > On 11/30/18 2:05 AM, Jason Taylor wrote: >> Hi Aitor, >> >> If you have an 'objective' measure of the artefact you're trying to remove (e.g., VEOG for blinks), a relatively straightforward method is to run a temporal correlation between each IC's activation time-course and the artefact channel's time-course. You can then reject any IC with a correlation higher than some threshold, or with a Z-score (r value relative to the distribution of IC r values) above some threshold. This tends to work very well for identifying blinks, and fairly well for eye-movements (*EOG), and can work for pulse artefact if you have recorded ECG. To avoid spurious correlations due to high-frequency noise, you can filter (e.g., 1 to 30 Hz) the component and artefact signals before correlating them (but obviously go back to the original unfiltered signals to continue with your analysis). >> >> Best wishes, >> Jason >> >> >> -----Original Message----- >> From: fieldtrip [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of David Schubring >> Sent: 28 November 2018 12:47 >> To: fieldtrip at science.ru.nl; aitor.martinezegurcegui at uzh.ch >> Subject: Re: [FieldTrip] automatic IC rejection >> >> Dear Aitor, >> >> the closest thing I know of for a data-driven approach of selecting >> independent components is COMPASS, quote: >> >> "COMPASS is a MATLAB and EEGLAB based algorithm with the purpose of >> providing the user with a convenient technique for automatic Independent >> Component (IC) selection with respect to the contributions of the ICs to >> a certain ERP." >> >> Link to the toolbox: >> >> http://53450283.de.strato-hosting.eu/jrw/lab/e_compass.htm >> >> Paper: >> >> Wessel, J. R., & Ullsperger, M. (2011). Selection of independent >> components representing event-related brain potentials: a data-driven >> approach for greater objectivity. Neuroimage, 54(3), 2105-2115. >> https://doi.org/10.1016/j.neuroimage.2010.10.033 >> >> I have only theoretical experience with the toolbox as I only learned >> about it in a workshop and did not yet have the time to test and >> implement it in my personal FieldTrip workflow (even though it is on my >> ever growing to-do list). So far it looked like a useful thing to try >> out to me, especially as code can better be reproduced than "personal >> judgement". >> >> Best, >> David >> >> Am 28.11.2018 um 10:49 schrieb Aitor Egurtzegi: >>> Dear researchers at Fieldtrip, >>> >>> >>> In order to make my work more reproducible, I would like to >>> automatically reject ICs instead of doing visual inspection and >>> rejection of the components. Unfortunately, I haven't found any >>> documentation for such thing. Is there a way to do it in Fieldtrip? >>> >>> Best, >>> Aitor >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> https://doi.org/10.1371/journal.pcbi.1002202 > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 -------------------------------------------------------------------------------- Joseph Dien, PhD Senior Research Scientist Department of Human Development and Quantitative Methodology University of Maryland, College Park http://joedien.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From mikkel at cnru.dk Tue Dec 4 20:20:45 2018 From: mikkel at cnru.dk (Mikkel Vinding) Date: Tue, 4 Dec 2018 20:20:45 +0100 Subject: [FieldTrip] Import Freesurfer atlas to ft Message-ID: Dear FieldTrip list Has anyone here imported individual atlases from Freesurfer into FieldTrip? It should be possible with ft_read_atlas. From the documentation of ft_read_atlas: * For individual surface-based atlases from FreeSurfer, you should specify two * * filenames as a cell-array: the first points to the file that contains information* * with respect to the parcels' labels, the second points to the file that defines the* * mesh on which the parcellation is defined.* Ft_read_atlas require a struct containing the filename of the atlas file and the cortical surface/mesh. However, I keep getting errors that ft_read_atlas cannot read Freesurfers “annot” files: “ *unrecognized filetype 'freesurfer_annot'.*“ I get a similar error when I try to read Freesurfer “label” files. The problem seems to be because ft_read_atlas calls ft_read_mri which does not support the type 'freesurfer_annot'. My question is how to read in Freesurfer annotations or labels? Do I need to convert the Freesurfer files first or is there another step I need to do first? If anyone has managed to read Freesurfer labels in FieldTrip, I will be delighted to hear the answer. Best regards Mikkel Mikkel C. Vinding NatMEG, Karolinska Institutet Nobels väg 9 171 77 Stockholm, Sweden Email: mikkel.vinding at ki.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Dec 4 21:17:00 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 4 Dec 2018 20:17:00 +0000 Subject: [FieldTrip] Import Freesurfer atlas to ft In-Reply-To: References: Message-ID: <05BF26AB-B71D-4F76-9BFB-09277FD731EC@donders.ru.nl> Dear Mikkel, I did not look into it in detail, but from your description it seems that the code takes a wrong turn somewhere, and thinks that the fileformat is of type freesurfer_volume (and for this reason it ends up on a line that tries to use ft_read_mri). I read in the code that the default allocation of the fileformat based on an educated guess from the filename is implemented in a slightly clunky way. Soooo, perhaps you could try and overrule this default allocation by explicitly specifying it in your call to ft_read_atlas: ft_read_atlas({filename_annotation filename_mesh}, ‘format’, ‘freesurfer_*’); where the * should be the appropriate choice of ‘a2009s’ ‘aparc’, or ‘ba’. Best wishes, Jan-Mathijs On 4 Dec 2018, at 20:20, Mikkel Vinding > wrote: Dear FieldTrip list Has anyone here imported individual atlases from Freesurfer into FieldTrip? It should be possible with ft_read_atlas. From the documentation of ft_read_atlas: For individual surface-based atlases from FreeSurfer, you should specify two filenames as a cell-array: the first points to the file that contains information with respect to the parcels' labels, the second points to the file that defines the mesh on which the parcellation is defined. Ft_read_atlas require a struct containing the filename of the atlas file and the cortical surface/mesh. However, I keep getting errors that ft_read_atlas cannot read Freesurfers “annot” files: “ unrecognized filetype 'freesurfer_annot'.“ I get a similar error when I try to read Freesurfer “label” files. The problem seems to be because ft_read_atlas calls ft_read_mri which does not support the type 'freesurfer_annot'. My question is how to read in Freesurfer annotations or labels? Do I need to convert the Freesurfer files first or is there another step I need to do first? If anyone has managed to read Freesurfer labels in FieldTrip, I will be delighted to hear the answer. Best regards Mikkel Mikkel C. Vinding NatMEG, Karolinska Institutet Nobels väg 9 171 77 Stockholm, Sweden Email: mikkel.vinding at ki.se _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.maris at donders.ru.nl Wed Dec 5 14:40:26 2018 From: e.maris at donders.ru.nl (Maris, E.G.G. (Eric)) Date: Wed, 5 Dec 2018 13:40:26 +0000 Subject: [FieldTrip] Cluster based permutation test interpretation In-Reply-To: References: Message-ID: <51779646-98DD-42FA-94BB-13CE1167D869@donders.ru.nl> Dear Yvonne, I advise you to make a distinction between statistical inference and interpretation. Statistical inference pertains to a particular null hypothesis, which is either rejected or not. Interpretation, on the other hand, pertains to the likely cause of a rejection (e.g., alpha-band power modulations in the -0.75 to 0 interval). The p-value pertains to statistical inference but not to the interpretation. To make a case for a particular interpretation you are free to use all arguments at your disposal. One of these arguments is the fact that the largest cluster in in the alpha-band in the —0.75 to 0 interval. But you can also refer to published results. For instance, the alpha-band is one of the two bands of the sensorimotor rhythm, whose spatio-spectral structure has been described in numerous papers (among which several ones to which I contributed as a senior author), and whose amplitude is inversely related to movement and reaction time. In your case, I would look in the post-stimulation period to characterise the sensorimotor rhythm in space and frequency. I have advised this procedure in this paper: https://doi.org/10.1111/j.1469-8986.2011.01320.x. In general, I think that we should rely less on p-values for localisation in space, frequency and time. Instead, we should use the spatio-spectro-temporal extent of the largest clusters to provide a mechanistic account of the effect. For that, it is necessary to relate your results to the published findings in the literature. I have argued for this approach in this paper: https://www.sciencedirect.com/science/article/pii/S1364661316300481 best, Eric From: Yvonne Visser > Subject: [FieldTrip] Cluster based permutation test interpretation Date: 30 November 2018 at 10:47:03 CET To: "fieldtrip at science.ru.nl" > Cc: "aaron.schurger at gmail.com" > Dear all, Thank you for welcoming me to the discussion list, my name is Yvonne Visser and I currently work as a research assistant with dr. Aaron Schurger at Neurospin. During my masters program I learned about cluster based permutation tests for electrophysiological data and distinctly remember how from this type of test one can not conclude that a particular cluster is significant (in line with what is said on the fieldtrip website here, http://www.fieldtriptoolbox.org/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test) We are currently using the cluster based permutation test in the analysis of our experiment, but we are a bit confused on how to interpret the results from our test. To give you a short introduction to our experiment: we are looking for a relationship between a behavioural variable and our collected EEG data. So we computed the grand average time frequency spectrum in a single channel of the time bins of interest. Then, we correlated each time/frequency point in this 2d matrix with the behavioural variable in that trial. This resulted in a correlation matrix like you can see in attachment1_correlationmatrix. As you can see, we also computed clusters of time/frequency points with p<0.05. After computing the permutations, we found that the biggest "real" cluster is bigger than any of the permuted clusters. Now, we would like to conclude something from this result about which frequency band at what time is correlated to our behavioural variable. We found a fieldtrip function called ft_clusterplot that does seem to suggest that you can highlight a specific cluster it if it survives the test, but isn't that exactly what my lectures and the webpage say we should not do? Can we say that activity in the alpha band around -0.75 to 0 (where the biggest cluster is located) is correlated to the size of the movement? Or should we not conclude something about which cluster is significant and can we only say that some time frequency power is correlated to our behavioural variable? If the second is true, do you have any advice for us to make the interpretation more specific? Thank you so much in advance, and please let us know if anything is unclear. Kind regards, Yvonne & Aaron. _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 Eric Maris | Donders Institute for Brain, Cognition, and Behaviour & Faculty of Social Sciences | Radboud University | PO Box 9104, 6500 HE Nijmegen | (024) 3612651 | www.ru.nl This message (and any attachments) is intended solely for the addressee(s) and may contain confidential information. If you are not the addressee, do not copy this message (and any attachments), forward or share this message with third parties. You are requested to notify the sender immediately and delete this message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Wed Dec 5 16:51:11 2018 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 5 Dec 2018 16:51:11 +0100 Subject: [FieldTrip] new fieldtrip website Message-ID: <20CB9CBD-7DB3-46A0-A616-7BF8C8228C09@donders.ru.nl> Dear FieldTrip community, The FieldTrip website has been implemented as a wiki using the Dokuwiki CMS for more than 10 years now. But the ongoing struggles in updating the underlying code base to prevent being hacked (which happened a few times), the effort to keep the website/wiki free of spam (which happened too often), and to maintain and extend the documentation of thee website have triggered us to move to a new system. You may already have noticed that the wiki was not editable for some weeks: this was to allow us the opportunity to copy all content over. We now have a new website that is implemented using Jekyll (which some of you might know from github pages). It is technically not a wiki any more, but importantly: you can still directly contribute. The important difference is that contributions are now done by editing markdown documents and using github . This allows us to review them for correctness and consistency and (importantly) to prevent spam. Furthermore, having all pages in one easily accessible place makes maintenance and large edits easier, and properly gives credits to the documentation contributors. To edit, you need a github account. You can do edits directly on the github website, or fork/clone the repository and send PRs. The new website can be found on new.fieldtriptoolbox.org , Up to now the main address www.fieldtriptoolbox.org is pointing to the old one, but I will redirect it so that it points to the new one. It might take some time for you to see the change. The old website will remain available for some time on old.fieldtriptoolbox.org . All content has been moved over and (almost) all URLs from the old website should point to the same page on the new website. The overall menu structure has been changed/simplified; hopefully you can still find the pages you are familiar with. The search functionality has been significantly improved and now automatically returns results both from website and email list. The new website also loads much faster than the old one, and you could actually get a fully functional offline copy on your hard disk or own server. We are still (as always) working on improving the new website. Especially the overall organization of the documentation has gotten a bit messy over the years (in true wiki style ;-) and we will try to restructure it more and make the wealth(*) of documentation more accessible. Furthermore, you can expect some technical improvements and more to come in the future (check out the new matlab2markdown and markdown2matlab functions in fieldtrip/utilities). If you have suggestions, or if you are skilled with jekyll/html/css/javascript, or want to help out in any other way, please open an issue here to contribute. best regards, Robert, Eelke, Jan-Mathijs and the others that helped transitioning to the new website PS (*) the FieldTrip website now has 944 pages of documentation (excluding the reference documentation) and 1022 figures. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dlozanosoldevilla at gmail.com Wed Dec 5 18:54:13 2018 From: dlozanosoldevilla at gmail.com (Diego Lozano-Soldevilla) Date: Wed, 5 Dec 2018 18:54:13 +0100 Subject: [FieldTrip] new fieldtrip website In-Reply-To: <20CB9CBD-7DB3-46A0-A616-7BF8C8228C09@donders.ru.nl> References: <20CB9CBD-7DB3-46A0-A616-7BF8C8228C09@donders.ru.nl> Message-ID: Thank you for this great effort! A perfect Sinterklaas gift ;) On Wed, Dec 5, 2018, 17:22 Robert Oostenveld Dear FieldTrip community, > > The FieldTrip website has been implemented as a wiki using the Dokuwiki > CMS for more than 10 years now. But the ongoing > struggles in updating the underlying code base to prevent being hacked > (which happened a few times), the effort to keep the website/wiki free of > spam (which happened too often), and to maintain and extend the > documentation of thee website have triggered us to move to a new system. > You may already have noticed that the wiki was not editable for some weeks: > this was to allow us the opportunity to copy all content over. > > We now have a new website that is implemented using Jekyll > (which some of you might know from github pages). > It is technically not a wiki any more, but importantly: you can still > directly contribute. The important difference is that contributions are now > done by editing markdown documents and using github > . This allows us to review them for > correctness and consistency and (importantly) to prevent spam. Furthermore, > having all pages in one easily accessible place makes maintenance and large > edits easier, and properly gives credits to the documentation contributors. > To edit, you need a github account. You can do edits directly on the github > website, or fork/clone the repository and send PRs. > > The new website can be found on new.fieldtriptoolbox.org, Up to now the > main address www.fieldtriptoolbox.org is pointing to the old one, but I > will redirect it so that it points to the new one. It might take some time > for you to see the change. The old website will remain available for some > time on old.fieldtriptoolbox.org. > > All content has been moved over and (almost) all URLs from the old website > should point to the same page on the new website. The overall menu > structure has been changed/simplified; hopefully you can still find the > pages you are familiar with. The search functionality has been > significantly improved and now automatically returns results both from > website and email list. The new website also loads much faster than the old > one, and you could actually get a fully functional offline copy on your > hard disk or own server. > > We are still (as always) working on improving the new website. Especially > the overall organization of the documentation has gotten a bit messy over > the years (in true wiki style ;-) and we will try to restructure it more > and make the wealth(*) of documentation more accessible. Furthermore, you > can expect some technical improvements and more to come in the future > (check out the new matlab2markdown and markdown2matlab functions in > fieldtrip/utilities). If you have suggestions, or if you are skilled with > jekyll/html/css/javascript, or want to help out in any other way, please > open an issue here to contribute. > > best regards, > Robert, Eelke, Jan-Mathijs and the others that helped transitioning to the > new website > > > PS (*) the FieldTrip website now has 944 pages of documentation (excluding > the reference documentation) and 1022 figures. > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mikkel at cnru.dk Thu Dec 6 10:50:32 2018 From: mikkel at cnru.dk (Mikkel Vinding) Date: Thu, 6 Dec 2018 10:50:32 +0100 Subject: [FieldTrip] Import Freesurfer atlas to ft In-Reply-To: <05BF26AB-B71D-4F76-9BFB-09277FD731EC@donders.ru.nl> References: <05BF26AB-B71D-4F76-9BFB-09277FD731EC@donders.ru.nl> Message-ID: Dear Jan-Mathijs Thank you for the answer. It worked! Best regards Mikkel Mikkel C. Vinding NatMEG, Karolinska Institutet Nobels väg 9 171 77 Stockholm, Sweden Email: mikkel.vinding at ki.se On Tue, Dec 4, 2018 at 9:45 PM Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Dear Mikkel, > > I did not look into it in detail, but from your description it seems that > the code takes a wrong turn somewhere, and thinks that the fileformat is of > type freesurfer_volume (and for this reason it ends up on a line that tries > to use ft_read_mri). I read in the code that the default allocation of the > fileformat based on an educated guess from the filename is implemented in > a slightly clunky way. Soooo, perhaps you could try and overrule this > default allocation by explicitly specifying it in your call to > ft_read_atlas: > > ft_read_atlas({filename_annotation filename_mesh}, ‘format’, > ‘freesurfer_*’); > > where the * should be the appropriate choice of ‘a2009s’ ‘aparc’, or ‘ba’. > > Best wishes, > Jan-Mathijs > > On 4 Dec 2018, at 20:20, Mikkel Vinding wrote: > > Dear FieldTrip list > > > Has anyone here imported individual atlases from Freesurfer into > FieldTrip? It should be possible with ft_read_atlas. From the documentation > of ft_read_atlas: > > > * For individual surface-based atlases from FreeSurfer, you should > specify two * > * filenames as a cell-array: the first points to the file that contains > information* > * with respect to the parcels' labels, the second points to the file that > defines the* > * mesh on which the parcellation is defined.* > > > Ft_read_atlas require a struct containing the filename of the atlas file > and the cortical surface/mesh. However, I keep getting errors that > ft_read_atlas cannot read Freesurfers “annot” files: “ *unrecognized > filetype 'freesurfer_annot'.*“ I get a similar error when I try to read > Freesurfer “label” files. > > > The problem seems to be because ft_read_atlas calls ft_read_mri which does > not support the type 'freesurfer_annot'. My question is how to read in > Freesurfer annotations or labels? Do I need to convert the Freesurfer files > first or is there another step I need to do first? If anyone has managed to > read Freesurfer labels in FieldTrip, I will be delighted to hear the answer. > > > Best regards > Mikkel > > Mikkel C. Vinding > NatMEG, Karolinska Institutet > Nobels väg 9 > 171 77 Stockholm, Sweden > Email: mikkel.vinding at ki.se > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From p.gaur at ulster.ac.uk Thu Dec 6 20:10:51 2018 From: p.gaur at ulster.ac.uk (Gaur, Pramod) Date: Thu, 6 Dec 2018 19:10:51 +0000 Subject: [FieldTrip] Connectivity analysis in Source level Message-ID: Dear Team, I have identified 3 sources in the source level which are showing significant difference using machine learning techniques in MCI group and control group. Can please advise is it possible to perform connectivity analysis in the identified sources? Thanks, Pramod This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster at ulster.ac.uk and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Ulster University. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. Ulster University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The Ulster University was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for Ulster University in Northern Ireland is Cromore Road, Coleraine, Co. Londonderry BT52 1SA -------------- next part -------------- An HTML attachment was scrubbed... URL: From y.visser at hotmail.com Fri Dec 7 16:04:02 2018 From: y.visser at hotmail.com (Yvonne Visser) Date: Fri, 7 Dec 2018 15:04:02 +0000 Subject: [FieldTrip] Cluster based permutation test interpretation In-Reply-To: <51779646-98DD-42FA-94BB-13CE1167D869@donders.ru.nl> References: , <51779646-98DD-42FA-94BB-13CE1167D869@donders.ru.nl> Message-ID: Dear Eric, Thank you for your extensive reply, we will take it into account for the interpretation of our results! Best, Yvonne ________________________________ From: fieldtrip on behalf of Maris, E.G.G. (Eric) Sent: Wednesday, December 5, 2018 2:40 PM To: fieldtrip at science.ru.nl Subject: Re: [FieldTrip] Cluster based permutation test interpretation Dear Yvonne, I advise you to make a distinction between statistical inference and interpretation. Statistical inference pertains to a particular null hypothesis, which is either rejected or not. Interpretation, on the other hand, pertains to the likely cause of a rejection (e.g., alpha-band power modulations in the -0.75 to 0 interval). The p-value pertains to statistical inference but not to the interpretation. To make a case for a particular interpretation you are free to use all arguments at your disposal. One of these arguments is the fact that the largest cluster in in the alpha-band in the —0.75 to 0 interval. But you can also refer to published results. For instance, the alpha-band is one of the two bands of the sensorimotor rhythm, whose spatio-spectral structure has been described in numerous papers (among which several ones to which I contributed as a senior author), and whose amplitude is inversely related to movement and reaction time. In your case, I would look in the post-stimulation period to characterise the sensorimotor rhythm in space and frequency. I have advised this procedure in this paper: https://doi.org/10.1111/j.1469-8986.2011.01320.x. In general, I think that we should rely less on p-values for localisation in space, frequency and time. Instead, we should use the spatio-spectro-temporal extent of the largest clusters to provide a mechanistic account of the effect. For that, it is necessary to relate your results to the published findings in the literature. I have argued for this approach in this paper: https://www.sciencedirect.com/science/article/pii/S1364661316300481 best, Eric From: Yvonne Visser > Subject: [FieldTrip] Cluster based permutation test interpretation Date: 30 November 2018 at 10:47:03 CET To: "fieldtrip at science.ru.nl" > Cc: "aaron.schurger at gmail.com" > Dear all, Thank you for welcoming me to the discussion list, my name is Yvonne Visser and I currently work as a research assistant with dr. Aaron Schurger at Neurospin. During my masters program I learned about cluster based permutation tests for electrophysiological data and distinctly remember how from this type of test one can not conclude that a particular cluster is significant (in line with what is said on the fieldtrip website here, http://www.fieldtriptoolbox.org/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test) We are currently using the cluster based permutation test in the analysis of our experiment, but we are a bit confused on how to interpret the results from our test. To give you a short introduction to our experiment: we are looking for a relationship between a behavioural variable and our collected EEG data. So we computed the grand average time frequency spectrum in a single channel of the time bins of interest. Then, we correlated each time/frequency point in this 2d matrix with the behavioural variable in that trial. This resulted in a correlation matrix like you can see in attachment1_correlationmatrix. As you can see, we also computed clusters of time/frequency points with p<0.05. After computing the permutations, we found that the biggest "real" cluster is bigger than any of the permuted clusters. Now, we would like to conclude something from this result about which frequency band at what time is correlated to our behavioural variable. We found a fieldtrip function called ft_clusterplot that does seem to suggest that you can highlight a specific cluster it if it survives the test, but isn't that exactly what my lectures and the webpage say we should not do? Can we say that activity in the alpha band around -0.75 to 0 (where the biggest cluster is located) is correlated to the size of the movement? Or should we not conclude something about which cluster is significant and can we only say that some time frequency power is correlated to our behavioural variable? If the second is true, do you have any advice for us to make the interpretation more specific? Thank you so much in advance, and please let us know if anything is unclear. Kind regards, Yvonne & Aaron. _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 Eric Maris | Donders Institute for Brain, Cognition, and Behaviour & Faculty of Social Sciences | Radboud University | PO Box 9104, 6500 HE Nijmegen | (024) 3612651 | www.ru.nl This message (and any attachments) is intended solely for the addressee(s) and may contain confidential information. If you are not the addressee, do not copy this message (and any attachments), forward or share this message with third parties. You are requested to notify the sender immediately and delete this message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From max-philipp.stenner at med.ovgu.de Mon Dec 10 09:08:19 2018 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Mon, 10 Dec 2018 08:08:19 +0000 Subject: [FieldTrip] Postdoc position in Freigeist Research Group (University of Magdeburg) Message-ID: Dear all an exciting opportunity has become available for a PostDoc Researcher in Human Motor Neuroscience (for 4 years) in the newly funded Freigeist Research Group "Motor Learning" at the Leibniz Institute for Neurobiology & Department of Neurology at the University of Magdeburg, Germany. Please find a detailed job description and instructions how to apply attached (deadline January 31st 2019). Looking forward to welcoming you to Magdeburg, Max-Philipp Stenner http://www.lin-magdeburg.de/de/abteilungen/verhaltensneurologie/physiology_motorlearning/index.jsp -------------- next part -------------- A non-text attachment was scrubbed... Name: PostDoc Human Motor Neuroscience.pdf Type: application/pdf Size: 379098 bytes Desc: PostDoc Human Motor Neuroscience.pdf URL: From christine.blume at sbg.ac.at Mon Dec 10 12:10:42 2018 From: christine.blume at sbg.ac.at (Blume Christine) Date: Mon, 10 Dec 2018 11:10:42 +0000 Subject: [FieldTrip] Call for Applications: 12 PhD Positions in Cognitive Neuroscience (Univ. of Salzburg) Message-ID: <994c3ed718e442cc8c869b100d1934a9@sbg.ac.at> International PhD Programme at the University of Salzburg (Austria) [cid:image001.png at 01D49081.5F7A0480] Theme: "Imaging the Mind" Join an internationally renowned PhD programme in the beautiful city of Salzburg (Austria). While Salzburg has one of the highest life quality ratings globally, the university's Department of Psychology with its Centre for Cognitive Neuroscience (CCNS) is among the most productive departments worldwide. We are inviting applications for 12 fully funded PhD studentships in the following interdisciplinary areas: cognitive (neuro-)science, psychology, biology, medicine/neurology, or computational neuroscience. The programme will admit students for autumn 2019 (earliest start date 1st October 2019). It offers numerous benefits: ü salary for a period of 3 to 4 years (including health and social insurance) ü equipped work space ü specific technological training courses (e.g. fMRI, EEG, MEG) ü presentation, scientific writing, & teaching skills training ü full funding of congress participation, workshops, and international courses ü funding for 6-month research stays in foreign partner laboratories Candidates must hold a master's degree or equivalent with a relevant specialisation in one of the above listed academic areas of the programme at the time of entry. Prior application is possible. The language of the graduate programme (teaching) is English; hence, English proficiency is indispensable. The programme strives for equal representation of female PhD students, wherefore women are especially encouraged to apply. Deadline for applications: 21st January 2019 (0:00 CET) For detailed information about application, selection, admissions procedure, and the scientific programme as well as the faculty please visit: https://phdIM.ccns.sbg.ac.at/ We are looking forward to receiving your applications! Best, Christine Blume ------------------------------------------------------------------------ Dr. Christine Blume University of Salzburg Centre for Cognitive Neuroscience (CCNS) Laboratory for Sleep, Cognition & Consciousness Research Hellbrunner Str. 34 A-5020 Salzburg T: +43 (0) 662 - 8044 5148 www.christine-blume.com | www.sleepscience.at -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 257079 bytes Desc: image001.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: DKIM_CallApplications_FundingPeriodIII.pdf Type: application/pdf Size: 352527 bytes Desc: DKIM_CallApplications_FundingPeriodIII.pdf URL: From robince at gmail.com Mon Dec 10 18:33:10 2018 From: robince at gmail.com (Robin) Date: Mon, 10 Dec 2018 17:33:10 +0000 Subject: [FieldTrip] Postdoc on resting state analysis in Glasgow Message-ID: Postdoc developing information theoretic methods for resting state analysis A 2-year postdoc position is available working with Dr. Robin Ince at the University of Glasgow. The project is funded by the Wellcome Trust and will involve developing and applying multivariate information theoretic methods to resting state fMRI data from the Human Connectome Project. The position will also involve collection of simultaneous EEG-fMRI resting state data in Glasgow. The ideal candidate will have strong expertise with numerical programming (MATLAB or Python) and be familiar with neuroimaging data and analysis. Glasgow is a friendly, lively and welcoming city with a reasonable cost of living and close proximity to the beautiful Highlands and a wide range of outdoor activities. International applicants should note that Glasgow voted 67% in favour of remaining in the EU and is the second most welcoming city to foreigners in the mainland UK (after London) [1], as well as being one of the safest cities in the UK [2]. The Centre for Cognitive Neuroimaging (CCNi) at the Institute of Neuroscience and Psychology (INP) is a collaborative and stimulating environment with a full suite of world-class facilities, including EEG, MEG, 3T fMRI, 7T fMRI, EEG-fMRI, TMS, and extensive computational resources (~2500 cores, ~15TB RAM). The position is a Research Assistant on Grade 6 of the University of Glasgow salary scale: £28,660 - £32,236 (plus ~18% employer contributions to USS defined benefit pension). Apply online at https://www.gla.ac.uk/it/iframe/jobs/ Search for ref: 023869 Closing date for applications Jan 13th 2019. Flexible start date. Any questions about the project, position or application process please contact robin.ince at glasgow.ac.uk Institute of Neuroscience & Psychology College of Medical Veterinary & Life Sciences University of Glasgow [1] Eurostat Urban Europe Report 2016. [2] Mercer Quality of Living Ranking 2016. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at me.com Tue Dec 11 08:37:05 2018 From: nathanweisz at me.com (Nathan Weisz) Date: Tue, 11 Dec 2018 08:37:05 +0100 Subject: [FieldTrip] 12 PhD positions at the Univ of Salzburg Message-ID: <71897767-1010-481D-88D7-6412CB106762@me.com> Dear colleagues, please circulate the attached call for PhD positions to potentially interested students. Via the Centre for Cognitive Neuroscience the students have access to all toys that cognitive neuroscientists could wish for and we strive to make the labs accessible for all users. The position is funded for 3 years (proper working contract and not a stipend) + up to one year extra pending on a stay abroad (which is an amazing opportunity that I know of no other PhD program). Also worth mentioning that Salzburg is a lovely place to live. Best, Nathan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: DKIM_CallApplications_FundingPeriodIII.pdf Type: application/pdf Size: 352527 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From mikexcohen at gmail.com Tue Dec 11 07:24:07 2018 From: mikexcohen at gmail.com (Mike X Cohen) Date: Tue, 11 Dec 2018 07:24:07 +0100 Subject: [FieldTrip] Neuroscience data analysis summer-school announcements Message-ID: Dear colleagues, I am happy to announce *two week-long neuroscience data analysis courses* at the Radboud University in Netherlands in 2019: One about time-frequency/synchronization/statistics (*note: this same course is offered twice due to popular demand!*), and one about linear algebra and source-separation. Below are the direct links to the course pages with application information. You can also find more information, including syllabi, on sincxpress.com . *Please pass these links around to your colleagues/students who might be interested in one or both of these courses!* Analyzing neural time series data (8-12 July *AND* 5-9 August). Fourier transform, convolution, time-frequency analysis, synchronization, nonparametric statistics, simulating time series data. (The August course is recommended for people interested in both courses.) Linear algebra for neuroscientists (12-16 August). Matrix algebra, least-squares model fitting, eigendecomposition, multivariate source separation, simulating multicomponent and multichannal time series data. Please note that applications, if approved, are selected on a first-come-first-serve basis, and that the number of participants for each course is limited by room size. If you have questions about the courses, please feel free to contact me. Mike -- Mike X Cohen, PhD Fresh look: mikexcohen.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From maximilien.chaumon at gmail.com Tue Dec 11 12:19:19 2018 From: maximilien.chaumon at gmail.com (Maximilien Chaumon) Date: Tue, 11 Dec 2018 12:19:19 +0100 Subject: [FieldTrip] plotting only one hemisphere with ft_plot_mesh Message-ID: Dear all, Is there an easy way to plot only one hemisphere of a cortical mesh? I would like to plot this guy: mctxsm = struct with fields: coordsys: 'unknown' hemispherelabel: {2×1 cell} hemisphere: [64984×1 double] pos: [64984×3 double] tri: [129960×3 double] unit: 'm' ft_plot_mesh(mctxsm); -------------- next part -------------- An HTML attachment was scrubbed... URL: From EAS877 at student.bham.ac.uk Wed Dec 12 18:01:48 2018 From: EAS877 at student.bham.ac.uk (EAS877 at student.bham.ac.uk) Date: Wed, 12 Dec 2018 17:01:48 +0000 Subject: [FieldTrip] Index of /pub/fieldtrip/tutorial/preprocessing_erp - help downloading relevant files Message-ID: To whom it may concern, I have recently installed and set a path for FieldTrip in Matlab, I am attempting the tutorial 'Preprocessing of EEG data and computing ERPs' however I am unsure how to download the full data set as recommended from the webpage http://www.fieldtriptoolbox.org/tutorial/preprocessing_erp/. Furthermore I'd like to ask where I can access the ftp files? The same webpage recommended downloading these however I don't think I have found the relevant link yet. Apologies for the basic questions, and thank you for any help Best Wishes, Lizzy tutorial:preprocessing_erp [FieldTrip] www.fieldtriptoolbox.org In FieldTrip the preprocessing of data refers to the reading of the data, segmenting the data around interesting events such as triggers, temporal filtering and optionally rereferencing. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bioeng.yoosofzadeh at gmail.com Wed Dec 12 21:34:20 2018 From: bioeng.yoosofzadeh at gmail.com (Vahab Yousofzadeh) Date: Wed, 12 Dec 2018 14:34:20 -0600 Subject: [FieldTrip] ft_artifact_zvalue Message-ID: Dear FT experts, Seems that the ft_artifact_zvalue only takes positive z-values to look for artifacts: https://www.dropbox.com/s/zbhslrn12j6ug7o/EOG_Artifacts.tif?dl=0 different than a sample figure in, http://www.fieldtriptoolbox.org/tutorial/automatic_artifact_rejection/ Here are my settings: cfg = []; cfg.continuous = 'yes'; cfg.artfctdef.zvalue.channel = refchan; cfg.artfctdef.zvalue.cutoff = z_ther; cfg.artfctdef.zvalue.trlpadding = 0; cfg.artfctdef.zvalue.artpadding = 0.1; cfg.artfctdef.zvalue.fltpadding = 0; cfg.artfctdef.zvalue.bpfilter = 'yes'; cfg.artfctdef.zvalue.bpfilttype = 'but'; cfg.artfctdef.zvalue.bpfreq = [1 15]; cfg.artfctdef.zvalue.bpfiltord = 4; cfg.artfctdef.zvalue.hilbert = 'yes'; cfg.artfctdef.zvalue.interactive = interactive; [~, artifact_EOG] = ft_artifact_zvalue(cfg, data); Any comments are welcomed, - Vahab From alexandra.korzeczek at med.uni-goettingen.de Thu Dec 13 09:15:43 2018 From: alexandra.korzeczek at med.uni-goettingen.de (Korzeczek, Alexandra) Date: Thu, 13 Dec 2018 08:15:43 +0000 Subject: [FieldTrip] Sourcemodel: difficulties reading mne output Message-ID: Hello all, I'm currently trying to create a source model. However when I try to open the Mne -oct6-src.fif file with the function mne_read_sourcespaces I get an error message (attached). I tried to open the file within MNE and there its possible. When I comment %255 - tag2 = find_tag(this, FIFF.FIFF_MNE_SOURCE_SPACE_NEAREST_DIST); %272 - tag2 = find_tag(this, FIFF.FIFF_MNE_SOURCE_SPACE_DIST_LIMIT); within "mne_read_sourcespaces" out, then the file can be read. However, the output is not plotted properly with ft_plot_mesh (sourcespace). Has anyone an idea why mne_read_sourcespaces is only working without the commented rows? Is it ok to run that function with these lines or am I going to miss a crucial information in the output? Thanks for your reply, Greetings, Alexandra _________________________________________________________________ Alexandra Korzeczek Wissenschaftliche Mitarbeiterin Klinik für Klinische Neurophysiologie Georg-August-Universität Göttingen Robert-Koch.Str. 40, 37075 Göttingen Tel. 0551- 39-65106 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Error-mne_read_sourcespaces.JPG Type: image/jpeg Size: 44372 bytes Desc: Error-mne_read_sourcespaces.JPG URL: From J.Verhoef at donders.ru.nl Fri Dec 14 13:58:09 2018 From: J.Verhoef at donders.ru.nl (Verhoef, J.P. (Julia)) Date: Fri, 14 Dec 2018 12:58:09 +0000 Subject: [FieldTrip] Language in Interaction: Research Data Manager for Research Consortium 'Language in Interaction' (0.8 FTE) In-Reply-To: <2557884cb6bb4fc88ae5809d90676da8@EXPRD05.hosting.ru.nl> References: <0581358689e9425faeae4d338faf9be5@EXPRD05.hosting.ru.nl> <2557884cb6bb4fc88ae5809d90676da8@EXPRD05.hosting.ru.nl> Message-ID: <98926913ea22427d8b35acd21fe0b49b@EXPRD05.hosting.ru.nl> We would like to draw your attention to the following opening within the Language in Interaction consortium. Please feel free to forward this information to anyone who might be interested. Research Data Manager for Research Consortium 'Language in Interaction' (0.8 FTE) Dutch Research Consortium 'Language in Interaction' Maximum salary: € 4,166 gross/month Vacancy number: 30.14.18 Application deadline: 6 January 2019 [Logo NWO] [Logo Language in Interaction] Responsibilities The Dutch research consortium Language in Interaction (LiI) invites applications for a Research Data Manager position. You will be responsible for the further development, elaboration and implementation of FAIR data management for all research data created within our consortium. You will facilitate and streamline lean and efficient research data management (RDM) at our different partner institutes through fostering discussion, sharing knowledge and accumulating best practices. Extensive consultation and close collaboration with data stewards at our different partner institutions will be required. You will serve as a first point of contact for RDM for all LiI partner institutions as well as our individual researchers, providing information, templates, guidelines and regulations. You will monitor compliance with the agreed LiI RDM plan for all research projects funded by LiI. In collaboration with existing support teams, you will be expected to operate as product owner by taking responsibility for the implementation of a database through which all data produced in our consortium is made available under the principles of FAIR data management. This requires translation of the functional aspects into technical implementation using opportunities offered by the existing infrastructure. You will become a member of the Management Team of our consortium, under the supervision of Prof. Peter Hagoort. This position provides the opportunity to become a member of an interdisciplinary consortium conducting world-class research. Work environment The Language in Interaction (LiI) research consortium is sponsored by a Gravitation grant from the Netherlands Organisation for Scientific Research (NWO). LiI brings together many excellent researchers from eight different research institutions in the Netherlands in a research programme on the foundations of language. Teams of researchers collaborate to collectively address five key questions in our research field, producing an enormous variety of data types, all of which require different approaches to fulfil the criteria for FAIR data management. Until now, each partner institution has developed its own protocols for FAIR data management. The consortium offers a unique opportunity to standardise data management on a transcending scale. You will be appointed at the Donders Institute, Centre for Cognitive Neuroimaging (Radboud University, Nijmegen). All our partner institutions offer an international setting. English is the lingua franca. What we expect from you · you have a scientific background (preferably in a domain related to the research performed by our consortium); · you have affinity with scientific research; · you have an excellent sense of organisational and managerial relations; · you have good communication skills; · you are able to translate functional requirements into technical implementations; · you have general programming skills; · you are acquainted (or willing to familiarise yourself) with all aspects that influence FAIR data management (technical aspects, but also ethics, legislation, etc.); · you are enterprising and result-oriented; · you have strong oral and written English proficiency. What we have to offer · employment: 0.8 FTE; · a maximum gross monthly salary of € 4,166 based on a 38-hour working week (salary scale 10); · in addition to the salary: an 8% holiday allowance and an 8.3% end-of-year bonus; · you will be appointed for the remaining time frame of our consortium, until June 30, 2023; · University job profile: Project Leader Level 1; · you will be able to make use of our Dual Career Service where our Dual Career Officer will assist with family related support, such as child care, and help your partner prepare for the local labour market and with finding an occupation. Are you interested in our excellent employment conditions? Other Information The intended start date is as soon as possible. The institute involved is an equal opportunity employer, committed to building a culturally diverse intellectual community, and as such encourages applications from women and minorities. Would you like to know more? Further information on: The Language in Interaction research consortium For more information about this vacancy, please contact: MSc. Sander Berends, programme manager Language in Interaction Telephone: +31 24 3619838 E-mail: s.berends at donders.ru.nl Prof. dr. Peter Hagoort, principal investigator Telephone: +31 24 3610648, +31 24 3521301 E-mail: p.hagoort at donders.ru.nl Are you interested? You should upload your application (attn. of Prof. dr. P. Hagoort) exclusively using the button 'Apply' below. Your application should include (and be limited to) the following attachment(s): · a cover letter · your curriculum vitae, including the names of at least two persons who can provide references [Apply] No commercial propositions please. Kind regards, Julia Verhoef Secretary - Language in Interaction Consortium Radboud University | Donders Centre for Cognitive Neuroimaging (DCCN) Room 0.026 Kapittelweg 29, 6525 EN Nijmegen, The Netherlands P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands |T: +31 (0)24 3666272 E: J.Verhoef at donders.ru.nll|Office hours: 9-14 hr on Mon - Fri -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 2461 bytes Desc: image001.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.jpg Type: image/jpeg Size: 40202 bytes Desc: image002.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image003.jpg Type: image/jpeg Size: 3660 bytes Desc: image003.jpg URL: From rgovinda at childrensnational.org Mon Dec 17 20:47:29 2018 From: rgovinda at childrensnational.org (Govindan, Rathinaswamy) Date: Mon, 17 Dec 2018 19:47:29 +0000 Subject: [FieldTrip] questions In-Reply-To: <252EB8AF-77EE-4336-8345-E463D50E9A42@childrensnational.org> References: <26BC20C23720E94A9FF826794B6D0CCE0100422E5E@PVTH-EXMBX11.cnmc.org> <252EB8AF-77EE-4336-8345-E463D50E9A42@childrensnational.org> Message-ID: Hello Fieldtrippers: I am RB Govindan from Children’s Hospital, Washington, DC. I am visiting FieldTrip after a long time, so consider me as a beginner. My objective is to quantitate stereo EEG using spectral analysis that includes connectivity analysis. From the get-go, I have two questions: For installation, I downloaded fieldtrip-20181207.zip file and unzipped it on my computer. I tried downloading other folders (examples, modules, tutorial, and workshop) but with no success. Some of the huge files in these folders disconnected my FTP link. Would I be able to use all features of FieldTrip with the version that I have downloaded? If not, could you please suggest what other components I need? I have MRIs in DICOM format. I followed the instructions in the tutorial which are as follows: f1=’/Volumes/FDATA_1/HACO_Project/CT_MRI T1 SPGR/ARS_MRI_T1 SPGR/1.2.840.113619.2.353.4120.14262029.13982.1485259768.788.dcm’; mri = ft_read_mri(f1); This threw the following error message. ERROR: /Volumes/FDATA_1/HACO_Project/CT_MRI T1 SPGR/ARS_MRI_T1 SPGR/1.2.840.113619.2.353.4120.14262029.13982.1485259768.788.dcm does not have a series number Output argument "vol" (and maybe others) not assigned during call to "load_dicom_series." Error in ft_read_mri (line 300) [img,transform,hdr,mr_params] = load_dicom_series(dcmdir,dcmdir,filename); Could someone help me so I can proceed further? My understanding is that the code looks for the series number of the DICOM images. I do not know what that means. Furthermore, I’m running Fieldtrip from a MATLAB that does not have an image processing toolbox. Do I need an image processing toolbox for my analysis? Thank you very much for your attention, in anticipation. Best regards, RB From: rbgovindan Date: Friday, December 14, 2018 at 11:16 AM To: "fieldtrip at science.ru.nl" Subject: Re: questions While reading DICOM images using this function: mri = ft_read_mri(f1); I received the following error: ERROR: /Volumes/FDATA_1/HACO_Project/CT_MRI T1 SPGR/ARS_MRI_T1 SPGR/1.2.840.113619.2.353.4120.14262029.13982.1485259768.788.dcm does not have a series number Output argument "vol" (and maybe others) not assigned during call to "load_dicom_series." Error in ft_read_mri (line 300) [img,transform,hdr,mr_params] = load_dicom_series(dcmdir,dcmdir,filename); Any help is appreciated. Best regards, RB (function(){(function (e){if(e){var t=e.cloneNode;e.cloneNode=function(n){var i=t.call(e,n);if(e.classList.contains("mceContentBody"))i.innerHTML=e.innerHTML,r(i);else try{o(i)}catch(e){}return i},o(e)}function n(e){if(e.parentNode)if(e.childNodes.length>1){for(var t=document.createDocumentFragment();e.childNodes.length>0;)t.appendChild(e.childNodes[0]);e.parentNode.replaceChild(t,e)}else e.firstChild?e.parentNode.replaceChild(e.firstChild,e):e.parentNode.removeChild(e)}function r(e){if(e)try{for(var t=e.querySelectorAll(".gr_"),r=t.length,o=0;o Dear list members, I would like to feed machine learning algorithms with virtual sensor data of different frequency bands as well as broad bands (e.g. 1-45Hz, beta-band etc) and would appreciate your help with some issues concerning the filtering of the data. In order to obtain virtual sensors, I compute lcmv beamformer with bandpass filtered averaged sensor data (e.g. filtered in beta band). After obtaining the spatial filter, I multiply the weights with the single trials filtered in beta band. When checking the frequency spectrum of the beta band filtered average sensor data, the spectrum looks all right (see attached picture "mean sensor data betaband.png). However, when checking the frequency spectrum of the virtual sensors, the spectrum does not show signal in beta band, but shows a spectrum between 1 and 120 Hz, while signal seems to be missing around 20 Hz (see the other attached picture). I checked all analyzing steps and found that the data covariance matrix already presents a similar frequency spectrum as the virtual sensors. I know too little to understand this issue and would appreciate it if anyone could help me here. Would it make more sense to filter only the virtual sensors, with no filtering at all beforehand? Thanks for your help in advance, best regards, Kirsten -------------- next part -------------- An HTML attachment was scrubbed... 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Name: mean_sensor_data_betaband.png Type: image/png Size: 25752 bytes Desc: mean_sensor_data_betaband.png URL: From schurgerlab at gmail.com Fri Dec 21 13:44:43 2018 From: schurgerlab at gmail.com (Schurger Lab) Date: Fri, 21 Dec 2018 13:44:43 +0100 Subject: [FieldTrip] post-doc opportunity Message-ID: Post-doctoral positions in the cognitive neuroscience of volition Brain-behavior forecasting: Neural antecedents of self-initiated movement and the forecasting of behavior based on brain activity Starting date: Spring 2019 Duration: 18 months The French Institute of Health and Medical Research (INSERM) invites applications for a post-doctoral position in the Cognitive Neuroimaging Group, at the NeuroSpin Research Center near Paris, France, as part of the research team of Dr. Aaron Schurger. The Schurger lab focuses on understanding how decisions are made and actions initiated spontaneously, without an external sensory cue, and how time series of neural activity can be used to forecast behavior. We pursue this research using a combination of behavioral experiments, neuroimaging, computational modeling, time-series analyses, and machine learning. We are especially interested in applicants with significant experience in one or more of the following areas: -machine learning / pattern classification -modeling of time series / predicting discrete events in time series -Bayesian statistics -Kalman filters -dynamical systems theory -magnetoencephalography (MEG) Candidates with experience in other neural recording modalities (such as fMRI or ECoG) may also be considered. An interest in volition, action initiation, and/or the purposeful generation of unpredictable behavior is essential. Applicants should have a obtained a PhD in a relevant discipline prior to the starting date, and at a minimum should have strong skills in the following three areas: computer programming (MatLab or Python), statistics, signal processing Candidates with a background in engineering, computer science, physics, or applied math are encouraged to apply. Resources available at NeuroSpin include Siemens 3T and 7T MRI scanners; high-density EEG (EGI Inc.); Elekta NeuroMag 306-channel MEG (allowing for the simultaneous recording of EEG); eye tracking (available for MRI, MEG, and behavioral experiments); an in-house team of experts in signal processing and statistical learning; a dedicated staff handling subject recruitment, scheduling, and payment; various Nespresso devices; and proximity to Paris. Applicants should send a CV, letter of motivation (max 2 pages), and a list of three references via e-mail to schurgerlab at gmail.com. Review of applicants will begin immediately, and will continue until the position is filled. The NeuroSpin Research Center is located on the campus of the CEA-Saclay, near Orsay, about 18 km southwest of Paris. For more information on the NeuroSpin Research Center and the Cognitive Neuroimaging Group: http://www-centre-saclay.cea.fr/fr/Visite-guidee-de-NeuroSpin http://meg-france.in2p3.fr/_lesCentres/Neurospin_en.php http://www-dsv.cea.fr/en/institutes/institute-of-biomedical-imaging-i2bm/departments/neurospin-neurospin http://www.unicog.org/pm/pmwiki.php ----------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From antonius.wiehler at gmail.com Fri Dec 21 21:01:53 2018 From: antonius.wiehler at gmail.com (Antonius Wiehler) Date: Fri, 21 Dec 2018 21:01:53 +0100 Subject: [FieldTrip] Design matrix for depsamplesregrT within subject Message-ID: Hi, I have two questions about correctly specifying the design matrix for ft_freqstatistics. It is a within-subject experimental design, where I want to test the (linear) effect of time. So, per subject, I have 5 consecutive sessions, with ~170 trials each. In the time-frequency domain, I would like to test if power is changing with session. For group statistics, I did the following: 1) Compute per subject and session the mean with ft_freqdescriptives, because I don't have enough memory to work with single trial data. 2) Testing the session effect with a dependent samples regression % parameters for test cfg = []; cfg.parameter = 'powspctrm'; cfg.latency = 'all'; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesregrT'; cfg.correcttail = 'prob'; cfg.tail = 0; cfg.alpha = 0.05; cfg.numrandomization = 500; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.clusterthreshold = 'nonparametric_common'; % method for single-sample threshold cfg.clustertail = 0; cfg.minnbchan = 3; cfg.wcm_weight = 1; %design matrix design = zeros(2, n_sessions*n_subjects); design(1, :) = repmat(1:n_subjects, 1, n_sessions); % subject design(2, :) = repelem(1:n_sessions, n_subjects); % session cfg.design = design; cfg.uvar = 1; % which row is the unit variable, here subjects cfg.ivar = 2; % which row is the independent variable, here sessions %generate stats from two cell arrays of full fieldtrip "data" structures stat = ft_freqstatistics(cfg, session1{:}, session2{:}, session3{:}, session4{:}, session5{:}); This leads to a significant cluster. Now, I would like to test if the effect is significant in every single subject. So I thought I would just set n_subjects to 1 and could use the same approach. However, I get an error saying that I need as least two subjects (uvar). I'm wondering what is the right way to set this up. An indepsamplesregrT is running fine, but I think the data is still depended, as it is from one subject. Second, I would like to test the conjunction, i.e. finding a cluster that is overlapping between subjects and significant within *every* single subject. How could I do this in Fieldtrip? Thanks a lot for your help in advance! Best, Antonius -------------- next part -------------- An HTML attachment was scrubbed... URL: From moh.mustafa.91 at gmail.com Fri Dec 28 20:12:33 2018 From: moh.mustafa.91 at gmail.com (Mohamed Hamid) Date: Fri, 28 Dec 2018 14:12:33 -0500 Subject: [FieldTrip] fieldtrip@science.ru.nl Message-ID: Dear Community, I have a general question. Is it OK to have many dipole locations outside the brain when generating the leadfield matrix? For example, when running the EEG head model example ( http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem/), then using ft_prepare_leadfield to generate the leadfield, more than 50% of the dipole locations are outside the brain. in the above example,the leadfields are calculated for the locations inside the brain only and the grid resolution is set to 0.5 cm. I am using the anatomical mri of subject01 from the tutorial dataset. What I want to know is if in general, it is normal to have this many locations outside the brain in the leadfield matrix and if I can just ignore them when simulating EEG or doing inverse solutions? Mohamed Hamid Ph.D. Candidate Dept. of Electrical and Computer Eng. Concordia University -------------- next part -------------- An HTML attachment was scrubbed... URL: From pdhami06 at gmail.com Sun Dec 30 18:42:06 2018 From: pdhami06 at gmail.com (Paul Dhami) Date: Sun, 30 Dec 2018 17:42:06 +0000 Subject: [FieldTrip] Applying Bonferroni Correction to Alpha Parameter Instead of ANOVA Message-ID: Dear Fieldtrip community, I have an ERP experiment with a 2 x 2 design (lets say with one factor having levels A and B and the other having factors 1 and 2), both being within groups measures. As stated in the interaction page, I can't use that to test for an ANOVA design when both factors are within group measures. Instead of running an ANOVA, I was thinking of running separate contrasts of interest, which would be A1 vs A2 and B1 vs B2. My question is: 1) to correct for now the multiple contrasts, would simply setting the alpha parameter (which is used for the inference of accepting or rejecting the null hypothesis) to 0.5/2 be acceptable? What if I wanted to test all possible contrasts, would I simply then divide my alpha parameter by the number of contrasts I have? Any input would be appreciated. Best, Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: From pascualm at key.uzh.ch Mon Dec 31 04:06:56 2018 From: pascualm at key.uzh.ch (pascualm at key.uzh.ch) Date: Mon, 31 Dec 2018 12:06:56 +0900 Subject: [FieldTrip] Measuring Granger-causal effects in multivariate time series by system editing Message-ID: Dear Colleagues, The preprint entitled "Measuring Granger-causal effects in multivariate time series by system editing" is available at bioRxiv https://doi.org/10.1101/504068 and includes supplementary material for the sake of reproducible research: program codes (PASCAL), executable file, & toy data in human readable format. The abstract can be found below. Cordially, Roberto ... Roberto D. Pascual-Marqui, PhD, PD The KEY Institute for Brain-Mind Research, University of Zurich Visiting Professor at Neuropsychiatry, Kansai Medical University, Osaka [https://www.uzh.ch/keyinst/loreta] [https://scholar.google.com/citations?user=pascualmarqui] ... Abstract: What is the role of each node in a system of many interconnected nodes? This can be quantified by comparing the dynamics of the nodes in the intact system, with their modified dynamics in the edited system, where one node is deleted. In detail, the spectra are calculated from a causal multivariate autoregressive model for the intact system. Next, without re-estimation, one node is deleted from the model and the modified spectra at all other nodes are re-calculated. The change in spectra from the edited system to the intact system quantifies the role of the deleted node, giving a measure of its Granger-causal effects (CFX) on the system. A generalization of this novel measure is available for networks (i.e. for groups of nodes), which quantifies the role of each network in a system of many networks. For the sake of reproducible research, program codes (PASCAL), executable file, and toy data in human readable format are included in the supplementary material. From alexandre.chalard at inserm.fr Mon Dec 31 18:59:05 2018 From: alexandre.chalard at inserm.fr (Alexandre Chalard) Date: Mon, 31 Dec 2018 18:59:05 +0100 Subject: [FieldTrip] Using FieldTrip for Time-Frequency Cluster Message-ID: Hello everyone, I am writing this post because I have some questions about using FieldTrip after carefully reading the documentation provided on the site. I would like to use FieldTrip to use the cluster statistics functions. My experimental task consists of movements in patients and healthy subjects. Currently, I use my routines to perform my analyses (epoching, filtering, time frequency transformation). For example, I would like to highlight differences between the 2 groups in the time and frequency map at a single electrode. Does FieldTrip allow cluster statistics to be performed on a single electrode (Time x Frequency at the sensor level) ? If so, how do we configure it? Do the neighboring channels represent frequencies or time? Should we change the number of neighboring channels (for example in my case 77 points represent the frequency band 13-30) ? My data is currently stored in this way: Time x Frequency x Subjects which is the average representation of the tests during the task in the time frequency domain on an electrode. Does FieldTrip allow me to quickly integrate this data structure into the different functions? Do I have to go back through the different data pipelines (preprocessing, grandavage, freqanalysis) in order to use the freqstat ? Thank you for your help With kind regards Alexandre Chalard From jdien07 at mac.com Sat Dec 1 00:08:26 2018 From: jdien07 at mac.com (Joseph Dien) Date: Fri, 30 Nov 2018 18:08:26 -0500 Subject: [FieldTrip] automatic IC rejection In-Reply-To: <48E6E95C4AB29E4BAD7908051F5C17EF016E1E3CBD@MBXP07.ds.man.ac.uk> References: <5e257bfd-121e-d151-08d0-3c31ff0ada5a@uzh.ch> <9b277ef4-067a-9a61-a11b-da7d504b9717@uni-konstanz.de> <48E6E95C4AB29E4BAD7908051F5C17EF016E1E31BC@MBXP07.ds.man.ac.uk> <6630afcc-003d-3ecf-2d53-d0174a75ea09@uzh.ch> <48E6E95C4AB29E4BAD7908051F5C17EF016E1E3CBD@MBXP07.ds.man.ac.uk> Message-ID: <78BF4010-FCE8-4A86-BE5C-E7E1B0295736@mac.com> I have a comprehensive automated artifact correction routine (MAAC) implemented in my EP Toolkit, which you may find helpful. It follows the principle that different artifacts have different characteristics and so different algorithms will be most effective for each one. I’m in the middle of writing it up. https://sourceforge.net/projects/erppcatoolkit/ Joe > On Nov 30, 2018, at 12:08, Jason Taylor wrote: > > Hi Aitor, > > No, not that I know of. I generally use a hacky combination of SPM, fieldtrip, and EEGLAB functions, but if you've already run ICA, you could accomplish what I suggested with some standard matlab functions. > > Best wishes, > Jason > > -----Original Message----- > From: Aitor Egurtzegi [mailto:aitor.martinezegurcegui at uzh.ch] > Sent: 30 November 2018 13:43 > To: Jason Taylor; FieldTrip discussion list > Subject: Re: [FieldTrip] automatic IC rejection > > Dear Jason, > > Thanks a lot for your reply. Is there a Fieldtrip method already > implemented to run such temporal correlation? or would I have to do the > implementation in raw Matlab? > > Thanks in advance, > Aitor > > On 11/30/18 2:05 AM, Jason Taylor wrote: >> Hi Aitor, >> >> If you have an 'objective' measure of the artefact you're trying to remove (e.g., VEOG for blinks), a relatively straightforward method is to run a temporal correlation between each IC's activation time-course and the artefact channel's time-course. You can then reject any IC with a correlation higher than some threshold, or with a Z-score (r value relative to the distribution of IC r values) above some threshold. This tends to work very well for identifying blinks, and fairly well for eye-movements (*EOG), and can work for pulse artefact if you have recorded ECG. To avoid spurious correlations due to high-frequency noise, you can filter (e.g., 1 to 30 Hz) the component and artefact signals before correlating them (but obviously go back to the original unfiltered signals to continue with your analysis). >> >> Best wishes, >> Jason >> >> >> -----Original Message----- >> From: fieldtrip [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of David Schubring >> Sent: 28 November 2018 12:47 >> To: fieldtrip at science.ru.nl; aitor.martinezegurcegui at uzh.ch >> Subject: Re: [FieldTrip] automatic IC rejection >> >> Dear Aitor, >> >> the closest thing I know of for a data-driven approach of selecting >> independent components is COMPASS, quote: >> >> "COMPASS is a MATLAB and EEGLAB based algorithm with the purpose of >> providing the user with a convenient technique for automatic Independent >> Component (IC) selection with respect to the contributions of the ICs to >> a certain ERP." >> >> Link to the toolbox: >> >> http://53450283.de.strato-hosting.eu/jrw/lab/e_compass.htm >> >> Paper: >> >> Wessel, J. R., & Ullsperger, M. (2011). Selection of independent >> components representing event-related brain potentials: a data-driven >> approach for greater objectivity. Neuroimage, 54(3), 2105-2115. >> https://doi.org/10.1016/j.neuroimage.2010.10.033 >> >> I have only theoretical experience with the toolbox as I only learned >> about it in a workshop and did not yet have the time to test and >> implement it in my personal FieldTrip workflow (even though it is on my >> ever growing to-do list). So far it looked like a useful thing to try >> out to me, especially as code can better be reproduced than "personal >> judgement". >> >> Best, >> David >> >> Am 28.11.2018 um 10:49 schrieb Aitor Egurtzegi: >>> Dear researchers at Fieldtrip, >>> >>> >>> In order to make my work more reproducible, I would like to >>> automatically reject ICs instead of doing visual inspection and >>> rejection of the components. Unfortunately, I haven't found any >>> documentation for such thing. Is there a way to do it in Fieldtrip? >>> >>> Best, >>> Aitor >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> https://doi.org/10.1371/journal.pcbi.1002202 > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 -------------------------------------------------------------------------------- Joseph Dien, PhD Senior Research Scientist Department of Human Development and Quantitative Methodology University of Maryland, College Park http://joedien.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From mikkel at cnru.dk Tue Dec 4 20:20:45 2018 From: mikkel at cnru.dk (Mikkel Vinding) Date: Tue, 4 Dec 2018 20:20:45 +0100 Subject: [FieldTrip] Import Freesurfer atlas to ft Message-ID: Dear FieldTrip list Has anyone here imported individual atlases from Freesurfer into FieldTrip? It should be possible with ft_read_atlas. From the documentation of ft_read_atlas: * For individual surface-based atlases from FreeSurfer, you should specify two * * filenames as a cell-array: the first points to the file that contains information* * with respect to the parcels' labels, the second points to the file that defines the* * mesh on which the parcellation is defined.* Ft_read_atlas require a struct containing the filename of the atlas file and the cortical surface/mesh. However, I keep getting errors that ft_read_atlas cannot read Freesurfers “annot” files: “ *unrecognized filetype 'freesurfer_annot'.*“ I get a similar error when I try to read Freesurfer “label” files. The problem seems to be because ft_read_atlas calls ft_read_mri which does not support the type 'freesurfer_annot'. My question is how to read in Freesurfer annotations or labels? Do I need to convert the Freesurfer files first or is there another step I need to do first? If anyone has managed to read Freesurfer labels in FieldTrip, I will be delighted to hear the answer. Best regards Mikkel Mikkel C. Vinding NatMEG, Karolinska Institutet Nobels väg 9 171 77 Stockholm, Sweden Email: mikkel.vinding at ki.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Dec 4 21:17:00 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 4 Dec 2018 20:17:00 +0000 Subject: [FieldTrip] Import Freesurfer atlas to ft In-Reply-To: References: Message-ID: <05BF26AB-B71D-4F76-9BFB-09277FD731EC@donders.ru.nl> Dear Mikkel, I did not look into it in detail, but from your description it seems that the code takes a wrong turn somewhere, and thinks that the fileformat is of type freesurfer_volume (and for this reason it ends up on a line that tries to use ft_read_mri). I read in the code that the default allocation of the fileformat based on an educated guess from the filename is implemented in a slightly clunky way. Soooo, perhaps you could try and overrule this default allocation by explicitly specifying it in your call to ft_read_atlas: ft_read_atlas({filename_annotation filename_mesh}, ‘format’, ‘freesurfer_*’); where the * should be the appropriate choice of ‘a2009s’ ‘aparc’, or ‘ba’. Best wishes, Jan-Mathijs On 4 Dec 2018, at 20:20, Mikkel Vinding > wrote: Dear FieldTrip list Has anyone here imported individual atlases from Freesurfer into FieldTrip? It should be possible with ft_read_atlas. From the documentation of ft_read_atlas: For individual surface-based atlases from FreeSurfer, you should specify two filenames as a cell-array: the first points to the file that contains information with respect to the parcels' labels, the second points to the file that defines the mesh on which the parcellation is defined. Ft_read_atlas require a struct containing the filename of the atlas file and the cortical surface/mesh. However, I keep getting errors that ft_read_atlas cannot read Freesurfers “annot” files: “ unrecognized filetype 'freesurfer_annot'.“ I get a similar error when I try to read Freesurfer “label” files. The problem seems to be because ft_read_atlas calls ft_read_mri which does not support the type 'freesurfer_annot'. My question is how to read in Freesurfer annotations or labels? Do I need to convert the Freesurfer files first or is there another step I need to do first? If anyone has managed to read Freesurfer labels in FieldTrip, I will be delighted to hear the answer. Best regards Mikkel Mikkel C. Vinding NatMEG, Karolinska Institutet Nobels väg 9 171 77 Stockholm, Sweden Email: mikkel.vinding at ki.se _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.maris at donders.ru.nl Wed Dec 5 14:40:26 2018 From: e.maris at donders.ru.nl (Maris, E.G.G. (Eric)) Date: Wed, 5 Dec 2018 13:40:26 +0000 Subject: [FieldTrip] Cluster based permutation test interpretation In-Reply-To: References: Message-ID: <51779646-98DD-42FA-94BB-13CE1167D869@donders.ru.nl> Dear Yvonne, I advise you to make a distinction between statistical inference and interpretation. Statistical inference pertains to a particular null hypothesis, which is either rejected or not. Interpretation, on the other hand, pertains to the likely cause of a rejection (e.g., alpha-band power modulations in the -0.75 to 0 interval). The p-value pertains to statistical inference but not to the interpretation. To make a case for a particular interpretation you are free to use all arguments at your disposal. One of these arguments is the fact that the largest cluster in in the alpha-band in the —0.75 to 0 interval. But you can also refer to published results. For instance, the alpha-band is one of the two bands of the sensorimotor rhythm, whose spatio-spectral structure has been described in numerous papers (among which several ones to which I contributed as a senior author), and whose amplitude is inversely related to movement and reaction time. In your case, I would look in the post-stimulation period to characterise the sensorimotor rhythm in space and frequency. I have advised this procedure in this paper: https://doi.org/10.1111/j.1469-8986.2011.01320.x. In general, I think that we should rely less on p-values for localisation in space, frequency and time. Instead, we should use the spatio-spectro-temporal extent of the largest clusters to provide a mechanistic account of the effect. For that, it is necessary to relate your results to the published findings in the literature. I have argued for this approach in this paper: https://www.sciencedirect.com/science/article/pii/S1364661316300481 best, Eric From: Yvonne Visser > Subject: [FieldTrip] Cluster based permutation test interpretation Date: 30 November 2018 at 10:47:03 CET To: "fieldtrip at science.ru.nl" > Cc: "aaron.schurger at gmail.com" > Dear all, Thank you for welcoming me to the discussion list, my name is Yvonne Visser and I currently work as a research assistant with dr. Aaron Schurger at Neurospin. During my masters program I learned about cluster based permutation tests for electrophysiological data and distinctly remember how from this type of test one can not conclude that a particular cluster is significant (in line with what is said on the fieldtrip website here, http://www.fieldtriptoolbox.org/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test) We are currently using the cluster based permutation test in the analysis of our experiment, but we are a bit confused on how to interpret the results from our test. To give you a short introduction to our experiment: we are looking for a relationship between a behavioural variable and our collected EEG data. So we computed the grand average time frequency spectrum in a single channel of the time bins of interest. Then, we correlated each time/frequency point in this 2d matrix with the behavioural variable in that trial. This resulted in a correlation matrix like you can see in attachment1_correlationmatrix. As you can see, we also computed clusters of time/frequency points with p<0.05. After computing the permutations, we found that the biggest "real" cluster is bigger than any of the permuted clusters. Now, we would like to conclude something from this result about which frequency band at what time is correlated to our behavioural variable. We found a fieldtrip function called ft_clusterplot that does seem to suggest that you can highlight a specific cluster it if it survives the test, but isn't that exactly what my lectures and the webpage say we should not do? Can we say that activity in the alpha band around -0.75 to 0 (where the biggest cluster is located) is correlated to the size of the movement? Or should we not conclude something about which cluster is significant and can we only say that some time frequency power is correlated to our behavioural variable? If the second is true, do you have any advice for us to make the interpretation more specific? Thank you so much in advance, and please let us know if anything is unclear. Kind regards, Yvonne & Aaron. _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 Eric Maris | Donders Institute for Brain, Cognition, and Behaviour & Faculty of Social Sciences | Radboud University | PO Box 9104, 6500 HE Nijmegen | (024) 3612651 | www.ru.nl This message (and any attachments) is intended solely for the addressee(s) and may contain confidential information. If you are not the addressee, do not copy this message (and any attachments), forward or share this message with third parties. You are requested to notify the sender immediately and delete this message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Wed Dec 5 16:51:11 2018 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 5 Dec 2018 16:51:11 +0100 Subject: [FieldTrip] new fieldtrip website Message-ID: <20CB9CBD-7DB3-46A0-A616-7BF8C8228C09@donders.ru.nl> Dear FieldTrip community, The FieldTrip website has been implemented as a wiki using the Dokuwiki CMS for more than 10 years now. But the ongoing struggles in updating the underlying code base to prevent being hacked (which happened a few times), the effort to keep the website/wiki free of spam (which happened too often), and to maintain and extend the documentation of thee website have triggered us to move to a new system. You may already have noticed that the wiki was not editable for some weeks: this was to allow us the opportunity to copy all content over. We now have a new website that is implemented using Jekyll (which some of you might know from github pages). It is technically not a wiki any more, but importantly: you can still directly contribute. The important difference is that contributions are now done by editing markdown documents and using github . This allows us to review them for correctness and consistency and (importantly) to prevent spam. Furthermore, having all pages in one easily accessible place makes maintenance and large edits easier, and properly gives credits to the documentation contributors. To edit, you need a github account. You can do edits directly on the github website, or fork/clone the repository and send PRs. The new website can be found on new.fieldtriptoolbox.org , Up to now the main address www.fieldtriptoolbox.org is pointing to the old one, but I will redirect it so that it points to the new one. It might take some time for you to see the change. The old website will remain available for some time on old.fieldtriptoolbox.org . All content has been moved over and (almost) all URLs from the old website should point to the same page on the new website. The overall menu structure has been changed/simplified; hopefully you can still find the pages you are familiar with. The search functionality has been significantly improved and now automatically returns results both from website and email list. The new website also loads much faster than the old one, and you could actually get a fully functional offline copy on your hard disk or own server. We are still (as always) working on improving the new website. Especially the overall organization of the documentation has gotten a bit messy over the years (in true wiki style ;-) and we will try to restructure it more and make the wealth(*) of documentation more accessible. Furthermore, you can expect some technical improvements and more to come in the future (check out the new matlab2markdown and markdown2matlab functions in fieldtrip/utilities). If you have suggestions, or if you are skilled with jekyll/html/css/javascript, or want to help out in any other way, please open an issue here to contribute. best regards, Robert, Eelke, Jan-Mathijs and the others that helped transitioning to the new website PS (*) the FieldTrip website now has 944 pages of documentation (excluding the reference documentation) and 1022 figures. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dlozanosoldevilla at gmail.com Wed Dec 5 18:54:13 2018 From: dlozanosoldevilla at gmail.com (Diego Lozano-Soldevilla) Date: Wed, 5 Dec 2018 18:54:13 +0100 Subject: [FieldTrip] new fieldtrip website In-Reply-To: <20CB9CBD-7DB3-46A0-A616-7BF8C8228C09@donders.ru.nl> References: <20CB9CBD-7DB3-46A0-A616-7BF8C8228C09@donders.ru.nl> Message-ID: Thank you for this great effort! A perfect Sinterklaas gift ;) On Wed, Dec 5, 2018, 17:22 Robert Oostenveld Dear FieldTrip community, > > The FieldTrip website has been implemented as a wiki using the Dokuwiki > CMS for more than 10 years now. But the ongoing > struggles in updating the underlying code base to prevent being hacked > (which happened a few times), the effort to keep the website/wiki free of > spam (which happened too often), and to maintain and extend the > documentation of thee website have triggered us to move to a new system. > You may already have noticed that the wiki was not editable for some weeks: > this was to allow us the opportunity to copy all content over. > > We now have a new website that is implemented using Jekyll > (which some of you might know from github pages). > It is technically not a wiki any more, but importantly: you can still > directly contribute. The important difference is that contributions are now > done by editing markdown documents and using github > . This allows us to review them for > correctness and consistency and (importantly) to prevent spam. Furthermore, > having all pages in one easily accessible place makes maintenance and large > edits easier, and properly gives credits to the documentation contributors. > To edit, you need a github account. You can do edits directly on the github > website, or fork/clone the repository and send PRs. > > The new website can be found on new.fieldtriptoolbox.org, Up to now the > main address www.fieldtriptoolbox.org is pointing to the old one, but I > will redirect it so that it points to the new one. It might take some time > for you to see the change. The old website will remain available for some > time on old.fieldtriptoolbox.org. > > All content has been moved over and (almost) all URLs from the old website > should point to the same page on the new website. The overall menu > structure has been changed/simplified; hopefully you can still find the > pages you are familiar with. The search functionality has been > significantly improved and now automatically returns results both from > website and email list. The new website also loads much faster than the old > one, and you could actually get a fully functional offline copy on your > hard disk or own server. > > We are still (as always) working on improving the new website. Especially > the overall organization of the documentation has gotten a bit messy over > the years (in true wiki style ;-) and we will try to restructure it more > and make the wealth(*) of documentation more accessible. Furthermore, you > can expect some technical improvements and more to come in the future > (check out the new matlab2markdown and markdown2matlab functions in > fieldtrip/utilities). If you have suggestions, or if you are skilled with > jekyll/html/css/javascript, or want to help out in any other way, please > open an issue here to contribute. > > best regards, > Robert, Eelke, Jan-Mathijs and the others that helped transitioning to the > new website > > > PS (*) the FieldTrip website now has 944 pages of documentation (excluding > the reference documentation) and 1022 figures. > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mikkel at cnru.dk Thu Dec 6 10:50:32 2018 From: mikkel at cnru.dk (Mikkel Vinding) Date: Thu, 6 Dec 2018 10:50:32 +0100 Subject: [FieldTrip] Import Freesurfer atlas to ft In-Reply-To: <05BF26AB-B71D-4F76-9BFB-09277FD731EC@donders.ru.nl> References: <05BF26AB-B71D-4F76-9BFB-09277FD731EC@donders.ru.nl> Message-ID: Dear Jan-Mathijs Thank you for the answer. It worked! Best regards Mikkel Mikkel C. Vinding NatMEG, Karolinska Institutet Nobels väg 9 171 77 Stockholm, Sweden Email: mikkel.vinding at ki.se On Tue, Dec 4, 2018 at 9:45 PM Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Dear Mikkel, > > I did not look into it in detail, but from your description it seems that > the code takes a wrong turn somewhere, and thinks that the fileformat is of > type freesurfer_volume (and for this reason it ends up on a line that tries > to use ft_read_mri). I read in the code that the default allocation of the > fileformat based on an educated guess from the filename is implemented in > a slightly clunky way. Soooo, perhaps you could try and overrule this > default allocation by explicitly specifying it in your call to > ft_read_atlas: > > ft_read_atlas({filename_annotation filename_mesh}, ‘format’, > ‘freesurfer_*’); > > where the * should be the appropriate choice of ‘a2009s’ ‘aparc’, or ‘ba’. > > Best wishes, > Jan-Mathijs > > On 4 Dec 2018, at 20:20, Mikkel Vinding wrote: > > Dear FieldTrip list > > > Has anyone here imported individual atlases from Freesurfer into > FieldTrip? It should be possible with ft_read_atlas. From the documentation > of ft_read_atlas: > > > * For individual surface-based atlases from FreeSurfer, you should > specify two * > * filenames as a cell-array: the first points to the file that contains > information* > * with respect to the parcels' labels, the second points to the file that > defines the* > * mesh on which the parcellation is defined.* > > > Ft_read_atlas require a struct containing the filename of the atlas file > and the cortical surface/mesh. However, I keep getting errors that > ft_read_atlas cannot read Freesurfers “annot” files: “ *unrecognized > filetype 'freesurfer_annot'.*“ I get a similar error when I try to read > Freesurfer “label” files. > > > The problem seems to be because ft_read_atlas calls ft_read_mri which does > not support the type 'freesurfer_annot'. My question is how to read in > Freesurfer annotations or labels? Do I need to convert the Freesurfer files > first or is there another step I need to do first? If anyone has managed to > read Freesurfer labels in FieldTrip, I will be delighted to hear the answer. > > > Best regards > Mikkel > > Mikkel C. Vinding > NatMEG, Karolinska Institutet > Nobels väg 9 > 171 77 Stockholm, Sweden > Email: mikkel.vinding at ki.se > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From p.gaur at ulster.ac.uk Thu Dec 6 20:10:51 2018 From: p.gaur at ulster.ac.uk (Gaur, Pramod) Date: Thu, 6 Dec 2018 19:10:51 +0000 Subject: [FieldTrip] Connectivity analysis in Source level Message-ID: Dear Team, I have identified 3 sources in the source level which are showing significant difference using machine learning techniques in MCI group and control group. Can please advise is it possible to perform connectivity analysis in the identified sources? Thanks, Pramod This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster at ulster.ac.uk and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Ulster University. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. Ulster University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The Ulster University was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for Ulster University in Northern Ireland is Cromore Road, Coleraine, Co. Londonderry BT52 1SA -------------- next part -------------- An HTML attachment was scrubbed... URL: From y.visser at hotmail.com Fri Dec 7 16:04:02 2018 From: y.visser at hotmail.com (Yvonne Visser) Date: Fri, 7 Dec 2018 15:04:02 +0000 Subject: [FieldTrip] Cluster based permutation test interpretation In-Reply-To: <51779646-98DD-42FA-94BB-13CE1167D869@donders.ru.nl> References: , <51779646-98DD-42FA-94BB-13CE1167D869@donders.ru.nl> Message-ID: Dear Eric, Thank you for your extensive reply, we will take it into account for the interpretation of our results! Best, Yvonne ________________________________ From: fieldtrip on behalf of Maris, E.G.G. (Eric) Sent: Wednesday, December 5, 2018 2:40 PM To: fieldtrip at science.ru.nl Subject: Re: [FieldTrip] Cluster based permutation test interpretation Dear Yvonne, I advise you to make a distinction between statistical inference and interpretation. Statistical inference pertains to a particular null hypothesis, which is either rejected or not. Interpretation, on the other hand, pertains to the likely cause of a rejection (e.g., alpha-band power modulations in the -0.75 to 0 interval). The p-value pertains to statistical inference but not to the interpretation. To make a case for a particular interpretation you are free to use all arguments at your disposal. One of these arguments is the fact that the largest cluster in in the alpha-band in the —0.75 to 0 interval. But you can also refer to published results. For instance, the alpha-band is one of the two bands of the sensorimotor rhythm, whose spatio-spectral structure has been described in numerous papers (among which several ones to which I contributed as a senior author), and whose amplitude is inversely related to movement and reaction time. In your case, I would look in the post-stimulation period to characterise the sensorimotor rhythm in space and frequency. I have advised this procedure in this paper: https://doi.org/10.1111/j.1469-8986.2011.01320.x. In general, I think that we should rely less on p-values for localisation in space, frequency and time. Instead, we should use the spatio-spectro-temporal extent of the largest clusters to provide a mechanistic account of the effect. For that, it is necessary to relate your results to the published findings in the literature. I have argued for this approach in this paper: https://www.sciencedirect.com/science/article/pii/S1364661316300481 best, Eric From: Yvonne Visser > Subject: [FieldTrip] Cluster based permutation test interpretation Date: 30 November 2018 at 10:47:03 CET To: "fieldtrip at science.ru.nl" > Cc: "aaron.schurger at gmail.com" > Dear all, Thank you for welcoming me to the discussion list, my name is Yvonne Visser and I currently work as a research assistant with dr. Aaron Schurger at Neurospin. During my masters program I learned about cluster based permutation tests for electrophysiological data and distinctly remember how from this type of test one can not conclude that a particular cluster is significant (in line with what is said on the fieldtrip website here, http://www.fieldtriptoolbox.org/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test) We are currently using the cluster based permutation test in the analysis of our experiment, but we are a bit confused on how to interpret the results from our test. To give you a short introduction to our experiment: we are looking for a relationship between a behavioural variable and our collected EEG data. So we computed the grand average time frequency spectrum in a single channel of the time bins of interest. Then, we correlated each time/frequency point in this 2d matrix with the behavioural variable in that trial. This resulted in a correlation matrix like you can see in attachment1_correlationmatrix. As you can see, we also computed clusters of time/frequency points with p<0.05. After computing the permutations, we found that the biggest "real" cluster is bigger than any of the permuted clusters. Now, we would like to conclude something from this result about which frequency band at what time is correlated to our behavioural variable. We found a fieldtrip function called ft_clusterplot that does seem to suggest that you can highlight a specific cluster it if it survives the test, but isn't that exactly what my lectures and the webpage say we should not do? Can we say that activity in the alpha band around -0.75 to 0 (where the biggest cluster is located) is correlated to the size of the movement? Or should we not conclude something about which cluster is significant and can we only say that some time frequency power is correlated to our behavioural variable? If the second is true, do you have any advice for us to make the interpretation more specific? Thank you so much in advance, and please let us know if anything is unclear. Kind regards, Yvonne & Aaron. _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 Eric Maris | Donders Institute for Brain, Cognition, and Behaviour & Faculty of Social Sciences | Radboud University | PO Box 9104, 6500 HE Nijmegen | (024) 3612651 | www.ru.nl This message (and any attachments) is intended solely for the addressee(s) and may contain confidential information. If you are not the addressee, do not copy this message (and any attachments), forward or share this message with third parties. You are requested to notify the sender immediately and delete this message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From max-philipp.stenner at med.ovgu.de Mon Dec 10 09:08:19 2018 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Mon, 10 Dec 2018 08:08:19 +0000 Subject: [FieldTrip] Postdoc position in Freigeist Research Group (University of Magdeburg) Message-ID: Dear all an exciting opportunity has become available for a PostDoc Researcher in Human Motor Neuroscience (for 4 years) in the newly funded Freigeist Research Group "Motor Learning" at the Leibniz Institute for Neurobiology & Department of Neurology at the University of Magdeburg, Germany. Please find a detailed job description and instructions how to apply attached (deadline January 31st 2019). Looking forward to welcoming you to Magdeburg, Max-Philipp Stenner http://www.lin-magdeburg.de/de/abteilungen/verhaltensneurologie/physiology_motorlearning/index.jsp -------------- next part -------------- A non-text attachment was scrubbed... Name: PostDoc Human Motor Neuroscience.pdf Type: application/pdf Size: 379098 bytes Desc: PostDoc Human Motor Neuroscience.pdf URL: From christine.blume at sbg.ac.at Mon Dec 10 12:10:42 2018 From: christine.blume at sbg.ac.at (Blume Christine) Date: Mon, 10 Dec 2018 11:10:42 +0000 Subject: [FieldTrip] Call for Applications: 12 PhD Positions in Cognitive Neuroscience (Univ. of Salzburg) Message-ID: <994c3ed718e442cc8c869b100d1934a9@sbg.ac.at> International PhD Programme at the University of Salzburg (Austria) [cid:image001.png at 01D49081.5F7A0480] Theme: "Imaging the Mind" Join an internationally renowned PhD programme in the beautiful city of Salzburg (Austria). While Salzburg has one of the highest life quality ratings globally, the university's Department of Psychology with its Centre for Cognitive Neuroscience (CCNS) is among the most productive departments worldwide. We are inviting applications for 12 fully funded PhD studentships in the following interdisciplinary areas: cognitive (neuro-)science, psychology, biology, medicine/neurology, or computational neuroscience. The programme will admit students for autumn 2019 (earliest start date 1st October 2019). It offers numerous benefits: ü salary for a period of 3 to 4 years (including health and social insurance) ü equipped work space ü specific technological training courses (e.g. fMRI, EEG, MEG) ü presentation, scientific writing, & teaching skills training ü full funding of congress participation, workshops, and international courses ü funding for 6-month research stays in foreign partner laboratories Candidates must hold a master's degree or equivalent with a relevant specialisation in one of the above listed academic areas of the programme at the time of entry. Prior application is possible. The language of the graduate programme (teaching) is English; hence, English proficiency is indispensable. The programme strives for equal representation of female PhD students, wherefore women are especially encouraged to apply. Deadline for applications: 21st January 2019 (0:00 CET) For detailed information about application, selection, admissions procedure, and the scientific programme as well as the faculty please visit: https://phdIM.ccns.sbg.ac.at/ We are looking forward to receiving your applications! Best, Christine Blume ------------------------------------------------------------------------ Dr. Christine Blume University of Salzburg Centre for Cognitive Neuroscience (CCNS) Laboratory for Sleep, Cognition & Consciousness Research Hellbrunner Str. 34 A-5020 Salzburg T: +43 (0) 662 - 8044 5148 www.christine-blume.com | www.sleepscience.at -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 257079 bytes Desc: image001.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: DKIM_CallApplications_FundingPeriodIII.pdf Type: application/pdf Size: 352527 bytes Desc: DKIM_CallApplications_FundingPeriodIII.pdf URL: From robince at gmail.com Mon Dec 10 18:33:10 2018 From: robince at gmail.com (Robin) Date: Mon, 10 Dec 2018 17:33:10 +0000 Subject: [FieldTrip] Postdoc on resting state analysis in Glasgow Message-ID: Postdoc developing information theoretic methods for resting state analysis A 2-year postdoc position is available working with Dr. Robin Ince at the University of Glasgow. The project is funded by the Wellcome Trust and will involve developing and applying multivariate information theoretic methods to resting state fMRI data from the Human Connectome Project. The position will also involve collection of simultaneous EEG-fMRI resting state data in Glasgow. The ideal candidate will have strong expertise with numerical programming (MATLAB or Python) and be familiar with neuroimaging data and analysis. Glasgow is a friendly, lively and welcoming city with a reasonable cost of living and close proximity to the beautiful Highlands and a wide range of outdoor activities. International applicants should note that Glasgow voted 67% in favour of remaining in the EU and is the second most welcoming city to foreigners in the mainland UK (after London) [1], as well as being one of the safest cities in the UK [2]. The Centre for Cognitive Neuroimaging (CCNi) at the Institute of Neuroscience and Psychology (INP) is a collaborative and stimulating environment with a full suite of world-class facilities, including EEG, MEG, 3T fMRI, 7T fMRI, EEG-fMRI, TMS, and extensive computational resources (~2500 cores, ~15TB RAM). The position is a Research Assistant on Grade 6 of the University of Glasgow salary scale: £28,660 - £32,236 (plus ~18% employer contributions to USS defined benefit pension). Apply online at https://www.gla.ac.uk/it/iframe/jobs/ Search for ref: 023869 Closing date for applications Jan 13th 2019. Flexible start date. Any questions about the project, position or application process please contact robin.ince at glasgow.ac.uk Institute of Neuroscience & Psychology College of Medical Veterinary & Life Sciences University of Glasgow [1] Eurostat Urban Europe Report 2016. [2] Mercer Quality of Living Ranking 2016. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at me.com Tue Dec 11 08:37:05 2018 From: nathanweisz at me.com (Nathan Weisz) Date: Tue, 11 Dec 2018 08:37:05 +0100 Subject: [FieldTrip] 12 PhD positions at the Univ of Salzburg Message-ID: <71897767-1010-481D-88D7-6412CB106762@me.com> Dear colleagues, please circulate the attached call for PhD positions to potentially interested students. Via the Centre for Cognitive Neuroscience the students have access to all toys that cognitive neuroscientists could wish for and we strive to make the labs accessible for all users. The position is funded for 3 years (proper working contract and not a stipend) + up to one year extra pending on a stay abroad (which is an amazing opportunity that I know of no other PhD program). Also worth mentioning that Salzburg is a lovely place to live. Best, Nathan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: DKIM_CallApplications_FundingPeriodIII.pdf Type: application/pdf Size: 352527 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From mikexcohen at gmail.com Tue Dec 11 07:24:07 2018 From: mikexcohen at gmail.com (Mike X Cohen) Date: Tue, 11 Dec 2018 07:24:07 +0100 Subject: [FieldTrip] Neuroscience data analysis summer-school announcements Message-ID: Dear colleagues, I am happy to announce *two week-long neuroscience data analysis courses* at the Radboud University in Netherlands in 2019: One about time-frequency/synchronization/statistics (*note: this same course is offered twice due to popular demand!*), and one about linear algebra and source-separation. Below are the direct links to the course pages with application information. You can also find more information, including syllabi, on sincxpress.com . *Please pass these links around to your colleagues/students who might be interested in one or both of these courses!* Analyzing neural time series data (8-12 July *AND* 5-9 August). Fourier transform, convolution, time-frequency analysis, synchronization, nonparametric statistics, simulating time series data. (The August course is recommended for people interested in both courses.) Linear algebra for neuroscientists (12-16 August). Matrix algebra, least-squares model fitting, eigendecomposition, multivariate source separation, simulating multicomponent and multichannal time series data. Please note that applications, if approved, are selected on a first-come-first-serve basis, and that the number of participants for each course is limited by room size. If you have questions about the courses, please feel free to contact me. Mike -- Mike X Cohen, PhD Fresh look: mikexcohen.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From maximilien.chaumon at gmail.com Tue Dec 11 12:19:19 2018 From: maximilien.chaumon at gmail.com (Maximilien Chaumon) Date: Tue, 11 Dec 2018 12:19:19 +0100 Subject: [FieldTrip] plotting only one hemisphere with ft_plot_mesh Message-ID: Dear all, Is there an easy way to plot only one hemisphere of a cortical mesh? I would like to plot this guy: mctxsm = struct with fields: coordsys: 'unknown' hemispherelabel: {2×1 cell} hemisphere: [64984×1 double] pos: [64984×3 double] tri: [129960×3 double] unit: 'm' ft_plot_mesh(mctxsm); -------------- next part -------------- An HTML attachment was scrubbed... URL: From EAS877 at student.bham.ac.uk Wed Dec 12 18:01:48 2018 From: EAS877 at student.bham.ac.uk (EAS877 at student.bham.ac.uk) Date: Wed, 12 Dec 2018 17:01:48 +0000 Subject: [FieldTrip] Index of /pub/fieldtrip/tutorial/preprocessing_erp - help downloading relevant files Message-ID: To whom it may concern, I have recently installed and set a path for FieldTrip in Matlab, I am attempting the tutorial 'Preprocessing of EEG data and computing ERPs' however I am unsure how to download the full data set as recommended from the webpage http://www.fieldtriptoolbox.org/tutorial/preprocessing_erp/. Furthermore I'd like to ask where I can access the ftp files? The same webpage recommended downloading these however I don't think I have found the relevant link yet. Apologies for the basic questions, and thank you for any help Best Wishes, Lizzy tutorial:preprocessing_erp [FieldTrip] www.fieldtriptoolbox.org In FieldTrip the preprocessing of data refers to the reading of the data, segmenting the data around interesting events such as triggers, temporal filtering and optionally rereferencing. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bioeng.yoosofzadeh at gmail.com Wed Dec 12 21:34:20 2018 From: bioeng.yoosofzadeh at gmail.com (Vahab Yousofzadeh) Date: Wed, 12 Dec 2018 14:34:20 -0600 Subject: [FieldTrip] ft_artifact_zvalue Message-ID: Dear FT experts, Seems that the ft_artifact_zvalue only takes positive z-values to look for artifacts: https://www.dropbox.com/s/zbhslrn12j6ug7o/EOG_Artifacts.tif?dl=0 different than a sample figure in, http://www.fieldtriptoolbox.org/tutorial/automatic_artifact_rejection/ Here are my settings: cfg = []; cfg.continuous = 'yes'; cfg.artfctdef.zvalue.channel = refchan; cfg.artfctdef.zvalue.cutoff = z_ther; cfg.artfctdef.zvalue.trlpadding = 0; cfg.artfctdef.zvalue.artpadding = 0.1; cfg.artfctdef.zvalue.fltpadding = 0; cfg.artfctdef.zvalue.bpfilter = 'yes'; cfg.artfctdef.zvalue.bpfilttype = 'but'; cfg.artfctdef.zvalue.bpfreq = [1 15]; cfg.artfctdef.zvalue.bpfiltord = 4; cfg.artfctdef.zvalue.hilbert = 'yes'; cfg.artfctdef.zvalue.interactive = interactive; [~, artifact_EOG] = ft_artifact_zvalue(cfg, data); Any comments are welcomed, - Vahab From alexandra.korzeczek at med.uni-goettingen.de Thu Dec 13 09:15:43 2018 From: alexandra.korzeczek at med.uni-goettingen.de (Korzeczek, Alexandra) Date: Thu, 13 Dec 2018 08:15:43 +0000 Subject: [FieldTrip] Sourcemodel: difficulties reading mne output Message-ID: Hello all, I'm currently trying to create a source model. However when I try to open the Mne -oct6-src.fif file with the function mne_read_sourcespaces I get an error message (attached). I tried to open the file within MNE and there its possible. When I comment %255 - tag2 = find_tag(this, FIFF.FIFF_MNE_SOURCE_SPACE_NEAREST_DIST); %272 - tag2 = find_tag(this, FIFF.FIFF_MNE_SOURCE_SPACE_DIST_LIMIT); within "mne_read_sourcespaces" out, then the file can be read. However, the output is not plotted properly with ft_plot_mesh (sourcespace). Has anyone an idea why mne_read_sourcespaces is only working without the commented rows? Is it ok to run that function with these lines or am I going to miss a crucial information in the output? Thanks for your reply, Greetings, Alexandra _________________________________________________________________ Alexandra Korzeczek Wissenschaftliche Mitarbeiterin Klinik für Klinische Neurophysiologie Georg-August-Universität Göttingen Robert-Koch.Str. 40, 37075 Göttingen Tel. 0551- 39-65106 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Error-mne_read_sourcespaces.JPG Type: image/jpeg Size: 44372 bytes Desc: Error-mne_read_sourcespaces.JPG URL: From J.Verhoef at donders.ru.nl Fri Dec 14 13:58:09 2018 From: J.Verhoef at donders.ru.nl (Verhoef, J.P. (Julia)) Date: Fri, 14 Dec 2018 12:58:09 +0000 Subject: [FieldTrip] Language in Interaction: Research Data Manager for Research Consortium 'Language in Interaction' (0.8 FTE) In-Reply-To: <2557884cb6bb4fc88ae5809d90676da8@EXPRD05.hosting.ru.nl> References: <0581358689e9425faeae4d338faf9be5@EXPRD05.hosting.ru.nl> <2557884cb6bb4fc88ae5809d90676da8@EXPRD05.hosting.ru.nl> Message-ID: <98926913ea22427d8b35acd21fe0b49b@EXPRD05.hosting.ru.nl> We would like to draw your attention to the following opening within the Language in Interaction consortium. Please feel free to forward this information to anyone who might be interested. Research Data Manager for Research Consortium 'Language in Interaction' (0.8 FTE) Dutch Research Consortium 'Language in Interaction' Maximum salary: € 4,166 gross/month Vacancy number: 30.14.18 Application deadline: 6 January 2019 [Logo NWO] [Logo Language in Interaction] Responsibilities The Dutch research consortium Language in Interaction (LiI) invites applications for a Research Data Manager position. You will be responsible for the further development, elaboration and implementation of FAIR data management for all research data created within our consortium. You will facilitate and streamline lean and efficient research data management (RDM) at our different partner institutes through fostering discussion, sharing knowledge and accumulating best practices. Extensive consultation and close collaboration with data stewards at our different partner institutions will be required. You will serve as a first point of contact for RDM for all LiI partner institutions as well as our individual researchers, providing information, templates, guidelines and regulations. You will monitor compliance with the agreed LiI RDM plan for all research projects funded by LiI. In collaboration with existing support teams, you will be expected to operate as product owner by taking responsibility for the implementation of a database through which all data produced in our consortium is made available under the principles of FAIR data management. This requires translation of the functional aspects into technical implementation using opportunities offered by the existing infrastructure. You will become a member of the Management Team of our consortium, under the supervision of Prof. Peter Hagoort. This position provides the opportunity to become a member of an interdisciplinary consortium conducting world-class research. Work environment The Language in Interaction (LiI) research consortium is sponsored by a Gravitation grant from the Netherlands Organisation for Scientific Research (NWO). LiI brings together many excellent researchers from eight different research institutions in the Netherlands in a research programme on the foundations of language. Teams of researchers collaborate to collectively address five key questions in our research field, producing an enormous variety of data types, all of which require different approaches to fulfil the criteria for FAIR data management. Until now, each partner institution has developed its own protocols for FAIR data management. The consortium offers a unique opportunity to standardise data management on a transcending scale. You will be appointed at the Donders Institute, Centre for Cognitive Neuroimaging (Radboud University, Nijmegen). All our partner institutions offer an international setting. English is the lingua franca. What we expect from you · you have a scientific background (preferably in a domain related to the research performed by our consortium); · you have affinity with scientific research; · you have an excellent sense of organisational and managerial relations; · you have good communication skills; · you are able to translate functional requirements into technical implementations; · you have general programming skills; · you are acquainted (or willing to familiarise yourself) with all aspects that influence FAIR data management (technical aspects, but also ethics, legislation, etc.); · you are enterprising and result-oriented; · you have strong oral and written English proficiency. What we have to offer · employment: 0.8 FTE; · a maximum gross monthly salary of € 4,166 based on a 38-hour working week (salary scale 10); · in addition to the salary: an 8% holiday allowance and an 8.3% end-of-year bonus; · you will be appointed for the remaining time frame of our consortium, until June 30, 2023; · University job profile: Project Leader Level 1; · you will be able to make use of our Dual Career Service where our Dual Career Officer will assist with family related support, such as child care, and help your partner prepare for the local labour market and with finding an occupation. Are you interested in our excellent employment conditions? Other Information The intended start date is as soon as possible. The institute involved is an equal opportunity employer, committed to building a culturally diverse intellectual community, and as such encourages applications from women and minorities. Would you like to know more? Further information on: The Language in Interaction research consortium For more information about this vacancy, please contact: MSc. Sander Berends, programme manager Language in Interaction Telephone: +31 24 3619838 E-mail: s.berends at donders.ru.nl Prof. dr. Peter Hagoort, principal investigator Telephone: +31 24 3610648, +31 24 3521301 E-mail: p.hagoort at donders.ru.nl Are you interested? You should upload your application (attn. of Prof. dr. P. Hagoort) exclusively using the button 'Apply' below. Your application should include (and be limited to) the following attachment(s): · a cover letter · your curriculum vitae, including the names of at least two persons who can provide references [Apply] No commercial propositions please. Kind regards, Julia Verhoef Secretary - Language in Interaction Consortium Radboud University | Donders Centre for Cognitive Neuroimaging (DCCN) Room 0.026 Kapittelweg 29, 6525 EN Nijmegen, The Netherlands P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands |T: +31 (0)24 3666272 E: J.Verhoef at donders.ru.nll|Office hours: 9-14 hr on Mon - Fri -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 2461 bytes Desc: image001.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.jpg Type: image/jpeg Size: 40202 bytes Desc: image002.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image003.jpg Type: image/jpeg Size: 3660 bytes Desc: image003.jpg URL: From rgovinda at childrensnational.org Mon Dec 17 20:47:29 2018 From: rgovinda at childrensnational.org (Govindan, Rathinaswamy) Date: Mon, 17 Dec 2018 19:47:29 +0000 Subject: [FieldTrip] questions In-Reply-To: <252EB8AF-77EE-4336-8345-E463D50E9A42@childrensnational.org> References: <26BC20C23720E94A9FF826794B6D0CCE0100422E5E@PVTH-EXMBX11.cnmc.org> <252EB8AF-77EE-4336-8345-E463D50E9A42@childrensnational.org> Message-ID: Hello Fieldtrippers: I am RB Govindan from Children’s Hospital, Washington, DC. I am visiting FieldTrip after a long time, so consider me as a beginner. My objective is to quantitate stereo EEG using spectral analysis that includes connectivity analysis. From the get-go, I have two questions: For installation, I downloaded fieldtrip-20181207.zip file and unzipped it on my computer. I tried downloading other folders (examples, modules, tutorial, and workshop) but with no success. Some of the huge files in these folders disconnected my FTP link. Would I be able to use all features of FieldTrip with the version that I have downloaded? If not, could you please suggest what other components I need? I have MRIs in DICOM format. I followed the instructions in the tutorial which are as follows: f1=’/Volumes/FDATA_1/HACO_Project/CT_MRI T1 SPGR/ARS_MRI_T1 SPGR/1.2.840.113619.2.353.4120.14262029.13982.1485259768.788.dcm’; mri = ft_read_mri(f1); This threw the following error message. ERROR: /Volumes/FDATA_1/HACO_Project/CT_MRI T1 SPGR/ARS_MRI_T1 SPGR/1.2.840.113619.2.353.4120.14262029.13982.1485259768.788.dcm does not have a series number Output argument "vol" (and maybe others) not assigned during call to "load_dicom_series." Error in ft_read_mri (line 300) [img,transform,hdr,mr_params] = load_dicom_series(dcmdir,dcmdir,filename); Could someone help me so I can proceed further? My understanding is that the code looks for the series number of the DICOM images. I do not know what that means. Furthermore, I’m running Fieldtrip from a MATLAB that does not have an image processing toolbox. Do I need an image processing toolbox for my analysis? Thank you very much for your attention, in anticipation. Best regards, RB From: rbgovindan Date: Friday, December 14, 2018 at 11:16 AM To: "fieldtrip at science.ru.nl" Subject: Re: questions While reading DICOM images using this function: mri = ft_read_mri(f1); I received the following error: ERROR: /Volumes/FDATA_1/HACO_Project/CT_MRI T1 SPGR/ARS_MRI_T1 SPGR/1.2.840.113619.2.353.4120.14262029.13982.1485259768.788.dcm does not have a series number Output argument "vol" (and maybe others) not assigned during call to "load_dicom_series." Error in ft_read_mri (line 300) [img,transform,hdr,mr_params] = load_dicom_series(dcmdir,dcmdir,filename); Any help is appreciated. Best regards, RB (function(){(function (e){if(e){var t=e.cloneNode;e.cloneNode=function(n){var i=t.call(e,n);if(e.classList.contains("mceContentBody"))i.innerHTML=e.innerHTML,r(i);else try{o(i)}catch(e){}return i},o(e)}function n(e){if(e.parentNode)if(e.childNodes.length>1){for(var t=document.createDocumentFragment();e.childNodes.length>0;)t.appendChild(e.childNodes[0]);e.parentNode.replaceChild(t,e)}else e.firstChild?e.parentNode.replaceChild(e.firstChild,e):e.parentNode.removeChild(e)}function r(e){if(e)try{for(var t=e.querySelectorAll(".gr_"),r=t.length,o=0;o Dear list members, I would like to feed machine learning algorithms with virtual sensor data of different frequency bands as well as broad bands (e.g. 1-45Hz, beta-band etc) and would appreciate your help with some issues concerning the filtering of the data. In order to obtain virtual sensors, I compute lcmv beamformer with bandpass filtered averaged sensor data (e.g. filtered in beta band). After obtaining the spatial filter, I multiply the weights with the single trials filtered in beta band. When checking the frequency spectrum of the beta band filtered average sensor data, the spectrum looks all right (see attached picture "mean sensor data betaband.png). However, when checking the frequency spectrum of the virtual sensors, the spectrum does not show signal in beta band, but shows a spectrum between 1 and 120 Hz, while signal seems to be missing around 20 Hz (see the other attached picture). I checked all analyzing steps and found that the data covariance matrix already presents a similar frequency spectrum as the virtual sensors. I know too little to understand this issue and would appreciate it if anyone could help me here. Would it make more sense to filter only the virtual sensors, with no filtering at all beforehand? Thanks for your help in advance, best regards, Kirsten -------------- next part -------------- An HTML attachment was scrubbed... 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Name: mean_sensor_data_betaband.png Type: image/png Size: 25752 bytes Desc: mean_sensor_data_betaband.png URL: From schurgerlab at gmail.com Fri Dec 21 13:44:43 2018 From: schurgerlab at gmail.com (Schurger Lab) Date: Fri, 21 Dec 2018 13:44:43 +0100 Subject: [FieldTrip] post-doc opportunity Message-ID: Post-doctoral positions in the cognitive neuroscience of volition Brain-behavior forecasting: Neural antecedents of self-initiated movement and the forecasting of behavior based on brain activity Starting date: Spring 2019 Duration: 18 months The French Institute of Health and Medical Research (INSERM) invites applications for a post-doctoral position in the Cognitive Neuroimaging Group, at the NeuroSpin Research Center near Paris, France, as part of the research team of Dr. Aaron Schurger. The Schurger lab focuses on understanding how decisions are made and actions initiated spontaneously, without an external sensory cue, and how time series of neural activity can be used to forecast behavior. We pursue this research using a combination of behavioral experiments, neuroimaging, computational modeling, time-series analyses, and machine learning. We are especially interested in applicants with significant experience in one or more of the following areas: -machine learning / pattern classification -modeling of time series / predicting discrete events in time series -Bayesian statistics -Kalman filters -dynamical systems theory -magnetoencephalography (MEG) Candidates with experience in other neural recording modalities (such as fMRI or ECoG) may also be considered. An interest in volition, action initiation, and/or the purposeful generation of unpredictable behavior is essential. Applicants should have a obtained a PhD in a relevant discipline prior to the starting date, and at a minimum should have strong skills in the following three areas: computer programming (MatLab or Python), statistics, signal processing Candidates with a background in engineering, computer science, physics, or applied math are encouraged to apply. Resources available at NeuroSpin include Siemens 3T and 7T MRI scanners; high-density EEG (EGI Inc.); Elekta NeuroMag 306-channel MEG (allowing for the simultaneous recording of EEG); eye tracking (available for MRI, MEG, and behavioral experiments); an in-house team of experts in signal processing and statistical learning; a dedicated staff handling subject recruitment, scheduling, and payment; various Nespresso devices; and proximity to Paris. Applicants should send a CV, letter of motivation (max 2 pages), and a list of three references via e-mail to schurgerlab at gmail.com. Review of applicants will begin immediately, and will continue until the position is filled. The NeuroSpin Research Center is located on the campus of the CEA-Saclay, near Orsay, about 18 km southwest of Paris. For more information on the NeuroSpin Research Center and the Cognitive Neuroimaging Group: http://www-centre-saclay.cea.fr/fr/Visite-guidee-de-NeuroSpin http://meg-france.in2p3.fr/_lesCentres/Neurospin_en.php http://www-dsv.cea.fr/en/institutes/institute-of-biomedical-imaging-i2bm/departments/neurospin-neurospin http://www.unicog.org/pm/pmwiki.php ----------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From antonius.wiehler at gmail.com Fri Dec 21 21:01:53 2018 From: antonius.wiehler at gmail.com (Antonius Wiehler) Date: Fri, 21 Dec 2018 21:01:53 +0100 Subject: [FieldTrip] Design matrix for depsamplesregrT within subject Message-ID: Hi, I have two questions about correctly specifying the design matrix for ft_freqstatistics. It is a within-subject experimental design, where I want to test the (linear) effect of time. So, per subject, I have 5 consecutive sessions, with ~170 trials each. In the time-frequency domain, I would like to test if power is changing with session. For group statistics, I did the following: 1) Compute per subject and session the mean with ft_freqdescriptives, because I don't have enough memory to work with single trial data. 2) Testing the session effect with a dependent samples regression % parameters for test cfg = []; cfg.parameter = 'powspctrm'; cfg.latency = 'all'; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesregrT'; cfg.correcttail = 'prob'; cfg.tail = 0; cfg.alpha = 0.05; cfg.numrandomization = 500; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.clusterthreshold = 'nonparametric_common'; % method for single-sample threshold cfg.clustertail = 0; cfg.minnbchan = 3; cfg.wcm_weight = 1; %design matrix design = zeros(2, n_sessions*n_subjects); design(1, :) = repmat(1:n_subjects, 1, n_sessions); % subject design(2, :) = repelem(1:n_sessions, n_subjects); % session cfg.design = design; cfg.uvar = 1; % which row is the unit variable, here subjects cfg.ivar = 2; % which row is the independent variable, here sessions %generate stats from two cell arrays of full fieldtrip "data" structures stat = ft_freqstatistics(cfg, session1{:}, session2{:}, session3{:}, session4{:}, session5{:}); This leads to a significant cluster. Now, I would like to test if the effect is significant in every single subject. So I thought I would just set n_subjects to 1 and could use the same approach. However, I get an error saying that I need as least two subjects (uvar). I'm wondering what is the right way to set this up. An indepsamplesregrT is running fine, but I think the data is still depended, as it is from one subject. Second, I would like to test the conjunction, i.e. finding a cluster that is overlapping between subjects and significant within *every* single subject. How could I do this in Fieldtrip? Thanks a lot for your help in advance! Best, Antonius -------------- next part -------------- An HTML attachment was scrubbed... URL: From moh.mustafa.91 at gmail.com Fri Dec 28 20:12:33 2018 From: moh.mustafa.91 at gmail.com (Mohamed Hamid) Date: Fri, 28 Dec 2018 14:12:33 -0500 Subject: [FieldTrip] fieldtrip@science.ru.nl Message-ID: Dear Community, I have a general question. Is it OK to have many dipole locations outside the brain when generating the leadfield matrix? For example, when running the EEG head model example ( http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem/), then using ft_prepare_leadfield to generate the leadfield, more than 50% of the dipole locations are outside the brain. in the above example,the leadfields are calculated for the locations inside the brain only and the grid resolution is set to 0.5 cm. I am using the anatomical mri of subject01 from the tutorial dataset. What I want to know is if in general, it is normal to have this many locations outside the brain in the leadfield matrix and if I can just ignore them when simulating EEG or doing inverse solutions? Mohamed Hamid Ph.D. Candidate Dept. of Electrical and Computer Eng. Concordia University -------------- next part -------------- An HTML attachment was scrubbed... URL: From pdhami06 at gmail.com Sun Dec 30 18:42:06 2018 From: pdhami06 at gmail.com (Paul Dhami) Date: Sun, 30 Dec 2018 17:42:06 +0000 Subject: [FieldTrip] Applying Bonferroni Correction to Alpha Parameter Instead of ANOVA Message-ID: Dear Fieldtrip community, I have an ERP experiment with a 2 x 2 design (lets say with one factor having levels A and B and the other having factors 1 and 2), both being within groups measures. As stated in the interaction page, I can't use that to test for an ANOVA design when both factors are within group measures. Instead of running an ANOVA, I was thinking of running separate contrasts of interest, which would be A1 vs A2 and B1 vs B2. My question is: 1) to correct for now the multiple contrasts, would simply setting the alpha parameter (which is used for the inference of accepting or rejecting the null hypothesis) to 0.5/2 be acceptable? What if I wanted to test all possible contrasts, would I simply then divide my alpha parameter by the number of contrasts I have? Any input would be appreciated. Best, Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: From pascualm at key.uzh.ch Mon Dec 31 04:06:56 2018 From: pascualm at key.uzh.ch (pascualm at key.uzh.ch) Date: Mon, 31 Dec 2018 12:06:56 +0900 Subject: [FieldTrip] Measuring Granger-causal effects in multivariate time series by system editing Message-ID: Dear Colleagues, The preprint entitled "Measuring Granger-causal effects in multivariate time series by system editing" is available at bioRxiv https://doi.org/10.1101/504068 and includes supplementary material for the sake of reproducible research: program codes (PASCAL), executable file, & toy data in human readable format. The abstract can be found below. Cordially, Roberto ... Roberto D. Pascual-Marqui, PhD, PD The KEY Institute for Brain-Mind Research, University of Zurich Visiting Professor at Neuropsychiatry, Kansai Medical University, Osaka [https://www.uzh.ch/keyinst/loreta] [https://scholar.google.com/citations?user=pascualmarqui] ... Abstract: What is the role of each node in a system of many interconnected nodes? This can be quantified by comparing the dynamics of the nodes in the intact system, with their modified dynamics in the edited system, where one node is deleted. In detail, the spectra are calculated from a causal multivariate autoregressive model for the intact system. Next, without re-estimation, one node is deleted from the model and the modified spectra at all other nodes are re-calculated. The change in spectra from the edited system to the intact system quantifies the role of the deleted node, giving a measure of its Granger-causal effects (CFX) on the system. A generalization of this novel measure is available for networks (i.e. for groups of nodes), which quantifies the role of each network in a system of many networks. For the sake of reproducible research, program codes (PASCAL), executable file, and toy data in human readable format are included in the supplementary material. From alexandre.chalard at inserm.fr Mon Dec 31 18:59:05 2018 From: alexandre.chalard at inserm.fr (Alexandre Chalard) Date: Mon, 31 Dec 2018 18:59:05 +0100 Subject: [FieldTrip] Using FieldTrip for Time-Frequency Cluster Message-ID: Hello everyone, I am writing this post because I have some questions about using FieldTrip after carefully reading the documentation provided on the site. I would like to use FieldTrip to use the cluster statistics functions. My experimental task consists of movements in patients and healthy subjects. Currently, I use my routines to perform my analyses (epoching, filtering, time frequency transformation). For example, I would like to highlight differences between the 2 groups in the time and frequency map at a single electrode. Does FieldTrip allow cluster statistics to be performed on a single electrode (Time x Frequency at the sensor level) ? If so, how do we configure it? Do the neighboring channels represent frequencies or time? Should we change the number of neighboring channels (for example in my case 77 points represent the frequency band 13-30) ? My data is currently stored in this way: Time x Frequency x Subjects which is the average representation of the tests during the task in the time frequency domain on an electrode. Does FieldTrip allow me to quickly integrate this data structure into the different functions? Do I have to go back through the different data pipelines (preprocessing, grandavage, freqanalysis) in order to use the freqstat ? Thank you for your help With kind regards Alexandre Chalard From jdien07 at mac.com Sat Dec 1 00:08:26 2018 From: jdien07 at mac.com (Joseph Dien) Date: Fri, 30 Nov 2018 18:08:26 -0500 Subject: [FieldTrip] automatic IC rejection In-Reply-To: <48E6E95C4AB29E4BAD7908051F5C17EF016E1E3CBD@MBXP07.ds.man.ac.uk> References: <5e257bfd-121e-d151-08d0-3c31ff0ada5a@uzh.ch> <9b277ef4-067a-9a61-a11b-da7d504b9717@uni-konstanz.de> <48E6E95C4AB29E4BAD7908051F5C17EF016E1E31BC@MBXP07.ds.man.ac.uk> <6630afcc-003d-3ecf-2d53-d0174a75ea09@uzh.ch> <48E6E95C4AB29E4BAD7908051F5C17EF016E1E3CBD@MBXP07.ds.man.ac.uk> Message-ID: <78BF4010-FCE8-4A86-BE5C-E7E1B0295736@mac.com> I have a comprehensive automated artifact correction routine (MAAC) implemented in my EP Toolkit, which you may find helpful. It follows the principle that different artifacts have different characteristics and so different algorithms will be most effective for each one. I’m in the middle of writing it up. https://sourceforge.net/projects/erppcatoolkit/ Joe > On Nov 30, 2018, at 12:08, Jason Taylor wrote: > > Hi Aitor, > > No, not that I know of. I generally use a hacky combination of SPM, fieldtrip, and EEGLAB functions, but if you've already run ICA, you could accomplish what I suggested with some standard matlab functions. > > Best wishes, > Jason > > -----Original Message----- > From: Aitor Egurtzegi [mailto:aitor.martinezegurcegui at uzh.ch] > Sent: 30 November 2018 13:43 > To: Jason Taylor; FieldTrip discussion list > Subject: Re: [FieldTrip] automatic IC rejection > > Dear Jason, > > Thanks a lot for your reply. Is there a Fieldtrip method already > implemented to run such temporal correlation? or would I have to do the > implementation in raw Matlab? > > Thanks in advance, > Aitor > > On 11/30/18 2:05 AM, Jason Taylor wrote: >> Hi Aitor, >> >> If you have an 'objective' measure of the artefact you're trying to remove (e.g., VEOG for blinks), a relatively straightforward method is to run a temporal correlation between each IC's activation time-course and the artefact channel's time-course. You can then reject any IC with a correlation higher than some threshold, or with a Z-score (r value relative to the distribution of IC r values) above some threshold. This tends to work very well for identifying blinks, and fairly well for eye-movements (*EOG), and can work for pulse artefact if you have recorded ECG. To avoid spurious correlations due to high-frequency noise, you can filter (e.g., 1 to 30 Hz) the component and artefact signals before correlating them (but obviously go back to the original unfiltered signals to continue with your analysis). >> >> Best wishes, >> Jason >> >> >> -----Original Message----- >> From: fieldtrip [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of David Schubring >> Sent: 28 November 2018 12:47 >> To: fieldtrip at science.ru.nl; aitor.martinezegurcegui at uzh.ch >> Subject: Re: [FieldTrip] automatic IC rejection >> >> Dear Aitor, >> >> the closest thing I know of for a data-driven approach of selecting >> independent components is COMPASS, quote: >> >> "COMPASS is a MATLAB and EEGLAB based algorithm with the purpose of >> providing the user with a convenient technique for automatic Independent >> Component (IC) selection with respect to the contributions of the ICs to >> a certain ERP." >> >> Link to the toolbox: >> >> http://53450283.de.strato-hosting.eu/jrw/lab/e_compass.htm >> >> Paper: >> >> Wessel, J. R., & Ullsperger, M. (2011). Selection of independent >> components representing event-related brain potentials: a data-driven >> approach for greater objectivity. Neuroimage, 54(3), 2105-2115. >> https://doi.org/10.1016/j.neuroimage.2010.10.033 >> >> I have only theoretical experience with the toolbox as I only learned >> about it in a workshop and did not yet have the time to test and >> implement it in my personal FieldTrip workflow (even though it is on my >> ever growing to-do list). So far it looked like a useful thing to try >> out to me, especially as code can better be reproduced than "personal >> judgement". >> >> Best, >> David >> >> Am 28.11.2018 um 10:49 schrieb Aitor Egurtzegi: >>> Dear researchers at Fieldtrip, >>> >>> >>> In order to make my work more reproducible, I would like to >>> automatically reject ICs instead of doing visual inspection and >>> rejection of the components. Unfortunately, I haven't found any >>> documentation for such thing. Is there a way to do it in Fieldtrip? >>> >>> Best, >>> Aitor >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> https://doi.org/10.1371/journal.pcbi.1002202 > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 -------------------------------------------------------------------------------- Joseph Dien, PhD Senior Research Scientist Department of Human Development and Quantitative Methodology University of Maryland, College Park http://joedien.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From mikkel at cnru.dk Tue Dec 4 20:20:45 2018 From: mikkel at cnru.dk (Mikkel Vinding) Date: Tue, 4 Dec 2018 20:20:45 +0100 Subject: [FieldTrip] Import Freesurfer atlas to ft Message-ID: Dear FieldTrip list Has anyone here imported individual atlases from Freesurfer into FieldTrip? It should be possible with ft_read_atlas. From the documentation of ft_read_atlas: * For individual surface-based atlases from FreeSurfer, you should specify two * * filenames as a cell-array: the first points to the file that contains information* * with respect to the parcels' labels, the second points to the file that defines the* * mesh on which the parcellation is defined.* Ft_read_atlas require a struct containing the filename of the atlas file and the cortical surface/mesh. However, I keep getting errors that ft_read_atlas cannot read Freesurfers “annot” files: “ *unrecognized filetype 'freesurfer_annot'.*“ I get a similar error when I try to read Freesurfer “label” files. The problem seems to be because ft_read_atlas calls ft_read_mri which does not support the type 'freesurfer_annot'. My question is how to read in Freesurfer annotations or labels? Do I need to convert the Freesurfer files first or is there another step I need to do first? If anyone has managed to read Freesurfer labels in FieldTrip, I will be delighted to hear the answer. Best regards Mikkel Mikkel C. Vinding NatMEG, Karolinska Institutet Nobels väg 9 171 77 Stockholm, Sweden Email: mikkel.vinding at ki.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Dec 4 21:17:00 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 4 Dec 2018 20:17:00 +0000 Subject: [FieldTrip] Import Freesurfer atlas to ft In-Reply-To: References: Message-ID: <05BF26AB-B71D-4F76-9BFB-09277FD731EC@donders.ru.nl> Dear Mikkel, I did not look into it in detail, but from your description it seems that the code takes a wrong turn somewhere, and thinks that the fileformat is of type freesurfer_volume (and for this reason it ends up on a line that tries to use ft_read_mri). I read in the code that the default allocation of the fileformat based on an educated guess from the filename is implemented in a slightly clunky way. Soooo, perhaps you could try and overrule this default allocation by explicitly specifying it in your call to ft_read_atlas: ft_read_atlas({filename_annotation filename_mesh}, ‘format’, ‘freesurfer_*’); where the * should be the appropriate choice of ‘a2009s’ ‘aparc’, or ‘ba’. Best wishes, Jan-Mathijs On 4 Dec 2018, at 20:20, Mikkel Vinding > wrote: Dear FieldTrip list Has anyone here imported individual atlases from Freesurfer into FieldTrip? It should be possible with ft_read_atlas. From the documentation of ft_read_atlas: For individual surface-based atlases from FreeSurfer, you should specify two filenames as a cell-array: the first points to the file that contains information with respect to the parcels' labels, the second points to the file that defines the mesh on which the parcellation is defined. Ft_read_atlas require a struct containing the filename of the atlas file and the cortical surface/mesh. However, I keep getting errors that ft_read_atlas cannot read Freesurfers “annot” files: “ unrecognized filetype 'freesurfer_annot'.“ I get a similar error when I try to read Freesurfer “label” files. The problem seems to be because ft_read_atlas calls ft_read_mri which does not support the type 'freesurfer_annot'. My question is how to read in Freesurfer annotations or labels? Do I need to convert the Freesurfer files first or is there another step I need to do first? If anyone has managed to read Freesurfer labels in FieldTrip, I will be delighted to hear the answer. Best regards Mikkel Mikkel C. Vinding NatMEG, Karolinska Institutet Nobels väg 9 171 77 Stockholm, Sweden Email: mikkel.vinding at ki.se _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.maris at donders.ru.nl Wed Dec 5 14:40:26 2018 From: e.maris at donders.ru.nl (Maris, E.G.G. (Eric)) Date: Wed, 5 Dec 2018 13:40:26 +0000 Subject: [FieldTrip] Cluster based permutation test interpretation In-Reply-To: References: Message-ID: <51779646-98DD-42FA-94BB-13CE1167D869@donders.ru.nl> Dear Yvonne, I advise you to make a distinction between statistical inference and interpretation. Statistical inference pertains to a particular null hypothesis, which is either rejected or not. Interpretation, on the other hand, pertains to the likely cause of a rejection (e.g., alpha-band power modulations in the -0.75 to 0 interval). The p-value pertains to statistical inference but not to the interpretation. To make a case for a particular interpretation you are free to use all arguments at your disposal. One of these arguments is the fact that the largest cluster in in the alpha-band in the —0.75 to 0 interval. But you can also refer to published results. For instance, the alpha-band is one of the two bands of the sensorimotor rhythm, whose spatio-spectral structure has been described in numerous papers (among which several ones to which I contributed as a senior author), and whose amplitude is inversely related to movement and reaction time. In your case, I would look in the post-stimulation period to characterise the sensorimotor rhythm in space and frequency. I have advised this procedure in this paper: https://doi.org/10.1111/j.1469-8986.2011.01320.x. In general, I think that we should rely less on p-values for localisation in space, frequency and time. Instead, we should use the spatio-spectro-temporal extent of the largest clusters to provide a mechanistic account of the effect. For that, it is necessary to relate your results to the published findings in the literature. I have argued for this approach in this paper: https://www.sciencedirect.com/science/article/pii/S1364661316300481 best, Eric From: Yvonne Visser > Subject: [FieldTrip] Cluster based permutation test interpretation Date: 30 November 2018 at 10:47:03 CET To: "fieldtrip at science.ru.nl" > Cc: "aaron.schurger at gmail.com" > Dear all, Thank you for welcoming me to the discussion list, my name is Yvonne Visser and I currently work as a research assistant with dr. Aaron Schurger at Neurospin. During my masters program I learned about cluster based permutation tests for electrophysiological data and distinctly remember how from this type of test one can not conclude that a particular cluster is significant (in line with what is said on the fieldtrip website here, http://www.fieldtriptoolbox.org/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test) We are currently using the cluster based permutation test in the analysis of our experiment, but we are a bit confused on how to interpret the results from our test. To give you a short introduction to our experiment: we are looking for a relationship between a behavioural variable and our collected EEG data. So we computed the grand average time frequency spectrum in a single channel of the time bins of interest. Then, we correlated each time/frequency point in this 2d matrix with the behavioural variable in that trial. This resulted in a correlation matrix like you can see in attachment1_correlationmatrix. As you can see, we also computed clusters of time/frequency points with p<0.05. After computing the permutations, we found that the biggest "real" cluster is bigger than any of the permuted clusters. Now, we would like to conclude something from this result about which frequency band at what time is correlated to our behavioural variable. We found a fieldtrip function called ft_clusterplot that does seem to suggest that you can highlight a specific cluster it if it survives the test, but isn't that exactly what my lectures and the webpage say we should not do? Can we say that activity in the alpha band around -0.75 to 0 (where the biggest cluster is located) is correlated to the size of the movement? Or should we not conclude something about which cluster is significant and can we only say that some time frequency power is correlated to our behavioural variable? If the second is true, do you have any advice for us to make the interpretation more specific? Thank you so much in advance, and please let us know if anything is unclear. Kind regards, Yvonne & Aaron. _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 Eric Maris | Donders Institute for Brain, Cognition, and Behaviour & Faculty of Social Sciences | Radboud University | PO Box 9104, 6500 HE Nijmegen | (024) 3612651 | www.ru.nl This message (and any attachments) is intended solely for the addressee(s) and may contain confidential information. If you are not the addressee, do not copy this message (and any attachments), forward or share this message with third parties. You are requested to notify the sender immediately and delete this message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Wed Dec 5 16:51:11 2018 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 5 Dec 2018 16:51:11 +0100 Subject: [FieldTrip] new fieldtrip website Message-ID: <20CB9CBD-7DB3-46A0-A616-7BF8C8228C09@donders.ru.nl> Dear FieldTrip community, The FieldTrip website has been implemented as a wiki using the Dokuwiki CMS for more than 10 years now. But the ongoing struggles in updating the underlying code base to prevent being hacked (which happened a few times), the effort to keep the website/wiki free of spam (which happened too often), and to maintain and extend the documentation of thee website have triggered us to move to a new system. You may already have noticed that the wiki was not editable for some weeks: this was to allow us the opportunity to copy all content over. We now have a new website that is implemented using Jekyll (which some of you might know from github pages). It is technically not a wiki any more, but importantly: you can still directly contribute. The important difference is that contributions are now done by editing markdown documents and using github . This allows us to review them for correctness and consistency and (importantly) to prevent spam. Furthermore, having all pages in one easily accessible place makes maintenance and large edits easier, and properly gives credits to the documentation contributors. To edit, you need a github account. You can do edits directly on the github website, or fork/clone the repository and send PRs. The new website can be found on new.fieldtriptoolbox.org , Up to now the main address www.fieldtriptoolbox.org is pointing to the old one, but I will redirect it so that it points to the new one. It might take some time for you to see the change. The old website will remain available for some time on old.fieldtriptoolbox.org . All content has been moved over and (almost) all URLs from the old website should point to the same page on the new website. The overall menu structure has been changed/simplified; hopefully you can still find the pages you are familiar with. The search functionality has been significantly improved and now automatically returns results both from website and email list. The new website also loads much faster than the old one, and you could actually get a fully functional offline copy on your hard disk or own server. We are still (as always) working on improving the new website. Especially the overall organization of the documentation has gotten a bit messy over the years (in true wiki style ;-) and we will try to restructure it more and make the wealth(*) of documentation more accessible. Furthermore, you can expect some technical improvements and more to come in the future (check out the new matlab2markdown and markdown2matlab functions in fieldtrip/utilities). If you have suggestions, or if you are skilled with jekyll/html/css/javascript, or want to help out in any other way, please open an issue here to contribute. best regards, Robert, Eelke, Jan-Mathijs and the others that helped transitioning to the new website PS (*) the FieldTrip website now has 944 pages of documentation (excluding the reference documentation) and 1022 figures. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dlozanosoldevilla at gmail.com Wed Dec 5 18:54:13 2018 From: dlozanosoldevilla at gmail.com (Diego Lozano-Soldevilla) Date: Wed, 5 Dec 2018 18:54:13 +0100 Subject: [FieldTrip] new fieldtrip website In-Reply-To: <20CB9CBD-7DB3-46A0-A616-7BF8C8228C09@donders.ru.nl> References: <20CB9CBD-7DB3-46A0-A616-7BF8C8228C09@donders.ru.nl> Message-ID: Thank you for this great effort! A perfect Sinterklaas gift ;) On Wed, Dec 5, 2018, 17:22 Robert Oostenveld Dear FieldTrip community, > > The FieldTrip website has been implemented as a wiki using the Dokuwiki > CMS for more than 10 years now. But the ongoing > struggles in updating the underlying code base to prevent being hacked > (which happened a few times), the effort to keep the website/wiki free of > spam (which happened too often), and to maintain and extend the > documentation of thee website have triggered us to move to a new system. > You may already have noticed that the wiki was not editable for some weeks: > this was to allow us the opportunity to copy all content over. > > We now have a new website that is implemented using Jekyll > (which some of you might know from github pages). > It is technically not a wiki any more, but importantly: you can still > directly contribute. The important difference is that contributions are now > done by editing markdown documents and using github > . This allows us to review them for > correctness and consistency and (importantly) to prevent spam. Furthermore, > having all pages in one easily accessible place makes maintenance and large > edits easier, and properly gives credits to the documentation contributors. > To edit, you need a github account. You can do edits directly on the github > website, or fork/clone the repository and send PRs. > > The new website can be found on new.fieldtriptoolbox.org, Up to now the > main address www.fieldtriptoolbox.org is pointing to the old one, but I > will redirect it so that it points to the new one. It might take some time > for you to see the change. The old website will remain available for some > time on old.fieldtriptoolbox.org. > > All content has been moved over and (almost) all URLs from the old website > should point to the same page on the new website. The overall menu > structure has been changed/simplified; hopefully you can still find the > pages you are familiar with. The search functionality has been > significantly improved and now automatically returns results both from > website and email list. The new website also loads much faster than the old > one, and you could actually get a fully functional offline copy on your > hard disk or own server. > > We are still (as always) working on improving the new website. Especially > the overall organization of the documentation has gotten a bit messy over > the years (in true wiki style ;-) and we will try to restructure it more > and make the wealth(*) of documentation more accessible. Furthermore, you > can expect some technical improvements and more to come in the future > (check out the new matlab2markdown and markdown2matlab functions in > fieldtrip/utilities). If you have suggestions, or if you are skilled with > jekyll/html/css/javascript, or want to help out in any other way, please > open an issue here to contribute. > > best regards, > Robert, Eelke, Jan-Mathijs and the others that helped transitioning to the > new website > > > PS (*) the FieldTrip website now has 944 pages of documentation (excluding > the reference documentation) and 1022 figures. > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mikkel at cnru.dk Thu Dec 6 10:50:32 2018 From: mikkel at cnru.dk (Mikkel Vinding) Date: Thu, 6 Dec 2018 10:50:32 +0100 Subject: [FieldTrip] Import Freesurfer atlas to ft In-Reply-To: <05BF26AB-B71D-4F76-9BFB-09277FD731EC@donders.ru.nl> References: <05BF26AB-B71D-4F76-9BFB-09277FD731EC@donders.ru.nl> Message-ID: Dear Jan-Mathijs Thank you for the answer. It worked! Best regards Mikkel Mikkel C. Vinding NatMEG, Karolinska Institutet Nobels väg 9 171 77 Stockholm, Sweden Email: mikkel.vinding at ki.se On Tue, Dec 4, 2018 at 9:45 PM Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Dear Mikkel, > > I did not look into it in detail, but from your description it seems that > the code takes a wrong turn somewhere, and thinks that the fileformat is of > type freesurfer_volume (and for this reason it ends up on a line that tries > to use ft_read_mri). I read in the code that the default allocation of the > fileformat based on an educated guess from the filename is implemented in > a slightly clunky way. Soooo, perhaps you could try and overrule this > default allocation by explicitly specifying it in your call to > ft_read_atlas: > > ft_read_atlas({filename_annotation filename_mesh}, ‘format’, > ‘freesurfer_*’); > > where the * should be the appropriate choice of ‘a2009s’ ‘aparc’, or ‘ba’. > > Best wishes, > Jan-Mathijs > > On 4 Dec 2018, at 20:20, Mikkel Vinding wrote: > > Dear FieldTrip list > > > Has anyone here imported individual atlases from Freesurfer into > FieldTrip? It should be possible with ft_read_atlas. From the documentation > of ft_read_atlas: > > > * For individual surface-based atlases from FreeSurfer, you should > specify two * > * filenames as a cell-array: the first points to the file that contains > information* > * with respect to the parcels' labels, the second points to the file that > defines the* > * mesh on which the parcellation is defined.* > > > Ft_read_atlas require a struct containing the filename of the atlas file > and the cortical surface/mesh. However, I keep getting errors that > ft_read_atlas cannot read Freesurfers “annot” files: “ *unrecognized > filetype 'freesurfer_annot'.*“ I get a similar error when I try to read > Freesurfer “label” files. > > > The problem seems to be because ft_read_atlas calls ft_read_mri which does > not support the type 'freesurfer_annot'. My question is how to read in > Freesurfer annotations or labels? Do I need to convert the Freesurfer files > first or is there another step I need to do first? If anyone has managed to > read Freesurfer labels in FieldTrip, I will be delighted to hear the answer. > > > Best regards > Mikkel > > Mikkel C. Vinding > NatMEG, Karolinska Institutet > Nobels väg 9 > 171 77 Stockholm, Sweden > Email: mikkel.vinding at ki.se > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From p.gaur at ulster.ac.uk Thu Dec 6 20:10:51 2018 From: p.gaur at ulster.ac.uk (Gaur, Pramod) Date: Thu, 6 Dec 2018 19:10:51 +0000 Subject: [FieldTrip] Connectivity analysis in Source level Message-ID: Dear Team, I have identified 3 sources in the source level which are showing significant difference using machine learning techniques in MCI group and control group. Can please advise is it possible to perform connectivity analysis in the identified sources? Thanks, Pramod This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster at ulster.ac.uk and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Ulster University. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. Ulster University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The Ulster University was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for Ulster University in Northern Ireland is Cromore Road, Coleraine, Co. Londonderry BT52 1SA -------------- next part -------------- An HTML attachment was scrubbed... URL: From y.visser at hotmail.com Fri Dec 7 16:04:02 2018 From: y.visser at hotmail.com (Yvonne Visser) Date: Fri, 7 Dec 2018 15:04:02 +0000 Subject: [FieldTrip] Cluster based permutation test interpretation In-Reply-To: <51779646-98DD-42FA-94BB-13CE1167D869@donders.ru.nl> References: , <51779646-98DD-42FA-94BB-13CE1167D869@donders.ru.nl> Message-ID: Dear Eric, Thank you for your extensive reply, we will take it into account for the interpretation of our results! Best, Yvonne ________________________________ From: fieldtrip on behalf of Maris, E.G.G. (Eric) Sent: Wednesday, December 5, 2018 2:40 PM To: fieldtrip at science.ru.nl Subject: Re: [FieldTrip] Cluster based permutation test interpretation Dear Yvonne, I advise you to make a distinction between statistical inference and interpretation. Statistical inference pertains to a particular null hypothesis, which is either rejected or not. Interpretation, on the other hand, pertains to the likely cause of a rejection (e.g., alpha-band power modulations in the -0.75 to 0 interval). The p-value pertains to statistical inference but not to the interpretation. To make a case for a particular interpretation you are free to use all arguments at your disposal. One of these arguments is the fact that the largest cluster in in the alpha-band in the —0.75 to 0 interval. But you can also refer to published results. For instance, the alpha-band is one of the two bands of the sensorimotor rhythm, whose spatio-spectral structure has been described in numerous papers (among which several ones to which I contributed as a senior author), and whose amplitude is inversely related to movement and reaction time. In your case, I would look in the post-stimulation period to characterise the sensorimotor rhythm in space and frequency. I have advised this procedure in this paper: https://doi.org/10.1111/j.1469-8986.2011.01320.x. In general, I think that we should rely less on p-values for localisation in space, frequency and time. Instead, we should use the spatio-spectro-temporal extent of the largest clusters to provide a mechanistic account of the effect. For that, it is necessary to relate your results to the published findings in the literature. I have argued for this approach in this paper: https://www.sciencedirect.com/science/article/pii/S1364661316300481 best, Eric From: Yvonne Visser > Subject: [FieldTrip] Cluster based permutation test interpretation Date: 30 November 2018 at 10:47:03 CET To: "fieldtrip at science.ru.nl" > Cc: "aaron.schurger at gmail.com" > Dear all, Thank you for welcoming me to the discussion list, my name is Yvonne Visser and I currently work as a research assistant with dr. Aaron Schurger at Neurospin. During my masters program I learned about cluster based permutation tests for electrophysiological data and distinctly remember how from this type of test one can not conclude that a particular cluster is significant (in line with what is said on the fieldtrip website here, http://www.fieldtriptoolbox.org/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test) We are currently using the cluster based permutation test in the analysis of our experiment, but we are a bit confused on how to interpret the results from our test. To give you a short introduction to our experiment: we are looking for a relationship between a behavioural variable and our collected EEG data. So we computed the grand average time frequency spectrum in a single channel of the time bins of interest. Then, we correlated each time/frequency point in this 2d matrix with the behavioural variable in that trial. This resulted in a correlation matrix like you can see in attachment1_correlationmatrix. As you can see, we also computed clusters of time/frequency points with p<0.05. After computing the permutations, we found that the biggest "real" cluster is bigger than any of the permuted clusters. Now, we would like to conclude something from this result about which frequency band at what time is correlated to our behavioural variable. We found a fieldtrip function called ft_clusterplot that does seem to suggest that you can highlight a specific cluster it if it survives the test, but isn't that exactly what my lectures and the webpage say we should not do? Can we say that activity in the alpha band around -0.75 to 0 (where the biggest cluster is located) is correlated to the size of the movement? Or should we not conclude something about which cluster is significant and can we only say that some time frequency power is correlated to our behavioural variable? If the second is true, do you have any advice for us to make the interpretation more specific? Thank you so much in advance, and please let us know if anything is unclear. Kind regards, Yvonne & Aaron. _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 Eric Maris | Donders Institute for Brain, Cognition, and Behaviour & Faculty of Social Sciences | Radboud University | PO Box 9104, 6500 HE Nijmegen | (024) 3612651 | www.ru.nl This message (and any attachments) is intended solely for the addressee(s) and may contain confidential information. If you are not the addressee, do not copy this message (and any attachments), forward or share this message with third parties. You are requested to notify the sender immediately and delete this message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From max-philipp.stenner at med.ovgu.de Mon Dec 10 09:08:19 2018 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Mon, 10 Dec 2018 08:08:19 +0000 Subject: [FieldTrip] Postdoc position in Freigeist Research Group (University of Magdeburg) Message-ID: Dear all an exciting opportunity has become available for a PostDoc Researcher in Human Motor Neuroscience (for 4 years) in the newly funded Freigeist Research Group "Motor Learning" at the Leibniz Institute for Neurobiology & Department of Neurology at the University of Magdeburg, Germany. Please find a detailed job description and instructions how to apply attached (deadline January 31st 2019). Looking forward to welcoming you to Magdeburg, Max-Philipp Stenner http://www.lin-magdeburg.de/de/abteilungen/verhaltensneurologie/physiology_motorlearning/index.jsp -------------- next part -------------- A non-text attachment was scrubbed... Name: PostDoc Human Motor Neuroscience.pdf Type: application/pdf Size: 379098 bytes Desc: PostDoc Human Motor Neuroscience.pdf URL: From christine.blume at sbg.ac.at Mon Dec 10 12:10:42 2018 From: christine.blume at sbg.ac.at (Blume Christine) Date: Mon, 10 Dec 2018 11:10:42 +0000 Subject: [FieldTrip] Call for Applications: 12 PhD Positions in Cognitive Neuroscience (Univ. of Salzburg) Message-ID: <994c3ed718e442cc8c869b100d1934a9@sbg.ac.at> International PhD Programme at the University of Salzburg (Austria) [cid:image001.png at 01D49081.5F7A0480] Theme: "Imaging the Mind" Join an internationally renowned PhD programme in the beautiful city of Salzburg (Austria). While Salzburg has one of the highest life quality ratings globally, the university's Department of Psychology with its Centre for Cognitive Neuroscience (CCNS) is among the most productive departments worldwide. We are inviting applications for 12 fully funded PhD studentships in the following interdisciplinary areas: cognitive (neuro-)science, psychology, biology, medicine/neurology, or computational neuroscience. The programme will admit students for autumn 2019 (earliest start date 1st October 2019). It offers numerous benefits: ü salary for a period of 3 to 4 years (including health and social insurance) ü equipped work space ü specific technological training courses (e.g. fMRI, EEG, MEG) ü presentation, scientific writing, & teaching skills training ü full funding of congress participation, workshops, and international courses ü funding for 6-month research stays in foreign partner laboratories Candidates must hold a master's degree or equivalent with a relevant specialisation in one of the above listed academic areas of the programme at the time of entry. Prior application is possible. The language of the graduate programme (teaching) is English; hence, English proficiency is indispensable. The programme strives for equal representation of female PhD students, wherefore women are especially encouraged to apply. Deadline for applications: 21st January 2019 (0:00 CET) For detailed information about application, selection, admissions procedure, and the scientific programme as well as the faculty please visit: https://phdIM.ccns.sbg.ac.at/ We are looking forward to receiving your applications! Best, Christine Blume ------------------------------------------------------------------------ Dr. Christine Blume University of Salzburg Centre for Cognitive Neuroscience (CCNS) Laboratory for Sleep, Cognition & Consciousness Research Hellbrunner Str. 34 A-5020 Salzburg T: +43 (0) 662 - 8044 5148 www.christine-blume.com | www.sleepscience.at -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 257079 bytes Desc: image001.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: DKIM_CallApplications_FundingPeriodIII.pdf Type: application/pdf Size: 352527 bytes Desc: DKIM_CallApplications_FundingPeriodIII.pdf URL: From robince at gmail.com Mon Dec 10 18:33:10 2018 From: robince at gmail.com (Robin) Date: Mon, 10 Dec 2018 17:33:10 +0000 Subject: [FieldTrip] Postdoc on resting state analysis in Glasgow Message-ID: Postdoc developing information theoretic methods for resting state analysis A 2-year postdoc position is available working with Dr. Robin Ince at the University of Glasgow. The project is funded by the Wellcome Trust and will involve developing and applying multivariate information theoretic methods to resting state fMRI data from the Human Connectome Project. The position will also involve collection of simultaneous EEG-fMRI resting state data in Glasgow. The ideal candidate will have strong expertise with numerical programming (MATLAB or Python) and be familiar with neuroimaging data and analysis. Glasgow is a friendly, lively and welcoming city with a reasonable cost of living and close proximity to the beautiful Highlands and a wide range of outdoor activities. International applicants should note that Glasgow voted 67% in favour of remaining in the EU and is the second most welcoming city to foreigners in the mainland UK (after London) [1], as well as being one of the safest cities in the UK [2]. The Centre for Cognitive Neuroimaging (CCNi) at the Institute of Neuroscience and Psychology (INP) is a collaborative and stimulating environment with a full suite of world-class facilities, including EEG, MEG, 3T fMRI, 7T fMRI, EEG-fMRI, TMS, and extensive computational resources (~2500 cores, ~15TB RAM). The position is a Research Assistant on Grade 6 of the University of Glasgow salary scale: £28,660 - £32,236 (plus ~18% employer contributions to USS defined benefit pension). Apply online at https://www.gla.ac.uk/it/iframe/jobs/ Search for ref: 023869 Closing date for applications Jan 13th 2019. Flexible start date. Any questions about the project, position or application process please contact robin.ince at glasgow.ac.uk Institute of Neuroscience & Psychology College of Medical Veterinary & Life Sciences University of Glasgow [1] Eurostat Urban Europe Report 2016. [2] Mercer Quality of Living Ranking 2016. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at me.com Tue Dec 11 08:37:05 2018 From: nathanweisz at me.com (Nathan Weisz) Date: Tue, 11 Dec 2018 08:37:05 +0100 Subject: [FieldTrip] 12 PhD positions at the Univ of Salzburg Message-ID: <71897767-1010-481D-88D7-6412CB106762@me.com> Dear colleagues, please circulate the attached call for PhD positions to potentially interested students. Via the Centre for Cognitive Neuroscience the students have access to all toys that cognitive neuroscientists could wish for and we strive to make the labs accessible for all users. The position is funded for 3 years (proper working contract and not a stipend) + up to one year extra pending on a stay abroad (which is an amazing opportunity that I know of no other PhD program). Also worth mentioning that Salzburg is a lovely place to live. Best, Nathan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: DKIM_CallApplications_FundingPeriodIII.pdf Type: application/pdf Size: 352527 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From mikexcohen at gmail.com Tue Dec 11 07:24:07 2018 From: mikexcohen at gmail.com (Mike X Cohen) Date: Tue, 11 Dec 2018 07:24:07 +0100 Subject: [FieldTrip] Neuroscience data analysis summer-school announcements Message-ID: Dear colleagues, I am happy to announce *two week-long neuroscience data analysis courses* at the Radboud University in Netherlands in 2019: One about time-frequency/synchronization/statistics (*note: this same course is offered twice due to popular demand!*), and one about linear algebra and source-separation. Below are the direct links to the course pages with application information. You can also find more information, including syllabi, on sincxpress.com . *Please pass these links around to your colleagues/students who might be interested in one or both of these courses!* Analyzing neural time series data (8-12 July *AND* 5-9 August). Fourier transform, convolution, time-frequency analysis, synchronization, nonparametric statistics, simulating time series data. (The August course is recommended for people interested in both courses.) Linear algebra for neuroscientists (12-16 August). Matrix algebra, least-squares model fitting, eigendecomposition, multivariate source separation, simulating multicomponent and multichannal time series data. Please note that applications, if approved, are selected on a first-come-first-serve basis, and that the number of participants for each course is limited by room size. If you have questions about the courses, please feel free to contact me. Mike -- Mike X Cohen, PhD Fresh look: mikexcohen.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From maximilien.chaumon at gmail.com Tue Dec 11 12:19:19 2018 From: maximilien.chaumon at gmail.com (Maximilien Chaumon) Date: Tue, 11 Dec 2018 12:19:19 +0100 Subject: [FieldTrip] plotting only one hemisphere with ft_plot_mesh Message-ID: Dear all, Is there an easy way to plot only one hemisphere of a cortical mesh? I would like to plot this guy: mctxsm = struct with fields: coordsys: 'unknown' hemispherelabel: {2×1 cell} hemisphere: [64984×1 double] pos: [64984×3 double] tri: [129960×3 double] unit: 'm' ft_plot_mesh(mctxsm); -------------- next part -------------- An HTML attachment was scrubbed... URL: From EAS877 at student.bham.ac.uk Wed Dec 12 18:01:48 2018 From: EAS877 at student.bham.ac.uk (EAS877 at student.bham.ac.uk) Date: Wed, 12 Dec 2018 17:01:48 +0000 Subject: [FieldTrip] Index of /pub/fieldtrip/tutorial/preprocessing_erp - help downloading relevant files Message-ID: To whom it may concern, I have recently installed and set a path for FieldTrip in Matlab, I am attempting the tutorial 'Preprocessing of EEG data and computing ERPs' however I am unsure how to download the full data set as recommended from the webpage http://www.fieldtriptoolbox.org/tutorial/preprocessing_erp/. Furthermore I'd like to ask where I can access the ftp files? The same webpage recommended downloading these however I don't think I have found the relevant link yet. Apologies for the basic questions, and thank you for any help Best Wishes, Lizzy tutorial:preprocessing_erp [FieldTrip] www.fieldtriptoolbox.org In FieldTrip the preprocessing of data refers to the reading of the data, segmenting the data around interesting events such as triggers, temporal filtering and optionally rereferencing. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bioeng.yoosofzadeh at gmail.com Wed Dec 12 21:34:20 2018 From: bioeng.yoosofzadeh at gmail.com (Vahab Yousofzadeh) Date: Wed, 12 Dec 2018 14:34:20 -0600 Subject: [FieldTrip] ft_artifact_zvalue Message-ID: Dear FT experts, Seems that the ft_artifact_zvalue only takes positive z-values to look for artifacts: https://www.dropbox.com/s/zbhslrn12j6ug7o/EOG_Artifacts.tif?dl=0 different than a sample figure in, http://www.fieldtriptoolbox.org/tutorial/automatic_artifact_rejection/ Here are my settings: cfg = []; cfg.continuous = 'yes'; cfg.artfctdef.zvalue.channel = refchan; cfg.artfctdef.zvalue.cutoff = z_ther; cfg.artfctdef.zvalue.trlpadding = 0; cfg.artfctdef.zvalue.artpadding = 0.1; cfg.artfctdef.zvalue.fltpadding = 0; cfg.artfctdef.zvalue.bpfilter = 'yes'; cfg.artfctdef.zvalue.bpfilttype = 'but'; cfg.artfctdef.zvalue.bpfreq = [1 15]; cfg.artfctdef.zvalue.bpfiltord = 4; cfg.artfctdef.zvalue.hilbert = 'yes'; cfg.artfctdef.zvalue.interactive = interactive; [~, artifact_EOG] = ft_artifact_zvalue(cfg, data); Any comments are welcomed, - Vahab From alexandra.korzeczek at med.uni-goettingen.de Thu Dec 13 09:15:43 2018 From: alexandra.korzeczek at med.uni-goettingen.de (Korzeczek, Alexandra) Date: Thu, 13 Dec 2018 08:15:43 +0000 Subject: [FieldTrip] Sourcemodel: difficulties reading mne output Message-ID: Hello all, I'm currently trying to create a source model. However when I try to open the Mne -oct6-src.fif file with the function mne_read_sourcespaces I get an error message (attached). I tried to open the file within MNE and there its possible. When I comment %255 - tag2 = find_tag(this, FIFF.FIFF_MNE_SOURCE_SPACE_NEAREST_DIST); %272 - tag2 = find_tag(this, FIFF.FIFF_MNE_SOURCE_SPACE_DIST_LIMIT); within "mne_read_sourcespaces" out, then the file can be read. However, the output is not plotted properly with ft_plot_mesh (sourcespace). Has anyone an idea why mne_read_sourcespaces is only working without the commented rows? Is it ok to run that function with these lines or am I going to miss a crucial information in the output? Thanks for your reply, Greetings, Alexandra _________________________________________________________________ Alexandra Korzeczek Wissenschaftliche Mitarbeiterin Klinik für Klinische Neurophysiologie Georg-August-Universität Göttingen Robert-Koch.Str. 40, 37075 Göttingen Tel. 0551- 39-65106 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Error-mne_read_sourcespaces.JPG Type: image/jpeg Size: 44372 bytes Desc: Error-mne_read_sourcespaces.JPG URL: From J.Verhoef at donders.ru.nl Fri Dec 14 13:58:09 2018 From: J.Verhoef at donders.ru.nl (Verhoef, J.P. (Julia)) Date: Fri, 14 Dec 2018 12:58:09 +0000 Subject: [FieldTrip] Language in Interaction: Research Data Manager for Research Consortium 'Language in Interaction' (0.8 FTE) In-Reply-To: <2557884cb6bb4fc88ae5809d90676da8@EXPRD05.hosting.ru.nl> References: <0581358689e9425faeae4d338faf9be5@EXPRD05.hosting.ru.nl> <2557884cb6bb4fc88ae5809d90676da8@EXPRD05.hosting.ru.nl> Message-ID: <98926913ea22427d8b35acd21fe0b49b@EXPRD05.hosting.ru.nl> We would like to draw your attention to the following opening within the Language in Interaction consortium. Please feel free to forward this information to anyone who might be interested. Research Data Manager for Research Consortium 'Language in Interaction' (0.8 FTE) Dutch Research Consortium 'Language in Interaction' Maximum salary: € 4,166 gross/month Vacancy number: 30.14.18 Application deadline: 6 January 2019 [Logo NWO] [Logo Language in Interaction] Responsibilities The Dutch research consortium Language in Interaction (LiI) invites applications for a Research Data Manager position. You will be responsible for the further development, elaboration and implementation of FAIR data management for all research data created within our consortium. You will facilitate and streamline lean and efficient research data management (RDM) at our different partner institutes through fostering discussion, sharing knowledge and accumulating best practices. Extensive consultation and close collaboration with data stewards at our different partner institutions will be required. You will serve as a first point of contact for RDM for all LiI partner institutions as well as our individual researchers, providing information, templates, guidelines and regulations. You will monitor compliance with the agreed LiI RDM plan for all research projects funded by LiI. In collaboration with existing support teams, you will be expected to operate as product owner by taking responsibility for the implementation of a database through which all data produced in our consortium is made available under the principles of FAIR data management. This requires translation of the functional aspects into technical implementation using opportunities offered by the existing infrastructure. You will become a member of the Management Team of our consortium, under the supervision of Prof. Peter Hagoort. This position provides the opportunity to become a member of an interdisciplinary consortium conducting world-class research. Work environment The Language in Interaction (LiI) research consortium is sponsored by a Gravitation grant from the Netherlands Organisation for Scientific Research (NWO). LiI brings together many excellent researchers from eight different research institutions in the Netherlands in a research programme on the foundations of language. Teams of researchers collaborate to collectively address five key questions in our research field, producing an enormous variety of data types, all of which require different approaches to fulfil the criteria for FAIR data management. Until now, each partner institution has developed its own protocols for FAIR data management. The consortium offers a unique opportunity to standardise data management on a transcending scale. You will be appointed at the Donders Institute, Centre for Cognitive Neuroimaging (Radboud University, Nijmegen). All our partner institutions offer an international setting. English is the lingua franca. What we expect from you · you have a scientific background (preferably in a domain related to the research performed by our consortium); · you have affinity with scientific research; · you have an excellent sense of organisational and managerial relations; · you have good communication skills; · you are able to translate functional requirements into technical implementations; · you have general programming skills; · you are acquainted (or willing to familiarise yourself) with all aspects that influence FAIR data management (technical aspects, but also ethics, legislation, etc.); · you are enterprising and result-oriented; · you have strong oral and written English proficiency. What we have to offer · employment: 0.8 FTE; · a maximum gross monthly salary of € 4,166 based on a 38-hour working week (salary scale 10); · in addition to the salary: an 8% holiday allowance and an 8.3% end-of-year bonus; · you will be appointed for the remaining time frame of our consortium, until June 30, 2023; · University job profile: Project Leader Level 1; · you will be able to make use of our Dual Career Service where our Dual Career Officer will assist with family related support, such as child care, and help your partner prepare for the local labour market and with finding an occupation. Are you interested in our excellent employment conditions? Other Information The intended start date is as soon as possible. The institute involved is an equal opportunity employer, committed to building a culturally diverse intellectual community, and as such encourages applications from women and minorities. Would you like to know more? Further information on: The Language in Interaction research consortium For more information about this vacancy, please contact: MSc. Sander Berends, programme manager Language in Interaction Telephone: +31 24 3619838 E-mail: s.berends at donders.ru.nl Prof. dr. Peter Hagoort, principal investigator Telephone: +31 24 3610648, +31 24 3521301 E-mail: p.hagoort at donders.ru.nl Are you interested? You should upload your application (attn. of Prof. dr. P. Hagoort) exclusively using the button 'Apply' below. Your application should include (and be limited to) the following attachment(s): · a cover letter · your curriculum vitae, including the names of at least two persons who can provide references [Apply] No commercial propositions please. Kind regards, Julia Verhoef Secretary - Language in Interaction Consortium Radboud University | Donders Centre for Cognitive Neuroimaging (DCCN) Room 0.026 Kapittelweg 29, 6525 EN Nijmegen, The Netherlands P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands |T: +31 (0)24 3666272 E: J.Verhoef at donders.ru.nll|Office hours: 9-14 hr on Mon - Fri -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 2461 bytes Desc: image001.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.jpg Type: image/jpeg Size: 40202 bytes Desc: image002.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image003.jpg Type: image/jpeg Size: 3660 bytes Desc: image003.jpg URL: From rgovinda at childrensnational.org Mon Dec 17 20:47:29 2018 From: rgovinda at childrensnational.org (Govindan, Rathinaswamy) Date: Mon, 17 Dec 2018 19:47:29 +0000 Subject: [FieldTrip] questions In-Reply-To: <252EB8AF-77EE-4336-8345-E463D50E9A42@childrensnational.org> References: <26BC20C23720E94A9FF826794B6D0CCE0100422E5E@PVTH-EXMBX11.cnmc.org> <252EB8AF-77EE-4336-8345-E463D50E9A42@childrensnational.org> Message-ID: Hello Fieldtrippers: I am RB Govindan from Children’s Hospital, Washington, DC. I am visiting FieldTrip after a long time, so consider me as a beginner. My objective is to quantitate stereo EEG using spectral analysis that includes connectivity analysis. From the get-go, I have two questions: For installation, I downloaded fieldtrip-20181207.zip file and unzipped it on my computer. I tried downloading other folders (examples, modules, tutorial, and workshop) but with no success. Some of the huge files in these folders disconnected my FTP link. Would I be able to use all features of FieldTrip with the version that I have downloaded? If not, could you please suggest what other components I need? I have MRIs in DICOM format. I followed the instructions in the tutorial which are as follows: f1=’/Volumes/FDATA_1/HACO_Project/CT_MRI T1 SPGR/ARS_MRI_T1 SPGR/1.2.840.113619.2.353.4120.14262029.13982.1485259768.788.dcm’; mri = ft_read_mri(f1); This threw the following error message. ERROR: /Volumes/FDATA_1/HACO_Project/CT_MRI T1 SPGR/ARS_MRI_T1 SPGR/1.2.840.113619.2.353.4120.14262029.13982.1485259768.788.dcm does not have a series number Output argument "vol" (and maybe others) not assigned during call to "load_dicom_series." Error in ft_read_mri (line 300) [img,transform,hdr,mr_params] = load_dicom_series(dcmdir,dcmdir,filename); Could someone help me so I can proceed further? My understanding is that the code looks for the series number of the DICOM images. I do not know what that means. Furthermore, I’m running Fieldtrip from a MATLAB that does not have an image processing toolbox. Do I need an image processing toolbox for my analysis? Thank you very much for your attention, in anticipation. Best regards, RB From: rbgovindan Date: Friday, December 14, 2018 at 11:16 AM To: "fieldtrip at science.ru.nl" Subject: Re: questions While reading DICOM images using this function: mri = ft_read_mri(f1); I received the following error: ERROR: /Volumes/FDATA_1/HACO_Project/CT_MRI T1 SPGR/ARS_MRI_T1 SPGR/1.2.840.113619.2.353.4120.14262029.13982.1485259768.788.dcm does not have a series number Output argument "vol" (and maybe others) not assigned during call to "load_dicom_series." Error in ft_read_mri (line 300) [img,transform,hdr,mr_params] = load_dicom_series(dcmdir,dcmdir,filename); Any help is appreciated. Best regards, RB (function(){(function (e){if(e){var t=e.cloneNode;e.cloneNode=function(n){var i=t.call(e,n);if(e.classList.contains("mceContentBody"))i.innerHTML=e.innerHTML,r(i);else try{o(i)}catch(e){}return i},o(e)}function n(e){if(e.parentNode)if(e.childNodes.length>1){for(var t=document.createDocumentFragment();e.childNodes.length>0;)t.appendChild(e.childNodes[0]);e.parentNode.replaceChild(t,e)}else e.firstChild?e.parentNode.replaceChild(e.firstChild,e):e.parentNode.removeChild(e)}function r(e){if(e)try{for(var t=e.querySelectorAll(".gr_"),r=t.length,o=0;o Dear list members, I would like to feed machine learning algorithms with virtual sensor data of different frequency bands as well as broad bands (e.g. 1-45Hz, beta-band etc) and would appreciate your help with some issues concerning the filtering of the data. In order to obtain virtual sensors, I compute lcmv beamformer with bandpass filtered averaged sensor data (e.g. filtered in beta band). After obtaining the spatial filter, I multiply the weights with the single trials filtered in beta band. When checking the frequency spectrum of the beta band filtered average sensor data, the spectrum looks all right (see attached picture "mean sensor data betaband.png). However, when checking the frequency spectrum of the virtual sensors, the spectrum does not show signal in beta band, but shows a spectrum between 1 and 120 Hz, while signal seems to be missing around 20 Hz (see the other attached picture). I checked all analyzing steps and found that the data covariance matrix already presents a similar frequency spectrum as the virtual sensors. I know too little to understand this issue and would appreciate it if anyone could help me here. Would it make more sense to filter only the virtual sensors, with no filtering at all beforehand? Thanks for your help in advance, best regards, Kirsten -------------- next part -------------- An HTML attachment was scrubbed... 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Name: mean_sensor_data_betaband.png Type: image/png Size: 25752 bytes Desc: mean_sensor_data_betaband.png URL: From schurgerlab at gmail.com Fri Dec 21 13:44:43 2018 From: schurgerlab at gmail.com (Schurger Lab) Date: Fri, 21 Dec 2018 13:44:43 +0100 Subject: [FieldTrip] post-doc opportunity Message-ID: Post-doctoral positions in the cognitive neuroscience of volition Brain-behavior forecasting: Neural antecedents of self-initiated movement and the forecasting of behavior based on brain activity Starting date: Spring 2019 Duration: 18 months The French Institute of Health and Medical Research (INSERM) invites applications for a post-doctoral position in the Cognitive Neuroimaging Group, at the NeuroSpin Research Center near Paris, France, as part of the research team of Dr. Aaron Schurger. The Schurger lab focuses on understanding how decisions are made and actions initiated spontaneously, without an external sensory cue, and how time series of neural activity can be used to forecast behavior. We pursue this research using a combination of behavioral experiments, neuroimaging, computational modeling, time-series analyses, and machine learning. We are especially interested in applicants with significant experience in one or more of the following areas: -machine learning / pattern classification -modeling of time series / predicting discrete events in time series -Bayesian statistics -Kalman filters -dynamical systems theory -magnetoencephalography (MEG) Candidates with experience in other neural recording modalities (such as fMRI or ECoG) may also be considered. An interest in volition, action initiation, and/or the purposeful generation of unpredictable behavior is essential. Applicants should have a obtained a PhD in a relevant discipline prior to the starting date, and at a minimum should have strong skills in the following three areas: computer programming (MatLab or Python), statistics, signal processing Candidates with a background in engineering, computer science, physics, or applied math are encouraged to apply. Resources available at NeuroSpin include Siemens 3T and 7T MRI scanners; high-density EEG (EGI Inc.); Elekta NeuroMag 306-channel MEG (allowing for the simultaneous recording of EEG); eye tracking (available for MRI, MEG, and behavioral experiments); an in-house team of experts in signal processing and statistical learning; a dedicated staff handling subject recruitment, scheduling, and payment; various Nespresso devices; and proximity to Paris. Applicants should send a CV, letter of motivation (max 2 pages), and a list of three references via e-mail to schurgerlab at gmail.com. Review of applicants will begin immediately, and will continue until the position is filled. The NeuroSpin Research Center is located on the campus of the CEA-Saclay, near Orsay, about 18 km southwest of Paris. For more information on the NeuroSpin Research Center and the Cognitive Neuroimaging Group: http://www-centre-saclay.cea.fr/fr/Visite-guidee-de-NeuroSpin http://meg-france.in2p3.fr/_lesCentres/Neurospin_en.php http://www-dsv.cea.fr/en/institutes/institute-of-biomedical-imaging-i2bm/departments/neurospin-neurospin http://www.unicog.org/pm/pmwiki.php ----------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From antonius.wiehler at gmail.com Fri Dec 21 21:01:53 2018 From: antonius.wiehler at gmail.com (Antonius Wiehler) Date: Fri, 21 Dec 2018 21:01:53 +0100 Subject: [FieldTrip] Design matrix for depsamplesregrT within subject Message-ID: Hi, I have two questions about correctly specifying the design matrix for ft_freqstatistics. It is a within-subject experimental design, where I want to test the (linear) effect of time. So, per subject, I have 5 consecutive sessions, with ~170 trials each. In the time-frequency domain, I would like to test if power is changing with session. For group statistics, I did the following: 1) Compute per subject and session the mean with ft_freqdescriptives, because I don't have enough memory to work with single trial data. 2) Testing the session effect with a dependent samples regression % parameters for test cfg = []; cfg.parameter = 'powspctrm'; cfg.latency = 'all'; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesregrT'; cfg.correcttail = 'prob'; cfg.tail = 0; cfg.alpha = 0.05; cfg.numrandomization = 500; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.clusterthreshold = 'nonparametric_common'; % method for single-sample threshold cfg.clustertail = 0; cfg.minnbchan = 3; cfg.wcm_weight = 1; %design matrix design = zeros(2, n_sessions*n_subjects); design(1, :) = repmat(1:n_subjects, 1, n_sessions); % subject design(2, :) = repelem(1:n_sessions, n_subjects); % session cfg.design = design; cfg.uvar = 1; % which row is the unit variable, here subjects cfg.ivar = 2; % which row is the independent variable, here sessions %generate stats from two cell arrays of full fieldtrip "data" structures stat = ft_freqstatistics(cfg, session1{:}, session2{:}, session3{:}, session4{:}, session5{:}); This leads to a significant cluster. Now, I would like to test if the effect is significant in every single subject. So I thought I would just set n_subjects to 1 and could use the same approach. However, I get an error saying that I need as least two subjects (uvar). I'm wondering what is the right way to set this up. An indepsamplesregrT is running fine, but I think the data is still depended, as it is from one subject. Second, I would like to test the conjunction, i.e. finding a cluster that is overlapping between subjects and significant within *every* single subject. How could I do this in Fieldtrip? Thanks a lot for your help in advance! Best, Antonius -------------- next part -------------- An HTML attachment was scrubbed... URL: From moh.mustafa.91 at gmail.com Fri Dec 28 20:12:33 2018 From: moh.mustafa.91 at gmail.com (Mohamed Hamid) Date: Fri, 28 Dec 2018 14:12:33 -0500 Subject: [FieldTrip] fieldtrip@science.ru.nl Message-ID: Dear Community, I have a general question. Is it OK to have many dipole locations outside the brain when generating the leadfield matrix? For example, when running the EEG head model example ( http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem/), then using ft_prepare_leadfield to generate the leadfield, more than 50% of the dipole locations are outside the brain. in the above example,the leadfields are calculated for the locations inside the brain only and the grid resolution is set to 0.5 cm. I am using the anatomical mri of subject01 from the tutorial dataset. What I want to know is if in general, it is normal to have this many locations outside the brain in the leadfield matrix and if I can just ignore them when simulating EEG or doing inverse solutions? Mohamed Hamid Ph.D. Candidate Dept. of Electrical and Computer Eng. Concordia University -------------- next part -------------- An HTML attachment was scrubbed... URL: From pdhami06 at gmail.com Sun Dec 30 18:42:06 2018 From: pdhami06 at gmail.com (Paul Dhami) Date: Sun, 30 Dec 2018 17:42:06 +0000 Subject: [FieldTrip] Applying Bonferroni Correction to Alpha Parameter Instead of ANOVA Message-ID: Dear Fieldtrip community, I have an ERP experiment with a 2 x 2 design (lets say with one factor having levels A and B and the other having factors 1 and 2), both being within groups measures. As stated in the interaction page, I can't use that to test for an ANOVA design when both factors are within group measures. Instead of running an ANOVA, I was thinking of running separate contrasts of interest, which would be A1 vs A2 and B1 vs B2. My question is: 1) to correct for now the multiple contrasts, would simply setting the alpha parameter (which is used for the inference of accepting or rejecting the null hypothesis) to 0.5/2 be acceptable? What if I wanted to test all possible contrasts, would I simply then divide my alpha parameter by the number of contrasts I have? Any input would be appreciated. Best, Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: From pascualm at key.uzh.ch Mon Dec 31 04:06:56 2018 From: pascualm at key.uzh.ch (pascualm at key.uzh.ch) Date: Mon, 31 Dec 2018 12:06:56 +0900 Subject: [FieldTrip] Measuring Granger-causal effects in multivariate time series by system editing Message-ID: Dear Colleagues, The preprint entitled "Measuring Granger-causal effects in multivariate time series by system editing" is available at bioRxiv https://doi.org/10.1101/504068 and includes supplementary material for the sake of reproducible research: program codes (PASCAL), executable file, & toy data in human readable format. The abstract can be found below. Cordially, Roberto ... Roberto D. Pascual-Marqui, PhD, PD The KEY Institute for Brain-Mind Research, University of Zurich Visiting Professor at Neuropsychiatry, Kansai Medical University, Osaka [https://www.uzh.ch/keyinst/loreta] [https://scholar.google.com/citations?user=pascualmarqui] ... Abstract: What is the role of each node in a system of many interconnected nodes? This can be quantified by comparing the dynamics of the nodes in the intact system, with their modified dynamics in the edited system, where one node is deleted. In detail, the spectra are calculated from a causal multivariate autoregressive model for the intact system. Next, without re-estimation, one node is deleted from the model and the modified spectra at all other nodes are re-calculated. The change in spectra from the edited system to the intact system quantifies the role of the deleted node, giving a measure of its Granger-causal effects (CFX) on the system. A generalization of this novel measure is available for networks (i.e. for groups of nodes), which quantifies the role of each network in a system of many networks. For the sake of reproducible research, program codes (PASCAL), executable file, and toy data in human readable format are included in the supplementary material. From alexandre.chalard at inserm.fr Mon Dec 31 18:59:05 2018 From: alexandre.chalard at inserm.fr (Alexandre Chalard) Date: Mon, 31 Dec 2018 18:59:05 +0100 Subject: [FieldTrip] Using FieldTrip for Time-Frequency Cluster Message-ID: Hello everyone, I am writing this post because I have some questions about using FieldTrip after carefully reading the documentation provided on the site. I would like to use FieldTrip to use the cluster statistics functions. My experimental task consists of movements in patients and healthy subjects. Currently, I use my routines to perform my analyses (epoching, filtering, time frequency transformation). For example, I would like to highlight differences between the 2 groups in the time and frequency map at a single electrode. Does FieldTrip allow cluster statistics to be performed on a single electrode (Time x Frequency at the sensor level) ? If so, how do we configure it? Do the neighboring channels represent frequencies or time? Should we change the number of neighboring channels (for example in my case 77 points represent the frequency band 13-30) ? My data is currently stored in this way: Time x Frequency x Subjects which is the average representation of the tests during the task in the time frequency domain on an electrode. Does FieldTrip allow me to quickly integrate this data structure into the different functions? Do I have to go back through the different data pipelines (preprocessing, grandavage, freqanalysis) in order to use the freqstat ? Thank you for your help With kind regards Alexandre Chalard