[FieldTrip] fieldtrip Digest, Vol 31, Issue 27

[Stolk, A.]

Hi Steve, With respect to the cube vs. brain-shaped grid; this seems to be plotting-related? template_grid.inside in the snippet of code below selects only the grid points that have been determined as inside the brain, but with a negative inwardshift, hence it's also outside. ft_plot_mesh ( template_grid. pos ( template_grid. inside ,: ) ) ; % taken from the wiki Hopefully someone else has up-to-date knowledge to answer your question pertaining to the units (mm vs. cm) of the volume conductor and the source model. Best regards, Arjen ----- Oorspronkelijk bericht -----
> Van: "Stephen Politzer-Ahles" <politzerahless at gmail.com>
> Aan: fieldtrip at science.ru.nl
> Verzonden: Maandag 24 juni 2013 17:19:59
> Onderwerp: Re: [FieldTrip] fieldtrip Digest, Vol 31, Issue 27
> Hi everyone,
> I recently tried
> http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space
> and noticed some inconsistencies between the example code and the
> results; I updated the code on the wiki but I wanted to send a message
> to the list to double-check whether my changes are ok. Firstly, I had
> to add a call to ft_convert_units, because otherwise the vol was
> expressed in mm and the grid in cm, causing the grid to be much
> smaller than the volume conductor (see http://i.imgur.com/gzct9Dm.png
> ). Is this change ok?
> The result I get is still not quite consistent with the examples shown
> on that page, though; in my result, the grid is a cube (
> http://i.imgur.com/NSgCFpg.png ), whereas in the example the grid is
> brain-shaped. I used the same Fieldtrip brain template and the same
> code from the example (except for the change above), so I'm not sure
> if the difference is due to different plot settings, a change in the
> Fieldtrip code since this example was made, or a change in the sample
> brain included in Fieldtrip since the example was made.
> Best,
> Steve
> On Thu, Jun 13, 2013 at 5:05 AM, < fieldtrip-request at science.ru.nl >
> wrote:
> >
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> > than "Re: Contents of fieldtrip digest..."
> >
> >
> > Today's Topics:
> >
> > 1. Re: Source statistics on spatio-temporal source
> > reconstruction data (MNE) (Nicolai Mersebak)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Thu, 13 Jun 2013 12:04:34 +0200
> > From: Nicolai Mersebak < nicolai at mersebak.dk >
> > To: FieldTrip discussion list < fieldtrip at science.ru.nl >
> > Subject: Re: [FieldTrip] Source statistics on spatio-temporal source
> > reconstruction data (MNE)
> > Message-ID: < 6F3697BB-194F-422F-A1BF-EBBB132F805B at mersebak.dk >
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Thanks to all of you for your comments and ideas - they are very
> > helpful!
> >
> > I ( off course :) ) have some follow up questions.
> >
> > I have created an ERP structure for my MNE source, so the only think
> > which I need and that is not straight forward is the neighbour
> > structure.
> >
> > I am using the standard bem template
> > (fieldtrip-20130124/template/headmodel/standard_bem.mat) as a head
> > model and use the following code to get a grid for all subjects as I
> > don't have any subject specific information regarding the anatomy.
> >
> > cfg = [];
> > cfg.grid.xgrid = -100:10:100;
> > cfg.grid.ygrid = -100:10:100;
> > cfg.grid.zgrid = -100:10:100;
> > cfg.grid.tight = 'yes';
> > cfg.grid.unit = hdm.unit; % unit: mm
> > cfg.vol = hdm;
> > grid = ft_prepare_sourcemodel(cfg);
> >
> >
> > @Jan-Mathijs and Stephan: I guess making a subject specific grid
> > based on a warped template requires anatomic information for each
> > subject, e.g. a MRI image like this tutorial shows:
> > http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space?s%5B
> >
> > The final grid output in the tutorial - does it have this 3D grid
> > which can be used as a neighbour structure ?
> >
> > I am not sure how to go from my cortical sheet [vertices x
> > coordinates(x,y,z)] to a 3D grid, which I can use as a neighbour
> > structure ?
> >
> > A second thing I would like to know is, if any of you have tried to
> > use an atlas (e.g ALL template atlas) where the regions now are
> > channels in the permutation test? Going from source points to atlas
> > regions can be done through ft_sourcestatistics, but I am still
> > interested in keeping the temporal dimension. The reason to use
> > atlas regions instead of source points is to decrease the
> > computation time.
> >
> > Best,
> >
> > Nicolai
> >
> >
> On Thu, Jun 13, 2013 at 5:05 AM, < fieldtrip-request at science.ru.nl >
> wrote:
> > Send fieldtrip mailing list submissions to
> > fieldtrip at science.ru.nl
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > or, via email, send a message with subject or body 'help' to
> > fieldtrip-request at science.ru.nl
> > You can reach the person managing the list at
> > fieldtrip-owner at science.ru.nl
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of fieldtrip digest..."
> > Today's Topics:
> > 1. Re: Source statistics on spatio-temporal source
> > reconstruction data (MNE) (Nicolai Mersebak)
> > ----------------------------------------------------------------------
> > Message: 1
> > Date: Thu, 13 Jun 2013 12:04:34 +0200
> > From: Nicolai Mersebak < nicolai at mersebak.dk >
> > To: FieldTrip discussion list < fieldtrip at science.ru.nl >
> > Subject: Re: [FieldTrip] Source statistics on spatio-temporal source
> > reconstruction data (MNE)
> > Message-ID: < 6F3697BB-194F-422F-A1BF-EBBB132F805B at mersebak.dk >
> > Content-Type: text/plain; charset="iso-8859-1"
> > Thanks to all of you for your comments and ideas - they are very
> > helpful!
> > I ( off course :) ) have some follow up questions.
> > I have created an ERP structure for my MNE source, so the only think
> > which I need and that is not straight forward is the neighbour
> > structure.
> > I am using the standard bem template
> > (fieldtrip-20130124/template/headmodel/standard_bem.mat) as a head
> > model and use the following code to get a grid for all subjects as I
> > don't have any subject specific information regarding the anatomy.
> > cfg = [];
> > cfg.grid.xgrid = -100:10:100;
> > cfg.grid.ygrid = -100:10:100;
> > cfg.grid.zgrid = -100:10:100;
> > cfg.grid.tight = 'yes';
> > cfg.grid.unit = hdm.unit; % unit: mm
> > cfg.vol = hdm;
> > grid = ft_prepare_sourcemodel(cfg);
> > @Jan-Mathijs and Stephan: I guess making a subject specific grid
> > based
> > on a warped template requires anatomic information for each subject,
> > e.g. a MRI image like this tutorial shows:
> > http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space?s%5B
> > The final grid output in the tutorial - does it have this 3D grid
> > which can be used as a neighbour structure ?
> > I am not sure how to go from my cortical sheet [vertices x
> > coordinates(x,y,z)] to a 3D grid, which I can use as a neighbour
> > structure ?
> > A second thing I would like to know is, if any of you have tried to
> > use an atlas (e.g ALL template atlas) where the regions now are
> > channels in the permutation test? Going from source points to atlas
> > regions can be done through ft_sourcestatistics, but I am still
> > interested in keeping the temporal dimension. The reason to use
> > atlas
> > regions instead of source points is to decrease the computation
> > time.
> > Best,
> > Nicolai
> > Den 12/06/2013 kl. 18.58 skrev " smoratti at psi.ucm.es " <
> > smoratti at psi.ucm.es >:
> > >
> > > I think Jan.Mathijs alternative suggestion is quite attractive.
> > > With
> > > the neighbors on a cortical sheet I also had the problems that
> > > sometimes the vertices do not have the same distance and then
> > > clustering may be biased to smaller or bigger clusters as the
> > > number
> > > of neighbors does not guarantee same cluster sizes. With the
> > > interpolation onto a 3D grid, you won't have that problem.
> > >
> > > best,
> > >
> > > Stephan
> > >
> > >
> > > ________________________________________________________
> > > Stephan Moratti, PhD
> > >
> > > see also: http://web.me.com/smoratti/
> > >
> > > Universidad Complutense de Madrid
> > > Facultad de Psicolog?a
> > > Departamento de Psicolog?a B?sica I
> > > Campus de Somosaguas
> > > 28223 Pozuelo de Alarc?n (Madrid)
> > > Spain
> > >
> > > and
> > >
> > > Center for Biomedical Technology
> > > Laboratory for Cognitive and Computational Neuroscience
> > > Parque Cient?fico y Tecnol?gico de la Universidad Politecnica de
> > > Madrid
> > > Campus Montegancedo
> > > 28223 Pozuelo de Alarc?n (Madrid)
> > > Spain
> > >
> > >
> > > email: smoratti at psi.ucm.es
> > > Tel.: +34 679219982
> > >
> > > El 12/06/2013, a las 18:00, jan-mathijs schoffelen escribi?:
> > >
> > >> An alternative would be to interpolate the cortical sheet to a 3D
> > >> grid (where the grid is defined for each subject based on a
> > >> warped
> > >> template grid defined in a standard space), and then do
> > >> clustering
> > >> using a regular 3D spatial neighbourhood structure. The rationale
> > >> being that two vertices on the sheet may appear as disconnected
> > >> (e.g. being on two sides of a sulcus) whereas, given the poor
> > >> spatial resolution, they belong to the same spatial blob.
> > >>
> > >> Best,
> > >> Jan-Mathijs
> > >>
> > >> On Jun 12, 2013, at 5:44 PM, smoratti at psi.ucm.es wrote:
> > >>
> > >>> Dear Nicolai,
> > >>>
> > >>> Indeed I have used ft_timelockstatistics for minimum norm source
> > >>> data. The trick is to put the source level data into a ERF
> > >>> structure. Determining the neighbors of a source surface with
> > >>> vertices is not trivial. However I used tess_vertconn.m from the
> > >>> BrainStorm toolbox to get the connectivity matrix that tells you
> > >>> who is a neighbor. This you can feed into timelockstats.
> > >>>
> > >>> Hope that helps,
> > >>>
> > >>> Stephan
> > >>>
> > >>> ________________________________________________________
> > >>> Stephan Moratti, PhD
> > >>>
> > >>> see also: http://web.me.com/smoratti/
> > >>>
> > >>> Universidad Complutense de Madrid
> > >>> Facultad de Psicolog?a
> > >>> Departamento de Psicolog?a B?sica I
> > >>> Campus de Somosaguas
> > >>> 28223 Pozuelo de Alarc?n (Madrid)
> > >>> Spain
> > >>>
> > >>> and
> > >>>
> > >>> Center for Biomedical Technology
> > >>> Laboratory for Cognitive and Computational Neuroscience
> > >>> Parque Cient?fico y Tecnol?gico de la Universidad Politecnica de
> > >>> Madrid
> > >>> Campus Montegancedo
> > >>> 28223 Pozuelo de Alarc?n (Madrid)
> > >>> Spain
> > >>>
> > >>>
> > >>> email: smoratti at psi.ucm.es
> > >>> Tel.: +34 679219982
> > >>>
> > >>> El 12/06/2013, a las 15:44, Nicolai Mersebak escribi?:
> > >>>
> > >>>> Dear all,
> > >>>>
> > >>>> I have a question concerning the usage of ft_sourcegrandaverage
> > >>>> and ft_sourcestatistics.
> > >>>>
> > >>>> After using ft_sourceanalysis (method: MNE), I get
> > >>>> spatio-temporal source reconstructed data in source.avg.pow
> > >>>> (4050
> > >>>> x 897): 4050 sources and 897 time points.
> > >>>>
> > >>>> Now I would like to use the cluster-based permutation test on
> > >>>> my
> > >>>> source reconstructed data. However it seems like
> > >>>> ft_sourcegrandaverage and ft_sourcestatistics don't support
> > >>>> source level time courses. E.g when I am using
> > >>>> ft_sourcegrandaverage I am getting the following error:
> > >>>>
> > >>>> Error in ft_sourcegrandaverage (line 158)
> > >>>> dat(:,i) = tmp(:);
> > >>>>
> > >>>> Looking into the code:
> > >>>>
> > >>>> for i=1:Nsubject
> > >>>> tmp = getsubfield(varargin{i},
> > >>>> parameterselection(cfg.parameter,
> > >>>> varargin{i}));
> > >>>> dat(:,i) = tmp(:);
> > >>>> tmp = getsubfield(varargin{i}, 'inside');
> > >>>> inside(tmp,i) = 1;
> > >>>> end
> > >>>>
> > >>>> I see that "tmp" are getting the structure [N_sources x
> > >>>> timepoints] from source.avg.pow for one subject, where "dat"
> > >>>> requires the structure [N_sources x 1].
> > >>>>
> > >>>> I seached the mailing list for similar issues and found this
> > >>>> thread:
> > >>>>
> > >>>> http://mailman.science.ru.nl/pipermail/fieldtrip/2010-September/003122.html
> > >>>>
> > >>>> Since I am interested in using the temporal dimension in my
> > >>>> statistics, I would like to know if it is still not possible to
> > >>>> use spatio-temporal source reconstructed data in
> > >>>> ft_sourcestatistics and ft_sourcegrandaverage ?
> > >>>>
> > >>>> Or if any have succeeded in using the cluster-based permutation
> > >>>> test on source level also including the temporal dimension ?
> > >>>>
> > >>>> Alternative I was thinking that I might could use
> > >>>> ft_timelockstatistics, where I substituted the channels with
> > >>>> sources, e.g instead of having 64 channels, I would now have
> > >>>> 4050
> > >>>> "channels".
> > >>>> If so I need to calculate a label structure and an appropriate
> > >>>> neighbor structure, which I guess is possible as I have all the
> > >>>> 3D coordinates for each source, e.g in leadfield.pos ?
> > >>>> I know this is a work around solution, but have anyone tried or
> > >>>> have any experience using such an approach ?
> > >>>>
> > >>>> Best,
> > >>>>
> > >>>> Nicolai
> > >>>>
> > >>>> _______________________________________________
> > >>>> fieldtrip mailing list
> > >>>> fieldtrip at donders.ru.nl
> > >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > >>>
> > >>> _______________________________________________
> > >>> fieldtrip mailing list
> > >>> fieldtrip at donders.ru.nl
> > >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > >>
> > >> Jan-Mathijs Schoffelen, MD PhD
> > >>
> > >> Donders Institute for Brain, Cognition and Behaviour,
> > >> Centre for Cognitive Neuroimaging,
> > >> Radboud University Nijmegen, The Netherlands
> > >>
> > >> Max Planck Institute for Psycholinguistics,
> > >> Nijmegen, The Netherlands
> > >>
> > >> J.Schoffelen at donders.ru.nl
> > >> Telephone: +31-24-3614793
> > >>
> > >> http://www.hettaligebrein.nl
> > >>
> > >> _______________________________________________
> > >> fieldtrip mailing list
> > >> fieldtrip at donders.ru.nl
> > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > >
> > > _______________________________________________
> > > fieldtrip mailing list
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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> > End of fieldtrip Digest, Vol 31, Issue 27
> > *****************************************
> --
> Stephen Politzer-Ahles
> University of Kansas
> Linguistics Department
> http://people.ku.edu/~sjpa/
> _______________________________________________
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