[FieldTrip] The compartment nesting cannot be determined

[Cristiano Micheli]

Dear Saeed,

it might depend on the boundaries. If they are not nested (one is inside
another, which is inside another, etc... like chinese boxes) then you have
a fundamental problem. This is a constraint of the BEM algorithm in order
for it to work properly.

Have you tried plotting the triangulated meshes? Do they look nested?

I hope this helps for now,
Cris


On Thu, Jan 21, 2016 at 7:22 PM, saeed zahran <saeedzahran at hotmail.com>
wrote:

> Dear Fieldtrip Community,
>
> Dear Fieldtrip community,
>
>
> What does the error of the surface nesting means;
>
> I define the volume conductor as:
>
> vol = [];
> vol.bnd(1).pnt=skinpnt
> vol.bnd(1).tri=skinf
>
> vol.bnd(2).pnt=uteruspnt
> vol.bnd(2).tri=uterusf
>
> vol.bnd(3).pnt=uterinecontentpnt
> vol.bnd(3).tri=uterinecontentf
>
> vol.cond = c;
>
>
> But it result with the below error:
>
> Error using surface_nesting (line 26)
> the compartment nesting cannot be determined
>
> Error in ft_headmodel_bemcp (line 66)
> order = surface_nesting(vol.bnd, 'insidefirst');
>
> Error in ft_prepare_headmodel (line 253)
> vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity);
>
> Error in openmeeg_eeg_leadfield_example (line 100)
> vol = ft_prepare_headmodel(cfg, vol);
> Thank you very much in advance for your help!
>
> Best regards
> Saeed Zahran
>
>
>
> > From: fieldtrip-request at science.ru.nl
> > Subject: fieldtrip Digest, Vol 62, Issue 20
> > To: fieldtrip at science.ru.nl
> > Date: Thu, 21 Jan 2016 19:14:24 +0100
> >
> > Send fieldtrip mailing list submissions to
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> >
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> >
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> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of fieldtrip digest..."
> >
> >
> > Today's Topics:
> >
> > 1. Re: fieldtrip Digest, Vol 62, Issue 18 (Cristiano Micheli)
> > 2. difficulty in loading BCI-IV-2a dataset into fieldtrip for
> > preprocessing (Muhammad Naveed Iqbal Qureshi)
> > 3. Re: fieldtrip Digest, Vol 62, Issue 19 (saeed zahran)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Thu, 21 Jan 2016 12:06:13 +0100
> > From: Cristiano Micheli <michelic72 at gmail.com>
> > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18
> > Message-ID:
> > <CADW7XCC0y_YAKLq48QEPPOo+MF0S0neT9ZjakmgbuhBHUVbD1g at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi Saeed,
> > if the content of your triangulation connectivity matrices *skinf,
> > uterusf, **uterinecontentf* is not made of integers you probably get the
> > error you mentioned. Could this be the case?
> > Out of curiosity, are you doing fetal recordings?
> >
> > Cris
> >
> >
> > On Wed, Jan 20, 2016 at 6:37 PM, saeed zahran <saeedzahran at hotmail.com>
> > wrote:
> >
> > > Dear Fieldtrip community,
> > >
> > > I define the volume conductor as:
> > >
> > > vol = [];
> > > vol.bnd(1).pnt=skinpnt
> > > vol.bnd(1).tri=skinf
> > >
> > > vol.bnd(2).pnt=uteruspnt
> > > vol.bnd(2).tri=uterusf
> > >
> > > vol.bnd(3).pnt=uterinecontentpnt
> > > vol.bnd(3).tri=uterinecontentf
> > >
> > > vol.cond = c;
> > >
> > >
> > > But it result with the below error:
> > >
> > > Subscript indices must either be real positive integers or logicals.
> > >
> > > Error in triangle4pt (line 57)
> > > sph_pnt = pnt([tri(jj,:) lv],:);
> > >
> > > Error in ft_headmodel_bemcp (line 101)
> > > vol = triangle4pt(vol);
> > >
> > > Error in ft_prepare_headmodel (line 253)
> > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity);
> > >
> > > Error in openmeeg_eeg_leadfield_example_me (line 91)
> > > vol = ft_prepare_headmodel(cfg, vol);
> > >
> > >
> > > Thank you very much in advance for your help!
> > >
> > > Best regards
> > > Saeed Zahran
> > >
> > > > From: fieldtrip-request at science.ru.nl
> > > > Subject: fieldtrip Digest, Vol 62, Issue 18
> > > > To: fieldtrip at science.ru.nl
> > > > Date: Wed, 20 Jan 2016 12:00:02 +0100
> > > >
> > > > 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. Standard BEM or FEM models for use with 256-electrode EEG
> > > > data recorded with EGI caps (Laith Hamid)
> > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG
> > > > data recorded with EGI caps (Cristiano Micheli)
> > > > 3. Standard BEM or FEM models for use with 256-electrode EEG
> > > > data recorded with EGI caps (Laith Hamid)
> > > > 4. Source Localisation (aishwarya selvaraj)
> > > > 5. Re: Source Localisation (Hom?lle)
> > > > 6. Re: plotting neighbours (victoria schroeder)
> > > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG
> > > > data recorded with EGI caps (Cristiano Micheli)
> > > > 8. Re: Source Localisation (Munsif Jatoi)
> > > > 9. problems with mri interpolation (Olga Sysoeva)
> > > >
> > > >
> > > >
> ----------------------------------------------------------------------
> > > >
> > > > Message: 1
> > > > Date: Tue, 19 Jan 2016 15:35:00 +0100
> > > > From: Laith Hamid <lah at pedneuro.uni-kiel.de>
> > > > To: fieldtrip at science.ru.nl
> > > > Subject: [FieldTrip] Standard BEM or FEM models for use with
> > > > 256-electrode EEG data recorded with EGI caps
> > > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de>
> > > > Content-Type: text/plain; charset="us-ascii"
> > > >
> > > >
> > > >
> > > > Dear community,
> > > >
> > > > My name is Laith Hamid and I am working in the University Medical
> > > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic
> > > > spikes and seizures. Currently I am analysing an EEG data set that
> was
> > > > recorded using a 256-channel EGI system and I wanted to ask whether
> you
> > > > have a standard BEM or FEM head Subscript indices must either be real
> > > positive integers or logicals.
> > >
> > > Error in triangle4pt (line 57)
> > > sph_pnt = pnt([tri(jj,:) lv],:);
> > >
> > > Error in ft_headmodel_bemcp (line 101)
> > > vol = triangle4pt(vol);
> > >
> > > Error in ft_prepare_headmodel (line 253)
> > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity);
> > >
> > > Error in openmeeg_eeg_leadfield_example_me (line 91)
> > > vol = ft_prepare_headmodel(cfg, vol);
> > > model that extends enough downwards to
> > > > accomodate all 256 electrodes. The current standard BEM model in the
> > > > template folder of Fieldtrip isn't appropriate for source analysis of
> > > > 256-channel EGI data.
> > > >
> > > > Thank you very much in advance for your help!
> > > >
> > > > Best,
> > > >
> > > > Laith
> > > >
> > > >
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> > >
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/f8805c11/attachment-0001.html
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 2
> > > > Date: Tue, 19 Jan 2016 16:16:54 +0100
> > > > From: Cristiano Micheli <michelic72 at gmail.com>
> > > > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with
> > > > 256-electrode EEG data recorded with EGI caps
> > > > Message-ID:
> > > > <CADW7XCCywrPeWqGTqfP6jWoeLuvBo52poPfRyAPy9__VvkbDLg at mail.gmail.com>
> > > > Content-Type: text/plain; charset="utf-8"
> > > >
> > > > Dear Laith,
> > > >
> > > > thanks for your question. You could refer to a factory schematic
> layout
> > > > such as the one in figure 4 of this publication:
> > > >
> http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract
> > > >
> > > > and subsequently use the function ft_prepare_layout to manually
> track the
> > > > points of the custom design on your own (if you dont want to wait for
> > > > somebody from the FT to do the same for you).
> > > >
> > > > cfg = [];
> > > > cfg.image = 'figure4_layout_256_Frontiers.png';
> > > > lay = ft_prepare_layout(cfg);
> > > >
> > > > The following tutorial describes the procedure in more details:
> > > > http://www.fieldtriptoolbox.org/tutorial/layout
> > > >
> > > > Please do not hesitate to get in touch with me for this and other
> > > matters.
> > > >
> > > > All the best
> > > > Cris Micheli
> > > >
> > > >
> > > >
> > > >
> > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid <
> lah at pedneuro.uni-kiel.de>
> > > > wrote:
> > > >
> > > > > Dear community,
> > > > >
> > > > > My name is Laith Hamid and I am working in the University Medical
> > > Complex
> > > > > of Schleswig-Holstein in Kiel on source analysis of epileptic
> spikes
> > > and
> > > > > seizures. Currently I am analysing an EEG data set that was
> recorded
> > > using
> > > > > a 256-channel EGI system and I wanted to ask whether you have a
> > > standard
> > > > > BEM or FEM head model that extends enough downwards to accomodate
> all
> > > 256
> > > > > electrodes. The current standard BEM model in the template folder
> of
> > > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI
> > > data.
> > > > >
> > > > > Thank you very much in advance for your help!
> > > > >
> > > > > Best,
> > > > >
> > > > > Laith
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > fieldtrip mailing list
> > > > > fieldtrip at donders.ru.nl
> > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > > >
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> > >
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/659988fa/attachment-0001.html
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 3
> > > > Date: Tue, 19 Jan 2016 17:41:48 +0100
> > > > From: Laith Hamid <lah at pedneuro.uni-kiel.de>
> > > > To: Fieldtrip <fieldtrip at science.ru.nl>
> > > > Subject: [FieldTrip] Standard BEM or FEM models for use with
> > > > 256-electrode EEG data recorded with EGI caps
> > > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de>
> > > > Content-Type: text/plain; charset="us-ascii"
> > > >
> > > >
> > > >
> > > > Dear Cris,
> > > >
> > > > thank you very much for your answer. I am refering to an issue that
> was
> > > > discussed in this thread from April 2013:
> > > >
> > > > [FieldTrip] source analysis EEG data without MRI
> > > >
> > > > The thread however does not offer a segmentation or head model for
> > > > download. Some electrodes in the EGI 256-electrodes cap are placed on
> > > > the cheeks or on the back of the neck and these areas are not
> modeled by
> > > > the standard BEM skin compartment in the standard BEM model. My
> question
> > > > was about a standard segmentation that extends the skin (and skull)
> > > > compartment downwards to allow these electrodes to sit on the nodes
> of
> > > > the skin mesh.
> > > >
> > > > Best,
> > > > Laith
> > > >
> > > >
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> > >
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/49665b0c/attachment-0001.html
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 4
> > > > Date: Tue, 19 Jan 2016 16:52:55 +0000
> > > > From: aishwarya selvaraj <aishwaryaselvaraj1708 at gmail.com>
> > > > To: "fieldtrip, donders" <fieldtrip at donders.ru.nl>
> > > > Subject: [FieldTrip] Source Localisation
> > > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl>
> > > > Content-Type: text/plain; charset="us-ascii"
> > > >
> > > > Hi guys,
> > > > I'm currently working on source localization of EEG signals .
> > > > Im very new to it .
> > > >
> > > >
> > > > Can Anyone provide any inputs ??
> > > > It would be of great help .
> > > >
> > > > --
> > > > Regards,
> > > > Aishwarya
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> > >
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/3459ed12/attachment-0001.html
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 5
> > > > Date: Tue, 19 Jan 2016 17:06:13 +0000
> > > > From: Hom?lle, S. (Simon) <S.Homolle at donders.ru.nl>
> > > > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > > > Subject: Re: [FieldTrip] Source Localisation
> > > > Message-ID:
> > > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl>
> > > > Content-Type: text/plain; charset="iso-8859-1"
> > > >
> > > > Dear Aishwarya,
> > > >
> > > > Under http://www.fieldtriptoolbox.org/tutorial there are several
> > > tutorials about source reconstruction.
> > > >
> > > > My recommended start would be:
> > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem
> > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate
> > > >
> > > >
> > > > Hopefully this provides you good start working with EEG source
> > > reconstruction
> > > >
> > > > Best regards,
> > > >
> > > > Simon Hom?lle
> > > > PhD Candidate
> > > > Donders Institute for Brain, Cognition and Behaviour
> > > > Centre for Cognitive Neuroimaging
> > > > Radboud University Nijmegen
> > > > Phone: +31-(0)24-36-65059
> > > > ________________________________
> > > > From: fieldtrip-bounces at science.ru.nl [
> fieldtrip-bounces at science.ru.nl]
> > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com]
> > > > Sent: Tuesday, January 19, 2016 5:52 PM
> > > > To: fieldtrip, donders
> > > > Subject: [FieldTrip] Source Localisation
> > > >
> > > > Hi guys,
> > > > I'm currently working on source localization of EEG signals .
> > > > Im very new to it .
> > > >
> > > >
> > > > Can Anyone provide any inputs ??
> > > > It would be of great help .
> > > >
> > > > --
> > > > Regards,
> > > > Aishwarya
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> > >
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/d2425227/attachment-0001.html
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 6
> > > > Date: Tue, 19 Jan 2016 17:49:21 +0000
> > > > From: victoria schroeder <vic.schroeder2 at gmail.com>
> > > > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > > > Subject: Re: [FieldTrip] plotting neighbours
> > > > Message-ID:
> > > > <CAOWWpozcLgcLNqgF4rMrTRZ_=e8cYCvXgeY5ZJYXx_9YmWnJ_w at mail.gmail.com>
> > > > Content-Type: text/plain; charset="utf-8"
> > > >
> > > > Thank you very much Philipp and Tzvetan!
> > > >
> > > > Things have become much clearer now.
> > > >
> > > > I would like to follow up with a very related question. I am trying
> to
> > > > replicate the analysis for the cluster based permutation test using
> the
> > > > code and the data provided. However, i run into two problems here
> > > >
> > > > First, i get the following error if i use the original code:
> > > > Attempted to access cfg.frequency(2); index out of bounds because
> > > > numel(cfg.frequency)=1.
> > > >
> > > > Error in ft_freqstatistics (line 187)
> > > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2),
> > > fmax)];
> > > >
> > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20
> 20].
> > > > However, then no significant clusters are found. Which becomes clear
> when
> > > > trying to plot the cluster or by looking at the output of
> > > > ft_freqstatistics.
> > > >
> > > > Does the change in the code , change the output? How can i avoid the
> > > error
> > > > mentioned above and still get the same output from ft_freqstatistics
> as
> > > the
> > > > one provided on the webpage?
> > > >
> > > >
> > > > The relevant section of the toturial is provided below.
> > > > Thank you!
> > > >
> > > > Victoria
> > > >
> > > > Permutation test
> > > >
> > > > Now, run *ft_freqstatistics
> > > > <http://www.fieldtriptoolbox.org/reference/ft_freqstatistics>* to
> > > compare
> > > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field
> > > cfg.latency,
> > > > the following configuration is identical to the configuration that
> was
> > > used
> > > > for comparing event-related averages in the cluster-based permutation
> > > tests
> > > > on event related fields tutorial
> > > > <
> http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock>.
> > > > Also see this tutorial
> > > > <
> http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock>
> > > for
> > > > a detailed explanation of all the configuration settings. You can
> read
> > > more
> > > > about the *ft_prepare_neighbours
> > > > <http://www.fieldtriptoolbox.org/reference/ft_prepare_neighbours>*
> > > function
> > > > in the FAQ's
> > > > <
> http://www.fieldtriptoolbox.org/faq/how_does_ft_prepare_neighbours_work
> > > >.
> > > >
> > > > To load the planar gradient TFRs (also available on the FieldTrip FTP
> > > > servers,freqFIC_planar_cmb.mat
> > > > <
> > >
> ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFIC_planar_cmb.mat
> > > >
> > > > and freqFC_planar_cmb.mat
> > > > <
> > >
> ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFC_planar_cmb.mat
> > > >),
> > > > use:
> > > >
> > > > load freqFIC_planar_cmb
> > > > load freqFC_planar_cmb
> > > >
> > > > cfg = [];
> > > > cfg.channel = {'MEG', '-MLP31', '-MLO12'};
> > > > cfg.latency = 'all';
> > > > cfg.frequency = 20;
> > > > cfg.method = 'montecarlo';
> > > > cfg.statistic = 'ft_statfun_indepsamplesT';
> > > > cfg.correctm = 'cluster';
> > > > cfg.clusteralpha = 0.05;
> > > > cfg.clusterstatistic = 'maxsum';
> > > > cfg.minnbchan = 2;
> > > > cfg.tail = 0;
> > > > cfg.clustertail = 0;
> > > > cfg.alpha = 0.025;
> > > > cfg.numrandomization = 500;
> > > > % prepare_neighbours determines what sensors may form clusters
> > > > cfg_neighb.method = 'distance';
> > > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC);
> > > >
> > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) +
> > > > size(freqFC_planar_cmb.powspctrm,1));
> > > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1;
> > > >
> > >
> design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+...
> > > > size(freqFC_planar_cmb.powspctrm,1))) = 2;
> > > >
> > > > cfg.design = design;
> > > > cfg.ivar = 1;
> > > >
> > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb,
> freqFC_planar_cmb);
> > > >
> > > >
> > > >
> > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov <
> tzvetan.popov at uni-konstanz.de
> > > >:
> > > >
> > > > >
> > > > > Hi Victoria,
> > > > >
> > > > > oopsy, I think I confused you dramatically. I?m sorry for this.
> You are
> > > > > right I was only scrolling up to the part where the mags were
> > > analyzed. As
> > > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course
> you
> > > can
> > > > > threat them separately, as I was naively thinking as non-neuormag
> > > user, but
> > > > > indeed combination of both is recommended as I have now learned
> > > :-)(thanks
> > > > > Phillip). I ran the following steps and I guess this should work
> for
> > > you.
> > > > > best
> > > > > tzvetan
> > > > >
> > > > > %%
> > > > > cfg = [];
> > > > > ComCon = ft_combineplanar(cfg,FreqCon);
> > > > > %%
> > > > > cfg = []
> > > > > cfg.method = 'triangulation';
> > > > > cfg.layout = 'neuromag306cmb.lay';
> > > > > cfg.senstype = 'MEG';
> > > > > neighbours = ft_prepare_neighbours(cfg, ComCon)
> > > > > %%
> > > > > % plot neighbours
> > > > > cfg=[];
> > > > > cfg.neighbours = neighbours;
> > > > > cfg.layout = 'neuromag306cmb.lay';
> > > > > ft_neighbourplot(cfg);
> > > > >
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > fieldtrip mailing list
> > > > > fieldtrip at donders.ru.nl
> > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > > >
> > > > -------------- next part --------------
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> > >
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> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 7
> > > > Date: Tue, 19 Jan 2016 20:50:24 +0100
> > > > From: Cristiano Micheli <michelic72 at gmail.com>
> > > > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with
> > > > 256-electrode EEG data recorded with EGI caps
> > > > Message-ID:
> > > > <CADW7XCC8BvdVKRAEMw4Jt8v3T6zXjF2zHF_T_4h8ZkuvTbc=1Q at mail.gmail.com>
> > > > Content-Type: text/plain; charset="utf-8"
> > > >
> > > > Dear Laith,
> > > >
> > > > this might be possible if you have the subject-specific MRI by
> following
> > > > the tutorial here:
> > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem
> > > >
> > > > and using the function ft_prepare_mesh and the tutorial command:
> > > >
> > > > cfg=[];
> > > > cfg.tissue={'brain','skull','scalp'};
> > > > cfg.numvertices = [3000 2000 1000];
> > > > bnd=ft_prepare_mesh(cfg,segmentedmri);
> > > >
> > > >
> > > > which uses the segmented MRI (see tutorial). The bnd(3) variable
> should
> > > > contain your triangulated surface with 1000 vertices. Let me know if
> that
> > > > works. Of course you should see the skin and the neck in the original
> > > MRI.
> > > >
> > > > If you do not have an anatomical MRI that extends down to the chin
> you
> > > > could try with a template, such as this:
> > > >
> > >
> ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri
> > > > and the corresponding segmented version
> > > >
> > >
> ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat
> > > >
> > > > This goes down to the chin. Then you take care of rearranging the
> > > position
> > > > of the EEG electrodes according to this:
> > > >
> > > >
> > >
> http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel
> > > >
> > > > I hope this helped
> > > > Cris
> > > >
> > > >
> > > >
> > > >
> > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid <
> lah at pedneuro.uni-kiel.de>
> > > > wrote:
> > > >
> > > > > Dear Cris,
> > > > >
> > > > > thank you very much for your answer. I am refering to an issue
> that was
> > > > > discussed in this thread from April 2013:
> > > > >
> > > > >
> > > > > [FieldTrip] source analysis EEG data without MRI
> > > > >
> > > > >
> > > > > The thread however does not offer a segmentation or head model for
> > > > > download. Some electrodes in the EGI 256-electrodes cap are placed
> on
> > > the
> > > > > cheeks or on the back of the neck and these areas are not modeled
> by
> > > the
> > > > > standard BEM skin compartment in the standard BEM model. My
> question
> > > was
> > > > > about a standard segmentation that extends the skin (and skull)
> > > compartment
> > > > > downwards to allow these electrodes to sit on the nodes of the skin
> > > mesh.
> > > > >
> > > > > Best,
> > > > > Laith
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > fieldtrip mailing list
> > > > > fieldtrip at donders.ru.nl
> > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > > >
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> > >
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> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 8
> > > > Date: Wed, 20 Jan 2016 12:17:12 +0800
> > > > From: Munsif Jatoi <munsif.jatoi at gmail.com>
> > > > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > > > Subject: Re: [FieldTrip] Source Localisation
> > > > Message-ID:
> > > > <CAHnJ=SUHe84yNDVnTLKhGdJBri0mvOdbU0rPqM-Z3-0Gv71Ycg at mail.gmail.com>
> > > > Content-Type: text/plain; charset="utf-8"
> > > >
> > > > Dear Aishwarya,
> > > >
> > > > Please refer to main help tutorials.
> > > >
> > > > Also, you can find out the survey papers written in this area. For
> more,
> > > > SPM website can provide good help.
> > > >
> > > > Best,
> > > > Munsif.
> > > >
> > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) <
> > > > S.Homolle at donders.ru.nl> wrote:
> > > >
> > > > > Dear Aishwarya,
> > > > >
> > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several
> > > > > tutorials about source reconstruction.
> > > > >
> > > > > My recommended start would be:
> > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem
> > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate
> > > > >
> > > > >
> > > > > Hopefully this provides you good start working with EEG source
> > > > > reconstruction
> > > > >
> > > > > Best regards,
> > > > >
> > > > > Simon Hom?lle
> > > > > PhD Candidate
> > > > > Donders Institute for Brain, Cognition and Behaviour
> > > > > Centre for Cognitive Neuroimaging
> > > > > Radboud University Nijmegen
> > > > > Phone: +31-(0)24-36-65059
> > > > > ------------------------------
> > > > > *From:* fieldtrip-bounces at science.ru.nl [
> > > fieldtrip-bounces at science.ru.nl]
> > > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com]
> > > > > *Sent:* Tuesday, January 19, 2016 5:52 PM
> > > > > *To:* fieldtrip, donders
> > > > > *Subject:* [FieldTrip] Source Localisation
> > > > >
> > > > > Hi guys,
> > > > > I'm currently working on source localization of EEG signals .
> > > > > Im very new to it .
> > > > >
> > > > >
> > > > > Can Anyone provide any inputs ??
> > > > > It would be of great help .
> > > > >
> > > > > --
> > > > > Regards,
> > > > > Aishwarya
> > > > >
> > > > > _______________________________________________
> > > > > fieldtrip mailing list
> > > > > fieldtrip at donders.ru.nl
> > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Munsif Ali H.Jatoi,
> > > >
> > > > Ph D Scholar,
> > > > Centre for Intelligent Signals and Imaging Research,
> > > > Universiti Teknologi PETRONAS,
> > > > Malaysia.
> > > >
> > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> > >
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> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 9
> > > > Date: Wed, 20 Jan 2016 13:36:16 +0300
> > > > From: Olga Sysoeva <olga.v.sysoeva at gmail.com>
> > > > To: fieldtrip at science.ru.nl
> > > > Subject: [FieldTrip] problems with mri interpolation
> > > > Message-ID:
> > > > <CADtsnVcJLhrPPfq-P1Htj-RmfgzDDgqNhr8vsAoJ2mxxCV7seQ at mail.gmail.com>
> > > > Content-Type: text/plain; charset="utf-8"
> > > >
> > > > Dear Fieldtrippers,
> > > >
> > > >
> > > > I'm encounter the problem with MRI interpolation and reslicing using
> > > >
> > > > FT_VOLUMERESLICE.
> > > >
> > > > I have read my MRI from fif.file and this mri variable contains
> > > >
> > > > mri_K0012.unit, 'm'
> > > >
> > > > mri_K0012.dim, [432, 512, 180]
> > > >
> > > > mri_K0012.anatomy, <432, 512, 180 int16>
> > > >
> > > > mri_K0012.hdr, (1*1 structure)
> > > >
> > > > mri_K0012.transform, (4*4 double)
> > > >
> > > > mri_K0012.coordsys 'neuromag'.
> > > >
> > > >
> > > > Than I used
> > > >
> > > >
> > > > mri = ft_volumereslice([], mri);
> > > >
> > > >
> > > > the output is
> > > >
> > > >
> > > > ?the input is volume data with dimensions [432
> > > > 512 180]
> > > >
> > > > reslicing from [432 512 180] to [256 256 256]
> > > >
> > > > the input is volume data with dimensions [256
> > > > 256 256]
> > > >
> > > > the input is volume data with dimensions [432
> > > > 512 180]
> > > >
> > > > selecting subvolume of 0.0%
> > > >
> > > > reslicing and interpolating anatomy
> > > >
> > > > interpolating
> > > >
> > > > ??? Attempted to access sel(1); index out of
> > > > bounds because numel(sel)=0.
> > > >
> > > >
> > > > Error in ==> ft_sourceinterpolate>my_interpn
> > > > at 663
> > > >
> > > > ft_progress(sel(1)/num, 'interpolating
> > > > %.1f%%\n', 100*sel(1)/num);
> > > >
> > > >
> > > > Error in ==> ft_sourceinterpolate at 583
> > > >
> > > > av( sel) = my_interpn(fv, ax(sel),
> > > > ay(sel), az(sel), cfg.interpmethod,
> > > >
> > > > cfg.feedback);
> > > >
> > > >
> > > > Error in ==> ft_volumereslice at 176
> > > >
> > > > resliced = ft_sourceinterpolate(tmpcfg, mri,
> > > > resliced);?
> > > >
> > > >
> > > > I'm using matlab 7.6.0 (R2008a) and recently
> > > > downloaded fieltrip (also in my previous version of 2013 the error
> > > > was the same).
> > > >
> > > >
> > > > I'd be thankful for the comments.
> > > >
> > > >
> > > > Best Regards,
> > > >
> > > > Olga.
> > > >
> > > > P.S.Actually, I can project my sources
> > > > meaningfully into not interpolated MRI, altoough the images are
> > > > plotted upside down.
> > > > -------------- next part --------------
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> > >
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> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > _______________________________________________
> > > > fieldtrip mailing list
> > > > fieldtrip at donders.ru.nl
> > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > >
> > > > End of fieldtrip Digest, Vol 62, Issue 18
> > > > *****************************************
> > >
> > > _______________________________________________
> > > fieldtrip mailing list
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > >
> > -------------- next part --------------
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> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Thu, 21 Jan 2016 21:59:06 +0900
> > From: "Muhammad Naveed Iqbal Qureshi" <mniqureshi at gist.ac.kr>
> > To: <fieldtrip at science.ru.nl>
> > Subject: [FieldTrip] difficulty in loading BCI-IV-2a dataset into
> > fieldtrip for preprocessing
> > Message-ID: <000b01d1544b$8323d8e0$896b8aa0$@gist.ac.kr>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > Hi,
> >
> >
> >
> > I am using BCI competition IV dataset 2a for my experiment.
> >
> > I want to preprocess it with field trip.
> >
> >
> >
> > I have written the following code for this task.
> >
> >
> >
> > addpath(genpath('E:\bbci_data\fieldtrip-20160118\fieldtrip-20160118'));
> >
> > cd 'E:\bbci_data\BCICIV_2a_gdf\';
> >
> >
> >
> > %% Field Trip preprocessing code
> >
> > for i=1:9
> >
> > file=num2str(i);
> >
> > file=strcat('A0',file,'T.gdf');
> >
> > cfg = [];
> >
> > cfg.dataset = file ;
> >
> > cfg.trialdef.eventtype = 'Stimulus';
> >
> > cfg.trialdef.eventvalue = {'left', 'right', 'both feet', 'tongue'};
> >
> > cfg.trialdef.triallength = 8; % duration in seconds
> >
> > cfg.trialdef.ntrials = inf; % number of trials, inf
> > results in as many as possible
> >
> > cfg.trialdef.prestim = 3;
> >
> > cfg.trialdef.poststim = 6;
> >
> > cfg = ft_definetrial(cfg);
> >
> >
> >
> > cfg.bpfilter = 'yes';
> >
> > cfg.bpfreq = [0.5 100];
> >
> > cfg.bpfilttype = 'but';
> >
> > cfg.bpfiltord = 5;
> >
> > cfg.demean = 'yes';
> >
> > cfg.detrend = 'yes';
> >
> > trialdata_EO{i} = ft_preprocessing(cfg);
> >
> > end
> >
> >
> >
> > However, this code does not import the event and trigger information from
> > the header file of the data.
> >
> > I will be highly obliged if anyone can help me in this regard.
> >
> >
> >
> > Thank in advance.
> >
> >
> >
> > Best Regards,
> > Muhammad Naveed Iqbal Qureshi
> >
> >
> >
> >
> >
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
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> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Thu, 21 Jan 2016 20:14:01 +0200
> > From: saeed zahran <saeedzahran at hotmail.com>
> > To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 19
> > Message-ID: <DUB125-W30A23224F6DFC1BFBEED32B7C30 at phx.gbl>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Thank you Jan and Cristiano;
> >
> > I downloaded another version of Fieldtrip thus the below error disappear:
> > Error in triangle4pt (line 57)
> > sph_pnt = pnt([tri(jj,:) lv],:);
> >
> > But now I have another error:
> >
> > Error using surface_nesting (line 26)
> > the compartment nesting cannot be determined
> >
> > Error in ft_headmodel_bemcp (line 66)
> > order = surface_nesting(vol.bnd, 'insidefirst');
> >
> > Error in ft_prepare_headmodel (line 253)
> > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity);
> >
> > Error in openmeeg_eeg_leadfield_example (line 100)
> > vol = ft_prepare_headmodel(cfg, vol);
> > Thank you for any suggestion
> >
> > Cristiano, I record the contraction of the uterus;
> >
> >
> > Best regards
> > Saeed Zahran
> >
> > > From: fieldtrip-request at science.ru.nl
> > > Subject: fieldtrip Digest, Vol 62, Issue 19
> > > To: fieldtrip at science.ru.nl
> > > Date: Thu, 21 Jan 2016 12:00:02 +0100
> > >
> > > 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. Standard BEM or FEM models for use with 256-electrode EEG
> > > data recorded with EGI caps (Laith Hamid)
> > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG
> > > data recorded with EGI caps (Laith Hamid) (RICHARDS, JOHN)
> > > 3. Re: fieldtrip Digest, Vol 62, Issue 18 (saeed zahran)
> > > 4. Re: fieldtrip Digest, Vol 62, Issue 18
> > > (Schoffelen, J.M. (Jan Mathijs))
> > >
> > >
> > > ----------------------------------------------------------------------
> > >
> > > Message: 1
> > > Date: Wed, 20 Jan 2016 13:39:30 +0100
> > > From: Laith Hamid <lah at pedneuro.uni-kiel.de>
> > > To: Fieldtrip <fieldtrip at science.ru.nl>
> > > Subject: [FieldTrip] Standard BEM or FEM models for use with
> > > 256-electrode EEG data recorded with EGI caps
> > > Message-ID: <5ee6eeedb5d8a3a42f96840711d87ef1 at mail.uni-kiel.de>
> > > Content-Type: text/plain; charset="us-ascii"
> > >
> > >
> > >
> > > Dear Cris,
> > >
> > > thank you very much for your answers yesterday. The segmentedmri
> > > contained 'white', 'grey' and 'csf' so I needed to repeat the
> > > segmentation using 'brain', 'skull' and 'scalp' as described in the
> > > tutorial "Creating a BEM volume conduction model of the head for
> > > source-reconstruction of EEG data" and everything worked smoothly
> > > afterwards. The problem is solved now.
> > >
> > > Best,
> > > Laith
> > >
> > >
> > > -------------- next part --------------
> > > An HTML attachment was scrubbed...
> > > URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/e700c8d6/attachment-0001.html
> >
> > >
> > > ------------------------------
> > >
> > > Message: 2
> > > Date: Wed, 20 Jan 2016 14:39:13 +0000
> > > From: "RICHARDS, JOHN" <RICHARDS at mailbox.sc.edu>
> > > To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>,
> > > "lah at pedneuro.uni-kiel.de" <lah at pedneuro.uni-kiel.de>
> > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with
> > > 256-electrode EEG data recorded with EGI caps (Laith Hamid)
> > > Message-ID: <D0C0492E-CD7A-43AA-960D-189E95D5309B at mailbox.sc.edu>
> > > Content-Type: text/plain; charset="utf-8"
> > >
> > > Laith:
> > >
> > > I have a ?neurodevelopmental MRI database? (Richards, Sanchez et al.,
> 2015; see my www site) that has average MRI templates that could be used.
> Each average has the whole head down to about the top of the neck. I did
> these purposely since I use EEG recording and the MNI template did not even
> go down far enough for the EGI 128 channel net.
> > >
> > > The database has average MRI templates for head (T1, T2) and brain. I
> also have FEM segmented heads for the entire head that could be used for
> this. Additionally, I have BEM segmented heads (e.g., brain, csf, skull,
> scalp), but ironically, I cut these off about 10% below the EGI 128 channel
> electrodes. However, you could use the three inner compartments for this
> and just add the rest of the head below the compartment?or use the
> whole-head FEM as is for a FEM-model, or use the segmented area below the
> skull for a whole-head BEM model. I also have average 128-channel EGI
> electrodes for each template.
> > >
> > > Additionally, the ?developmental? part of the ?neurodevelopmental MRI
> database? is that I have these for a wide range of ages (all ages?). I have
> a average for young adults (20-24 yrs), and average templates and FEM/BEM
> models for groups from 3 months through adulthood, and into late adulthood.
> So if you have specific neuro-pediatric applications you might be
> interested in using an age appropriate MRI average template rather than an
> adult template.
> > >
> > > See my www site for journal article references re this, and
> http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/
> > >
> > > Finally? I have been using these head models for FT-based FEM and BEM
> models. Possibly some of the actually field trip models I have would be
> useful to you. Some of the parts of the model do not use the electrodes
> (e.g., grid-dipoles, head-model) whereas the final models (leadfield)
> requires the electrode locations. The database also includes ?virtual?
> electrodes for the 10-10 system, which might be used to generate the 256
> channel locations by knowing the relation between the 10-10 system and the
> EGI system based on EGI ELP files for the 256 channels.
> > >
> > > John
> > >
> > > ***********************************************
> > > John E. Richards Carolina Distinguished Professor
> > > Department of Psychology
> > > University of South Carolina
> > > Columbia, SC 29208
> > > Dept Phone: 803 777 2079
> > > Fax: 803 777 9558
> > > Email: richards-john at sc.edu
> > > HTTP: jerlab.psych.sc.edu
> > > ***********************************************
> > >
> > >
> > >
> > >
> > > >----------------------------------------------------------------------
> > > >
> > > >Message: 1
> > > >Date: Tue, 19 Jan 2016 15:35:00 +0100
> > > >From: Laith Hamid <lah at pedneuro.uni-kiel.de>
> > > >To: fieldtrip at science.ru.nl
> > > >Subject: [FieldTrip] Standard BEM or FEM models for use with
> > > > 256-electrode EEG data recorded with EGI caps
> > > >Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de>
> > > >Content-Type: text/plain; charset="us-ascii"
> > > >
> > > >
> > > >
> > > >Dear community,
> > > >
> > > >My name is Laith Hamid and I am working in the University Medical
> > > >Complex of Schleswig-Holstein in Kiel on source analysis of epileptic
> > > >spikes and seizures. Currently I am analysing an EEG data set that was
> > > >recorded using a 256-channel EGI system and I wanted to ask whether
> you
> > > >have a standard BEM or FEM head model that extends enough downwards to
> > > >accomodate all 256 electrodes. The current standard BEM model in the
> > > >template folder of Fieldtrip isn't appropriate for source analysis of
> > > >256-channel EGI data.
> > > >
> > > >Thank you very much in advance for your help!
> > > >
> > > >Best,
> > > >
> > > >Laith
> > >
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 3
> > > Date: Wed, 20 Jan 2016 19:37:32 +0200
> > > From: saeed zahran <saeedzahran at hotmail.com>
> > > To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> > > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18
> > > Message-ID: <DUB125-W5597106FD75ADF3E7BD054B7C20 at phx.gbl>
> > > Content-Type: text/plain; charset="iso-8859-1"
> > >
> > > Dear Fieldtrip community,
> > >
> > > I define the volume conductor as:
> > >
> > > vol = [];
> > > vol.bnd(1).pnt=skinpnt
> > > vol.bnd(1).tri=skinf
> > >
> > > vol.bnd(2).pnt=uteruspnt
> > > vol.bnd(2).tri=uterusf
> > >
> > > vol.bnd(3).pnt=uterinecontentpnt
> > > vol.bnd(3).tri=uterinecontentf
> > >
> > > vol.cond = c;
> > >
> > >
> > > But it result with the below error:
> > >
> > > Subscript indices must either be real positive integers or logicals.
> > >
> > > Error in triangle4pt (line 57)
> > > sph_pnt = pnt([tri(jj,:) lv],:);
> > >
> > > Error in ft_headmodel_bemcp (line 101)
> > > vol = triangle4pt(vol);
> > >
> > > Error in ft_prepare_headmodel (line 253)
> > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity);
> > >
> > > Error in openmeeg_eeg_leadfield_example_me (line 91)
> > > vol = ft_prepare_headmodel(cfg, vol);
> > >
> > >
> > > Thank you very much in advance for your help!
> > >
> > > Best regards
> > > Saeed Zahran
> > >
> > > > From: fieldtrip-request at science.ru.nl
> > > > Subject: fieldtrip Digest, Vol 62, Issue 18
> > > > To: fieldtrip at science.ru.nl
> > > > Date: Wed, 20 Jan 2016 12:00:02 +0100
> > > >
> > > > 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. Standard BEM or FEM models for use with 256-electrode EEG
> > > > data recorded with EGI caps (Laith Hamid)
> > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG
> > > > data recorded with EGI caps (Cristiano Micheli)
> > > > 3. Standard BEM or FEM models for use with 256-electrode EEG
> > > > data recorded with EGI caps (Laith Hamid)
> > > > 4. Source Localisation (aishwarya selvaraj)
> > > > 5. Re: Source Localisation (Hom?lle)
> > > > 6. Re: plotting neighbours (victoria schroeder)
> > > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG
> > > > data recorded with EGI caps (Cristiano Micheli)
> > > > 8. Re: Source Localisation (Munsif Jatoi)
> > > > 9. problems with mri interpolation (Olga Sysoeva)
> > > >
> > > >
> > > >
> ----------------------------------------------------------------------
> > > >
> > > > Message: 1
> > > > Date: Tue, 19 Jan 2016 15:35:00 +0100
> > > > From: Laith Hamid <lah at pedneuro.uni-kiel.de>
> > > > To: fieldtrip at science.ru.nl
> > > > Subject: [FieldTrip] Standard BEM or FEM models for use with
> > > > 256-electrode EEG data recorded with EGI caps
> > > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de>
> > > > Content-Type: text/plain; charset="us-ascii"
> > > >
> > > >
> > > >
> > > > Dear community,
> > > >
> > > > My name is Laith Hamid and I am working in the University Medical
> > > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic
> > > > spikes and seizures. Currently I am analysing an EEG data set that
> was
> > > > recorded using a 256-channel EGI system and I wanted to ask whether
> you
> > > > have a standard BEM or FEM head Subscript indices must either be
> real positive integers or logicals.
> > >
> > > Error in triangle4pt (line 57)
> > > sph_pnt = pnt([tri(jj,:) lv],:);
> > >
> > > Error in ft_headmodel_bemcp (line 101)
> > > vol = triangle4pt(vol);
> > >
> > > Error in ft_prepare_headmodel (line 253)
> > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity);
> > >
> > > Error in openmeeg_eeg_leadfield_example_me (line 91)
> > > vol = ft_prepare_headmodel(cfg, vol);
> > > model that extends enough downwards to
> > > > accomodate all 256 electrodes. The current standard BEM model in the
> > > > template folder of Fieldtrip isn't appropriate for source analysis of
> > > > 256-channel EGI data.
> > > >
> > > > Thank you very much in advance for your help!
> > > >
> > > > Best,
> > > >
> > > > Laith
> > > >
> > > >
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/f8805c11/attachment-0001.html
> >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 2
> > > > Date: Tue, 19 Jan 2016 16:16:54 +0100
> > > > From: Cristiano Micheli <michelic72 at gmail.com>
> > > > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with
> > > > 256-electrode EEG data recorded with EGI caps
> > > > Message-ID:
> > > > <CADW7XCCywrPeWqGTqfP6jWoeLuvBo52poPfRyAPy9__VvkbDLg at mail.gmail.com>
> > > > Content-Type: text/plain; charset="utf-8"
> > > >
> > > > Dear Laith,
> > > >
> > > > thanks for your question. You could refer to a factory schematic
> layout
> > > > such as the one in figure 4 of this publication:
> > > >
> http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract
> > > >
> > > > and subsequently use the function ft_prepare_layout to manually
> track the
> > > > points of the custom design on your own (if you dont want to wait for
> > > > somebody from the FT to do the same for you).
> > > >
> > > > cfg = [];
> > > > cfg.image = 'figure4_layout_256_Frontiers.png';
> > > > lay = ft_prepare_layout(cfg);
> > > >
> > > > The following tutorial describes the procedure in more details:
> > > > http://www.fieldtriptoolbox.org/tutorial/layout
> > > >
> > > > Please do not hesitate to get in touch with me for this and other
> matters.
> > > >
> > > > All the best
> > > > Cris Micheli
> > > >
> > > >
> > > >
> > > >
> > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid <
> lah at pedneuro.uni-kiel.de>
> > > > wrote:
> > > >
> > > > > Dear community,
> > > > >
> > > > > My name is Laith Hamid and I am working in the University Medical
> Complex
> > > > > of Schleswig-Holstein in Kiel on source analysis of epileptic
> spikes and
> > > > > seizures. Currently I am analysing an EEG data set that was
> recorded using
> > > > > a 256-channel EGI system and I wanted to ask whether you have a
> standard
> > > > > BEM or FEM head model that extends enough downwards to accomodate
> all 256
> > > > > electrodes. The current standard BEM model in the template folder
> of
> > > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI
> data.
> > > > >
> > > > > Thank you very much in advance for your help!
> > > > >
> > > > > Best,
> > > > >
> > > > > Laith
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > fieldtrip mailing list
> > > > > fieldtrip at donders.ru.nl
> > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > > >
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/659988fa/attachment-0001.html
> >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 3
> > > > Date: Tue, 19 Jan 2016 17:41:48 +0100
> > > > From: Laith Hamid <lah at pedneuro.uni-kiel.de>
> > > > To: Fieldtrip <fieldtrip at science.ru.nl>
> > > > Subject: [FieldTrip] Standard BEM or FEM models for use with
> > > > 256-electrode EEG data recorded with EGI caps
> > > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de>
> > > > Content-Type: text/plain; charset="us-ascii"
> > > >
> > > >
> > > >
> > > > Dear Cris,
> > > >
> > > > thank you very much for your answer. I am refering to an issue that
> was
> > > > discussed in this thread from April 2013:
> > > >
> > > > [FieldTrip] source analysis EEG data without MRI
> > > >
> > > > The thread however does not offer a segmentation or head model for
> > > > download. Some electrodes in the EGI 256-electrodes cap are placed on
> > > > the cheeks or on the back of the neck and these areas are not
> modeled by
> > > > the standard BEM skin compartment in the standard BEM model. My
> question
> > > > was about a standard segmentation that extends the skin (and skull)
> > > > compartment downwards to allow these electrodes to sit on the nodes
> of
> > > > the skin mesh.
> > > >
> > > > Best,
> > > > Laith
> > > >
> > > >
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/49665b0c/attachment-0001.html
> >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 4
> > > > Date: Tue, 19 Jan 2016 16:52:55 +0000
> > > > From: aishwarya selvaraj <aishwaryaselvaraj1708 at gmail.com>
> > > > To: "fieldtrip, donders" <fieldtrip at donders.ru.nl>
> > > > Subject: [FieldTrip] Source Localisation
> > > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl>
> > > > Content-Type: text/plain; charset="us-ascii"
> > > >
> > > > Hi guys,
> > > > I'm currently working on source localization of EEG signals .
> > > > Im very new to it .
> > > >
> > > >
> > > > Can Anyone provide any inputs ??
> > > > It would be of great help .
> > > >
> > > > --
> > > > Regards,
> > > > Aishwarya
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/3459ed12/attachment-0001.html
> >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 5
> > > > Date: Tue, 19 Jan 2016 17:06:13 +0000
> > > > From: Hom?lle, S. (Simon) <S.Homolle at donders.ru.nl>
> > > > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > > > Subject: Re: [FieldTrip] Source Localisation
> > > > Message-ID:
> > > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl>
> > > > Content-Type: text/plain; charset="iso-8859-1"
> > > >
> > > > Dear Aishwarya,
> > > >
> > > > Under http://www.fieldtriptoolbox.org/tutorial there are several
> tutorials about source reconstruction.
> > > >
> > > > My recommended start would be:
> > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem
> > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate
> > > >
> > > >
> > > > Hopefully this provides you good start working with EEG source
> reconstruction
> > > >
> > > > Best regards,
> > > >
> > > > Simon Hom?lle
> > > > PhD Candidate
> > > > Donders Institute for Brain, Cognition and Behaviour
> > > > Centre for Cognitive Neuroimaging
> > > > Radboud University Nijmegen
> > > > Phone: +31-(0)24-36-65059
> > > > ________________________________
> > > > From: fieldtrip-bounces at science.ru.nl [
> fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [
> aishwaryaselvaraj1708 at gmail.com]
> > > > Sent: Tuesday, January 19, 2016 5:52 PM
> > > > To: fieldtrip, donders
> > > > Subject: [FieldTrip] Source Localisation
> > > >
> > > > Hi guys,
> > > > I'm currently working on source localization of EEG signals .
> > > > Im very new to it .
> > > >
> > > >
> > > > Can Anyone provide any inputs ??
> > > > It would be of great help .
> > > >
> > > > --
> > > > Regards,
> > > > Aishwarya
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/d2425227/attachment-0001.html
> >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 6
> > > > Date: Tue, 19 Jan 2016 17:49:21 +0000
> > > > From: victoria schroeder <vic.schroeder2 at gmail.com>
> > > > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > > > Subject: Re: [FieldTrip] plotting neighbours
> > > > Message-ID:
> > > > <CAOWWpozcLgcLNqgF4rMrTRZ_=e8cYCvXgeY5ZJYXx_9YmWnJ_w at mail.gmail.com>
> > > > Content-Type: text/plain; charset="utf-8"
> > > >
> > > > Thank you very much Philipp and Tzvetan!
> > > >
> > > > Things have become much clearer now.
> > > >
> > > > I would like to follow up with a very related question. I am trying
> to
> > > > replicate the analysis for the cluster based permutation test using
> the
> > > > code and the data provided. However, i run into two problems here
> > > >
> > > > First, i get the following error if i use the original code:
> > > > Attempted to access cfg.frequency(2); index out of bounds because
> > > > numel(cfg.frequency)=1.
> > > >
> > > > Error in ft_freqstatistics (line 187)
> > > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2),
> fmax)];
> > > >
> > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20
> 20].
> > > > However, then no significant clusters are found. Which becomes clear
> when
> > > > trying to plot the cluster or by looking at the output of
> > > > ft_freqstatistics.
> > > >
> > > > Does the change in the code , change the output? How can i avoid the
> error
> > > > mentioned above and still get the same output from ft_freqstatistics
> as the
> > > > one provided on the webpage?
> > > >
> > > >
> > > > The relevant section of the toturial is provided below.
> > > > Thank you!
> > > >
> > > > Victoria
> > > >
> > > > Permutation test
> > > >
> > > > Now, run *ft_freqstatistics
> > > > <http://www.fieldtriptoolbox.org/reference/ft_freqstatistics>* to
> compare
> > > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field
> cfg.latency,
> > > > the following configuration is identical to the configuration that
> was used
> > > > for comparing event-related averages in the cluster-based
> permutation tests
> > > > on event related fields tutorial
> > > > <
> http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock>.
> > > > Also see this tutorial
> > > > <
> http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock> for
> > > > a detailed explanation of all the configuration settings. You can
> read more
> > > > about the *ft_prepare_neighbours
> > > > <http://www.fieldtriptoolbox.org/reference/ft_prepare_neighbours>*
> function
> > > > in the FAQ's
> > > > <
> http://www.fieldtriptoolbox.org/faq/how_does_ft_prepare_neighbours_work>.
> > > >
> > > > To load the planar gradient TFRs (also available on the FieldTrip FTP
> > > > servers,freqFIC_planar_cmb.mat
> > > > <
> ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFIC_planar_cmb.mat
> >
> > > > and freqFC_planar_cmb.mat
> > > > <
> ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFC_planar_cmb.mat
> >),
> > > > use:
> > > >
> > > > load freqFIC_planar_cmb
> > > > load freqFC_planar_cmb
> > > >
> > > > cfg = [];
> > > > cfg.channel = {'MEG', '-MLP31', '-MLO12'};
> > > > cfg.latency = 'all';
> > > > cfg.frequency = 20;
> > > > cfg.method = 'montecarlo';
> > > > cfg.statistic = 'ft_statfun_indepsamplesT';
> > > > cfg.correctm = 'cluster';
> > > > cfg.clusteralpha = 0.05;
> > > > cfg.clusterstatistic = 'maxsum';
> > > > cfg.minnbchan = 2;
> > > > cfg.tail = 0;
> > > > cfg.clustertail = 0;
> > > > cfg.alpha = 0.025;
> > > > cfg.numrandomization = 500;
> > > > % prepare_neighbours determines what sensors may form clusters
> > > > cfg_neighb.method = 'distance';
> > > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC);
> > > >
> > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) +
> > > > size(freqFC_planar_cmb.powspctrm,1));
> > > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1;
> > > >
> design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+...
> > > > size(freqFC_planar_cmb.powspctrm,1))) = 2;
> > > >
> > > > cfg.design = design;
> > > > cfg.ivar = 1;
> > > >
> > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb,
> freqFC_planar_cmb);
> > > >
> > > >
> > > >
> > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov <
> tzvetan.popov at uni-konstanz.de>:
> > > >
> > > > >
> > > > > Hi Victoria,
> > > > >
> > > > > oopsy, I think I confused you dramatically. I?m sorry for this.
> You are
> > > > > right I was only scrolling up to the part where the mags were
> analyzed. As
> > > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course
> you can
> > > > > threat them separately, as I was naively thinking as non-neuormag
> user, but
> > > > > indeed combination of both is recommended as I have now learned
> :-)(thanks
> > > > > Phillip). I ran the following steps and I guess this should work
> for you.
> > > > > best
> > > > > tzvetan
> > > > >
> > > > > %%
> > > > > cfg = [];
> > > > > ComCon = ft_combineplanar(cfg,FreqCon);
> > > > > %%
> > > > > cfg = []
> > > > > cfg.method = 'triangulation';
> > > > > cfg.layout = 'neuromag306cmb.lay';
> > > > > cfg.senstype = 'MEG';
> > > > > neighbours = ft_prepare_neighbours(cfg, ComCon)
> > > > > %%
> > > > > % plot neighbours
> > > > > cfg=[];
> > > > > cfg.neighbours = neighbours;
> > > > > cfg.layout = 'neuromag306cmb.lay';
> > > > > ft_neighbourplot(cfg);
> > > > >
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > fieldtrip mailing list
> > > > > fieldtrip at donders.ru.nl
> > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > > >
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/de08d8f1/attachment-0001.html
> >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 7
> > > > Date: Tue, 19 Jan 2016 20:50:24 +0100
> > > > From: Cristiano Micheli <michelic72 at gmail.com>
> > > > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with
> > > > 256-electrode EEG data recorded with EGI caps
> > > > Message-ID:
> > > > <CADW7XCC8BvdVKRAEMw4Jt8v3T6zXjF2zHF_T_4h8ZkuvTbc=1Q at mail.gmail.com>
> > > > Content-Type: text/plain; charset="utf-8"
> > > >
> > > > Dear Laith,
> > > >
> > > > this might be possible if you have the subject-specific MRI by
> following
> > > > the tutorial here:
> > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem
> > > >
> > > > and using the function ft_prepare_mesh and the tutorial command:
> > > >
> > > > cfg=[];
> > > > cfg.tissue={'brain','skull','scalp'};
> > > > cfg.numvertices = [3000 2000 1000];
> > > > bnd=ft_prepare_mesh(cfg,segmentedmri);
> > > >
> > > >
> > > > which uses the segmented MRI (see tutorial). The bnd(3) variable
> should
> > > > contain your triangulated surface with 1000 vertices. Let me know if
> that
> > > > works. Of course you should see the skin and the neck in the
> original MRI.
> > > >
> > > > If you do not have an anatomical MRI that extends down to the chin
> you
> > > > could try with a template, such as this:
> > > >
> ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri
> > > > and the corresponding segmented version
> > > >
> ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat
> > > >
> > > > This goes down to the chin. Then you take care of rearranging the
> position
> > > > of the EEG electrodes according to this:
> > > >
> > > >
> http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel
> > > >
> > > > I hope this helped
> > > > Cris
> > > >
> > > >
> > > >
> > > >
> > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid <
> lah at pedneuro.uni-kiel.de>
> > > > wrote:
> > > >
> > > > > Dear Cris,
> > > > >
> > > > > thank you very much for your answer. I am refering to an issue
> that was
> > > > > discussed in this thread from April 2013:
> > > > >
> > > > >
> > > > > [FieldTrip] source analysis EEG data without MRI
> > > > >
> > > > >
> > > > > The thread however does not offer a segmentation or head model for
> > > > > download. Some electrodes in the EGI 256-electrodes cap are placed
> on the
> > > > > cheeks or on the back of the neck and these areas are not modeled
> by the
> > > > > standard BEM skin compartment in the standard BEM model. My
> question was
> > > > > about a standard segmentation that extends the skin (and skull)
> compartment
> > > > > downwards to allow these electrodes to sit on the nodes of the
> skin mesh.
> > > > >
> > > > > Best,
> > > > > Laith
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > fieldtrip mailing list
> > > > > fieldtrip at donders.ru.nl
> > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > > >
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/0e42f0b5/attachment-0001.html
> >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 8
> > > > Date: Wed, 20 Jan 2016 12:17:12 +0800
> > > > From: Munsif Jatoi <munsif.jatoi at gmail.com>
> > > > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > > > Subject: Re: [FieldTrip] Source Localisation
> > > > Message-ID:
> > > > <CAHnJ=SUHe84yNDVnTLKhGdJBri0mvOdbU0rPqM-Z3-0Gv71Ycg at mail.gmail.com>
> > > > Content-Type: text/plain; charset="utf-8"
> > > >
> > > > Dear Aishwarya,
> > > >
> > > > Please refer to main help tutorials.
> > > >
> > > > Also, you can find out the survey papers written in this area. For
> more,
> > > > SPM website can provide good help.
> > > >
> > > > Best,
> > > > Munsif.
> > > >
> > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) <
> > > > S.Homolle at donders.ru.nl> wrote:
> > > >
> > > > > Dear Aishwarya,
> > > > >
> > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several
> > > > > tutorials about source reconstruction.
> > > > >
> > > > > My recommended start would be:
> > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem
> > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate
> > > > >
> > > > >
> > > > > Hopefully this provides you good start working with EEG source
> > > > > reconstruction
> > > > >
> > > > > Best regards,
> > > > >
> > > > > Simon Hom?lle
> > > > > PhD Candidate
> > > > > Donders Institute for Brain, Cognition and Behaviour
> > > > > Centre for Cognitive Neuroimaging
> > > > > Radboud University Nijmegen
> > > > > Phone: +31-(0)24-36-65059
> > > > > ------------------------------
> > > > > *From:* fieldtrip-bounces at science.ru.nl [
> fieldtrip-bounces at science.ru.nl]
> > > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com]
> > > > > *Sent:* Tuesday, January 19, 2016 5:52 PM
> > > > > *To:* fieldtrip, donders
> > > > > *Subject:* [FieldTrip] Source Localisation
> > > > >
> > > > > Hi guys,
> > > > > I'm currently working on source localization of EEG signals .
> > > > > Im very new to it .
> > > > >
> > > > >
> > > > > Can Anyone provide any inputs ??
> > > > > It would be of great help .
> > > > >
> > > > > --
> > > > > Regards,
> > > > > Aishwarya
> > > > >
> > > > > _______________________________________________
> > > > > fieldtrip mailing list
> > > > > fieldtrip at donders.ru.nl
> > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Munsif Ali H.Jatoi,
> > > >
> > > > Ph D Scholar,
> > > > Centre for Intelligent Signals and Imaging Research,
> > > > Universiti Teknologi PETRONAS,
> > > > Malaysia.
> > > >
> > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/4f6391e8/attachment-0001.html
> >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 9
> > > > Date: Wed, 20 Jan 2016 13:36:16 +0300
> > > > From: Olga Sysoeva <olga.v.sysoeva at gmail.com>
> > > > To: fieldtrip at science.ru.nl
> > > > Subject: [FieldTrip] problems with mri interpolation
> > > > Message-ID:
> > > > <CADtsnVcJLhrPPfq-P1Htj-RmfgzDDgqNhr8vsAoJ2mxxCV7seQ at mail.gmail.com>
> > > > Content-Type: text/plain; charset="utf-8"
> > > >
> > > > Dear Fieldtrippers,
> > > >
> > > >
> > > > I'm encounter the problem with MRI interpolation and reslicing using
> > > >
> > > > FT_VOLUMERESLICE.
> > > >
> > > > I have read my MRI from fif.file and this mri variable contains
> > > >
> > > > mri_K0012.unit, 'm'
> > > >
> > > > mri_K0012.dim, [432, 512, 180]
> > > >
> > > > mri_K0012.anatomy, <432, 512, 180 int16>
> > > >
> > > > mri_K0012.hdr, (1*1 structure)
> > > >
> > > > mri_K0012.transform, (4*4 double)
> > > >
> > > > mri_K0012.coordsys 'neuromag'.
> > > >
> > > >
> > > > Than I used
> > > >
> > > >
> > > > mri = ft_volumereslice([], mri);
> > > >
> > > >
> > > > the output is
> > > >
> > > >
> > > > ?the input is volume data with dimensions [432
> > > > 512 180]
> > > >
> > > > reslicing from [432 512 180] to [256 256 256]
> > > >
> > > > the input is volume data with dimensions [256
> > > > 256 256]
> > > >
> > > > the input is volume data with dimensions [432
> > > > 512 180]
> > > >
> > > > selecting subvolume of 0.0%
> > > >
> > > > reslicing and interpolating anatomy
> > > >
> > > > interpolating
> > > >
> > > > ??? Attempted to access sel(1); index out of
> > > > bounds because numel(sel)=0.
> > > >
> > > >
> > > > Error in ==> ft_sourceinterpolate>my_interpn
> > > > at 663
> > > >
> > > > ft_progress(sel(1)/num, 'interpolating
> > > > %.1f%%\n', 100*sel(1)/num);
> > > >
> > > >
> > > > Error in ==> ft_sourceinterpolate at 583
> > > >
> > > > av( sel) = my_interpn(fv, ax(sel),
> > > > ay(sel), az(sel), cfg.interpmethod,
> > > >
> > > > cfg.feedback);
> > > >
> > > >
> > > > Error in ==> ft_volumereslice at 176
> > > >
> > > > resliced = ft_sourceinterpolate(tmpcfg, mri,
> > > > resliced);?
> > > >
> > > >
> > > > I'm using matlab 7.6.0 (R2008a) and recently
> > > > downloaded fieltrip (also in my previous version of 2013 the error
> > > > was the same).
> > > >
> > > >
> > > > I'd be thankful for the comments.
> > > >
> > > >
> > > > Best Regards,
> > > >
> > > > Olga.
> > > >
> > > > P.S.Actually, I can project my sources
> > > > meaningfully into not interpolated MRI, altoough the images are
> > > > plotted upside down.
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/653068d3/attachment-0001.html
> >
> > > >
> > > > ------------------------------
> > > >
> > > > _______________________________________________
> > > > fieldtrip mailing list
> > > > fieldtrip at donders.ru.nl
> > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > >
> > > > End of fieldtrip Digest, Vol 62, Issue 18
> > > > *****************************************
> > >
> > > -------------- next part --------------
> > > An HTML attachment was scrubbed...
> > > URL: <
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> >
> > >
> > > ------------------------------
> > >
> > > Message: 4
> > > Date: Thu, 21 Jan 2016 08:16:55 +0000
> > > From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl>
> > > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18
> > > Message-ID: <BFFF5195-2F08-4233-B4D5-A0F8F69C17D7 at fcdonders.ru.nl>
> > > Content-Type: text/plain; charset="iso-8859-1"
> > >
> > > Saeed,
> > >
> > > are you using 0 or 1 indexing for your triangles? You probably want to
> use 1 indexing.
> > >
> > > Best,
> > > Jan-Mathijs
> > >
> > >
> > > On Jan 20, 2016, at 6:37 PM, saeed zahran <saeedzahran at hotmail.com
> <mailto:saeedzahran at hotmail.com>> wrote:
> > >
> > > Dear Fieldtrip community,
> > >
> > > I define the volume conductor as:
> > >
> > > vol = [];
> > > vol.bnd(1).pnt=skinpnt
> > > vol.bnd(1).tri=skinf
> > >
> > > vol.bnd(2).pnt=uteruspnt
> > > vol.bnd(2).tri=uterusf
> > >
> > > vol.bnd(3).pnt=uterinecontentpnt
> > > vol.bnd(3).tri=uterinecontentf
> > >
> > > vol.cond = c;
> > >
> > >
> > > But it result with the below error:
> > >
> > > Subscript indices must either be real positive integers or logicals.
> > >
> > > Error in triangle4pt (line 57)
> > > sph_pnt = pnt([tri(jj,:) lv],:);
> > >
> > > Error in ft_headmodel_bemcp (line 101)
> > > vol = triangle4pt(vol);
> > >
> > > Error in ft_prepare_headmodel (line 253)
> > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity);
> > >
> > > Error in openmeeg_eeg_leadfield_example_me (line 91)
> > > vol = ft_prepare_headmodel(cfg, vol);
> > >
> > >
> > > Thank you very much in advance for your help!
> > >
> > > Best regards
> > > Saeed Zahran
> > >
> > > > From: fieldtrip-request at science.ru.nl<mailto:
> fieldtrip-request at science.ru.nl>
> > > > Subject: fieldtrip Digest, Vol 62, Issue 18
> > > > To: fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>
> > > > Date: Wed, 20 Jan 2016 12:00:02 +0100
> > > >
> > > > Send fieldtrip mailing list submissions to
> > > > fieldtrip at science.ru.nl<mailto: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<mailto:
> fieldtrip-request at science.ru.nl>
> > > >
> > > > You can reach the person managing the list at
> > > > fieldtrip-owner at science.ru.nl<mailto: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. Standard BEM or FEM models for use with 256-electrode EEG
> > > > data recorded with EGI caps (Laith Hamid)
> > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG
> > > > data recorded with EGI caps (Cristiano Micheli)
> > > > 3. Standard BEM or FEM models for use with 256-electrode EEG
> > > > data recorded with EGI caps (Laith Hamid)
> > > > 4. Source Localisation (aishwarya selvaraj)
> > > > 5. Re: Source Localisation (Hom?lle)
> > > > 6. Re: plotting neighbours (victoria schroeder)
> > > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG
> > > > data recorded with EGI caps (Cristiano Micheli)
> > > > 8. Re: Source Localisation (Munsif Jatoi)
> > > > 9. problems with mri interpolation (Olga Sysoeva)
> > > >
> > > >
> > > >
> ----------------------------------------------------------------------
> > > >
> > > > Message: 1
> > > > Date: Tue, 19 Jan 2016 15:35:00 +0100
> > > > From: Laith Hamid <lah at pedneuro.uni-kiel.de<mailto:
> lah at pedneuro.uni-kiel.de>>
> > > > To: fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>
> > > > Subject: [FieldTrip] Standard BEM or FEM models for use with
> > > > 256-electrode EEG data recorded with EGI caps
> > > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de
> <mailto:0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de>>
> > > > Content-Type: text/plain; charset="us-ascii"
> > > >
> > > >
> > > >
> > > > Dear community,
> > > >
> > > > My name is Laith Hamid and I am working in the University Medical
> > > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic
> > > > spikes and seizures. Currently I am analysing an EEG data set that
> was
> > > > recorded using a 256-channel EGI system and I wanted to ask whether
> you
> > > > have a standard BEM or FEM head Subscript indices must either be
> real positive integers or logicals.
> > >
> > > Error in triangle4pt (line 57)
> > > sph_pnt = pnt([tri(jj,:) lv],:);
> > >
> > > Error in ft_headmodel_bemcp (line 101)
> > > vol = triangle4pt(vol);
> > >
> > > Error in ft_prepare_headmodel (line 253)
> > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity);
> > >
> > > Error in openmeeg_eeg_leadfield_example_me (line 91)
> > > vol = ft_prepare_headmodel(cfg, vol);
> > > model that extends enough downwards to
> > > > accomodate all 256 electrodes. The current standard BEM model in the
> > > > template folder of Fieldtrip isn't appropriate for source analysis of
> > > > 256-channel EGI data.
> > > >
> > > > Thank you very much in advance for your help!
> > > >
> > > > Best,
> > > >
> > > > Laith
> > > >
> > > >
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/f8805c11/attachment-0001.html
> >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 2
> > > > Date: Tue, 19 Jan 2016 16:16:54 +0100
> > > > From: Cristiano Micheli <michelic72 at gmail.com<mailto:
> michelic72 at gmail.com>>
> > > > To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:
> fieldtrip at science.ru.nl>>
> > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with
> > > > 256-electrode EEG data recorded with EGI caps
> > > > Message-ID:
> > > > <CADW7XCCywrPeWqGTqfP6jWoeLuvBo52poPfRyAPy9__VvkbDLg at mail.gmail.com
> <mailto:CADW7XCCywrPeWqGTqfP6jWoeLuvBo52poPfRyAPy9__VvkbDLg at mail.gmail.com
> >>
> > > > Content-Type: text/plain; charset="utf-8"
> > > >
> > > > Dear Laith,
> > > >
> > > > thanks for your question. You could refer to a factory schematic
> layout
> > > > such as the one in figure 4 of this publication:
> > > >
> http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract
> > > >
> > > > and subsequently use the function ft_prepare_layout to manually
> track the
> > > > points of the custom design on your own (if you dont want to wait for
> > > > somebody from the FT to do the same for you).
> > > >
> > > > cfg = [];
> > > > cfg.image = 'figure4_layout_256_Frontiers.png';
> > > > lay = ft_prepare_layout(cfg);
> > > >
> > > > The following tutorial describes the procedure in more details:
> > > > http://www.fieldtriptoolbox.org/tutorial/layout
> > > >
> > > > Please do not hesitate to get in touch with me for this and other
> matters.
> > > >
> > > > All the best
> > > > Cris Micheli
> > > >
> > > >
> > > >
> > > >
> > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid <
> lah at pedneuro.uni-kiel.de<mailto:lah at pedneuro.uni-kiel.de>>
> > > > wrote:
> > > >
> > > > > Dear community,
> > > > >
> > > > > My name is Laith Hamid and I am working in the University Medical
> Complex
> > > > > of Schleswig-Holstein in Kiel on source analysis of epileptic
> spikes and
> > > > > seizures. Currently I am analysing an EEG data set that was
> recorded using
> > > > > a 256-channel EGI system and I wanted to ask whether you have a
> standard
> > > > > BEM or FEM head model that extends enough downwards to accomodate
> all 256
> > > > > electrodes. The current standard BEM model in the template folder
> of
> > > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI
> data.
> > > > >
> > > > > Thank you very much in advance for your help!
> > > > >
> > > > > Best,
> > > > >
> > > > > Laith
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > fieldtrip mailing list
> > > > > fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
> > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > > >
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/659988fa/attachment-0001.html
> >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 3
> > > > Date: Tue, 19 Jan 2016 17:41:48 +0100
> > > > From: Laith Hamid <lah at pedneuro.uni-kiel.de<mailto:
> lah at pedneuro.uni-kiel.de>>
> > > > To: Fieldtrip <fieldtrip at science.ru.nl<mailto:
> fieldtrip at science.ru.nl>>
> > > > Subject: [FieldTrip] Standard BEM or FEM models for use with
> > > > 256-electrode EEG data recorded with EGI caps
> > > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de
> <mailto:61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de>>
> > > > Content-Type: text/plain; charset="us-ascii"
> > > >
> > > >
> > > >
> > > > Dear Cris,
> > > >
> > > > thank you very much for your answer. I am refering to an issue that
> was
> > > > discussed in this thread from April 2013:
> > > >
> > > > [FieldTrip] source analysis EEG data without MRI
> > > >
> > > > The thread however does not offer a segmentation or head model for
> > > > download. Some electrodes in the EGI 256-electrodes cap are placed on
> > > > the cheeks or on the back of the neck and these areas are not
> modeled by
> > > > the standard BEM skin compartment in the standard BEM model. My
> question
> > > > was about a standard segmentation that extends the skin (and skull)
> > > > compartment downwards to allow these electrodes to sit on the nodes
> of
> > > > the skin mesh.
> > > >
> > > > Best,
> > > > Laith
> > > >
> > > >
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/49665b0c/attachment-0001.html
> >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 4
> > > > Date: Tue, 19 Jan 2016 16:52:55 +0000
> > > > From: aishwarya selvaraj <aishwaryaselvaraj1708 at gmail.com<mailto:
> aishwaryaselvaraj1708 at gmail.com>>
> > > > To: "fieldtrip, donders" <fieldtrip at donders.ru.nl<mailto:
> fieldtrip at donders.ru.nl>>
> > > > Subject: [FieldTrip] Source Localisation
> > > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl
> <mailto:3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl>>
> > > > Content-Type: text/plain; charset="us-ascii"
> > > >
> > > > Hi guys,
> > > > I'm currently working on source localization of EEG signals .
> > > > Im very new to it .
> > > >
> > > >
> > > > Can Anyone provide any inputs ??
> > > > It would be of great help .
> > > >
> > > > --
> > > > Regards,
> > > > Aishwarya
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/3459ed12/attachment-0001.html
> >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 5
> > > > Date: Tue, 19 Jan 2016 17:06:13 +0000
> > > > From: Hom?lle, S. (Simon) <S.Homolle at donders.ru.nl<mailto:
> S.Homolle at donders.ru.nl>>
> > > > To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:
> fieldtrip at science.ru.nl>>
> > > > Subject: Re: [FieldTrip] Source Localisation
> > > > Message-ID:
> > > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl
> <mailto:2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl>>
> > > > Content-Type: text/plain; charset="iso-8859-1"
> > > >
> > > > Dear Aishwarya,
> > > >
> > > > Under http://www.fieldtriptoolbox.org/tutorial there are several
> tutorials about source reconstruction.
> > > >
> > > > My recommended start would be:
> > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem
> > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate
> > > >
> > > >
> > > > Hopefully this provides you good start working with EEG source
> reconstruction
> > > >
> > > > Best regards,
> > > >
> > > > Simon Hom?lle
> > > > PhD Candidate
> > > > Donders Institute for Brain, Cognition and Behaviour
> > > > Centre for Cognitive Neuroimaging
> > > > Radboud University Nijmegen
> > > > Phone: +31-(0)24-36-65059
> > > > ________________________________
> > > > From: fieldtrip-bounces at science.ru.nl<mailto:
> fieldtrip-bounces at science.ru.nl> [fieldtrip-bounces at science.ru.nl<mailto:
> fieldtrip-bounces at science.ru.nl>] on behalf of aishwarya selvaraj [
> aishwaryaselvaraj1708 at gmail.com<mailto:aishwaryaselvaraj1708 at gmail.com>]
> > > > Sent: Tuesday, January 19, 2016 5:52 PM
> > > > To: fieldtrip, donders
> > > > Subject: [FieldTrip] Source Localisation
> > > >
> > > > Hi guys,
> > > > I'm currently working on source localization of EEG signals .
> > > > Im very new to it .
> > > >
> > > >
> > > > Can Anyone provide any inputs ??
> > > > It would be of great help .
> > > >
> > > > --
> > > > Regards,
> > > > Aishwarya
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/d2425227/attachment-0001.html
> >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 6
> > > > Date: Tue, 19 Jan 2016 17:49:21 +0000
> > > > From: victoria schroeder <vic.schroeder2 at gmail.com<mailto:
> vic.schroeder2 at gmail.com>>
> > > > To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:
> fieldtrip at science.ru.nl>>
> > > > Subject: Re: [FieldTrip] plotting neighbours
> > > > Message-ID:
> > > > <CAOWWpozcLgcLNqgF4rMrTRZ_=e8cYCvXgeY5ZJYXx_9YmWnJ_w at mail.gmail.com
> <mailto:CAOWWpozcLgcLNqgF4rMrTRZ_=e8cYCvXgeY5ZJYXx_9YmWnJ_w at mail.gmail.com
> >>
> > > > Content-Type: text/plain; charset="utf-8"
> > > >
> > > > Thank you very much Philipp and Tzvetan!
> > > >
> > > > Things have become much clearer now.
> > > >
> > > > I would like to follow up with a very related question. I am trying
> to
> > > > replicate the analysis for the cluster based permutation test using
> the
> > > > code and the data provided. However, i run into two problems here
> > > >
> > > > First, i get the following error if i use the original code:
> > > > Attempted to access cfg.frequency(2); index out of bounds because
> > > > numel(cfg.frequency)=1.
> > > >
> > > > Error in ft_freqstatistics (line 187)
> > > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2),
> fmax)];
> > > >
> > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20
> 20].
> > > > However, then no significant clusters are found. Which becomes clear
> when
> > > > trying to plot the cluster or by looking at the output of
> > > > ft_freqstatistics.
> > > >
> > > > Does the change in the code , change the output? How can i avoid the
> error
> > > > mentioned above and still get the same output from ft_freqstatistics
> as the
> > > > one provided on the webpage?
> > > >
> > > >
> > > > The relevant section of the toturial is provided below.
> > > > Thank you!
> > > >
> > > > Victoria
> > > >
> > > > Permutation test
> > > >
> > > > Now, run *ft_freqstatistics
> > > > <http://www.fieldtriptoolbox.org/reference/ft_freqstatistics>* to
> compare
> > > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field
> cfg.latency,
> > > > the following configuration is identical to the configuration that
> was used
> > > > for comparing event-related averages in the cluster-based
> permutation tests
> > > > on event related fields tutorial
> > > > <
> http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock>.
> > > > Also see this tutorial
> > > > <
> http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock> for
> > > > a detailed explanation of all the configuration settings. You can
> read more
> > > > about the *ft_prepare_neighbours
> > > > <http://www.fieldtriptoolbox.org/reference/ft_prepare_neighbours>*
> function
> > > > in the FAQ's
> > > > <
> http://www.fieldtriptoolbox.org/faq/how_does_ft_prepare_neighbours_work>.
> > > >
> > > > To load the planar gradient TFRs (also available on the FieldTrip FTP
> > > > servers,freqFIC_planar_cmb.mat
> > > > <
> ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFIC_planar_cmb.mat
> >
> > > > and freqFC_planar_cmb.mat
> > > > <
> ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFC_planar_cmb.mat
> >),
> > > > use:
> > > >
> > > > load freqFIC_planar_cmb
> > > > load freqFC_planar_cmb
> > > >
> > > > cfg = [];
> > > > cfg.channel = {'MEG', '-MLP31', '-MLO12'};
> > > > cfg.latency = 'all';
> > > > cfg.frequency = 20;
> > > > cfg.method = 'montecarlo';
> > > > cfg.statistic = 'ft_statfun_indepsamplesT';
> > > > cfg.correctm = 'cluster';
> > > > cfg.clusteralpha = 0.05;
> > > > cfg.clusterstatistic = 'maxsum';
> > > > cfg.minnbchan = 2;
> > > > cfg.tail = 0;
> > > > cfg.clustertail = 0;
> > > > cfg.alpha = 0.025;
> > > > cfg.numrandomization = 500;
> > > > % prepare_neighbours determines what sensors may form clusters
> > > > cfg_neighb.method = 'distance';
> > > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC);
> > > >
> > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) +
> > > > size(freqFC_planar_cmb.powspctrm,1));
> > > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1;
> > > >
> design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+...
> > > > size(freqFC_planar_cmb.powspctrm,1))) = 2;
> > > >
> > > > cfg.design = design;
> > > > cfg.ivar = 1;
> > > >
> > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb,
> freqFC_planar_cmb);
> > > >
> > > >
> > > >
> > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov <
> tzvetan.popov at uni-konstanz.de<mailto:tzvetan.popov at uni-konstanz.de>>:
> > > >
> > > > >
> > > > > Hi Victoria,
> > > > >
> > > > > oopsy, I think I confused you dramatically. I?m sorry for this.
> You are
> > > > > right I was only scrolling up to the part where the mags were
> analyzed. As
> > > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course
> you can
> > > > > threat them separately, as I was naively thinking as non-neuormag
> user, but
> > > > > indeed combination of both is recommended as I have now learned
> :-)(thanks
> > > > > Phillip). I ran the following steps and I guess this should work
> for you.
> > > > > best
> > > > > tzvetan
> > > > >
> > > > > %%
> > > > > cfg = [];
> > > > > ComCon = ft_combineplanar(cfg,FreqCon);
> > > > > %%
> > > > > cfg = []
> > > > > cfg.method = 'triangulation';
> > > > > cfg.layout = 'neuromag306cmb.lay';
> > > > > cfg.senstype = 'MEG';
> > > > > neighbours = ft_prepare_neighbours(cfg, ComCon)
> > > > > %%
> > > > > % plot neighbours
> > > > > cfg=[];
> > > > > cfg.neighbours = neighbours;
> > > > > cfg.layout = 'neuromag306cmb.lay';
> > > > > ft_neighbourplot(cfg);
> > > > >
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > fieldtrip mailing list
> > > > > fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
> > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > > >
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/de08d8f1/attachment-0001.html
> >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 7
> > > > Date: Tue, 19 Jan 2016 20:50:24 +0100
> > > > From: Cristiano Micheli <michelic72 at gmail.com<mailto:
> michelic72 at gmail.com>>
> > > > To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:
> fieldtrip at science.ru.nl>>
> > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with
> > > > 256-electrode EEG data recorded with EGI caps
> > > > Message-ID:
> > > > <CADW7XCC8BvdVKRAEMw4Jt8v3T6zXjF2zHF_T_4h8ZkuvTbc=1Q at mail.gmail.com
> <mailto:CADW7XCC8BvdVKRAEMw4Jt8v3T6zXjF2zHF_T_4h8ZkuvTbc=1Q at mail.gmail.com
> >>
> > > > Content-Type: text/plain; charset="utf-8"
> > > >
> > > > Dear Laith,
> > > >
> > > > this might be possible if you have the subject-specific MRI by
> following
> > > > the tutorial here:
> > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem
> > > >
> > > > and using the function ft_prepare_mesh and the tutorial command:
> > > >
> > > > cfg=[];
> > > > cfg.tissue={'brain','skull','scalp'};
> > > > cfg.numvertices = [3000 2000 1000];
> > > > bnd=ft_prepare_mesh(cfg,segmentedmri);
> > > >
> > > >
> > > > which uses the segmented MRI (see tutorial). The bnd(3) variable
> should
> > > > contain your triangulated surface with 1000 vertices. Let me know if
> that
> > > > works. Of course you should see the skin and the neck in the
> original MRI.
> > > >
> > > > If you do not have an anatomical MRI that extends down to the chin
> you
> > > > could try with a template, such as this:
> > > >
> ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri
> > > > and the corresponding segmented version
> > > >
> ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat
> > > >
> > > > This goes down to the chin. Then you take care of rearranging the
> position
> > > > of the EEG electrodes according to this:
> > > >
> > > >
> http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel
> > > >
> > > > I hope this helped
> > > > Cris
> > > >
> > > >
> > > >
> > > >
> > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid <
> lah at pedneuro.uni-kiel.de<mailto:lah at pedneuro.uni-kiel.de>>
> > > > wrote:
> > > >
> > > > > Dear Cris,
> > > > >
> > > > > thank you very much for your answer. I am refering to an issue
> that was
> > > > > discussed in this thread from April 2013:
> > > > >
> > > > >
> > > > > [FieldTrip] source analysis EEG data without MRI
> > > > >
> > > > >
> > > > > The thread however does not offer a segmentation or head model for
> > > > > download. Some electrodes in the EGI 256-electrodes cap are placed
> on the
> > > > > cheeks or on the back of the neck and these areas are not modeled
> by the
> > > > > standard BEM skin compartment in the standard BEM model. My
> question was
> > > > > about a standard segmentation that extends the skin (and skull)
> compartment
> > > > > downwards to allow these electrodes to sit on the nodes of the
> skin mesh.
> > > > >
> > > > > Best,
> > > > > Laith
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > fieldtrip mailing list
> > > > > fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
> > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > > >
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/0e42f0b5/attachment-0001.html
> >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 8
> > > > Date: Wed, 20 Jan 2016 12:17:12 +0800
> > > > From: Munsif Jatoi <munsif.jatoi at gmail.com<mailto:
> munsif.jatoi at gmail.com>>
> > > > To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:
> fieldtrip at science.ru.nl>>
> > > > Subject: Re: [FieldTrip] Source Localisation
> > > > Message-ID:
> > > > <CAHnJ=SUHe84yNDVnTLKhGdJBri0mvOdbU0rPqM-Z3-0Gv71Ycg at mail.gmail.com
> <mailto:CAHnJ=SUHe84yNDVnTLKhGdJBri0mvOdbU0rPqM-Z3-0Gv71Ycg at mail.gmail.com
> >>
> > > > Content-Type: text/plain; charset="utf-8"
> > > >
> > > > Dear Aishwarya,
> > > >
> > > > Please refer to main help tutorials.
> > > >
> > > > Also, you can find out the survey papers written in this area. For
> more,
> > > > SPM website can provide good help.
> > > >
> > > > Best,
> > > > Munsif.
> > > >
> > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) <
> > > > S.Homolle at donders.ru.nl<mailto:S.Homolle at donders.ru.nl>> wrote:
> > > >
> > > > > Dear Aishwarya,
> > > > >
> > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several
> > > > > tutorials about source reconstruction.
> > > > >
> > > > > My recommended start would be:
> > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem
> > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate
> > > > >
> > > > >
> > > > > Hopefully this provides you good start working with EEG source
> > > > > reconstruction
> > > > >
> > > > > Best regards,
> > > > >
> > > > > Simon Hom?lle
> > > > > PhD Candidate
> > > > > Donders Institute for Brain, Cognition and Behaviour
> > > > > Centre for Cognitive Neuroimaging
> > > > > Radboud University Nijmegen
> > > > > Phone: +31-(0)24-36-65059
> > > > > ------------------------------
> > > > > *From:* fieldtrip-bounces at science.ru.nl<mailto:
> fieldtrip-bounces at science.ru.nl> [fieldtrip-bounces at science.ru.nl<mailto:
> fieldtrip-bounces at science.ru.nl>]
> > > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com
> <mailto:aishwaryaselvaraj1708 at gmail.com>]
> > > > > *Sent:* Tuesday, January 19, 2016 5:52 PM
> > > > > *To:* fieldtrip, donders
> > > > > *Subject:* [FieldTrip] Source Localisation
> > > > >
> > > > > Hi guys,
> > > > > I'm currently working on source localization of EEG signals .
> > > > > Im very new to it .
> > > > >
> > > > >
> > > > > Can Anyone provide any inputs ??
> > > > > It would be of great help .
> > > > >
> > > > > --
> > > > > Regards,
> > > > > Aishwarya
> > > > >
> > > > > _______________________________________________
> > > > > fieldtrip mailing list
> > > > > fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
> > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Munsif Ali H.Jatoi,
> > > >
> > > > Ph D Scholar,
> > > > Centre for Intelligent Signals and Imaging Research,
> > > > Universiti Teknologi PETRONAS,
> > > > Malaysia.
> > > >
> > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
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> >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 9
> > > > Date: Wed, 20 Jan 2016 13:36:16 +0300
> > > > From: Olga Sysoeva <olga.v.sysoeva at gmail.com<mailto:
> olga.v.sysoeva at gmail.com>>
> > > > To: fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>
> > > > Subject: [FieldTrip] problems with mri interpolation
> > > > Message-ID:
> > > > <CADtsnVcJLhrPPfq-P1Htj-RmfgzDDgqNhr8vsAoJ2mxxCV7seQ at mail.gmail.com
> <mailto:CADtsnVcJLhrPPfq-P1Htj-RmfgzDDgqNhr8vsAoJ2mxxCV7seQ at mail.gmail.com
> >>
> > > > Content-Type: text/plain; charset="utf-8"
> > > >
> > > > Dear Fieldtrippers,
> > > >
> > > >
> > > > I'm encounter the problem with MRI interpolation and reslicing using
> > > >
> > > > FT_VOLUMERESLICE.
> > > >
> > > > I have read my MRI from fif.file and this mri variable contains
> > > >
> > > > mri_K0012.unit, 'm'
> > > >
> > > > mri_K0012.dim, [432, 512, 180]
> > > >
> > > > mri_K0012.anatomy, <432, 512, 180 int16>
> > > >
> > > > mri_K0012.hdr, (1*1 structure)
> > > >
> > > > mri_K0012.transform, (4*4 double)
> > > >
> > > > mri_K0012.coordsys 'neuromag'.
> > > >
> > > >
> > > > Than I used
> > > >
> > > >
> > > > mri = ft_volumereslice([], mri);
> > > >
> > > >
> > > > the output is
> > > >
> > > >
> > > > ?the input is volume data with dimensions [432
> > > > 512 180]
> > > >
> > > > reslicing from [432 512 180] to [256 256 256]
> > > >
> > > > the input is volume data with dimensions [256
> > > > 256 256]
> > > >
> > > > the input is volume data with dimensions [432
> > > > 512 180]
> > > >
> > > > selecting subvolume of 0.0%
> > > >
> > > > reslicing and interpolating anatomy
> > > >
> > > > interpolating
> > > >
> > > > ??? Attempted to access sel(1); index out of
> > > > bounds because numel(sel)=0.
> > > >
> > > >
> > > > Error in ==> ft_sourceinterpolate>my_interpn
> > > > at 663
> > > >
> > > > ft_progress(sel(1)/num, 'interpolating
> > > > %.1f%%\n', 100*sel(1)/num);
> > > >
> > > >
> > > > Error in ==> ft_sourceinterpolate at 583
> > > >
> > > > av( sel) = my_interpn(fv, ax(sel),
> > > > ay(sel), az(sel), cfg.interpmethod,
> > > >
> > > > cfg.feedback);
> > > >
> > > >
> > > > Error in ==> ft_volumereslice at 176
> > > >
> > > > resliced = ft_sourceinterpolate(tmpcfg, mri,
> > > > resliced);?
> > > >
> > > >
> > > > I'm using matlab 7.6.0 (R2008a) and recently
> > > > downloaded fieltrip (also in my previous version of 2013 the error
> > > > was the same).
> > > >
> > > >
> > > > I'd be thankful for the comments.
> > > >
> > > >
> > > > Best Regards,
> > > >
> > > > Olga.
> > > >
> > > > P.S.Actually, I can project my sources
> > > > meaningfully into not interpolated MRI, altoough the images are
> > > > plotted upside down.
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> > > >
> > > > ------------------------------
> > > >
> > > > _______________________________________________
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> > > > fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
> > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > >
> > > > End of fieldtrip Digest, Vol 62, Issue 18
> > > > *****************************************
> > > _______________________________________________
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> > >
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> > > fieldtrip mailing list
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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