[FieldTrip] fieldtrip Digest, Vol 62, Issue 19
saeed zahran
saeedzahran at hotmail.com
Thu Jan 21 19:14:01 CET 2016
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 --------------
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>
> ------------------------------
>
> 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...
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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: <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 --------------
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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 --------------
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> >
> > ------------------------------
> >
> > 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 --------------
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> >
> > ------------------------------
> >
> > 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 --------------
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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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> >
> > _______________________________________________
> > fieldtrip mailing list
> > 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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