[FieldTrip] fieldtrip Digest, Vol 62, Issue 18
saeed zahran
saeedzahran at hotmail.com
Wed Jan 20 18:37:32 CET 2016
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
>
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>
> 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
>
>
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> ------------------------------
>
> 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
> >
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> ------------------------------
>
> 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
>
>
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> ------------------------------
>
> 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
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> ------------------------------
>
> 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 --------------
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>
> ------------------------------
>
> 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
> >
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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
> >
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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
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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.
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