[FieldTrip] fieldtrip Digest, Vol 62, Issue 18

Cristiano Micheli michelic72 at gmail.com
Thu Jan 21 12:06:13 CET 2016


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...
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> 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
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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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> >
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> >
> > End of fieldtrip Digest, Vol 62, Issue 18
> > *****************************************
>
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