From jm.horschig at donders.ru.nl  Thu Aug  1 12:37:08 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Thu, 01 Aug 2013 12:37:08 +0200
Subject: [FieldTrip] ancova for sources analysis
In-Reply-To: <2264a36963356fbe.51f8fb71@upo.es>
References: <167095db43e3fd69.51f8d35e@upo.es>
	<1763660954.2174368.1375257362812.JavaMail.root@sculptor.zimbra.ru.nl>
	<2264a36963356fbe.51f8fb71@upo.es>
Message-ID: <51FA3A54.8020001@donders.ru.nl>

Dear Gabriel,

if you have a .stat field, you did already run statistics on your data. 
I wouldn't regress anything out of e.g. t-values. Rather, the idea is to 
regress out confounding factors before doing statistics, so that you 
reduce variance across trials and subsequently maximize sensitivity of 
your statistical test. I could really advise you to read the paper I 
suggested, the rationale is explained there.
Moreover, if you are interested in a covariate like 'age', a simple 
correlational analysis might make more sense. As stated, the idea of 
regressconfound is to explain and remove variance across observations, 
but depending on what you want, a correlation might make more sense.
Want to improve your stats? Then go for regressconfound. Find out if 
there is age explains neural effects? Then go for a simple correlation.

Best,
Jörn

On 7/31/2013 11:56 AM, Gabriel Gonzalez Escamilla wrote:
> Thank you all for your responses.
>
> The last problem I did wrote is now solved, see below.
>
> I had a field called 'stat' instead of the 'pow', I'm guessing this 
> field was set before, so, now i'm using this field as if it was the 
> 'pow' I needed and it's working, Is that OK?
>
> Now it takes me to the next question, my data has the avg field, and 
> it says that will update the descriptives but that the 'method' is 
> missing, is this update necessary? or can I just skeep it?
>
>
> Many thanks in advanced,
> Gabriel
>
>
> ----- Mensaje original -----
> De: "Stolk, A." <a.stolk at fcdonders.ru.nl>
> Fecha: Miércoles, 31 de Julio de 2013, 10:04 am
> Asunto: Re: [FieldTrip] ancova for sources analysis
> A: FieldTrip discussion list <fieldtrip at science.ru.nl>
>
> >Dear Gabriel,
> >
> > This page demonstrates how to remove contributions to the data 
> originating from head movement, but one could as well follow the same 
> principle for any other type of covariate (e.g. eye movement related 
> activity).
> >
> > http://fieldtrip.fcdonders.nl/example/how_to_incorporate_head_movements_in_meg_analysis?
> >
> > Yours,
> > Arjen
> >
> ------------------------------------------------------------------------
>
>     *> Van: *"Gabriel Gonzalez Escamilla" <ggonesc at upo.es>
>     *> Aan: *"fieFieldTrip discussion list" <fieldtrip at science.ru.nl>
>     *> Verzonden: *Woensdag 31 juli 2013 09:05:34
>     *> Onderwerp: *[FieldTrip] ancova for sources analysis
>     >
>     > Dear fieldtrip experts,
>     >
>     > I'm wondering if it is possible to perform an ancova or to remove
>     the effect of a covariate in a source analysis?
>     >
>     > Many thanks in advanced,
>     > Gabriel
>     > _______________________________________________
>     > fieldtrip mailing list
>     > fieldtrip at donders.ru.nl
>     > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> <font size="3">--------------------------<br />PhD. student Gabriel 
> González-Escamilla<br />Laboratory of Functional Neuroscience<br 
> />Department of Physiology, Anatomy, and Cell Biology<br />University 
> Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br 
> />- Spain -<br /><br />Email: ggonesc at upo.es<br 
> />http://www.upo.es/neuroaging/es/</font>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From lzyang at ustc.edu.cn  Sat Aug  3 10:49:59 2013
From: lzyang at ustc.edu.cn (lzyang)
Date: Sat, 03 Aug 2013 16:49:59 +0800
Subject: [FieldTrip] units of data sample read from neuroscan avg file is
	incorrect
Message-ID: <51FCC437.5070409@ustc.edu.cn>

Dear fieldtrip list,
I used ft_read_data to read in .avg files (neuroscan format) to do some
advanced analysis.
data=ft_read_data('sham.avg', 'dataformat', 'ns_avg');
I noticed that the unit of data sample read by this function is incorrect.
Values of samples ranged from -0.1 to 0.1.
I will appreciate if anyone can give me some hints on how to import avg
files correctly using fieldtrip.

Thanks very much!

Best Regards,
-Lizhuang




From politzerahless at gmail.com  Sat Aug  3 13:48:58 2013
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Sat, 3 Aug 2013 07:48:58 -0400
Subject: [FieldTrip] fieldtrip Digest, Vol 33, Issue 3
In-Reply-To: <mailman.1.1375524018.6192.fieldtrip@science.ru.nl>
References: <mailman.1.1375524018.6192.fieldtrip@science.ru.nl>
Message-ID: <CAJT2k__JuKQth_DrjFDn39rJBMsNSAx1wsg=RAiq-mOq+D0N9g@mail.gmail.com>

Hi Lizhuang,

I haven't used Fieldtrip to import .avg files so I'm not sure about this,
but I wonder if this is related to the same problem in EEGLAB. EEGLAB also
scales .avg files like this when importing them, for some reason, so if the
Fieldtrip function is based on EEGLAB code these issues may be related.
(However, I just looked at read_ns_avg.m, which is what ft_read_data calls,
and it doesn't say it's copied from EEGLAB). If you have EEGLAB, you can
add the custom function loadavg_bcl.m to your path (it is available at
http://sccn.ucsd.edu/pipermail/eeglablist/2011/003986.html, as one of the
attachments near the bottom), use that to import the .avg file, and then
use the EEGLAB function eeglab2fieldtrip() to get the data into FieldTrip.

Also, have you tried reading the data with ft_preprocessing() instead of
ft_read_data? ft_read_data is kind of a low-level function; in the past I
think I've had better luck just using ft_preprocessing.

Best,
Steve


Stephen Politzer-Ahles
New York University, Abu Dhabi
Psychology Department


> Message: 1
> Date: Sat, 03 Aug 2013 16:49:59 +0800
> From: lzyang <lzyang at ustc.edu.cn>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] units of data sample read from neuroscan avg file
>         is      incorrect
> Message-ID: <51FCC437.5070409 at ustc.edu.cn>
> Content-Type: text/plain; charset=GB2312
>
> Dear fieldtrip list,
> I used ft_read_data to read in .avg files (neuroscan format) to do some
> advanced analysis.
> data=ft_read_data('sham.avg', 'dataformat', 'ns_avg');
> I noticed that the unit of data sample read by this function is incorrect.
> Values of samples ranged from -0.1 to 0.1.
> I will appreciate if anyone can give me some hints on how to import avg
> files correctly using fieldtrip.
>
> Thanks very much!
>
> Best Regards,
> -Lizhuang
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From politzerahless at gmail.com  Sat Aug  3 13:50:40 2013
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Sat, 3 Aug 2013 07:50:40 -0400
Subject: [FieldTrip] units of data sample read from neuroscan avg file
	is incorrect
Message-ID: <CAJT2k_8z9nv4YnX8AKYhUAwSv4cHnaPDDH7KqrjQ-T=f1RAAdg@mail.gmail.com>

Hi Lizhuang,

I haven't used Fieldtrip to import .avg files so I'm not sure about this,
but I wonder if this is related to the same problem in EEGLAB. EEGLAB also
scales .avg files like this when importing them, for some reason, so if the
Fieldtrip function is based on EEGLAB code these issues may be related.
(However, I just looked at read_ns_avg.m, which is what ft_read_data calls,
and it doesn't say it's copied from EEGLAB). If you have EEGLAB, you can
add the custom function loadavg_bcl.m to your path (it is available at
http://sccn.ucsd.edu/pipermail/eeglablist/2011/003986.html, as one of the
attachments near the bottom), use that to import the .avg file, and then
use the EEGLAB function eeglab2fieldtrip() to get the data into FieldTrip.

Also, have you tried reading the data with ft_preprocessing() instead of
ft_read_data? ft_read_data is kind of a low-level function; in the past I
think I've had better luck just using ft_preprocessing.

Best,
Steve



Stephen Politzer-Ahles
New York University, Abu Dhabi
Psychology Department


> Message: 1
> Date: Sat, 03 Aug 2013 16:49:59 +0800
> From: lzyang <lzyang at ustc.edu.cn>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] units of data sample read from neuroscan avg file
>         is      incorrect
> Message-ID: <51FCC437.5070409 at ustc.edu.cn>
> Content-Type: text/plain; charset=GB2312
>
> Dear fieldtrip list,
> I used ft_read_data to read in .avg files (neuroscan format) to do some
> advanced analysis.
> data=ft_read_data('sham.avg', 'dataformat', 'ns_avg');
> I noticed that the unit of data sample read by this function is incorrect.
> Values of samples ranged from -0.1 to 0.1.
> I will appreciate if anyone can give me some hints on how to import avg
> files correctly using fieldtrip.
>
> Thanks very much!
>
> Best Regards,
> -Lizhuang
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From Izabela.Mikula at mpi.nl  Tue Aug  6 12:10:32 2013
From: Izabela.Mikula at mpi.nl (Izabela Mikula)
Date: Tue, 6 Aug 2013 12:10:32 +0200
Subject: [FieldTrip] Error in ft_rejectartifact for the newest fieldtrip
	version
Message-ID: <9532B831-AB8E-4EBC-A984-5A3783E5313D@mpi.nl>

Dear all,
I was wondering if any of you have ever encountered similar problem and might know if I'm doing something wrong or it is a bug..

I have tried using (my old scripts for preprocessing) ft_rejectartifact(cfg, data) but I get an error:

evaluating artifact_jump
??? Error using ==> feval
Undefined function or method 'artifact_jump' for input arguments of type 'struct'.

Error in ==> ft_rejectartifact at 257
    cfg = feval(sprintf('artifact_%s', cfg.artfctdef.type{type}), cfg, data);

It is important to note that this error only occurs when using the newest fieldtrip version. For previous versions it works without any problems. I have also tried multiple datasets, but the problem remains.
 
data = 

       fsample: 1200
          grad: [1x1 struct]
    sampleinfo: [180x2 double]
     trialinfo: [180x1 double]
         trial: {1x180 cell}
          time: {1x180 cell}
         label: {273x1 cell}
           cfg: [1x1 struct]

and

cfg.artfctdef = 

          reject: 'complete'
            jump: [1x1 struct]
          muscle: [1x1 struct]
            type: {2x1 cell}
    minaccepttim: 0.1000
      crittoilim: []
        feedback: 'no'

Thanks in advance!

Best,
Izabela




From jan.schoffelen at donders.ru.nl  Tue Aug  6 13:13:09 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Tue, 6 Aug 2013 13:13:09 +0200
Subject: [FieldTrip] Error in ft_rejectartifact for the newest fieldtrip
	version
In-Reply-To: <9532B831-AB8E-4EBC-A984-5A3783E5313D@mpi.nl>
References: <9532B831-AB8E-4EBC-A984-5A3783E5313D@mpi.nl>
Message-ID: <C671E708-23FB-40E2-9094-1DFD80CAED92@donders.ru.nl>

Hi Izabela,

This is indeed a bug. We reorganized our compat-directory, that is dealing with backward compatibility issues. One of these issues was to support backward compatibility for calling ft-functions without the ft_prefix. E.g. calling freqanalysis should redirect to a call to ft_freqanalysis. With this feature removed, ft_rejectartifact cannot execute artifact_xxx, because it is not redirected anymore to ft_artifact_xxx.
I have fixed this. It should be available within 15 minutes on the DCCN Fieldtrip version, and in the download version as of tonight.

Thanks for reporting,
Jan-Mathijs

 
On Aug 6, 2013, at 12:10 PM, Izabela Mikula wrote:

> Dear all,
> I was wondering if any of you have ever encountered similar problem and might know if I'm doing something wrong or it is a bug..
> 
> I have tried using (my old scripts for preprocessing) ft_rejectartifact(cfg, data) but I get an error:
> 
> evaluating artifact_jump
> ??? Error using ==> feval
> Undefined function or method 'artifact_jump' for input arguments of type 'struct'.
> 
> Error in ==> ft_rejectartifact at 257
>    cfg = feval(sprintf('artifact_%s', cfg.artfctdef.type{type}), cfg, data);
> 
> It is important to note that this error only occurs when using the newest fieldtrip version. For previous versions it works without any problems. I have also tried multiple datasets, but the problem remains.
> 
> data = 
> 
>       fsample: 1200
>          grad: [1x1 struct]
>    sampleinfo: [180x2 double]
>     trialinfo: [180x1 double]
>         trial: {1x180 cell}
>          time: {1x180 cell}
>         label: {273x1 cell}
>           cfg: [1x1 struct]
> 
> and
> 
> cfg.artfctdef = 
> 
>          reject: 'complete'
>            jump: [1x1 struct]
>          muscle: [1x1 struct]
>            type: {2x1 cell}
>    minaccepttim: 0.1000
>      crittoilim: []
>        feedback: 'no'
> 
> Thanks in advance!
> 
> Best,
> Izabela
> 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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From ben.vanlier at bsse.ethz.ch  Tue Aug  6 17:56:55 2013
From: ben.vanlier at bsse.ethz.ch (van Lier  Ben)
Date: Tue, 6 Aug 2013 15:56:55 +0000
Subject: [FieldTrip] from trials to continuous and an error in selfromraw
Message-ID: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A6CBB0@MBX23.d.ethz.ch>

Hi guys,

for testing purposes im trying to use data in trials as one continuous piece of data. when i do freqanalysis with cfg.trials = 'all' and then singleplotTFR, i get to see only 1 trial. it should plot the spectra of all of them right? i do use cfg.continuous = yes
i can tell it is processing all the trials in the command window feedback and databrowser is putting them together fine.

i guess related, when i do cfg.trials = '1' (or any) and then freqanalysis it gives me the following error:

--------------------------
Error using selfromraw (line 13)
incorrect specification of requested repetitions

Error in ft_selectdata_old (line 547)
    data = selfromraw(data, 'rpt', selrpt);

Error in ft_selectdata (line 45)
  [varargout{1:nargout}] = ft_selectdata_old(varargin{:});

Error in ft_freqanalysis (line 225)
  data = ft_selectdata(data, 'rpt', cfg.trials);
----------------------------

i tried with data coming from ft_appendata (2 copies of the same file) and also with ft_definetrial from one continuous file.

i am using the version of 5 aug 13

anyone knows whats going wrong?

cheers
Ben




From eelke.spaak at donders.ru.nl  Tue Aug  6 19:44:33 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Tue, 6 Aug 2013 19:44:33 +0200
Subject: [FieldTrip] from trials to continuous and an error in selfromraw
In-Reply-To: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A6CBB0@MBX23.d.ethz.ch>
References: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A6CBB0@MBX23.d.ethz.ch>
Message-ID: <CABPNLUrc3FRn5V9h+kmsqDgoDPQBc26k+5kvfj_1OpzrSNDAqg@mail.gmail.com>

Hi Ben,

The cfg.trials option for ft_freqanalysis refers to which trials
should be used in the computation of the output. By default,
ft_freqanalysis returns the average over all those trials. If you want
to get estimates for each individual trial, you should specify
cfg.keeptrials = 'yes'. (See also
http://fieldtrip.fcdonders.nl/reference/ft_freqanalysis .) I am not
sure if ft_singleplotTFR will give you plots for individual trials,
though; I think it will do the averaging anyway. To get individual
trial plots, you probably have to call the plotting function several
times with cfg.trials = 1, 2, 3, etc.

Regarding cfg.trials = '1', it is important to use just a regular
scalar quantity, and not a string, so cfg.trials = 1.

Best,
Eelke

On 6 August 2013 17:56, van Lier  Ben <ben.vanlier at bsse.ethz.ch> wrote:
> Hi guys,
>
> for testing purposes im trying to use data in trials as one continuous piece of data. when i do freqanalysis with cfg.trials = 'all' and then singleplotTFR, i get to see only 1 trial. it should plot the spectra of all of them right? i do use cfg.continuous = yes
> i can tell it is processing all the trials in the command window feedback and databrowser is putting them together fine.
>
> i guess related, when i do cfg.trials = '1' (or any) and then freqanalysis it gives me the following error:
>
> --------------------------
> Error using selfromraw (line 13)
> incorrect specification of requested repetitions
>
> Error in ft_selectdata_old (line 547)
>     data = selfromraw(data, 'rpt', selrpt);
>
> Error in ft_selectdata (line 45)
>   [varargout{1:nargout}] = ft_selectdata_old(varargin{:});
>
> Error in ft_freqanalysis (line 225)
>   data = ft_selectdata(data, 'rpt', cfg.trials);
> ----------------------------
>
> i tried with data coming from ft_appendata (2 copies of the same file) and also with ft_definetrial from one continuous file.
>
> i am using the version of 5 aug 13
>
> anyone knows whats going wrong?
>
> cheers
> Ben
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From haristz at gmail.com  Tue Aug  6 20:24:55 2013
From: haristz at gmail.com (Charidimos Tzagarakis)
Date: Tue, 6 Aug 2013 13:24:55 -0500
Subject: [FieldTrip] question about virtual electrode MNI coordinates
Message-ID: <CAFN2X+fdvTW8jkx1EPS8C+J_FGRTQgTtYL38aYw7Gv6BbLtsxg@mail.gmail.com>

Hi there,
I have a question regarding virtual electrodes: How can I double check that
the MNI coordinates that I enter are correctly interpreted?
More specifically:
I have followed the the extended beamforming tutorial in the "Appendix" and
have been able to transpose it to my data (I have 4D/BTi MEG files and
Dicom mri volumes).The part I am not certain about is the call to the LCMV
beamformer.
Here it is in my case ( I just want to get the voxel were the power is max
in the previous analysis):
cfg              = [];
cfg.method       = 'lcmv';
cfg.vol          = volfcm;
cfg.grid.pos     = source_diff.pos(maxpowindx, :);
cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
cfg.grid.outside = [];
cfg.grad=senscm
source_idx       = ft_sourceanalysis(cfg, tlock);
My headmodel does not include MEG channel information so I need to also
define the cfg.grad parameter. What I don't understand is how cfg.grid.pos
(which is in MNI coordinates as per the previous part of the tutorial) can
be correctly applied to the coordinates of the headmodel and the channels
since these 2 are not in MNI coordinates (in my case they are in 4d/Bti
coordinates and rescaled to cm).In the previous part of the tutorial this
is (if I understand correctly) accomplished because the leadfield used when
calling ft_sourceanalysis was created using and MNI-warped template. I
don't see where the equivalent part is when estimating the virtual
electrode though.
Any advice you may have would be much appreciated.
Best,
Haris


Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
University of Minnesota Dept of Neuroscience and Brain Sciences Center
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From franziska.bilger at uni-ulm.de  Wed Aug  7 11:23:50 2013
From: franziska.bilger at uni-ulm.de (franziska.bilger at uni-ulm.de)
Date: Wed, 07 Aug 2013 11:23:50 +0200
Subject: [FieldTrip] topoplotER - how to plot a selection of channels ?
Message-ID: <20130807112350.i24h5npq80sgscws@imap.uni-ulm.de>

Dear subscribers,

I´m using fieldtrip to analyze the data for my bachelor thesis (topic:  
motor imagery in patientens in vegetative state) and I would be happy  
to get some help concerning the function ft_topoplotER.

Originally, my data derives from a 256-channel system, but I only like  
to plot a selection of 60 channels above the motor cortex.
This is my Region of Interest.
When I´m now plotting the data from these 60 channels with  
ft_topoplotER I receive a figure, which shows the plotted activation  
over the whole cortex.

My Question: Is there a possibility to plot only the activation in my  
Region of Interest/over the selected 60 channels above the motor cortex?

This would result in a figure where there´s only activation shown over  
the motor cortex and the rest of the plot is blank/white.

Thank you very much!

Kind regards,
Franziska





From jm.horschig at donders.ru.nl  Wed Aug  7 11:41:26 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 07 Aug 2013 11:41:26 +0200
Subject: [FieldTrip] topoplotER - how to plot a selection of channels ?
In-Reply-To: <20130807112350.i24h5npq80sgscws@imap.uni-ulm.de>
References: <20130807112350.i24h5npq80sgscws@imap.uni-ulm.de>
Message-ID: <52021646.4050203@donders.ru.nl>

Hi Franziska,

check out the help of ft_topoplotER and what options there are for 
cfg.interpolation, one of these does what you want (afair 'cubic'). An 
alternative would be to set datapoints of all irrelevant channels to nan 
and then use cfg.interpolatenan = 'no', but the former suggestion is 
cleaner/better/easier than the latter.

Good luck with writing your thesis!
Best,
Jörm

On 8/7/2013 11:23 AM, franziska.bilger at uni-ulm.de wrote:
> Dear subscribers,
>
> I´m using fieldtrip to analyze the data for my bachelor thesis (topic: 
> motor imagery in patientens in vegetative state) and I would be happy 
> to get some help concerning the function ft_topoplotER.
>
> Originally, my data derives from a 256-channel system, but I only like 
> to plot a selection of 60 channels above the motor cortex.
> This is my Region of Interest.
> When I´m now plotting the data from these 60 channels with 
> ft_topoplotER I receive a figure, which shows the plotted activation 
> over the whole cortex.
>
> My Question: Is there a possibility to plot only the activation in my 
> Region of Interest/over the selected 60 channels above the motor cortex?
>
> This would result in a figure where there´s only activation shown over 
> the motor cortex and the rest of the plot is blank/white.
>
> Thank you very much!
>
> Kind regards,
> Franziska
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands



From ben.vanlier at bsse.ethz.ch  Wed Aug  7 13:00:31 2013
From: ben.vanlier at bsse.ethz.ch (van Lier  Ben)
Date: Wed, 7 Aug 2013 11:00:31 +0000
Subject: [FieldTrip] from trials to continuous and an error in selfromraw
In-Reply-To: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A6CBB0@MBX23.d.ethz.ch>
References: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A6CBB0@MBX23.d.ethz.ch>
Message-ID: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A6CC10@MBX23.d.ethz.ch>

Hi Eelke,

thanks. its the little things you miss so cfg.trials = 1 works ofcourse :)

for plotting all the trials in a continuous spectrum i just merge them into 1 big trial first

cfg = [];
cfg.trl = [1 max(max(data.sampleinfo)) 0];
data = ft_redefinetrial(cfg, data);

perfect for my purposes, im trying to reanalyze old recordings chopped into several files but ft_append puts them in separate trials.

liking fieldtrip alot so far, very flexible :)

cheers
Ben



From jm.horschig at donders.ru.nl  Wed Aug  7 14:52:32 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 07 Aug 2013 14:52:32 +0200
Subject: [FieldTrip] question about virtual electrode MNI coordinates
In-Reply-To: <CAFN2X+fdvTW8jkx1EPS8C+J_FGRTQgTtYL38aYw7Gv6BbLtsxg@mail.gmail.com>
References: <CAFN2X+fdvTW8jkx1EPS8C+J_FGRTQgTtYL38aYw7Gv6BbLtsxg@mail.gmail.com>
Message-ID: <52024310.1020109@donders.ru.nl>

Dear Charidimos,

thanks very much for pointing to this, it is indeed an error in the 
appendix of the tutorial. cfg.grid.pos should be based on the 
subject-specific MRI or sourcemodel. So, correctly it should say that 
you need to load sourcemodel.mat (i.e. subject specific grid) and then 
use sourcemodel.pos(maxpowindx, :)
The rationale in principle is that the warped grid has the same size and 
is indexed the same as the original grid; that is why you can use the 
index variable obtained from the MNI-warped source reconstructed data. 
The virtual channel reconstruction should however still be done in 
whatever coordinate system the subject's anatomical data is in. I will 
update the appendix accordingly.

Best,
Jörn

On 8/6/2013 8:24 PM, Charidimos Tzagarakis wrote:
> Hi there,
> I have a question regarding virtual electrodes: How can I double check 
> that the MNI coordinates that I enter are correctly interpreted?
> More specifically:
> I have followed the the extended beamforming tutorial in the 
> "Appendix" and have been able to transpose it to my data (I have 
> 4D/BTi MEG files and Dicom mri volumes).The part I am not certain 
> about is the call to the LCMV beamformer.
> Here it is in my case ( I just want to get the voxel were the power is 
> max in the previous analysis):
> cfg              = [];
> cfg.method       = 'lcmv';
> cfg.vol          = volfcm;
> cfg.grid.pos     = source_diff.pos(maxpowindx, :);
> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
> cfg.grid.outside = [];
> cfg.grad=senscm
> source_idx       = ft_sourceanalysis(cfg, tlock);
> My headmodel does not include MEG channel information so I need to 
> also define the cfg.grad parameter. What I don't understand is how 
> cfg.grid.pos (which is in MNI coordinates as per the previous part of 
> the tutorial) can be correctly applied to the coordinates of the 
> headmodel and the channels since these 2 are not in MNI coordinates 
> (in my case they are in 4d/Bti coordinates and rescaled to cm).In the 
> previous part of the tutorial this is (if I understand correctly) 
> accomplished because the leadfield used when calling ft_sourceanalysis 
> was created using and MNI-warped template. I don't see where the 
> equivalent part is when estimating the virtual electrode though.
> Any advice you may have would be much appreciated.
> Best,
> Haris
>
>
> Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
> University of Minnesota Dept of Neuroscience and Brain Sciences Center
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From annevanhoogmoed at email.arizona.edu  Thu Aug  8 05:51:47 2013
From: annevanhoogmoed at email.arizona.edu (van Hoogmoed, Anne H - (annevanhoogmoed))
Date: Thu, 8 Aug 2013 03:51:47 +0000
Subject: [FieldTrip] reading in and segmenting Netstation data
Message-ID: <B4002ED52EC6814D8B6E1FF85B6AFBB30A198EA7@SPACEMT.catnet.arizona.edu>

Dear all,



I'm using Fieldtrip to analyze my Netstation data. The problem is that the segmented data (incl triggers) are shifted in Fieldtrip as compared to the Netstation analysis.

I've checked several things:

- The events are the same in Netstation and Fieldtrip

- The raw data look the same in both programs

- Fieldtrip produces the right trl based on the triggers.



The script I'm using is this:

cfg = [];

cfg.dataset = 'c007_raw';

cfg.continuous = 'yes';

data_eeg = ft_preprocessing(cfg);



hdr = ft_read_header('c007_raw');

event = ft_read_event('c007_raw');



cfg = [];

cfg.trialfun = 'trialfun_first_enc';

cfg_trials = ft_definetrial(cfg);

data_trials = ft_redefinetrial(cfg_trials, data_eeg);





The trialfun I'm using is this:

function [trl, event] = trialfun_first(cfg)

load event;

load hdr;





value = [event.value];

sample = [event.sample];

% determine the number of samples before and after the trigger

pretrig = -100; % = 200 ms

posttrig = 400; % = 800 ms

% for each trigger

trl = [];

for j = 1:length(event)

if (strcmp(event(1,j).value, '+Lrt') || strcmp(event(1,j).value, '+OOt')) || strcmp(event(1,j).value, '+SOt')

trlbegin = event(1,j).sample + pretrig;

trlend = event(1,j).sample + posttrig;

offset = pretrig;

newtrl = [trlbegin trlend offset];

trl = [trl; newtrl];

end

j = j + 1;

end





Does anyone know what I'm doing wrong here?



Thank you very much for your help!



Kind regards,



Anne



Anne van Hoogmoed

Down Syndrome Research Group

Department of Psychology, University of Arizona
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From d.lozanosoldevilla at fcdonders.ru.nl  Thu Aug  8 08:12:42 2013
From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego))
Date: Thu, 8 Aug 2013 08:12:42 +0200 (CEST)
Subject: [FieldTrip] reading in and segmenting Netstation data
In-Reply-To: <B4002ED52EC6814D8B6E1FF85B6AFBB30A198EA7@SPACEMT.catnet.arizona.edu>
Message-ID: <1178733115.2232641.1375942362693.JavaMail.root@sculptor.zimbra.ru.nl>

Hi Anne, What do you mean by "shifted"? Time samples mismatch might be? I don't see what's going wrong with the code you pasted but it'd be nice if you could file a bug (I'll assign to me) with a piece of preprocessed data with fieldtrip and a plot about how data looks like with Netstation to have a bit more info. best, Diego ps : do you have a non-integer eeg sampling rate, like 511.3Hz? ----- Original Message -----
> From: "van Hoogmoed , Anne H - ( annevanhoogmoed )" < annevanhoogmoed
> @email. arizona . edu >
> To: fieldtrip @science. ru . nl
> Sent: Thursday, 8 August, 2013 5:51:47 AM
> Subject: [ FieldTrip ] reading in and segmenting Netstation data
> Dear all,
> I'm using Fieldtrip to analyze my Netstation data. The problem is that
> the segmented data (incl triggers) are shifted in Fieldtrip as
> compared to the Netstation analysis.
> I've checked several things:
> - The events are the same in Netstation and Fieldtrip
> - The raw data look the same in both programs
> - Fieldtrip produces the right trl based on the triggers.
> The script I'm using is this:
> cfg = [];
> cfg . dataset = 'c007_ raw' ;
> cfg .continuous = 'yes' ;
> data_ eeg = ft_ preprocessing ( cfg );
> hdr = ft_read_header( 'c007_ raw' );
> event = ft_read_event( 'c007_ raw' );
> cfg = [];
> cfg . trialfun = 'trialfun _first_ enc' ;
> cfg _trials = ft_ definetrial ( cfg );
> data_trials = ft_ redefinetrial ( cfg _trials, data_ eeg );
> The trialfun I'm using is this:
> function [ trl , event] = trialfun _first( cfg )
> load event ;
> load hdr ;
> value = [event.value];
> sample = [event.sample];
> % determine the number of samples before and after the trigger
> pretrig = -100; % = 200 ms
> posttrig = 400; % = 800 ms
> % for each trigger
> trl = [];
> for j = 1:length(event)
> if ( strcmp (event(1,j).value, '+ Lrt' ) || strcmp (event(1,j).value,
> '+ OOt' )) || strcmp (event(1,j).value, '+ SOt' )
> trlbegin = event(1,j).sample + pretrig ;
> trlend = event(1,j).sample + posttrig ;
> offset = pretrig ;
> newtrl = [ trlbegin trlend offset];
> trl = [ trl ; newtrl ];
> end
> j = j + 1;
> end
> Does anyone know what I'm doing wrong here?
> Thank you very much for your help!
> Kind regards,
> Anne
> Anne van Hoogmoed
> Down Syndrome Research Group
> Department of Psychology, University of Arizona
> _______________________________________________
> fieldtrip mailing list
> fieldtrip @ donders . ru . nl
> http ://mailman.science. ru . nl /mailman/ listinfo / fieldtrip
-- PhD Student Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen NL-6525 EN Nijmegen The Netherlands http :// www . ru . nl /people/ donders /lozano-soldevilla-d/ 
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From elisa at csl.psychol.cam.ac.uk  Thu Aug  8 12:23:53 2013
From: elisa at csl.psychol.cam.ac.uk (Elisa Carrus)
Date: Thu, 08 Aug 2013 11:23:53 +0100
Subject: [FieldTrip] question about virtual electrode MNI coordinates
In-Reply-To: <52024310.1020109@donders.ru.nl>
References: <CAFN2X+fdvTW8jkx1EPS8C+J_FGRTQgTtYL38aYw7Gv6BbLtsxg@mail.gmail.com>
	<52024310.1020109@donders.ru.nl>
Message-ID: <520371B9.8060101@csl.psychol.cam.ac.uk>

Hi all,

 From the previous email it seems that I'm doing something wrong then. I 
have previously used the MNI-aligned subject grid (warped template) for 
the positions, hence I didn't encounter any problem. However, this seems 
to be wrong, as Jorn suggested. The question is the following:

The sourcediff.avg.pow is produced using the warped MNI template, 
therefore the grid positions and indexes will be different from the 
subject-specific MRI. Specifically in my case, the warped template has 
11000 x 3 pos, whereas the subject-specific has 2652 x 3.
My question is, when I therefore index the maxpos using:

[maxval, maxind] = max(sourcediff.avg.pow), my index is 3171, which 
exceeds the matrix dimensions of the subject-specific MRI (2652).

Which step am I missing?

Thanks for your help in advance,
Elisa






On 07/08/2013 13:52, "Jörn M. Horschig" wrote:
> Dear Charidimos,
>
> thanks very much for pointing to this, it is indeed an error in the 
> appendix of the tutorial. cfg.grid.pos should be based on the 
> subject-specific MRI or sourcemodel. So, correctly it should say that 
> you need to load sourcemodel.mat (i.e. subject specific grid) and then 
> use sourcemodel.pos(maxpowindx, :)
> The rationale in principle is that the warped grid has the same size 
> and is indexed the same as the original grid; that is why you can use 
> the index variable obtained from the MNI-warped source reconstructed 
> data. The virtual channel reconstruction should however still be done 
> in whatever coordinate system the subject's anatomical data is in. I 
> will update the appendix accordingly.
>
> Best,
> Jörn
>
> On 8/6/2013 8:24 PM, Charidimos Tzagarakis wrote:
>> Hi there,
>> I have a question regarding virtual electrodes: How can I double 
>> check that the MNI coordinates that I enter are correctly interpreted?
>> More specifically:
>> I have followed the the extended beamforming tutorial in the 
>> "Appendix" and have been able to transpose it to my data (I have 
>> 4D/BTi MEG files and Dicom mri volumes).The part I am not certain 
>> about is the call to the LCMV beamformer.
>> Here it is in my case ( I just want to get the voxel were the power 
>> is max in the previous analysis):
>> cfg              = [];
>> cfg.method       = 'lcmv';
>> cfg.vol          = volfcm;
>> cfg.grid.pos     = source_diff.pos(maxpowindx, :);
>> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
>> cfg.grid.outside = [];
>> cfg.grad=senscm
>> source_idx       = ft_sourceanalysis(cfg, tlock);
>> My headmodel does not include MEG channel information so I need to 
>> also define the cfg.grad parameter. What I don't understand is how 
>> cfg.grid.pos (which is in MNI coordinates as per the previous part of 
>> the tutorial) can be correctly applied to the coordinates of the 
>> headmodel and the channels since these 2 are not in MNI coordinates 
>> (in my case they are in 4d/Bti coordinates and rescaled to cm).In the 
>> previous part of the tutorial this is (if I understand correctly) 
>> accomplished because the leadfield used when calling 
>> ft_sourceanalysis was created using and MNI-warped template. I don't 
>> see where the equivalent part is when estimating the virtual 
>> electrode though.
>> Any advice you may have would be much appreciated.
>> Best,
>> Haris
>>
>>
>> Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
>> University of Minnesota Dept of Neuroscience and Brain Sciences Center
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> -- 
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
> FieldTrip Development Team
>
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>
> Contact:
> E-Mail:jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web:http://www.ru.nl/donders
>
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From jm.horschig at donders.ru.nl  Thu Aug  8 13:45:09 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Thu, 08 Aug 2013 13:45:09 +0200
Subject: [FieldTrip] question about virtual electrode MNI coordinates
In-Reply-To: <520371B9.8060101@csl.psychol.cam.ac.uk>
References: <CAFN2X+fdvTW8jkx1EPS8C+J_FGRTQgTtYL38aYw7Gv6BbLtsxg@mail.gmail.com>
	<52024310.1020109@donders.ru.nl>
	<520371B9.8060101@csl.psychol.cam.ac.uk>
Message-ID: <520384C5.80703@donders.ru.nl>

Dear Elisa,

hard to tell, because you are not telling us exactly what you are doing :)
The idea in the extended beamforming tutorial is that you first create 
an MNI template sourcemodel (or grid). Subsequently, you use exactly 
this grid and spatially transform it such that it fits to the 
subject-specific brain, based on the MRI. After following these steps, 
by definition, the number of grid points in the subject-specific grid 
and the MNI grid are the same - just the place where the grid points end 
up did change. (Otherwise, it would also not be possible to replace the 
.pos field from the source-reconstructed data by the template grid, as 
being done in the plotting part of the tutorial). The problem in the 
tutorial was exactly this replacement of the position description (which 
iself can be a perfectly fine step as e.g. earlier in the tutorial). 
Since we provide a sourcemodel based on the subject's mri, we need to 
specify the position based on that mri/sourcemodel and not based on the 
MNI template.

You, obviously, do not have the same number of grid points for the 
subject-specific sourcemodel as in the template sourcemodel. I cannot 
guarantee that what you did is correct, but at least I can tell you that 
what you did is not affects by this - else you would have had the same 
number of elements for both sourcemodels. I cross my fingers that you're 
doing the right thing :)

Best,
Jörn

On 8/8/2013 12:23 PM, Elisa Carrus wrote:
> Hi all,
>
> From the previous email it seems that I'm doing something wrong then. 
> I have previously used the MNI-aligned subject grid (warped template) 
> for the positions, hence I didn't encounter any problem. However, this 
> seems to be wrong, as Jorn suggested. The question is the following:
>
> The sourcediff.avg.pow is produced using the warped MNI template, 
> therefore the grid positions and indexes will be different from the 
> subject-specific MRI. Specifically in my case, the warped template has 
> 11000 x 3 pos, whereas the subject-specific has 2652 x 3.
> My question is, when I therefore index the maxpos using:
>
> [maxval, maxind] = max(sourcediff.avg.pow), my index is 3171, which 
> exceeds the matrix dimensions of the subject-specific MRI (2652).
>
> Which step am I missing?
>
> Thanks for your help in advance,
> Elisa
>
>
>
>
>
>
> On 07/08/2013 13:52, "Jörn M. Horschig" wrote:
>> Dear Charidimos,
>>
>> thanks very much for pointing to this, it is indeed an error in the 
>> appendix of the tutorial. cfg.grid.pos should be based on the 
>> subject-specific MRI or sourcemodel. So, correctly it should say that 
>> you need to load sourcemodel.mat (i.e. subject specific grid) and 
>> then use sourcemodel.pos(maxpowindx, :)
>> The rationale in principle is that the warped grid has the same size 
>> and is indexed the same as the original grid; that is why you can use 
>> the index variable obtained from the MNI-warped source reconstructed 
>> data. The virtual channel reconstruction should however still be done 
>> in whatever coordinate system the subject's anatomical data is in. I 
>> will update the appendix accordingly.
>>
>> Best,
>> Jörn
>>
>> On 8/6/2013 8:24 PM, Charidimos Tzagarakis wrote:
>>> Hi there,
>>> I have a question regarding virtual electrodes: How can I double 
>>> check that the MNI coordinates that I enter are correctly interpreted?
>>> More specifically:
>>> I have followed the the extended beamforming tutorial in the 
>>> "Appendix" and have been able to transpose it to my data (I have 
>>> 4D/BTi MEG files and Dicom mri volumes).The part I am not certain 
>>> about is the call to the LCMV beamformer.
>>> Here it is in my case ( I just want to get the voxel were the power 
>>> is max in the previous analysis):
>>> cfg              = [];
>>> cfg.method       = 'lcmv';
>>> cfg.vol          = volfcm;
>>> cfg.grid.pos     = source_diff.pos(maxpowindx, :);
>>> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
>>> cfg.grid.outside = [];
>>> cfg.grad=senscm
>>> source_idx       = ft_sourceanalysis(cfg, tlock);
>>> My headmodel does not include MEG channel information so I need to 
>>> also define the cfg.grad parameter. What I don't understand is how 
>>> cfg.grid.pos (which is in MNI coordinates as per the previous part 
>>> of the tutorial) can be correctly applied to the coordinates of the 
>>> headmodel and the channels since these 2 are not in MNI coordinates 
>>> (in my case they are in 4d/Bti coordinates and rescaled to cm).In 
>>> the previous part of the tutorial this is (if I understand 
>>> correctly) accomplished because the leadfield used when calling 
>>> ft_sourceanalysis was created using and MNI-warped template. I don't 
>>> see where the equivalent part is when estimating the virtual 
>>> electrode though.
>>> Any advice you may have would be much appreciated.
>>> Best,
>>> Haris
>>>
>>>
>>> Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
>>> University of Minnesota Dept of Neuroscience and Brain Sciences Center
>>>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>> -- 
>> Jörn M. Horschig
>> PhD Student
>> Donders Institute for Brain, Cognition and Behaviour
>> Centre for Cognitive Neuroimaging
>> Radboud University Nijmegen
>> Neuronal Oscillations Group
>> FieldTrip Development Team
>>
>> P.O. Box 9101
>> NL-6500 HB Nijmegen
>> The Netherlands
>>
>> Contact:
>> E-Mail:jm.horschig at donders.ru.nl
>> Tel:    +31-(0)24-36-68493
>> Web:http://www.ru.nl/donders
>>
>> Visiting address:
>> Trigon, room 2.30
>> Kapittelweg 29
>> NL-6525 EN Nijmegen
>> The Netherlands
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From K.Kalogianni at tudelft.nl  Fri Aug  9 09:59:18 2013
From: K.Kalogianni at tudelft.nl (Konstantina Kalogianni)
Date: Fri, 9 Aug 2013 07:59:18 +0000
Subject: [FieldTrip] ft_sourcegrandaverage & grid computation
Message-ID: <4DF682D3A10EAC46B462A46E16F0B049128EE308@SRV364.tudelft.net>

Dear fieldtripers,
I have experienced a problem with ft_sourcegrandaverage and the calculation of my grid and I want to ask for help.
The error I get is the following :different grid locations in source reconstructions.

I will describe briefly the processing to give you a better idea about my error.

For every subject I have 6 conditions and I want to average all subjects per condition.
After preprocessing I calculate the covariance matrix and then  I use the MUSIC algorithm for my sources.
For  the grid calculation I use a default MRI a default VOL and a default electrodes' positions.
However  for every subject the grid is not identical since  cfg.channel in ft_prepare_leadfield is dependent on the channels I've discarded as noisy during the preprocessing.
By the way for the grid calculation I had to change the order  of cfg.elec because it didn't agree with the order of cfg,channel in my data.
So apparently I end up with a different grid for every subject but still I want to average all of them per condition.

Do I have to use another function to average my sources in this case?
Because the grid would never be identical among subjects.


I hope somebody out there experienced that before and can probably help me.
Thank you.

Konstantina [Nadia] Kalogianni
PhD candidate, TU Delft


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From elisa at csl.psychol.cam.ac.uk  Fri Aug  9 11:25:15 2013
From: elisa at csl.psychol.cam.ac.uk (Elisa Carrus)
Date: Fri, 09 Aug 2013 10:25:15 +0100
Subject: [FieldTrip] question about virtual electrode MNI coordinates
In-Reply-To: <520384C5.80703@donders.ru.nl>
References: <CAFN2X+fdvTW8jkx1EPS8C+J_FGRTQgTtYL38aYw7Gv6BbLtsxg@mail.gmail.com>
	<52024310.1020109@donders.ru.nl>
	<520371B9.8060101@csl.psychol.cam.ac.uk>
	<520384C5.80703@donders.ru.nl>
Message-ID: <5204B57B.6040004@csl.psychol.cam.ac.uk>

Dear Jorn,

ah, I apologise for not writing a complete email! The good news is that 
I've done things correctly so far,  as I do have the same number of grid 
points in both the subject-specific and template, as expected :) I gave 
you the wrong indices because I thought that in your previous email you 
referred to the MRI rather than the sourcemodel. My bad. Sorry for the 
misunderstanding and thanks a lot for explaining this again!

Best,
Elisa


On 08/08/2013 12:45, "Jörn M. Horschig" wrote:
> Dear Elisa,
>
> hard to tell, because you are not telling us exactly what you are 
> doing :)
> The idea in the extended beamforming tutorial is that you first create 
> an MNI template sourcemodel (or grid). Subsequently, you use exactly 
> this grid and spatially transform it such that it fits to the 
> subject-specific brain, based on the MRI. After following these steps, 
> by definition, the number of grid points in the subject-specific grid 
> and the MNI grid are the same - just the place where the grid points 
> end up did change. (Otherwise, it would also not be possible to 
> replace the .pos field from the source-reconstructed data by the 
> template grid, as being done in the plotting part of the tutorial). 
> The problem in the tutorial was exactly this replacement of the 
> position description (which iself can be a perfectly fine step as e.g. 
> earlier in the tutorial). Since we provide a sourcemodel based on the 
> subject's mri, we need to specify the position based on that 
> mri/sourcemodel and not based on the MNI template.
>
> You, obviously, do not have the same number of grid points for the 
> subject-specific sourcemodel as in the template sourcemodel. I cannot 
> guarantee that what you did is correct, but at least I can tell you 
> that what you did is not affects by this - else you would have had the 
> same number of elements for both sourcemodels. I cross my fingers that 
> you're doing the right thing :)
>
> Best,
> Jörn
>
> On 8/8/2013 12:23 PM, Elisa Carrus wrote:
>> Hi all,
>>
>> From the previous email it seems that I'm doing something wrong then. 
>> I have previously used the MNI-aligned subject grid (warped template) 
>> for the positions, hence I didn't encounter any problem. However, 
>> this seems to be wrong, as Jorn suggested. The question is the following:
>>
>> The sourcediff.avg.pow is produced using the warped MNI template, 
>> therefore the grid positions and indexes will be different from the 
>> subject-specific MRI. Specifically in my case, the warped template 
>> has 11000 x 3 pos, whereas the subject-specific has 2652 x 3.
>> My question is, when I therefore index the maxpos using:
>>
>> [maxval, maxind] = max(sourcediff.avg.pow), my index is 3171, which 
>> exceeds the matrix dimensions of the subject-specific MRI (2652).
>>
>> Which step am I missing?
>>
>> Thanks for your help in advance,
>> Elisa
>>
>>
>>
>>
>>
>>
>> On 07/08/2013 13:52, "Jörn M. Horschig" wrote:
>>> Dear Charidimos,
>>>
>>> thanks very much for pointing to this, it is indeed an error in the 
>>> appendix of the tutorial. cfg.grid.pos should be based on the 
>>> subject-specific MRI or sourcemodel. So, correctly it should say 
>>> that you need to load sourcemodel.mat (i.e. subject specific grid) 
>>> and then use sourcemodel.pos(maxpowindx, :)
>>> The rationale in principle is that the warped grid has the same size 
>>> and is indexed the same as the original grid; that is why you can 
>>> use the index variable obtained from the MNI-warped source 
>>> reconstructed data. The virtual channel reconstruction should 
>>> however still be done in whatever coordinate system the subject's 
>>> anatomical data is in. I will update the appendix accordingly.
>>>
>>> Best,
>>> Jörn
>>>
>>> On 8/6/2013 8:24 PM, Charidimos Tzagarakis wrote:
>>>> Hi there,
>>>> I have a question regarding virtual electrodes: How can I double 
>>>> check that the MNI coordinates that I enter are correctly interpreted?
>>>> More specifically:
>>>> I have followed the the extended beamforming tutorial in the 
>>>> "Appendix" and have been able to transpose it to my data (I have 
>>>> 4D/BTi MEG files and Dicom mri volumes).The part I am not certain 
>>>> about is the call to the LCMV beamformer.
>>>> Here it is in my case ( I just want to get the voxel were the power 
>>>> is max in the previous analysis):
>>>> cfg              = [];
>>>> cfg.method       = 'lcmv';
>>>> cfg.vol          = volfcm;
>>>> cfg.grid.pos     = source_diff.pos(maxpowindx, :);
>>>> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
>>>> cfg.grid.outside = [];
>>>> cfg.grad=senscm
>>>> source_idx       = ft_sourceanalysis(cfg, tlock);
>>>> My headmodel does not include MEG channel information so I need to 
>>>> also define the cfg.grad parameter. What I don't understand is how 
>>>> cfg.grid.pos (which is in MNI coordinates as per the previous part 
>>>> of the tutorial) can be correctly applied to the coordinates of the 
>>>> headmodel and the channels since these 2 are not in MNI coordinates 
>>>> (in my case they are in 4d/Bti coordinates and rescaled to cm).In 
>>>> the previous part of the tutorial this is (if I understand 
>>>> correctly) accomplished because the leadfield used when calling 
>>>> ft_sourceanalysis was created using and MNI-warped template. I 
>>>> don't see where the equivalent part is when estimating the virtual 
>>>> electrode though.
>>>> Any advice you may have would be much appreciated.
>>>> Best,
>>>> Haris
>>>>
>>>>
>>>> Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
>>>> University of Minnesota Dept of Neuroscience and Brain Sciences Center
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>
>>> -- 
>>> Jörn M. Horschig
>>> PhD Student
>>> Donders Institute for Brain, Cognition and Behaviour
>>> Centre for Cognitive Neuroimaging
>>> Radboud University Nijmegen
>>> Neuronal Oscillations Group
>>> FieldTrip Development Team
>>>
>>> P.O. Box 9101
>>> NL-6500 HB Nijmegen
>>> The Netherlands
>>>
>>> Contact:
>>> E-Mail:jm.horschig at donders.ru.nl
>>> Tel:    +31-(0)24-36-68493
>>> Web:http://www.ru.nl/donders
>>>
>>> Visiting address:
>>> Trigon, room 2.30
>>> Kapittelweg 29
>>> NL-6525 EN Nijmegen
>>> The Netherlands
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> -- 
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
> FieldTrip Development Team
>
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>
> Contact:
> E-Mail:jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web:http://www.ru.nl/donders
>
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From g.dimitriadis at donders.ru.nl  Fri Aug  9 17:22:50 2013
From: g.dimitriadis at donders.ru.nl (Dimitriadis, G. (George))
Date: Fri, 9 Aug 2013 17:22:50 +0200 (CEST)
Subject: [FieldTrip] Error from postamble
Message-ID: <1463263304.1956192.1376061770792.JavaMail.root@monoceros.zimbra.ru.nl>


Hello guys,

I seem to be getting an error relating to the generation of warnings withing the postamble. I am not doing anything that I haven't been doing for the past year.

I had problems with the preamble (due to large file sizes) before and I am doing the cfg.stackcallinfo = 'no' trick.

But now I am getting the following series of errors:

---------------------------------------------------
Warning:
'@(hObject,eventdata)mainRatAnalysisGUI('pushbutton_run_analysis_Callback',hObject,eventdata,guidata(hObject))'
 exceeds MATLAB's maximum name length of 63 characters and has
been truncated to
 '@(hObject,eventdata)mainRatAnalysisGUI('pushbutton_run_analysis'. 
> In utilities/private/warning_once>fieldnameFromStack at 196
  In utilities/private/warning_once at 123
  In utilities/private/ft_postamble_history at 55
  In ft_postamble at 55
  In ft_preprocessing at 611
  In gd_eri_preprocratdata at 71
  In gd_eri_getratdatasignals at 39
  In mainRatAnalysisGUI>pushbutton_run_analysis_Callback at 120
  In gui_mainfcn at 96
  In mainRatAnalysisGUI at 42
  In @(hObject,eventdata)mainRatAnalysisGUI('pushbutton_run_analysis_Callback',hObject,eventdata,guidata(hObject)) 
Invalid field name:
'@(hObject,eventdata)mainRatAnalysisGUI('pushbutton_run_analysis'.

Error in warning_once>fieldnameFromStack (line 196)
  ft_previous_warnings.(stack(end).name) = []; % iteratively
  build up structure fields

Error in warning_once (line 123)
  [tmpfname ft_default.warning.identifier line] =
  fieldnameFromStack(ft_default.warning.identifier);

Error in ft_postamble_history (line 55)
warning_once('-clear');

Error in ft_postamble (line 55)
  evalin('caller', ['ft_postamble_' cmd]);

Error in ft_preprocessing (line 611)
ft_postamble history data

Error in gd_eri_preprocratdata (line 71)
  datacell{datindx}=ft_preprocessing(cfg_pp);

Error in gd_eri_getratdatasignals (line 39)
data=gd_eri_preprocratdata(cfg);

Error in mainRatAnalysisGUI>pushbutton_run_analysis_Callback
(line 120)
        data =gd_eri_getratdatasignals(cfg);

Error in gui_mainfcn (line 96)
        feval(varargin{:});

Error in mainRatAnalysisGUI (line 42)
    gui_mainfcn(gui_State, varargin{:});

Error in
@(hObject,eventdata)mainRatAnalysisGUI('pushbutton_run_analysis_Callback',hObject,eventdata,guidata(hObject))

 
Error while evaluating uicontrol Callback
----------------------------------------

I am calling my original function from within a gui.

So it seems that in the postamble_history a warning gets generated which then throws an error for some reason I would really like not to have to find out by myself.


Thanks for your time


George Dimitriadis


From r.cox at uva.nl  Tue Aug 13 11:29:23 2013
From: r.cox at uva.nl (Roy Cox)
Date: Tue, 13 Aug 2013 11:29:23 +0200
Subject: [FieldTrip] ft_freqstatistics
Message-ID: <CABafTZcchaOGyh1PVvx0KZ6v5rd+Cj2=KVhmgwgMEPN2LnaFDw@mail.gmail.com>

Hi,

Can anyone tell me how fieldtrip selects freq bins when calling
ft_freqstatistics with cfg.frequency?

That is, if I'm interested in two freq bands from, say, 10 to 20, and from
20 to 30 Hz, and I don't want a freq bin to be used twice, do I use
cfg.frequency=[10 20] and cfg.frequency=[20 30]? Or would the freq bin
closest to 20 be used twice?

I guess I'm asking how precisely the find function (with arguments 'first',
'last') is applied.

Best,

Roy


-- 
Roy Cox, M.Sc. | Brain & Cognition Group | Department of Psychology |
University of Amsterdam | Weesperplein 4 | 1018 XA Amsterdam | the
Netherlands | room 3.21 | phone: +31 20 525 6847 | email: r.cox at uva.nl
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From hweeling.lee at gmail.com  Wed Aug 14 16:51:23 2013
From: hweeling.lee at gmail.com (Hwee Ling Lee)
Date: Wed, 14 Aug 2013 16:51:23 +0200
Subject: [FieldTrip] newbie
Message-ID: <CABG7z0SvaX134oFfEbhasgrWRLtea+8=AxfcJDdrjHwR7veg_g@mail.gmail.com>

Hi to all!

I'm new to fieldtrip! I have a dataset that has been corrected for scanner
artifacts and BC artifacts using Brainvision Analyser. I would like to
export the corrected data as a .eeg file so that I can load the data onto
Matlab and use fieldtrip to perform further analyses.

However, I kept getting error messages from Matlab that the sub-file format
is unsupported. I've been searching online the best way to export the
corrected data from Brainvision Analyser, however, I could not find any
solution at all.

Would anyone please kindly instruct me the settings that I should have when
I export the corrected data?

Thanks!

Best wishes,
Hweeling
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From elisa at csl.psychol.cam.ac.uk  Wed Aug 14 17:32:42 2013
From: elisa at csl.psychol.cam.ac.uk (Elisa Carrus)
Date: Wed, 14 Aug 2013 16:32:42 +0100
Subject: [FieldTrip] newbie
In-Reply-To: <CABG7z0SvaX134oFfEbhasgrWRLtea+8=AxfcJDdrjHwR7veg_g@mail.gmail.com>
References: <CABG7z0SvaX134oFfEbhasgrWRLtea+8=AxfcJDdrjHwR7veg_g@mail.gmail.com>
Message-ID: <520BA31A.9040803@csl.psychol.cam.ac.uk>

Hi Hweeling,

Welcome! Can you give us a bit more information about the script you 
used to load the data? I haven't used BrainVision before but you should 
be able to read the .eeg data directly from Fieldtrip 
http://fieldtrip.fcdonders.nl/dataformat 
<http://fieldtrip.fcdonders.nl/dataformat>

Best,
Elisa



On 14/08/2013 15:51, Hwee Ling Lee wrote:
> Hi to all!
>
> I'm new to fieldtrip! I have a dataset that has been corrected for 
> scanner artifacts and BC artifacts using Brainvision Analyser. I would 
> like to export the corrected data as a .eeg file so that I can load 
> the data onto Matlab and use fieldtrip to perform further analyses.
>
> However, I kept getting error messages from Matlab that the sub-file 
> format is unsupported. I've been searching online the best way to 
> export the corrected data from Brainvision Analyser, however, I could 
> not find any solution at all.
>
> Would anyone please kindly instruct me the settings that I should have 
> when I export the corrected data?
>
> Thanks!
>
> Best wishes,
> Hweeling
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From r.oostenveld at donders.ru.nl  Wed Aug 14 21:34:02 2013
From: r.oostenveld at donders.ru.nl (Robert Oostenveld)
Date: Wed, 14 Aug 2013 21:34:02 +0200
Subject: [FieldTrip] newbie
In-Reply-To: <CABG7z0SvaX134oFfEbhasgrWRLtea+8=AxfcJDdrjHwR7veg_g@mail.gmail.com>
References: <CABG7z0SvaX134oFfEbhasgrWRLtea+8=AxfcJDdrjHwR7veg_g@mail.gmail.com>
Message-ID: <CA0DCF09-96E0-4D29-9CFE-9EE2C1B7EBFF@donders.ru.nl>

Hi Hweeling

The channel level data in the BrainVision data file can be represented in ascii and binary format. Furthermore, the order can be one channel at a time or sample-by-sample. Finally there are different numeric precisions (integer, float, etc).

This is something that you cannot see from the outside of the file, but if you open the *.vhdr file in a text editor you can see these details. Since there are so many possible combinations of these three factors, it is not difficult easy to support all possible variants. 

You could try storing the data as multiplexed and in single- or double-precision, which is the most common format. Otherwise, you can report it as feature request on http://bugzilla.fcdonders.nl and attach a small piece of data (with vhdr and vmrk file) there.

best regards,
Robert
 


On 14 Aug 2013, at 16:51, Hwee Ling Lee wrote:

> Hi to all!
> 
> I'm new to fieldtrip! I have a dataset that has been corrected for scanner artifacts and BC artifacts using Brainvision Analyser. I would like to export the corrected data as a .eeg file so that I can load the data onto Matlab and use fieldtrip to perform further analyses.
> 
> However, I kept getting error messages from Matlab that the sub-file format is unsupported. I've been searching online the best way to export the corrected data from Brainvision Analyser, however, I could not find any solution at all.
> 
> Would anyone please kindly instruct me the settings that I should have when I export the corrected data?
> 
> Thanks!
> 
> Best wishes,
> Hweeling
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip




From gopalar.ccf at gmail.com  Wed Aug 14 22:58:34 2013
From: gopalar.ccf at gmail.com (Raghavan Gopalakrishnan)
Date: Wed, 14 Aug 2013 16:58:34 -0400
Subject: [FieldTrip] Reading multiple NEX files
Message-ID: <CAHz=SkUQRqKD1reF53o4gL5Lw0mmW6FTzkAhd4T-x=JA2hfK6A@mail.gmail.com>

I have multiple nex files that have LFP and spike data. I would like to
read them and plot one raster, since the multple nex files are from same
subject. ft_appendspike does not append data structures with same channel
label. All my data structures from different nex files have same channel
label. Any ideas?
Thanks.
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From hweeling.lee at gmail.com  Thu Aug 15 11:34:33 2013
From: hweeling.lee at gmail.com (Hwee Ling Lee)
Date: Thu, 15 Aug 2013 11:34:33 +0200
Subject: [FieldTrip] EEG sensor position layout
Message-ID: <CABG7z0QLsEDt2O9Pth3Xe4aQOBtbHhGnROtCeGHqRHN4goUAtQ@mail.gmail.com>

Hi all!

After performing ICA, I used the command to browse the data in component
mode.

However, I got a warning message:

Warning: No layout specified - will try to construct one using sensor
positions
> In ft_databrowser at 217
Error using ft_databrowser (line 223)
cannot infer sensor type

I understand that one can manually create the layout, however, I was not
sure how I can do it. Could someone please help?

Thank you.

Best regards,
Hweeling
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From johanna.zumer at donders.ru.nl  Thu Aug 15 12:45:51 2013
From: johanna.zumer at donders.ru.nl (Johanna Zumer)
Date: Thu, 15 Aug 2013 12:45:51 +0200
Subject: [FieldTrip] EEG sensor position layout
In-Reply-To: <CABG7z0QLsEDt2O9Pth3Xe4aQOBtbHhGnROtCeGHqRHN4goUAtQ@mail.gmail.com>
References: <CABG7z0QLsEDt2O9Pth3Xe4aQOBtbHhGnROtCeGHqRHN4goUAtQ@mail.gmail.com>
Message-ID: <CAL4kA6d9A90HfXRErt5SxhDF4dTVhQzUWaU8Vvg=q1S2D=J=+g@mail.gmail.com>

Dear Hweeling,

You should indeed specify cfg.layout, naming the layout file for the data
that you have.
You can first check in the folder fieldtrip/template/layout to see if there
is already an existing template that you can use.
If not, please see ft_prepare_layout for more details.

If you're still stuck, please ask again with more specific details on your
layout.

Best,
Johanna



2013/8/15 Hwee Ling Lee <hweeling.lee at gmail.com>

> Hi all!
>
> After performing ICA, I used the command to browse the data in component
> mode.
>
> However, I got a warning message:
>
> Warning: No layout specified - will try to construct one using sensor
> positions
> > In ft_databrowser at 217
> Error using ft_databrowser (line 223)
> cannot infer sensor type
>
> I understand that one can manually create the layout, however, I was not
> sure how I can do it. Could someone please help?
>
> Thank you.
>
> Best regards,
> Hweeling
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From hweeling.lee at gmail.com  Thu Aug 15 13:21:19 2013
From: hweeling.lee at gmail.com (Hwee Ling Lee)
Date: Thu, 15 Aug 2013 13:21:19 +0200
Subject: [FieldTrip] EEG sensor position layout again
Message-ID: <CABG7z0TdTBH=c0e4szgPsSLnDgnmZvN6gh1Q6yTSAD6rDDnoWw@mail.gmail.com>

Hi,

A bit more details about my setup.

I'm using a Easycap MRI compatible 128 channels cap. I tried to search for
a layout on the templates/layout, and I found one that might closest fit to
my needs ('QuikCap_NSL_128').
To view my components, I tried these series of commands:

cfg = [];
cfg.viewmode = 'component';
cfg.continuous = 'yes';
cfg.layout = ft_prepare_layout('QuikCap_NSL_128');
ft_databrowser(cfg,ic_data);

However, I was prompted with error messages:
Warning: Struct field assignment overwrites a value with class "char". See
MATLAB R14SP2 Release Notes, Assigning Nonstructure
Variables As Structures Displays Warning, for details.
> In utilities\private\ft_preamble_provenance at 49
  In ft_preamble at 54
  In ft_prepare_layout at 91
Error using ft_prepare_layout (line 582)
no layout detected, please specify cfg.layout

Also when I tried the command,

cfg = [];
cfg.viewmode = 'component';
cfg.continuous = 'yes';
cfg.layout = 'QuikCap_NSL_128';
ft_databrowser(cfg,ic_data);

I get this error message:
Warning: could not open QuikCap_NSL_128
> In fileio\private\warning_once at 116
  In fileio\private\filetype_check_header at 54
  In ft_filetype at 328
  In ft_prepare_layout at 253
  In ft_databrowser at 226
Warning: could not determine filetype of QuikCap_NSL_128
> In fileio\private\warning_once at 116
  In ft_filetype at 1115
  In ft_prepare_layout at 253
  In ft_databrowser at 226
creating layout from electrode file QuikCap_NSL_128
Error using ft_read_sens (line 68)
file 'QuikCap_NSL_128' does not exist

Error in ft_prepare_layout (line 275)
  lay = sens2lay(ft_read_sens(cfg.layout), cfg.rotate, cfg.projection,
cfg.style, cfg.overlap);

Error in ft_databrowser (line 226)
  cfg.layout = ft_prepare_layout(tmpcfg);


Would anyone please help?

Cheers,
Hweeling
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From johanna.zumer at gmail.com  Thu Aug 15 13:33:57 2013
From: johanna.zumer at gmail.com (Johanna Zumer)
Date: Thu, 15 Aug 2013 13:33:57 +0200
Subject: [FieldTrip] EEG sensor position layout again
In-Reply-To: <CABG7z0TdTBH=c0e4szgPsSLnDgnmZvN6gh1Q6yTSAD6rDDnoWw@mail.gmail.com>
References: <CABG7z0TdTBH=c0e4szgPsSLnDgnmZvN6gh1Q6yTSAD6rDDnoWw@mail.gmail.com>
Message-ID: <CAL4kA6dXMDNUMcpiqi_1aaFYXmEHt2mTLgoT=dGH+c3L78miXQ@mail.gmail.com>

Hi Hweeling,

Since it says that it cannot find the Quikcap file, it sounds like it's not
on your path.    Run  ft_defaults on your Matlab command, then test if the
file is on your path:
>> ft_defaults
>> which QuikCap_NSL_128.mat

Assuming it finds the file on your path, then do you still get the browser
error?

Best,
Johanna


2013/8/15 Hwee Ling Lee <hweeling.lee at gmail.com>

> Hi,
>
> A bit more details about my setup.
>
> I'm using a Easycap MRI compatible 128 channels cap. I tried to search for
> a layout on the templates/layout, and I found one that might closest fit to
> my needs ('QuikCap_NSL_128').
> To view my components, I tried these series of commands:
>
> cfg = [];
> cfg.viewmode = 'component';
> cfg.continuous = 'yes';
> cfg.layout = ft_prepare_layout('QuikCap_NSL_128');
> ft_databrowser(cfg,ic_data);
>
> However, I was prompted with error messages:
> Warning: Struct field assignment overwrites a value with class "char". See
> MATLAB R14SP2 Release Notes, Assigning Nonstructure
> Variables As Structures Displays Warning, for details.
> > In utilities\private\ft_preamble_provenance at 49
>   In ft_preamble at 54
>   In ft_prepare_layout at 91
> Error using ft_prepare_layout (line 582)
> no layout detected, please specify cfg.layout
>
> Also when I tried the command,
>
> cfg = [];
> cfg.viewmode = 'component';
> cfg.continuous = 'yes';
> cfg.layout = 'QuikCap_NSL_128';
> ft_databrowser(cfg,ic_data);
>
> I get this error message:
> Warning: could not open QuikCap_NSL_128
> > In fileio\private\warning_once at 116
>   In fileio\private\filetype_check_header at 54
>   In ft_filetype at 328
>   In ft_prepare_layout at 253
>   In ft_databrowser at 226
> Warning: could not determine filetype of QuikCap_NSL_128
> > In fileio\private\warning_once at 116
>   In ft_filetype at 1115
>   In ft_prepare_layout at 253
>   In ft_databrowser at 226
> creating layout from electrode file QuikCap_NSL_128
> Error using ft_read_sens (line 68)
> file 'QuikCap_NSL_128' does not exist
>
> Error in ft_prepare_layout (line 275)
>   lay = sens2lay(ft_read_sens(cfg.layout), cfg.rotate, cfg.projection,
> cfg.style, cfg.overlap);
>
> Error in ft_databrowser (line 226)
>   cfg.layout = ft_prepare_layout(tmpcfg);
>
>
> Would anyone please help?
>
> Cheers,
> Hweeling
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From hweeling.lee at gmail.com  Thu Aug 15 13:59:17 2013
From: hweeling.lee at gmail.com (Hwee Ling Lee)
Date: Thu, 15 Aug 2013 13:59:17 +0200
Subject: [FieldTrip] EEG sensor position layout again
In-Reply-To: <CAL4kA6dXMDNUMcpiqi_1aaFYXmEHt2mTLgoT=dGH+c3L78miXQ@mail.gmail.com>
References: <CABG7z0TdTBH=c0e4szgPsSLnDgnmZvN6gh1Q6yTSAD6rDDnoWw@mail.gmail.com>
	<CAL4kA6dXMDNUMcpiqi_1aaFYXmEHt2mTLgoT=dGH+c3L78miXQ@mail.gmail.com>
Message-ID: <CABG7z0TQFuakrpr4zJDkP2TnfPvw0FwL+qqp9K_6o3owDsXFaw@mail.gmail.com>

Hi,

It states that:
'QuikCap_NSL_128.mat' not found.

However, when I checked fieldtrip/templates/layout, the mat file is stored
in this folder.

Cheers,
Hweeling



On 15 August 2013 13:33, Johanna Zumer <johanna.zumer at gmail.com> wrote:

> Hi Hweeling,
>
> Since it says that it cannot find the Quikcap file, it sounds like it's
> not on your path.    Run  ft_defaults on your Matlab command, then test if
> the file is on your path:
> >> ft_defaults
> >> which QuikCap_NSL_128.mat
>
> Assuming it finds the file on your path, then do you still get the browser
> error?
>
> Best,
> Johanna
>
>
> 2013/8/15 Hwee Ling Lee <hweeling.lee at gmail.com>
>
>> Hi,
>>
>> A bit more details about my setup.
>>
>> I'm using a Easycap MRI compatible 128 channels cap. I tried to search
>> for a layout on the templates/layout, and I found one that might closest
>> fit to my needs ('QuikCap_NSL_128').
>> To view my components, I tried these series of commands:
>>
>> cfg = [];
>> cfg.viewmode = 'component';
>> cfg.continuous = 'yes';
>> cfg.layout = ft_prepare_layout('QuikCap_NSL_128');
>> ft_databrowser(cfg,ic_data);
>>
>> However, I was prompted with error messages:
>> Warning: Struct field assignment overwrites a value with class "char".
>> See MATLAB R14SP2 Release Notes, Assigning Nonstructure
>> Variables As Structures Displays Warning, for details.
>> > In utilities\private\ft_preamble_provenance at 49
>>   In ft_preamble at 54
>>   In ft_prepare_layout at 91
>> Error using ft_prepare_layout (line 582)
>> no layout detected, please specify cfg.layout
>>
>> Also when I tried the command,
>>
>> cfg = [];
>> cfg.viewmode = 'component';
>> cfg.continuous = 'yes';
>> cfg.layout = 'QuikCap_NSL_128';
>> ft_databrowser(cfg,ic_data);
>>
>> I get this error message:
>> Warning: could not open QuikCap_NSL_128
>> > In fileio\private\warning_once at 116
>>   In fileio\private\filetype_check_header at 54
>>   In ft_filetype at 328
>>   In ft_prepare_layout at 253
>>   In ft_databrowser at 226
>> Warning: could not determine filetype of QuikCap_NSL_128
>> > In fileio\private\warning_once at 116
>>   In ft_filetype at 1115
>>   In ft_prepare_layout at 253
>>   In ft_databrowser at 226
>> creating layout from electrode file QuikCap_NSL_128
>> Error using ft_read_sens (line 68)
>> file 'QuikCap_NSL_128' does not exist
>>
>> Error in ft_prepare_layout (line 275)
>>   lay = sens2lay(ft_read_sens(cfg.layout), cfg.rotate, cfg.projection,
>> cfg.style, cfg.overlap);
>>
>> Error in ft_databrowser (line 226)
>>   cfg.layout = ft_prepare_layout(tmpcfg);
>>
>>
>> Would anyone please help?
>>
>> Cheers,
>> Hweeling
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>


-- 
=================================================
Dr. rer. nat. Lee, Hwee Ling
Postdoc
German Center for Neurodegenerative Diseases (DZNE) Bonn

Email 1: hwee-ling.lee<at>dzne.de
Email 2: hweeling.lee<at>gmail.com

https://sites.google.com/site/hweelinglee/home

Correspondence Address:
Ernst-Robert-Curtius Strasse 12, 53117, Bonn, Germany
=================================================
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From johanna.zumer at gmail.com  Thu Aug 15 14:01:39 2013
From: johanna.zumer at gmail.com (Johanna Zumer)
Date: Thu, 15 Aug 2013 14:01:39 +0200
Subject: [FieldTrip] EEG sensor position layout again
In-Reply-To: <CABG7z0TQFuakrpr4zJDkP2TnfPvw0FwL+qqp9K_6o3owDsXFaw@mail.gmail.com>
References: <CABG7z0TdTBH=c0e4szgPsSLnDgnmZvN6gh1Q6yTSAD6rDDnoWw@mail.gmail.com>
	<CAL4kA6dXMDNUMcpiqi_1aaFYXmEHt2mTLgoT=dGH+c3L78miXQ@mail.gmail.com>
	<CABG7z0TQFuakrpr4zJDkP2TnfPvw0FwL+qqp9K_6o3owDsXFaw@mail.gmail.com>
Message-ID: <CAL4kA6ddn8MoCfigmDq7nWnXy-UOBRJ842yBmucehOLoDFRw4Q@mail.gmail.com>

Hi Hweeling,

I just checked on my computer, and it helped to restart matlab and try
again.  Maybe there is something strange if ft_defaults is called (again)
during an already open session with previous calls to FT functions?

Best,
Johanna


2013/8/15 Hwee Ling Lee <hweeling.lee at gmail.com>

> Hi,
>
> It states that:
> 'QuikCap_NSL_128.mat' not found.
>
> However, when I checked fieldtrip/templates/layout, the mat file is stored
> in this folder.
>
> Cheers,
> Hweeling
>
>
>
> On 15 August 2013 13:33, Johanna Zumer <johanna.zumer at gmail.com> wrote:
>
>> Hi Hweeling,
>>
>> Since it says that it cannot find the Quikcap file, it sounds like it's
>> not on your path.    Run  ft_defaults on your Matlab command, then test if
>> the file is on your path:
>> >> ft_defaults
>> >> which QuikCap_NSL_128.mat
>>
>> Assuming it finds the file on your path, then do you still get the
>> browser error?
>>
>> Best,
>> Johanna
>>
>>
>> 2013/8/15 Hwee Ling Lee <hweeling.lee at gmail.com>
>>
>>> Hi,
>>>
>>> A bit more details about my setup.
>>>
>>> I'm using a Easycap MRI compatible 128 channels cap. I tried to search
>>> for a layout on the templates/layout, and I found one that might closest
>>> fit to my needs ('QuikCap_NSL_128').
>>> To view my components, I tried these series of commands:
>>>
>>> cfg = [];
>>> cfg.viewmode = 'component';
>>> cfg.continuous = 'yes';
>>> cfg.layout = ft_prepare_layout('QuikCap_NSL_128');
>>> ft_databrowser(cfg,ic_data);
>>>
>>> However, I was prompted with error messages:
>>> Warning: Struct field assignment overwrites a value with class "char".
>>> See MATLAB R14SP2 Release Notes, Assigning Nonstructure
>>> Variables As Structures Displays Warning, for details.
>>> > In utilities\private\ft_preamble_provenance at 49
>>>   In ft_preamble at 54
>>>   In ft_prepare_layout at 91
>>> Error using ft_prepare_layout (line 582)
>>> no layout detected, please specify cfg.layout
>>>
>>> Also when I tried the command,
>>>
>>> cfg = [];
>>> cfg.viewmode = 'component';
>>> cfg.continuous = 'yes';
>>> cfg.layout = 'QuikCap_NSL_128';
>>> ft_databrowser(cfg,ic_data);
>>>
>>> I get this error message:
>>> Warning: could not open QuikCap_NSL_128
>>> > In fileio\private\warning_once at 116
>>>   In fileio\private\filetype_check_header at 54
>>>   In ft_filetype at 328
>>>   In ft_prepare_layout at 253
>>>   In ft_databrowser at 226
>>> Warning: could not determine filetype of QuikCap_NSL_128
>>> > In fileio\private\warning_once at 116
>>>   In ft_filetype at 1115
>>>   In ft_prepare_layout at 253
>>>   In ft_databrowser at 226
>>> creating layout from electrode file QuikCap_NSL_128
>>> Error using ft_read_sens (line 68)
>>> file 'QuikCap_NSL_128' does not exist
>>>
>>> Error in ft_prepare_layout (line 275)
>>>   lay = sens2lay(ft_read_sens(cfg.layout), cfg.rotate, cfg.projection,
>>> cfg.style, cfg.overlap);
>>>
>>> Error in ft_databrowser (line 226)
>>>   cfg.layout = ft_prepare_layout(tmpcfg);
>>>
>>>
>>> Would anyone please help?
>>>
>>> Cheers,
>>> Hweeling
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>
>
> --
> =================================================
> Dr. rer. nat. Lee, Hwee Ling
> Postdoc
> German Center for Neurodegenerative Diseases (DZNE) Bonn
>
> Email 1: hwee-ling.lee<at>dzne.de
> Email 2: hweeling.lee<at>gmail.com
>
> https://sites.google.com/site/hweelinglee/home
>
> Correspondence Address:
> Ernst-Robert-Curtius Strasse 12, 53117, Bonn, Germany
> =================================================
>
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From hweeling.lee at gmail.com  Thu Aug 15 14:13:04 2013
From: hweeling.lee at gmail.com (Hwee Ling Lee)
Date: Thu, 15 Aug 2013 14:13:04 +0200
Subject: [FieldTrip] EEG sensor position layout again
In-Reply-To: <CAL4kA6ddn8MoCfigmDq7nWnXy-UOBRJ842yBmucehOLoDFRw4Q@mail.gmail.com>
References: <CABG7z0TdTBH=c0e4szgPsSLnDgnmZvN6gh1Q6yTSAD6rDDnoWw@mail.gmail.com>
	<CAL4kA6dXMDNUMcpiqi_1aaFYXmEHt2mTLgoT=dGH+c3L78miXQ@mail.gmail.com>
	<CABG7z0TQFuakrpr4zJDkP2TnfPvw0FwL+qqp9K_6o3owDsXFaw@mail.gmail.com>
	<CAL4kA6ddn8MoCfigmDq7nWnXy-UOBRJ842yBmucehOLoDFRw4Q@mail.gmail.com>
Message-ID: <CABG7z0SjsY7WSjM=PP5mfNq8oHY4NCv1pzRSjqV2FVVyVw92-Q@mail.gmail.com>

Hi,

Thanks for your advice. I restarted Matlab, and call for ft_defaults and
which QuikCap_NSL_128.mat, and I still get the same error message.

Also, is this the right layout file to use for my data?

Cheers,
Hweeling



On 15 August 2013 14:01, Johanna Zumer <johanna.zumer at gmail.com> wrote:

> Hi Hweeling,
>
> I just checked on my computer, and it helped to restart matlab and try
> again.  Maybe there is something strange if ft_defaults is called (again)
> during an already open session with previous calls to FT functions?
>
> Best,
> Johanna
>
>
> 2013/8/15 Hwee Ling Lee <hweeling.lee at gmail.com>
>
>> Hi,
>>
>> It states that:
>> 'QuikCap_NSL_128.mat' not found.
>>
>> However, when I checked fieldtrip/templates/layout, the mat file is
>> stored in this folder.
>>
>> Cheers,
>> Hweeling
>>
>>
>>
>> On 15 August 2013 13:33, Johanna Zumer <johanna.zumer at gmail.com> wrote:
>>
>>> Hi Hweeling,
>>>
>>> Since it says that it cannot find the Quikcap file, it sounds like it's
>>> not on your path.    Run  ft_defaults on your Matlab command, then test if
>>> the file is on your path:
>>> >> ft_defaults
>>> >> which QuikCap_NSL_128.mat
>>>
>>> Assuming it finds the file on your path, then do you still get the
>>> browser error?
>>>
>>> Best,
>>> Johanna
>>>
>>>
>>> 2013/8/15 Hwee Ling Lee <hweeling.lee at gmail.com>
>>>
>>>> Hi,
>>>>
>>>> A bit more details about my setup.
>>>>
>>>> I'm using a Easycap MRI compatible 128 channels cap. I tried to search
>>>> for a layout on the templates/layout, and I found one that might closest
>>>> fit to my needs ('QuikCap_NSL_128').
>>>> To view my components, I tried these series of commands:
>>>>
>>>> cfg = [];
>>>> cfg.viewmode = 'component';
>>>> cfg.continuous = 'yes';
>>>> cfg.layout = ft_prepare_layout('QuikCap_NSL_128');
>>>> ft_databrowser(cfg,ic_data);
>>>>
>>>> However, I was prompted with error messages:
>>>> Warning: Struct field assignment overwrites a value with class "char".
>>>> See MATLAB R14SP2 Release Notes, Assigning Nonstructure
>>>> Variables As Structures Displays Warning, for details.
>>>> > In utilities\private\ft_preamble_provenance at 49
>>>>   In ft_preamble at 54
>>>>   In ft_prepare_layout at 91
>>>> Error using ft_prepare_layout (line 582)
>>>> no layout detected, please specify cfg.layout
>>>>
>>>> Also when I tried the command,
>>>>
>>>> cfg = [];
>>>> cfg.viewmode = 'component';
>>>> cfg.continuous = 'yes';
>>>> cfg.layout = 'QuikCap_NSL_128';
>>>> ft_databrowser(cfg,ic_data);
>>>>
>>>> I get this error message:
>>>> Warning: could not open QuikCap_NSL_128
>>>> > In fileio\private\warning_once at 116
>>>>   In fileio\private\filetype_check_header at 54
>>>>   In ft_filetype at 328
>>>>   In ft_prepare_layout at 253
>>>>   In ft_databrowser at 226
>>>> Warning: could not determine filetype of QuikCap_NSL_128
>>>> > In fileio\private\warning_once at 116
>>>>   In ft_filetype at 1115
>>>>   In ft_prepare_layout at 253
>>>>   In ft_databrowser at 226
>>>> creating layout from electrode file QuikCap_NSL_128
>>>> Error using ft_read_sens (line 68)
>>>> file 'QuikCap_NSL_128' does not exist
>>>>
>>>> Error in ft_prepare_layout (line 275)
>>>>   lay = sens2lay(ft_read_sens(cfg.layout), cfg.rotate, cfg.projection,
>>>> cfg.style, cfg.overlap);
>>>>
>>>> Error in ft_databrowser (line 226)
>>>>   cfg.layout = ft_prepare_layout(tmpcfg);
>>>>
>>>>
>>>> Would anyone please help?
>>>>
>>>> Cheers,
>>>> Hweeling
>>>>
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>
>>>
>>>
>>
>>
>> --
>> =================================================
>> Dr. rer. nat. Lee, Hwee Ling
>> Postdoc
>> German Center for Neurodegenerative Diseases (DZNE) Bonn
>>
>> Email 1: hwee-ling.lee<at>dzne.de
>> Email 2: hweeling.lee<at>gmail.com
>>
>> https://sites.google.com/site/hweelinglee/home
>>
>> Correspondence Address:
>> Ernst-Robert-Curtius Strasse 12, 53117, Bonn, Germany
>> =================================================
>>
>
>


-- 
=================================================
Dr. rer. nat. Lee, Hwee Ling
Postdoc
German Center for Neurodegenerative Diseases (DZNE) Bonn

Email 1: hwee-ling.lee<at>dzne.de
Email 2: hweeling.lee<at>gmail.com

https://sites.google.com/site/hweelinglee/home

Correspondence Address:
Ernst-Robert-Curtius Strasse 12, 53117, Bonn, Germany
=================================================
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From m.kandula at uu.nl  Thu Aug 15 18:02:33 2013
From: m.kandula at uu.nl (Manasa Kandula)
Date: Thu, 15 Aug 2013 18:02:33 +0200
Subject: [FieldTrip] ft_databrowser No artifact.sampleinfo
Message-ID: <520CFB99.4060709@uu.nl>

I've been trying to use /ft_databrowser/ on segmented EEG data right 
after /ft_preprocessing/. However, at the subfunction /redraw_cb/, it's 
crashing as a call to /ft_fetch_data/ is resulting in an error as 
/opt.artdata.sampleinfo/ is not a field present in the /opt.artdata/ struct
(Error using ==> ft_fetch_data at 60 data does not contain a consistent 
trial definition, fetching data is not possible).
As far as I can tell, there is no point in the code that actually sets 
the /sampleinfo/ field for the /artifact/ struct.
Has anyone else encountered this problem?

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From pattersons076 at gmail.com  Thu Aug 15 20:01:32 2013
From: pattersons076 at gmail.com (Samantha Patterson)
Date: Thu, 15 Aug 2013 11:01:32 -0700
Subject: [FieldTrip] Fwd: error using freqdescriptives
In-Reply-To: <CACZDhUvHh-BRvcaPhKX7KXYMrSLX+fuEVqvDKZfUt7izwxBGjg@mail.gmail.com>
References: <CACZDhUvHh-BRvcaPhKX7KXYMrSLX+fuEVqvDKZfUt7izwxBGjg@mail.gmail.com>
Message-ID: <CACZDhUsnY6U5do=C0C3eJpX7sguUGJ1+Otbg-uybiZt3WpFEfg@mail.gmail.com>

Dear Fieldtrippers,


l am trying to use ft_freqdescriptives on freq data but i get an error
saying

Error using ft_checkdata (line 366)
This function requires freq or freqmvar data as input.

Error in ft_freqdescriptives (line 103)
freq = ft_checkdata(freq, 'datatype', {'freq', 'freqmvar'},
'feedback', 'yes');

Specfied cfg for freqdescriptives is

cfg = [];
cfg.foilim = [10 35];
cfg.toilim = [1.0 2.5];
cfg.keeptrials = 'yes';

test = ft_freqdescriptives(cfg,freq1);

output for freq1:

freq1

ans =

         label: {202x1 cell}
         dimord: 'rpt_chan_freq_time'
         freq: [1x22 double]
         time: [1x201 double]
         powspctrm: [4-D double]
         cumtapcnt: [26x18 double]
         grad: [1x1 struct]
         cfg: [1x1 struct]
         trialinfo: [26x3 double]

Any thoughts?

Thanks!!!!!

Samantha
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From M.Kandula at uu.nl  Thu Aug 15 22:26:54 2013
From: M.Kandula at uu.nl (Kandula, M. (Manasa))
Date: Thu, 15 Aug 2013 20:26:54 +0000
Subject: [FieldTrip] ft_databrowser No artifact.sampleinfo
In-Reply-To: <520CFB99.4060709@uu.nl>
References: <520CFB99.4060709@uu.nl>
Message-ID: <48A0B9F7F9A4BD4C836E1CC21805EB7E191D0BFC@ICTSC-W-S203.soliscom.uu.nl>

Hey all,
A minor correction.. I meant the artdata struct , not the artifact struct.
Thanks!!
Manasa
________________________________
From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Manasa Kandula [m.kandula at uu.nl]
Sent: Thursday, August 15, 2013 6:02 PM
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] ft_databrowser No artifact.sampleinfo

I've been trying to use ft_databrowser on segmented EEG data right after ft_preprocessing. However, at the subfunction redraw_cb, it's crashing as a call to ft_fetch_data is resulting in an error as opt.artdata.sampleinfo is not a field present in the opt.artdata struct
(Error using ==> ft_fetch_data at 60 data does not contain a consistent trial definition, fetching data is not possible).
As far as I can tell, there is no point in the code that actually sets the sampleinfo field for the artifact struct.
Has anyone else encountered this problem?

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From mbj0310 at gmail.com  Sun Aug 18 14:31:53 2013
From: mbj0310 at gmail.com (Beom Jun Min)
Date: Sun, 18 Aug 2013 21:31:53 +0900
Subject: [FieldTrip] Visualizing grand-averaged ERPs with different channels
Message-ID: <CA+v9jv+02_xb8sd-rQR14nqf5iA9Rs3HxYfbVgVx1=q+50YKkw@mail.gmail.com>

Dear all.

Hello

What I want to do is visualizing ERPs in different channels, simultaneously
in a single figure window.
For example, CZ, CPZ, & PZ or P4 & P5 in a group.

I use ft_singleplotER like below

*figure; *
*cfg = [];*
*cfg.ylim = [-8 8];*
*cfg.baseline = [-0.2 0];*
*cfg.linewidth = [2];*
*ft_singleplotER(cfg, group1_CP4, group1_CP3)*

I succeeded visualizing 3 different groups simultaneously with certain same
channel using the same manner above. (cfg, group1_CZ, group2_CZ)
However, when I try the same code with different channels, the result only
to show mean value (e.g. mean(CP4).

I do not know how to solve it.
Please help me.

With regards.

-- 
BeomJun Min, M.D.

Department of Medical System Engineering (DMSE)
Gwangju Institute of Science and Technology (GIST)
261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
500-712, Republic of Korea (South)
Phone: +82-62-715-3266 / Fax: +82-62-715-3244
E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
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From Sara.Bogels at mpi.nl  Mon Aug 19 11:39:54 2013
From: Sara.Bogels at mpi.nl (=?ISO-8859-1?Q?Sara_B=F6gels?=)
Date: Mon, 19 Aug 2013 11:39:54 +0200
Subject: [FieldTrip] problem with ft_multiplotER
In-Reply-To: <51E6838F.3050302@donders.ru.nl>
References: <CAPjpx=wTC727vv5fzqX_DdP-7wZi968TC13mkQR-bx80Faa-Zw@mail.gmail.com>
	<51E67229.8040001@mpi.nl> <51E6838F.3050302@donders.ru.nl>
Message-ID: <5211E7EA.8090907@mpi.nl>

Hi Jörn and others,

Some time ago, I posted the question below to the mailinglist. I now 
have had this error many times for both ft_timelockgrandaverage and 
ft_multiplotER. It happens for some datasets but not others and this 
appears quite random to me. The error message is:

"Subscripted assignment dimension mismatch"
Error in ft_timelockgrandaverage (line 182).
avgmat(s,:,:) = varargin{s}.(cfg.parameter{k});


It appears to have something to do with the different time limits of the 
different data I want to average or plot. I use cfg.latency to make sure 
the latency falls within the time limits of all files but this sometimes 
still does not help.

Any ideas?

Thank you,
Sara

"Jörn M. Horschig" wrote:
> Dear Sara,
>
> What you describe sounds like a bug to me. It looks like that in these
> lines the averages of the two conditions should be concatenated into one
> matrix, and apparently something goes wrong. However, you truncated the
> error message a bit (you pasted the line where the error occurs, but not
> the error message itself). If one of us developers should look into this
> further, it would be great if you register and create a bugreport on
> bugzilla.fconders.nl. Preferably would be to upload a snippet of your
> data, e.g. timelockstructures of one participant, and some lines of code
> which reproduce the error. We can then look into this further and fix
> this as soon as possible :)
>
> Best,
> Jörn
>
> On 7/17/2013 12:30 PM, Sara Bögels wrote:
>> Hi all,
>>
>> I have a very specific problem with the ft_multiplotER function. For 2
>> of my 24 participants, the function gives an error-message when I try
>> to plot the averages of two conditions at the same time. Plotting them
>> one by one is not a problem. There appears to be a specific point in
>> time (different for the two participants) when this goes wrong. If I
>> avoid that time (by using cfg.xlim) it works fine. My trials have
>> different lengths and I used "cfg.vartrllength = 2;" when calling
>> ft_timelockanalysis (not sure whether this is relevant).
>>
>> The error message I get is
>> "Error in ft_multiplotER (line 616)
>> yval(i,:) = datamatrix{i}(m,:);"
>>
>> I cannot find out what happens in this line. Can anyone tell me what
>> this might be referring to?
>>
>> Thank you,
>> Sara
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>


From frank.ye.mei at gmail.com  Mon Aug 19 22:18:39 2013
From: frank.ye.mei at gmail.com (Ye Mei)
Date: Mon, 19 Aug 2013 16:18:39 -0400
Subject: [FieldTrip] Can beamformer give both the location and the
 orientation of the source?
Message-ID: <52127D9F.3090102@gmail.com>

Hi all,

Can beamformer give both the location and the orientation of the source? 
If yes, how to do it in fieldtrip?

thanks ahead,
Ye




From arr at uvic.ca  Mon Aug 19 22:47:27 2013
From: arr at uvic.ca (Ashley Rose)
Date: Mon, 19 Aug 2013 13:47:27 -0700
Subject: [FieldTrip] fieldtrip question
Message-ID: <314d3147c1b422e458d033e10d7a6b17.squirrel@wm3.uvic.ca>


Hi there,

I'm having an issue running Fieldtrip.  I keep getting this warning:
"Warning: Dimensions of AlphaData must be 1x1, or must match CData."
But I haven't done anything to AlphaData or CData that would make them
inconsistent.  Has anyone had this problem before?

Thank you,
Ashley Rose




From imponderabilion at gmail.com  Tue Aug 20 00:54:49 2013
From: imponderabilion at gmail.com (=?ISO-8859-2?Q?Miko=B3aj_Magnuski?=)
Date: Tue, 20 Aug 2013 00:54:49 +0200
Subject: [FieldTrip] ft_neighbourplot does not plot new connections in 3D
Message-ID: <CAOb=78enLVbZZcApNNBGJALm=rZAtHH7CqiUqSSAimiDJYbmzw@mail.gmail.com>

Hi FieldTrippers!

just a short note in case it wasn'r reported before:
ft_neighbourplot with option .enableedit = 'on' (the bleeding option)
plots new connections (new - that means click-created) only as 2D
projections even if everything else is plotted in 3D.

changing lines 286 - 287 to something like:
    if size(proj,2) == 2
        Coord = {X, Y};
    elseif size(proj,2) > 2
        Z = [proj(curSensId,3) proj(lastSensId,3)];
        Coord = {X, Y, Z};
    end
    hl(curSensId, lastSensId) = line(Coord{:}, 'color', 'r');
    hl(lastSensId, curSensId) = line(Coord{:}, 'color', 'r');

fixes this problem.


Regards,
Mikołaj Magnuski
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From jm.horschig at donders.ru.nl  Fri Aug 23 09:28:18 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Fri, 23 Aug 2013 09:28:18 +0200
Subject: [FieldTrip] ft_neighbourplot does not plot new connections in 3D
In-Reply-To: <CAOb=78enLVbZZcApNNBGJALm=rZAtHH7CqiUqSSAimiDJYbmzw@mail.gmail.com>
References: <CAOb=78enLVbZZcApNNBGJALm=rZAtHH7CqiUqSSAimiDJYbmzw@mail.gmail.com>
Message-ID: <52170F12.9020107@donders.ru.nl>

Dear Miko?aj,

thanks very much for reporting this. I fixed it and the fix should be 
available inthe next FieldTrip release (i.e. tomorrow).

Best,
Jörn

On 8/20/2013 12:54 AM, Miko?aj Magnuski wrote:
> Hi FieldTrippers!
>
> just a short note in case it wasn'r reported before:
> ft_neighbourplot with option .enableedit = 'on' (the bleeding option)
> plots new connections (new - that means click-created) only as 2D
> projections even if everything else is plotted in 3D.
>
> changing lines 286 - 287 to something like:
>     if size(proj,2) == 2
>         Coord = {X, Y};
>     elseif size(proj,2) > 2
>         Z = [proj(curSensId,3) proj(lastSensId,3)];
>         Coord = {X, Y, Z};
>     end
>     hl(curSensId, lastSensId) = line(Coord{:}, 'color', 'r');
>     hl(lastSensId, curSensId) = line(Coord{:}, 'color', 'r');
>
> fixes this problem.
>
>
> Regards,
> Miko?aj Magnuski
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From narayan.ps at tut.fi  Fri Aug 23 12:37:20 2013
From: narayan.ps at tut.fi (Narayan Puthanmadam Subramaniyam)
Date: Fri, 23 Aug 2013 13:37:20 +0300
Subject: [FieldTrip] simulation of EOG
Message-ID: <001501ce9fec$bee80ce0$3cb826a0$@tut.fi>

Dear FT experts

I am not sure if I should be asking this question here. I want to simulate
'pure' EOG signal by placing rotating dipole in the eye. Can I use FT to
compute the lead field matrix from eye to  all scalp electrodes ? Has anyone
used a BEM model where eyes are segmented ?

Many Thanks
Narayan



From ingenieureniso at gmail.com  Fri Aug 23 19:40:14 2013
From: ingenieureniso at gmail.com (ingenieur eniso)
Date: Fri, 23 Aug 2013 18:40:14 +0100
Subject: [FieldTrip] how to open bdf and rdf files
Message-ID: <CAPjpx=yj73grOv58wwiLF4Ec2fLGzAiNpy7ziDZGpb+Lphynsg@mail.gmail.com>

Dear all,


I have EEG record files in rdf and bdf formats. but I do not know how to
open them.

Please can anyone send me a matlab function to open these files?

I hope you will send me positive and helpful response.

Thanks a lot in advance!

Best,

ahmed
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From johanna.zumer at gmail.com  Sun Aug 25 07:18:14 2013
From: johanna.zumer at gmail.com (Johanna Zumer)
Date: Sun, 25 Aug 2013 07:18:14 +0200
Subject: [FieldTrip] how to open bdf and rdf files
In-Reply-To: <CAPjpx=yj73grOv58wwiLF4Ec2fLGzAiNpy7ziDZGpb+Lphynsg@mail.gmail.com>
References: <CAPjpx=yj73grOv58wwiLF4Ec2fLGzAiNpy7ziDZGpb+Lphynsg@mail.gmail.com>
Message-ID: <CAL4kA6dwgo31sL43OMwpruHyOnF5O8MZW0Ha-Z682HfNs8gc=A@mail.gmail.com>

Dear Ahmed,

Does this help?  (http://fieldtrip.fcdonders.nl/getting_started/bdf )

If you are still stuck, maybe try EEGlab
import<http://sccn.ucsd.edu/wiki/A01:_Importing_Continuous_and_Epoched_Data>
and
then convert EEGlab format to FieldTrip format (
http://fieldtrip.fcdonders.nl/integrating_with/integrating_with_eeglab)

Best,
Johanna


2013/8/23 ingenieur eniso <ingenieureniso at gmail.com>

> Dear all,
>
>
> I have EEG record files in rdf and bdf formats. but I do not know how to
> open them.
>
> Please can anyone send me a matlab function to open these files?
>
> I hope you will send me positive and helpful response.
>
> Thanks a lot in advance!
>
> Best,
>
> ahmed
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From roeysc at gmail.com  Mon Aug 26 00:08:19 2013
From: roeysc at gmail.com (Roey Schurr)
Date: Mon, 26 Aug 2013 01:08:19 +0300
Subject: [FieldTrip] Source Analysis Normalisation in-subject and in-group
Message-ID: <CAHm4wZAWwHisWEPd41qxe6EiNAgkh_vqv2eMWvaGpNWdRQ1xww@mail.gmail.com>

Hi all,

We have a question regarding normalisation of EEG signals for source
reconstruction analysis.

We have EEG records (not ERP) of a few patients in two different conditions
(each condition consists of several 2 seconds segments/trials). Each
recording was done over a period of a few days, and in different sessions.
We also have anatomycal MRI scans for each patient (subject).

We would like to make two statistic comparisons:

1.    Compare the source analysis of the two conditions in each subject.

2.    Compare the source analysis of the two conditions, based upon all
subjects.

For the first comparison, we are puzzled about the appropriate way to
normalise and standardize our data, since each EEG segment was recorded at
a different time, and hence may be affected by different electrode
conductivity, for example. How would you normalise the data?

For the second comparison, of course, we would like to normalise the source
analysis results in the anatomycal level using ft_volumenormalise.

However, we are puzzled about the appropriate way to normalise and
standardize our data, since subjects differ from each other (for example,
anatomycally, resulting in changes of power spectrum).

How would you standartize the data between subjects?



Thank you very much,

best regards,

Aia and Roey
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From polomacnenad at gmail.com  Tue Aug 27 20:44:39 2013
From: polomacnenad at gmail.com (Nenad Polomac)
Date: Tue, 27 Aug 2013 20:44:39 +0200
Subject: [FieldTrip] ICA on highpass filtered MEG data
Message-ID: <CAEk4EpFExFt8U85CfTjz0MPQPQhOrV7R4LdCqLkVRjvahywiUQ@mail.gmail.com>

Dear Fieldtrip users,

I have CTF 275 channels MEG data and I am interested in gamma band. For
this purpose I would like to remove microsaccade artifacts from the data
using the ICA. In order to obtain the microsacade components I have
filtered data ( highpass and lowpass; 30-150 Hz) and than I've wanted to
run ICA calculation. However, I've read here
http://sccn.ucsd.edu/pipermail/eeglablist/2013/006710.html that after
filtering data are more dependent and that is a big problem for ICA
calculation. And I also experienced that ICA takes very long time and
sometimes doesn't converge. So, to overcome this problem, the data
dimensionality has to be reduced. I have found two different solutions from
different sources.

One solution might be to estimate variance with PCA and than choose the
amount of variance that should stay in the data. e.g.
[COEFF,SCORE,eigenvalues ] = princomp(data_matrix);
A= cumsum(eigenvalues);
num_of_comp=find(A/A(end)>0.98,1); % 98% is the percentage of variance that
will be used for the ICA, 2% will be discarded
This percentage will be the same for all subjects.

The second option might be to use the same eigenvalue cutoff value for all
subjects:
[COEFF,SCORE,eigenvalues ] = princomp(data_matrix);
A=(find(eigenvalues>0.005));  %0.005 here is just for example
num_of_comp=A(end);

The variable num_of_comp represents the number of component to which
filtered data will be reduced before ICA.
e.g.
    cfg = [];
    cfg.method = 'runica';
    cfg.runica.pca = num_of_comp;
    cfg.runica.maxsteps = 600;
    cfg.runica.stop = 1e-7;
    cfg.runica.extended = 1;
    ica_comp = ft_componentanalysis(cfg, data);



Finally, my question is which of this two methods is more objective? And is
there any other possibility I should consider?
I would like to add that in my case second calculation gives me less
variant number of components among 22 subjects.

Thank you in advance!

All the best!
Nenad
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From aaron.schurger at gmail.com  Tue Aug 27 21:49:21 2013
From: aaron.schurger at gmail.com (Aaron Schurger)
Date: Tue, 27 Aug 2013 21:49:21 +0200
Subject: [FieldTrip] ICA on highpass filtered MEG data
In-Reply-To: <CAEk4EpFExFt8U85CfTjz0MPQPQhOrV7R4LdCqLkVRjvahywiUQ@mail.gmail.com>
References: <CAEk4EpFExFt8U85CfTjz0MPQPQhOrV7R4LdCqLkVRjvahywiUQ@mail.gmail.com>
Message-ID: <CALeeyASWNx4+ZMfZuDqY-cfvrXma-0BquHNsbWUFrcE2xpjvCw@mail.gmail.com>

I am not aware of any good way to remove microsaccade artifacts from
EEG or MEG data. ICA might find a microsaccade component if you have
sufficient data, but you will have to hunt through the components to
find the "right" one. The difficult question is how to know which is
the right component, or whether or not microsaccades are incorporated
into two or more components (or not at all). Having an MEG-compatible
eye tracker with a high sampling rate is what I would want.
Best wishes,
Aaron

On Tue, Aug 27, 2013 at 8:44 PM, Nenad Polomac <polomacnenad at gmail.com> wrote:
> Dear Fieldtrip users,
>
> I have CTF 275 channels MEG data and I am interested in gamma band. For this
> purpose I would like to remove microsaccade artifacts from the data using
> the ICA. In order to obtain the microsacade components I have filtered data
> ( highpass and lowpass; 30-150 Hz) and than I've wanted to run ICA
> calculation. However, I've read here
> http://sccn.ucsd.edu/pipermail/eeglablist/2013/006710.html that after
> filtering data are more dependent and that is a big problem for ICA
> calculation. And I also experienced that ICA takes very long time and
> sometimes doesn't converge. So, to overcome this problem, the data
> dimensionality has to be reduced. I have found two different solutions from
> different sources.
>
> One solution might be to estimate variance with PCA and than choose the
> amount of variance that should stay in the data. e.g.
> [COEFF,SCORE,eigenvalues ] = princomp(data_matrix);
> A= cumsum(eigenvalues);
> num_of_comp=find(A/A(end)>0.98,1); % 98% is the percentage of variance that
> will be used for the ICA, 2% will be discarded
> This percentage will be the same for all subjects.
>
> The second option might be to use the same eigenvalue cutoff value for all
> subjects:
> [COEFF,SCORE,eigenvalues ] = princomp(data_matrix);
> A=(find(eigenvalues>0.005));  %0.005 here is just for example
> num_of_comp=A(end);
>
> The variable num_of_comp represents the number of component to which
> filtered data will be reduced before ICA.
> e.g.
>     cfg = [];
>     cfg.method = 'runica';
>     cfg.runica.pca = num_of_comp;
>     cfg.runica.maxsteps = 600;
>     cfg.runica.stop = 1e-7;
>     cfg.runica.extended = 1;
>     ica_comp = ft_componentanalysis(cfg, data);
>
>
>
> Finally, my question is which of this two methods is more objective? And is
> there any other possibility I should consider?
> I would like to add that in my case second calculation gives me less variant
> number of components among 22 subjects.
>
> Thank you in advance!
>
> All the best!
> Nenad
>
>
>
>
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



-- 
Aaron Schurger, PhD
Post-doctoral researcher
INSERM U992 / NeuroSpin
CEA - Saclay, France
+33-1-69-08-66-47
aaron.schurger at gmail.com
http://www.unicog.org


From sreenivasan.r.nadar at gmail.com  Tue Aug 27 22:17:03 2013
From: sreenivasan.r.nadar at gmail.com (Sreenivasan R. Nadar, Ph.D.)
Date: Tue, 27 Aug 2013 16:17:03 -0400
Subject: [FieldTrip] 19 channel EEG for source modeling of epileptic focus
Message-ID: <CAL+KoxgGx-BfL77H2VNL3dssfuB2FNAO5wFOB6p-gEKFLdNVFg@mail.gmail.com>

Hi All,

I have a 19 channel Nihon - Kohden EEG for epilepsy monitoring and I use
the following file for channel locations in
ftp://sccn.ucsd.edu/pub/locfiles/eeglab/Standard-10-20-Cap19.ced for data
analysis in EEGLab.

Please let me know if anybody has pre-processing script to import the data
in Fieldtrip and also for source localisation of epileptic focus.

Thank you.

Sreenivasan
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From jm.horschig at donders.ru.nl  Thu Aug 29 10:02:45 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Thu, 29 Aug 2013 10:02:45 +0200
Subject: [FieldTrip] 19 channel EEG for source modeling of epileptic
	focus
In-Reply-To: <CAL+KoxgGx-BfL77H2VNL3dssfuB2FNAO5wFOB6p-gEKFLdNVFg@mail.gmail.com>
References: <CAL+KoxgGx-BfL77H2VNL3dssfuB2FNAO5wFOB6p-gEKFLdNVFg@mail.gmail.com>
Message-ID: <521F0025.8090104@donders.ru.nl>

Dear Sreenivasan,

I am not sure whether you can read in .ced files with the ft_read_sens 
function. You could give it a try though by specifying cfg.elecfile = 
'PATH_TO_FILE/Standard-10-20-Cap19.ced'

Otherwise, I can see two ways how you can make this work.
First, you could change the content of the file to match the format of 
the other sensor-templates. For this, you can best have a look in 
fieldtrip/template/elec and have a look at one of these files. Then, you 
would need to rearrange the values of your .ced file to match the order 
of the .elc-format.
Alternatively, you could write your own wrapper function, which reads in 
the x-, y- and z-position of the electrodes from the .ced file and 
stores them in a matrix. Also, you need to store the corresponding 
channel label. Using these, you can create an elec-structure that you 
can use as cfg.elec for whatever function you want to do.

Maybe someone else here has worked with .ced files before and can thus 
can help with either of the two solutions. Good luck :)

Best,
Jörn

On 8/27/2013 10:17 PM, Sreenivasan R. Nadar, Ph.D. wrote:
> Hi All,
>
> I have a 19 channel Nihon - Kohden EEG for epilepsy monitoring and I 
> use the following file for channel locations in 
> ftp://sccn.ucsd.edu/pub/locfiles/eeglab/Standard-10-20-Cap19.ced for 
> data analysis in EEGLab.
>
> Please let me know if anybody has pre-processing script to import the 
> data in Fieldtrip and also for source localisation of epileptic focus.
>
> Thank you.
>
> Sreenivasan
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From ben.vanlier at bsse.ethz.ch  Thu Aug 29 13:53:26 2013
From: ben.vanlier at bsse.ethz.ch (van Lier  Ben)
Date: Thu, 29 Aug 2013 11:53:26 +0000
Subject: [FieldTrip] slow reading with ft_preprocessing of a fcdc_matbin
	file?
Message-ID: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A7B87E@MBX13.d.ethz.ch>

Hi all,

I have a pretty big data file of 120 channels for 20min continuous at 20khz. clearly i need to downsample. to do so, i convert the original file to fcdc_matbin, creating a 22gb bin file with all the data.

then its time for downsampling as shown on http://fieldtrip.fcdonders.nl/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory

this is very slow. ft_preprocessing takes 230 seconds per channel (using 380 mb), doing nothing but just reading 1 channel. the subsequent downsampling with ft_resample to 1khz is surprisingly fast with only 4 seconds.

does that make any sense? it seems like a very long time to read in 380mb... :(

Best,
Ben



From jan.schoffelen at donders.ru.nl  Thu Aug 29 14:01:59 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 29 Aug 2013 14:01:59 +0200
Subject: [FieldTrip] slow reading with ft_preprocessing of a fcdc_matbin
	file?
In-Reply-To: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A7B87E@MBX13.d.ethz.ch>
References: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A7B87E@MBX13.d.ethz.ch>
Message-ID: <264BF553-0691-4AC9-95B8-D78000F0CA6B@donders.ru.nl>

Hi Ben,

I guess MATLAB needs to read in the whole datafile each time (for each channel). What about creating separate files for each channel?

JM


On Aug 29, 2013, at 1:53 PM, van Lier Ben wrote:

> Hi all,
> 
> I have a pretty big data file of 120 channels for 20min continuous at 20khz. clearly i need to downsample. to do so, i convert the original file to fcdc_matbin, creating a 22gb bin file with all the data.
> 
> then its time for downsampling as shown on http://fieldtrip.fcdonders.nl/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory
> 
> this is very slow. ft_preprocessing takes 230 seconds per channel (using 380 mb), doing nothing but just reading 1 channel. the subsequent downsampling with ft_resample to 1khz is surprisingly fast with only 4 seconds.
> 
> does that make any sense? it seems like a very long time to read in 380mb... :(
> 
> Best,
> Ben
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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From jm.horschig at donders.ru.nl  Thu Aug  1 12:37:08 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Thu, 01 Aug 2013 12:37:08 +0200
Subject: [FieldTrip] ancova for sources analysis
In-Reply-To: <2264a36963356fbe.51f8fb71@upo.es>
References: <167095db43e3fd69.51f8d35e@upo.es>
	<1763660954.2174368.1375257362812.JavaMail.root@sculptor.zimbra.ru.nl>
	<2264a36963356fbe.51f8fb71@upo.es>
Message-ID: <51FA3A54.8020001@donders.ru.nl>

Dear Gabriel,

if you have a .stat field, you did already run statistics on your data. 
I wouldn't regress anything out of e.g. t-values. Rather, the idea is to 
regress out confounding factors before doing statistics, so that you 
reduce variance across trials and subsequently maximize sensitivity of 
your statistical test. I could really advise you to read the paper I 
suggested, the rationale is explained there.
Moreover, if you are interested in a covariate like 'age', a simple 
correlational analysis might make more sense. As stated, the idea of 
regressconfound is to explain and remove variance across observations, 
but depending on what you want, a correlation might make more sense.
Want to improve your stats? Then go for regressconfound. Find out if 
there is age explains neural effects? Then go for a simple correlation.

Best,
Jörn

On 7/31/2013 11:56 AM, Gabriel Gonzalez Escamilla wrote:
> Thank you all for your responses.
>
> The last problem I did wrote is now solved, see below.
>
> I had a field called 'stat' instead of the 'pow', I'm guessing this 
> field was set before, so, now i'm using this field as if it was the 
> 'pow' I needed and it's working, Is that OK?
>
> Now it takes me to the next question, my data has the avg field, and 
> it says that will update the descriptives but that the 'method' is 
> missing, is this update necessary? or can I just skeep it?
>
>
> Many thanks in advanced,
> Gabriel
>
>
> ----- Mensaje original -----
> De: "Stolk, A." <a.stolk at fcdonders.ru.nl>
> Fecha: Miércoles, 31 de Julio de 2013, 10:04 am
> Asunto: Re: [FieldTrip] ancova for sources analysis
> A: FieldTrip discussion list <fieldtrip at science.ru.nl>
>
> >Dear Gabriel,
> >
> > This page demonstrates how to remove contributions to the data 
> originating from head movement, but one could as well follow the same 
> principle for any other type of covariate (e.g. eye movement related 
> activity).
> >
> > http://fieldtrip.fcdonders.nl/example/how_to_incorporate_head_movements_in_meg_analysis?
> >
> > Yours,
> > Arjen
> >
> ------------------------------------------------------------------------
>
>     *> Van: *"Gabriel Gonzalez Escamilla" <ggonesc at upo.es>
>     *> Aan: *"fieFieldTrip discussion list" <fieldtrip at science.ru.nl>
>     *> Verzonden: *Woensdag 31 juli 2013 09:05:34
>     *> Onderwerp: *[FieldTrip] ancova for sources analysis
>     >
>     > Dear fieldtrip experts,
>     >
>     > I'm wondering if it is possible to perform an ancova or to remove
>     the effect of a covariate in a source analysis?
>     >
>     > Many thanks in advanced,
>     > Gabriel
>     > _______________________________________________
>     > fieldtrip mailing list
>     > fieldtrip at donders.ru.nl
>     > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> <font size="3">--------------------------<br />PhD. student Gabriel 
> González-Escamilla<br />Laboratory of Functional Neuroscience<br 
> />Department of Physiology, Anatomy, and Cell Biology<br />University 
> Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br 
> />- Spain -<br /><br />Email: ggonesc at upo.es<br 
> />http://www.upo.es/neuroaging/es/</font>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From lzyang at ustc.edu.cn  Sat Aug  3 10:49:59 2013
From: lzyang at ustc.edu.cn (lzyang)
Date: Sat, 03 Aug 2013 16:49:59 +0800
Subject: [FieldTrip] units of data sample read from neuroscan avg file is
	incorrect
Message-ID: <51FCC437.5070409@ustc.edu.cn>

Dear fieldtrip list,
I used ft_read_data to read in .avg files (neuroscan format) to do some
advanced analysis.
data=ft_read_data('sham.avg', 'dataformat', 'ns_avg');
I noticed that the unit of data sample read by this function is incorrect.
Values of samples ranged from -0.1 to 0.1.
I will appreciate if anyone can give me some hints on how to import avg
files correctly using fieldtrip.

Thanks very much!

Best Regards,
-Lizhuang




From politzerahless at gmail.com  Sat Aug  3 13:48:58 2013
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Sat, 3 Aug 2013 07:48:58 -0400
Subject: [FieldTrip] fieldtrip Digest, Vol 33, Issue 3
In-Reply-To: <mailman.1.1375524018.6192.fieldtrip@science.ru.nl>
References: <mailman.1.1375524018.6192.fieldtrip@science.ru.nl>
Message-ID: <CAJT2k__JuKQth_DrjFDn39rJBMsNSAx1wsg=RAiq-mOq+D0N9g@mail.gmail.com>

Hi Lizhuang,

I haven't used Fieldtrip to import .avg files so I'm not sure about this,
but I wonder if this is related to the same problem in EEGLAB. EEGLAB also
scales .avg files like this when importing them, for some reason, so if the
Fieldtrip function is based on EEGLAB code these issues may be related.
(However, I just looked at read_ns_avg.m, which is what ft_read_data calls,
and it doesn't say it's copied from EEGLAB). If you have EEGLAB, you can
add the custom function loadavg_bcl.m to your path (it is available at
http://sccn.ucsd.edu/pipermail/eeglablist/2011/003986.html, as one of the
attachments near the bottom), use that to import the .avg file, and then
use the EEGLAB function eeglab2fieldtrip() to get the data into FieldTrip.

Also, have you tried reading the data with ft_preprocessing() instead of
ft_read_data? ft_read_data is kind of a low-level function; in the past I
think I've had better luck just using ft_preprocessing.

Best,
Steve


Stephen Politzer-Ahles
New York University, Abu Dhabi
Psychology Department


> Message: 1
> Date: Sat, 03 Aug 2013 16:49:59 +0800
> From: lzyang <lzyang at ustc.edu.cn>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] units of data sample read from neuroscan avg file
>         is      incorrect
> Message-ID: <51FCC437.5070409 at ustc.edu.cn>
> Content-Type: text/plain; charset=GB2312
>
> Dear fieldtrip list,
> I used ft_read_data to read in .avg files (neuroscan format) to do some
> advanced analysis.
> data=ft_read_data('sham.avg', 'dataformat', 'ns_avg');
> I noticed that the unit of data sample read by this function is incorrect.
> Values of samples ranged from -0.1 to 0.1.
> I will appreciate if anyone can give me some hints on how to import avg
> files correctly using fieldtrip.
>
> Thanks very much!
>
> Best Regards,
> -Lizhuang
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From politzerahless at gmail.com  Sat Aug  3 13:50:40 2013
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Sat, 3 Aug 2013 07:50:40 -0400
Subject: [FieldTrip] units of data sample read from neuroscan avg file
	is incorrect
Message-ID: <CAJT2k_8z9nv4YnX8AKYhUAwSv4cHnaPDDH7KqrjQ-T=f1RAAdg@mail.gmail.com>

Hi Lizhuang,

I haven't used Fieldtrip to import .avg files so I'm not sure about this,
but I wonder if this is related to the same problem in EEGLAB. EEGLAB also
scales .avg files like this when importing them, for some reason, so if the
Fieldtrip function is based on EEGLAB code these issues may be related.
(However, I just looked at read_ns_avg.m, which is what ft_read_data calls,
and it doesn't say it's copied from EEGLAB). If you have EEGLAB, you can
add the custom function loadavg_bcl.m to your path (it is available at
http://sccn.ucsd.edu/pipermail/eeglablist/2011/003986.html, as one of the
attachments near the bottom), use that to import the .avg file, and then
use the EEGLAB function eeglab2fieldtrip() to get the data into FieldTrip.

Also, have you tried reading the data with ft_preprocessing() instead of
ft_read_data? ft_read_data is kind of a low-level function; in the past I
think I've had better luck just using ft_preprocessing.

Best,
Steve



Stephen Politzer-Ahles
New York University, Abu Dhabi
Psychology Department


> Message: 1
> Date: Sat, 03 Aug 2013 16:49:59 +0800
> From: lzyang <lzyang at ustc.edu.cn>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] units of data sample read from neuroscan avg file
>         is      incorrect
> Message-ID: <51FCC437.5070409 at ustc.edu.cn>
> Content-Type: text/plain; charset=GB2312
>
> Dear fieldtrip list,
> I used ft_read_data to read in .avg files (neuroscan format) to do some
> advanced analysis.
> data=ft_read_data('sham.avg', 'dataformat', 'ns_avg');
> I noticed that the unit of data sample read by this function is incorrect.
> Values of samples ranged from -0.1 to 0.1.
> I will appreciate if anyone can give me some hints on how to import avg
> files correctly using fieldtrip.
>
> Thanks very much!
>
> Best Regards,
> -Lizhuang
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From Izabela.Mikula at mpi.nl  Tue Aug  6 12:10:32 2013
From: Izabela.Mikula at mpi.nl (Izabela Mikula)
Date: Tue, 6 Aug 2013 12:10:32 +0200
Subject: [FieldTrip] Error in ft_rejectartifact for the newest fieldtrip
	version
Message-ID: <9532B831-AB8E-4EBC-A984-5A3783E5313D@mpi.nl>

Dear all,
I was wondering if any of you have ever encountered similar problem and might know if I'm doing something wrong or it is a bug..

I have tried using (my old scripts for preprocessing) ft_rejectartifact(cfg, data) but I get an error:

evaluating artifact_jump
??? Error using ==> feval
Undefined function or method 'artifact_jump' for input arguments of type 'struct'.

Error in ==> ft_rejectartifact at 257
    cfg = feval(sprintf('artifact_%s', cfg.artfctdef.type{type}), cfg, data);

It is important to note that this error only occurs when using the newest fieldtrip version. For previous versions it works without any problems. I have also tried multiple datasets, but the problem remains.
 
data = 

       fsample: 1200
          grad: [1x1 struct]
    sampleinfo: [180x2 double]
     trialinfo: [180x1 double]
         trial: {1x180 cell}
          time: {1x180 cell}
         label: {273x1 cell}
           cfg: [1x1 struct]

and

cfg.artfctdef = 

          reject: 'complete'
            jump: [1x1 struct]
          muscle: [1x1 struct]
            type: {2x1 cell}
    minaccepttim: 0.1000
      crittoilim: []
        feedback: 'no'

Thanks in advance!

Best,
Izabela




From jan.schoffelen at donders.ru.nl  Tue Aug  6 13:13:09 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Tue, 6 Aug 2013 13:13:09 +0200
Subject: [FieldTrip] Error in ft_rejectartifact for the newest fieldtrip
	version
In-Reply-To: <9532B831-AB8E-4EBC-A984-5A3783E5313D@mpi.nl>
References: <9532B831-AB8E-4EBC-A984-5A3783E5313D@mpi.nl>
Message-ID: <C671E708-23FB-40E2-9094-1DFD80CAED92@donders.ru.nl>

Hi Izabela,

This is indeed a bug. We reorganized our compat-directory, that is dealing with backward compatibility issues. One of these issues was to support backward compatibility for calling ft-functions without the ft_prefix. E.g. calling freqanalysis should redirect to a call to ft_freqanalysis. With this feature removed, ft_rejectartifact cannot execute artifact_xxx, because it is not redirected anymore to ft_artifact_xxx.
I have fixed this. It should be available within 15 minutes on the DCCN Fieldtrip version, and in the download version as of tonight.

Thanks for reporting,
Jan-Mathijs

 
On Aug 6, 2013, at 12:10 PM, Izabela Mikula wrote:

> Dear all,
> I was wondering if any of you have ever encountered similar problem and might know if I'm doing something wrong or it is a bug..
> 
> I have tried using (my old scripts for preprocessing) ft_rejectartifact(cfg, data) but I get an error:
> 
> evaluating artifact_jump
> ??? Error using ==> feval
> Undefined function or method 'artifact_jump' for input arguments of type 'struct'.
> 
> Error in ==> ft_rejectartifact at 257
>    cfg = feval(sprintf('artifact_%s', cfg.artfctdef.type{type}), cfg, data);
> 
> It is important to note that this error only occurs when using the newest fieldtrip version. For previous versions it works without any problems. I have also tried multiple datasets, but the problem remains.
> 
> data = 
> 
>       fsample: 1200
>          grad: [1x1 struct]
>    sampleinfo: [180x2 double]
>     trialinfo: [180x1 double]
>         trial: {1x180 cell}
>          time: {1x180 cell}
>         label: {273x1 cell}
>           cfg: [1x1 struct]
> 
> and
> 
> cfg.artfctdef = 
> 
>          reject: 'complete'
>            jump: [1x1 struct]
>          muscle: [1x1 struct]
>            type: {2x1 cell}
>    minaccepttim: 0.1000
>      crittoilim: []
>        feedback: 'no'
> 
> Thanks in advance!
> 
> Best,
> Izabela
> 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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From ben.vanlier at bsse.ethz.ch  Tue Aug  6 17:56:55 2013
From: ben.vanlier at bsse.ethz.ch (van Lier  Ben)
Date: Tue, 6 Aug 2013 15:56:55 +0000
Subject: [FieldTrip] from trials to continuous and an error in selfromraw
Message-ID: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A6CBB0@MBX23.d.ethz.ch>

Hi guys,

for testing purposes im trying to use data in trials as one continuous piece of data. when i do freqanalysis with cfg.trials = 'all' and then singleplotTFR, i get to see only 1 trial. it should plot the spectra of all of them right? i do use cfg.continuous = yes
i can tell it is processing all the trials in the command window feedback and databrowser is putting them together fine.

i guess related, when i do cfg.trials = '1' (or any) and then freqanalysis it gives me the following error:

--------------------------
Error using selfromraw (line 13)
incorrect specification of requested repetitions

Error in ft_selectdata_old (line 547)
    data = selfromraw(data, 'rpt', selrpt);

Error in ft_selectdata (line 45)
  [varargout{1:nargout}] = ft_selectdata_old(varargin{:});

Error in ft_freqanalysis (line 225)
  data = ft_selectdata(data, 'rpt', cfg.trials);
----------------------------

i tried with data coming from ft_appendata (2 copies of the same file) and also with ft_definetrial from one continuous file.

i am using the version of 5 aug 13

anyone knows whats going wrong?

cheers
Ben




From eelke.spaak at donders.ru.nl  Tue Aug  6 19:44:33 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Tue, 6 Aug 2013 19:44:33 +0200
Subject: [FieldTrip] from trials to continuous and an error in selfromraw
In-Reply-To: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A6CBB0@MBX23.d.ethz.ch>
References: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A6CBB0@MBX23.d.ethz.ch>
Message-ID: <CABPNLUrc3FRn5V9h+kmsqDgoDPQBc26k+5kvfj_1OpzrSNDAqg@mail.gmail.com>

Hi Ben,

The cfg.trials option for ft_freqanalysis refers to which trials
should be used in the computation of the output. By default,
ft_freqanalysis returns the average over all those trials. If you want
to get estimates for each individual trial, you should specify
cfg.keeptrials = 'yes'. (See also
http://fieldtrip.fcdonders.nl/reference/ft_freqanalysis .) I am not
sure if ft_singleplotTFR will give you plots for individual trials,
though; I think it will do the averaging anyway. To get individual
trial plots, you probably have to call the plotting function several
times with cfg.trials = 1, 2, 3, etc.

Regarding cfg.trials = '1', it is important to use just a regular
scalar quantity, and not a string, so cfg.trials = 1.

Best,
Eelke

On 6 August 2013 17:56, van Lier  Ben <ben.vanlier at bsse.ethz.ch> wrote:
> Hi guys,
>
> for testing purposes im trying to use data in trials as one continuous piece of data. when i do freqanalysis with cfg.trials = 'all' and then singleplotTFR, i get to see only 1 trial. it should plot the spectra of all of them right? i do use cfg.continuous = yes
> i can tell it is processing all the trials in the command window feedback and databrowser is putting them together fine.
>
> i guess related, when i do cfg.trials = '1' (or any) and then freqanalysis it gives me the following error:
>
> --------------------------
> Error using selfromraw (line 13)
> incorrect specification of requested repetitions
>
> Error in ft_selectdata_old (line 547)
>     data = selfromraw(data, 'rpt', selrpt);
>
> Error in ft_selectdata (line 45)
>   [varargout{1:nargout}] = ft_selectdata_old(varargin{:});
>
> Error in ft_freqanalysis (line 225)
>   data = ft_selectdata(data, 'rpt', cfg.trials);
> ----------------------------
>
> i tried with data coming from ft_appendata (2 copies of the same file) and also with ft_definetrial from one continuous file.
>
> i am using the version of 5 aug 13
>
> anyone knows whats going wrong?
>
> cheers
> Ben
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From haristz at gmail.com  Tue Aug  6 20:24:55 2013
From: haristz at gmail.com (Charidimos Tzagarakis)
Date: Tue, 6 Aug 2013 13:24:55 -0500
Subject: [FieldTrip] question about virtual electrode MNI coordinates
Message-ID: <CAFN2X+fdvTW8jkx1EPS8C+J_FGRTQgTtYL38aYw7Gv6BbLtsxg@mail.gmail.com>

Hi there,
I have a question regarding virtual electrodes: How can I double check that
the MNI coordinates that I enter are correctly interpreted?
More specifically:
I have followed the the extended beamforming tutorial in the "Appendix" and
have been able to transpose it to my data (I have 4D/BTi MEG files and
Dicom mri volumes).The part I am not certain about is the call to the LCMV
beamformer.
Here it is in my case ( I just want to get the voxel were the power is max
in the previous analysis):
cfg              = [];
cfg.method       = 'lcmv';
cfg.vol          = volfcm;
cfg.grid.pos     = source_diff.pos(maxpowindx, :);
cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
cfg.grid.outside = [];
cfg.grad=senscm
source_idx       = ft_sourceanalysis(cfg, tlock);
My headmodel does not include MEG channel information so I need to also
define the cfg.grad parameter. What I don't understand is how cfg.grid.pos
(which is in MNI coordinates as per the previous part of the tutorial) can
be correctly applied to the coordinates of the headmodel and the channels
since these 2 are not in MNI coordinates (in my case they are in 4d/Bti
coordinates and rescaled to cm).In the previous part of the tutorial this
is (if I understand correctly) accomplished because the leadfield used when
calling ft_sourceanalysis was created using and MNI-warped template. I
don't see where the equivalent part is when estimating the virtual
electrode though.
Any advice you may have would be much appreciated.
Best,
Haris


Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
University of Minnesota Dept of Neuroscience and Brain Sciences Center
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From franziska.bilger at uni-ulm.de  Wed Aug  7 11:23:50 2013
From: franziska.bilger at uni-ulm.de (franziska.bilger at uni-ulm.de)
Date: Wed, 07 Aug 2013 11:23:50 +0200
Subject: [FieldTrip] topoplotER - how to plot a selection of channels ?
Message-ID: <20130807112350.i24h5npq80sgscws@imap.uni-ulm.de>

Dear subscribers,

I´m using fieldtrip to analyze the data for my bachelor thesis (topic:  
motor imagery in patientens in vegetative state) and I would be happy  
to get some help concerning the function ft_topoplotER.

Originally, my data derives from a 256-channel system, but I only like  
to plot a selection of 60 channels above the motor cortex.
This is my Region of Interest.
When I´m now plotting the data from these 60 channels with  
ft_topoplotER I receive a figure, which shows the plotted activation  
over the whole cortex.

My Question: Is there a possibility to plot only the activation in my  
Region of Interest/over the selected 60 channels above the motor cortex?

This would result in a figure where there´s only activation shown over  
the motor cortex and the rest of the plot is blank/white.

Thank you very much!

Kind regards,
Franziska





From jm.horschig at donders.ru.nl  Wed Aug  7 11:41:26 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 07 Aug 2013 11:41:26 +0200
Subject: [FieldTrip] topoplotER - how to plot a selection of channels ?
In-Reply-To: <20130807112350.i24h5npq80sgscws@imap.uni-ulm.de>
References: <20130807112350.i24h5npq80sgscws@imap.uni-ulm.de>
Message-ID: <52021646.4050203@donders.ru.nl>

Hi Franziska,

check out the help of ft_topoplotER and what options there are for 
cfg.interpolation, one of these does what you want (afair 'cubic'). An 
alternative would be to set datapoints of all irrelevant channels to nan 
and then use cfg.interpolatenan = 'no', but the former suggestion is 
cleaner/better/easier than the latter.

Good luck with writing your thesis!
Best,
Jörm

On 8/7/2013 11:23 AM, franziska.bilger at uni-ulm.de wrote:
> Dear subscribers,
>
> I´m using fieldtrip to analyze the data for my bachelor thesis (topic: 
> motor imagery in patientens in vegetative state) and I would be happy 
> to get some help concerning the function ft_topoplotER.
>
> Originally, my data derives from a 256-channel system, but I only like 
> to plot a selection of 60 channels above the motor cortex.
> This is my Region of Interest.
> When I´m now plotting the data from these 60 channels with 
> ft_topoplotER I receive a figure, which shows the plotted activation 
> over the whole cortex.
>
> My Question: Is there a possibility to plot only the activation in my 
> Region of Interest/over the selected 60 channels above the motor cortex?
>
> This would result in a figure where there´s only activation shown over 
> the motor cortex and the rest of the plot is blank/white.
>
> Thank you very much!
>
> Kind regards,
> Franziska
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands



From ben.vanlier at bsse.ethz.ch  Wed Aug  7 13:00:31 2013
From: ben.vanlier at bsse.ethz.ch (van Lier  Ben)
Date: Wed, 7 Aug 2013 11:00:31 +0000
Subject: [FieldTrip] from trials to continuous and an error in selfromraw
In-Reply-To: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A6CBB0@MBX23.d.ethz.ch>
References: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A6CBB0@MBX23.d.ethz.ch>
Message-ID: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A6CC10@MBX23.d.ethz.ch>

Hi Eelke,

thanks. its the little things you miss so cfg.trials = 1 works ofcourse :)

for plotting all the trials in a continuous spectrum i just merge them into 1 big trial first

cfg = [];
cfg.trl = [1 max(max(data.sampleinfo)) 0];
data = ft_redefinetrial(cfg, data);

perfect for my purposes, im trying to reanalyze old recordings chopped into several files but ft_append puts them in separate trials.

liking fieldtrip alot so far, very flexible :)

cheers
Ben



From jm.horschig at donders.ru.nl  Wed Aug  7 14:52:32 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 07 Aug 2013 14:52:32 +0200
Subject: [FieldTrip] question about virtual electrode MNI coordinates
In-Reply-To: <CAFN2X+fdvTW8jkx1EPS8C+J_FGRTQgTtYL38aYw7Gv6BbLtsxg@mail.gmail.com>
References: <CAFN2X+fdvTW8jkx1EPS8C+J_FGRTQgTtYL38aYw7Gv6BbLtsxg@mail.gmail.com>
Message-ID: <52024310.1020109@donders.ru.nl>

Dear Charidimos,

thanks very much for pointing to this, it is indeed an error in the 
appendix of the tutorial. cfg.grid.pos should be based on the 
subject-specific MRI or sourcemodel. So, correctly it should say that 
you need to load sourcemodel.mat (i.e. subject specific grid) and then 
use sourcemodel.pos(maxpowindx, :)
The rationale in principle is that the warped grid has the same size and 
is indexed the same as the original grid; that is why you can use the 
index variable obtained from the MNI-warped source reconstructed data. 
The virtual channel reconstruction should however still be done in 
whatever coordinate system the subject's anatomical data is in. I will 
update the appendix accordingly.

Best,
Jörn

On 8/6/2013 8:24 PM, Charidimos Tzagarakis wrote:
> Hi there,
> I have a question regarding virtual electrodes: How can I double check 
> that the MNI coordinates that I enter are correctly interpreted?
> More specifically:
> I have followed the the extended beamforming tutorial in the 
> "Appendix" and have been able to transpose it to my data (I have 
> 4D/BTi MEG files and Dicom mri volumes).The part I am not certain 
> about is the call to the LCMV beamformer.
> Here it is in my case ( I just want to get the voxel were the power is 
> max in the previous analysis):
> cfg              = [];
> cfg.method       = 'lcmv';
> cfg.vol          = volfcm;
> cfg.grid.pos     = source_diff.pos(maxpowindx, :);
> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
> cfg.grid.outside = [];
> cfg.grad=senscm
> source_idx       = ft_sourceanalysis(cfg, tlock);
> My headmodel does not include MEG channel information so I need to 
> also define the cfg.grad parameter. What I don't understand is how 
> cfg.grid.pos (which is in MNI coordinates as per the previous part of 
> the tutorial) can be correctly applied to the coordinates of the 
> headmodel and the channels since these 2 are not in MNI coordinates 
> (in my case they are in 4d/Bti coordinates and rescaled to cm).In the 
> previous part of the tutorial this is (if I understand correctly) 
> accomplished because the leadfield used when calling ft_sourceanalysis 
> was created using and MNI-warped template. I don't see where the 
> equivalent part is when estimating the virtual electrode though.
> Any advice you may have would be much appreciated.
> Best,
> Haris
>
>
> Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
> University of Minnesota Dept of Neuroscience and Brain Sciences Center
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From annevanhoogmoed at email.arizona.edu  Thu Aug  8 05:51:47 2013
From: annevanhoogmoed at email.arizona.edu (van Hoogmoed, Anne H - (annevanhoogmoed))
Date: Thu, 8 Aug 2013 03:51:47 +0000
Subject: [FieldTrip] reading in and segmenting Netstation data
Message-ID: <B4002ED52EC6814D8B6E1FF85B6AFBB30A198EA7@SPACEMT.catnet.arizona.edu>

Dear all,



I'm using Fieldtrip to analyze my Netstation data. The problem is that the segmented data (incl triggers) are shifted in Fieldtrip as compared to the Netstation analysis.

I've checked several things:

- The events are the same in Netstation and Fieldtrip

- The raw data look the same in both programs

- Fieldtrip produces the right trl based on the triggers.



The script I'm using is this:

cfg = [];

cfg.dataset = 'c007_raw';

cfg.continuous = 'yes';

data_eeg = ft_preprocessing(cfg);



hdr = ft_read_header('c007_raw');

event = ft_read_event('c007_raw');



cfg = [];

cfg.trialfun = 'trialfun_first_enc';

cfg_trials = ft_definetrial(cfg);

data_trials = ft_redefinetrial(cfg_trials, data_eeg);





The trialfun I'm using is this:

function [trl, event] = trialfun_first(cfg)

load event;

load hdr;





value = [event.value];

sample = [event.sample];

% determine the number of samples before and after the trigger

pretrig = -100; % = 200 ms

posttrig = 400; % = 800 ms

% for each trigger

trl = [];

for j = 1:length(event)

if (strcmp(event(1,j).value, '+Lrt') || strcmp(event(1,j).value, '+OOt')) || strcmp(event(1,j).value, '+SOt')

trlbegin = event(1,j).sample + pretrig;

trlend = event(1,j).sample + posttrig;

offset = pretrig;

newtrl = [trlbegin trlend offset];

trl = [trl; newtrl];

end

j = j + 1;

end





Does anyone know what I'm doing wrong here?



Thank you very much for your help!



Kind regards,



Anne



Anne van Hoogmoed

Down Syndrome Research Group

Department of Psychology, University of Arizona
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From d.lozanosoldevilla at fcdonders.ru.nl  Thu Aug  8 08:12:42 2013
From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego))
Date: Thu, 8 Aug 2013 08:12:42 +0200 (CEST)
Subject: [FieldTrip] reading in and segmenting Netstation data
In-Reply-To: <B4002ED52EC6814D8B6E1FF85B6AFBB30A198EA7@SPACEMT.catnet.arizona.edu>
Message-ID: <1178733115.2232641.1375942362693.JavaMail.root@sculptor.zimbra.ru.nl>

Hi Anne, What do you mean by "shifted"? Time samples mismatch might be? I don't see what's going wrong with the code you pasted but it'd be nice if you could file a bug (I'll assign to me) with a piece of preprocessed data with fieldtrip and a plot about how data looks like with Netstation to have a bit more info. best, Diego ps : do you have a non-integer eeg sampling rate, like 511.3Hz? ----- Original Message -----
> From: "van Hoogmoed , Anne H - ( annevanhoogmoed )" < annevanhoogmoed
> @email. arizona . edu >
> To: fieldtrip @science. ru . nl
> Sent: Thursday, 8 August, 2013 5:51:47 AM
> Subject: [ FieldTrip ] reading in and segmenting Netstation data
> Dear all,
> I'm using Fieldtrip to analyze my Netstation data. The problem is that
> the segmented data (incl triggers) are shifted in Fieldtrip as
> compared to the Netstation analysis.
> I've checked several things:
> - The events are the same in Netstation and Fieldtrip
> - The raw data look the same in both programs
> - Fieldtrip produces the right trl based on the triggers.
> The script I'm using is this:
> cfg = [];
> cfg . dataset = 'c007_ raw' ;
> cfg .continuous = 'yes' ;
> data_ eeg = ft_ preprocessing ( cfg );
> hdr = ft_read_header( 'c007_ raw' );
> event = ft_read_event( 'c007_ raw' );
> cfg = [];
> cfg . trialfun = 'trialfun _first_ enc' ;
> cfg _trials = ft_ definetrial ( cfg );
> data_trials = ft_ redefinetrial ( cfg _trials, data_ eeg );
> The trialfun I'm using is this:
> function [ trl , event] = trialfun _first( cfg )
> load event ;
> load hdr ;
> value = [event.value];
> sample = [event.sample];
> % determine the number of samples before and after the trigger
> pretrig = -100; % = 200 ms
> posttrig = 400; % = 800 ms
> % for each trigger
> trl = [];
> for j = 1:length(event)
> if ( strcmp (event(1,j).value, '+ Lrt' ) || strcmp (event(1,j).value,
> '+ OOt' )) || strcmp (event(1,j).value, '+ SOt' )
> trlbegin = event(1,j).sample + pretrig ;
> trlend = event(1,j).sample + posttrig ;
> offset = pretrig ;
> newtrl = [ trlbegin trlend offset];
> trl = [ trl ; newtrl ];
> end
> j = j + 1;
> end
> Does anyone know what I'm doing wrong here?
> Thank you very much for your help!
> Kind regards,
> Anne
> Anne van Hoogmoed
> Down Syndrome Research Group
> Department of Psychology, University of Arizona
> _______________________________________________
> fieldtrip mailing list
> fieldtrip @ donders . ru . nl
> http ://mailman.science. ru . nl /mailman/ listinfo / fieldtrip
-- PhD Student Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen NL-6525 EN Nijmegen The Netherlands http :// www . ru . nl /people/ donders /lozano-soldevilla-d/ 
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From elisa at csl.psychol.cam.ac.uk  Thu Aug  8 12:23:53 2013
From: elisa at csl.psychol.cam.ac.uk (Elisa Carrus)
Date: Thu, 08 Aug 2013 11:23:53 +0100
Subject: [FieldTrip] question about virtual electrode MNI coordinates
In-Reply-To: <52024310.1020109@donders.ru.nl>
References: <CAFN2X+fdvTW8jkx1EPS8C+J_FGRTQgTtYL38aYw7Gv6BbLtsxg@mail.gmail.com>
	<52024310.1020109@donders.ru.nl>
Message-ID: <520371B9.8060101@csl.psychol.cam.ac.uk>

Hi all,

 From the previous email it seems that I'm doing something wrong then. I 
have previously used the MNI-aligned subject grid (warped template) for 
the positions, hence I didn't encounter any problem. However, this seems 
to be wrong, as Jorn suggested. The question is the following:

The sourcediff.avg.pow is produced using the warped MNI template, 
therefore the grid positions and indexes will be different from the 
subject-specific MRI. Specifically in my case, the warped template has 
11000 x 3 pos, whereas the subject-specific has 2652 x 3.
My question is, when I therefore index the maxpos using:

[maxval, maxind] = max(sourcediff.avg.pow), my index is 3171, which 
exceeds the matrix dimensions of the subject-specific MRI (2652).

Which step am I missing?

Thanks for your help in advance,
Elisa






On 07/08/2013 13:52, "Jörn M. Horschig" wrote:
> Dear Charidimos,
>
> thanks very much for pointing to this, it is indeed an error in the 
> appendix of the tutorial. cfg.grid.pos should be based on the 
> subject-specific MRI or sourcemodel. So, correctly it should say that 
> you need to load sourcemodel.mat (i.e. subject specific grid) and then 
> use sourcemodel.pos(maxpowindx, :)
> The rationale in principle is that the warped grid has the same size 
> and is indexed the same as the original grid; that is why you can use 
> the index variable obtained from the MNI-warped source reconstructed 
> data. The virtual channel reconstruction should however still be done 
> in whatever coordinate system the subject's anatomical data is in. I 
> will update the appendix accordingly.
>
> Best,
> Jörn
>
> On 8/6/2013 8:24 PM, Charidimos Tzagarakis wrote:
>> Hi there,
>> I have a question regarding virtual electrodes: How can I double 
>> check that the MNI coordinates that I enter are correctly interpreted?
>> More specifically:
>> I have followed the the extended beamforming tutorial in the 
>> "Appendix" and have been able to transpose it to my data (I have 
>> 4D/BTi MEG files and Dicom mri volumes).The part I am not certain 
>> about is the call to the LCMV beamformer.
>> Here it is in my case ( I just want to get the voxel were the power 
>> is max in the previous analysis):
>> cfg              = [];
>> cfg.method       = 'lcmv';
>> cfg.vol          = volfcm;
>> cfg.grid.pos     = source_diff.pos(maxpowindx, :);
>> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
>> cfg.grid.outside = [];
>> cfg.grad=senscm
>> source_idx       = ft_sourceanalysis(cfg, tlock);
>> My headmodel does not include MEG channel information so I need to 
>> also define the cfg.grad parameter. What I don't understand is how 
>> cfg.grid.pos (which is in MNI coordinates as per the previous part of 
>> the tutorial) can be correctly applied to the coordinates of the 
>> headmodel and the channels since these 2 are not in MNI coordinates 
>> (in my case they are in 4d/Bti coordinates and rescaled to cm).In the 
>> previous part of the tutorial this is (if I understand correctly) 
>> accomplished because the leadfield used when calling 
>> ft_sourceanalysis was created using and MNI-warped template. I don't 
>> see where the equivalent part is when estimating the virtual 
>> electrode though.
>> Any advice you may have would be much appreciated.
>> Best,
>> Haris
>>
>>
>> Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
>> University of Minnesota Dept of Neuroscience and Brain Sciences Center
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> -- 
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
> FieldTrip Development Team
>
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>
> Contact:
> E-Mail:jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web:http://www.ru.nl/donders
>
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From jm.horschig at donders.ru.nl  Thu Aug  8 13:45:09 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Thu, 08 Aug 2013 13:45:09 +0200
Subject: [FieldTrip] question about virtual electrode MNI coordinates
In-Reply-To: <520371B9.8060101@csl.psychol.cam.ac.uk>
References: <CAFN2X+fdvTW8jkx1EPS8C+J_FGRTQgTtYL38aYw7Gv6BbLtsxg@mail.gmail.com>
	<52024310.1020109@donders.ru.nl>
	<520371B9.8060101@csl.psychol.cam.ac.uk>
Message-ID: <520384C5.80703@donders.ru.nl>

Dear Elisa,

hard to tell, because you are not telling us exactly what you are doing :)
The idea in the extended beamforming tutorial is that you first create 
an MNI template sourcemodel (or grid). Subsequently, you use exactly 
this grid and spatially transform it such that it fits to the 
subject-specific brain, based on the MRI. After following these steps, 
by definition, the number of grid points in the subject-specific grid 
and the MNI grid are the same - just the place where the grid points end 
up did change. (Otherwise, it would also not be possible to replace the 
.pos field from the source-reconstructed data by the template grid, as 
being done in the plotting part of the tutorial). The problem in the 
tutorial was exactly this replacement of the position description (which 
iself can be a perfectly fine step as e.g. earlier in the tutorial). 
Since we provide a sourcemodel based on the subject's mri, we need to 
specify the position based on that mri/sourcemodel and not based on the 
MNI template.

You, obviously, do not have the same number of grid points for the 
subject-specific sourcemodel as in the template sourcemodel. I cannot 
guarantee that what you did is correct, but at least I can tell you that 
what you did is not affects by this - else you would have had the same 
number of elements for both sourcemodels. I cross my fingers that you're 
doing the right thing :)

Best,
Jörn

On 8/8/2013 12:23 PM, Elisa Carrus wrote:
> Hi all,
>
> From the previous email it seems that I'm doing something wrong then. 
> I have previously used the MNI-aligned subject grid (warped template) 
> for the positions, hence I didn't encounter any problem. However, this 
> seems to be wrong, as Jorn suggested. The question is the following:
>
> The sourcediff.avg.pow is produced using the warped MNI template, 
> therefore the grid positions and indexes will be different from the 
> subject-specific MRI. Specifically in my case, the warped template has 
> 11000 x 3 pos, whereas the subject-specific has 2652 x 3.
> My question is, when I therefore index the maxpos using:
>
> [maxval, maxind] = max(sourcediff.avg.pow), my index is 3171, which 
> exceeds the matrix dimensions of the subject-specific MRI (2652).
>
> Which step am I missing?
>
> Thanks for your help in advance,
> Elisa
>
>
>
>
>
>
> On 07/08/2013 13:52, "Jörn M. Horschig" wrote:
>> Dear Charidimos,
>>
>> thanks very much for pointing to this, it is indeed an error in the 
>> appendix of the tutorial. cfg.grid.pos should be based on the 
>> subject-specific MRI or sourcemodel. So, correctly it should say that 
>> you need to load sourcemodel.mat (i.e. subject specific grid) and 
>> then use sourcemodel.pos(maxpowindx, :)
>> The rationale in principle is that the warped grid has the same size 
>> and is indexed the same as the original grid; that is why you can use 
>> the index variable obtained from the MNI-warped source reconstructed 
>> data. The virtual channel reconstruction should however still be done 
>> in whatever coordinate system the subject's anatomical data is in. I 
>> will update the appendix accordingly.
>>
>> Best,
>> Jörn
>>
>> On 8/6/2013 8:24 PM, Charidimos Tzagarakis wrote:
>>> Hi there,
>>> I have a question regarding virtual electrodes: How can I double 
>>> check that the MNI coordinates that I enter are correctly interpreted?
>>> More specifically:
>>> I have followed the the extended beamforming tutorial in the 
>>> "Appendix" and have been able to transpose it to my data (I have 
>>> 4D/BTi MEG files and Dicom mri volumes).The part I am not certain 
>>> about is the call to the LCMV beamformer.
>>> Here it is in my case ( I just want to get the voxel were the power 
>>> is max in the previous analysis):
>>> cfg              = [];
>>> cfg.method       = 'lcmv';
>>> cfg.vol          = volfcm;
>>> cfg.grid.pos     = source_diff.pos(maxpowindx, :);
>>> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
>>> cfg.grid.outside = [];
>>> cfg.grad=senscm
>>> source_idx       = ft_sourceanalysis(cfg, tlock);
>>> My headmodel does not include MEG channel information so I need to 
>>> also define the cfg.grad parameter. What I don't understand is how 
>>> cfg.grid.pos (which is in MNI coordinates as per the previous part 
>>> of the tutorial) can be correctly applied to the coordinates of the 
>>> headmodel and the channels since these 2 are not in MNI coordinates 
>>> (in my case they are in 4d/Bti coordinates and rescaled to cm).In 
>>> the previous part of the tutorial this is (if I understand 
>>> correctly) accomplished because the leadfield used when calling 
>>> ft_sourceanalysis was created using and MNI-warped template. I don't 
>>> see where the equivalent part is when estimating the virtual 
>>> electrode though.
>>> Any advice you may have would be much appreciated.
>>> Best,
>>> Haris
>>>
>>>
>>> Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
>>> University of Minnesota Dept of Neuroscience and Brain Sciences Center
>>>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>> -- 
>> Jörn M. Horschig
>> PhD Student
>> Donders Institute for Brain, Cognition and Behaviour
>> Centre for Cognitive Neuroimaging
>> Radboud University Nijmegen
>> Neuronal Oscillations Group
>> FieldTrip Development Team
>>
>> P.O. Box 9101
>> NL-6500 HB Nijmegen
>> The Netherlands
>>
>> Contact:
>> E-Mail:jm.horschig at donders.ru.nl
>> Tel:    +31-(0)24-36-68493
>> Web:http://www.ru.nl/donders
>>
>> Visiting address:
>> Trigon, room 2.30
>> Kapittelweg 29
>> NL-6525 EN Nijmegen
>> The Netherlands
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From K.Kalogianni at tudelft.nl  Fri Aug  9 09:59:18 2013
From: K.Kalogianni at tudelft.nl (Konstantina Kalogianni)
Date: Fri, 9 Aug 2013 07:59:18 +0000
Subject: [FieldTrip] ft_sourcegrandaverage & grid computation
Message-ID: <4DF682D3A10EAC46B462A46E16F0B049128EE308@SRV364.tudelft.net>

Dear fieldtripers,
I have experienced a problem with ft_sourcegrandaverage and the calculation of my grid and I want to ask for help.
The error I get is the following :different grid locations in source reconstructions.

I will describe briefly the processing to give you a better idea about my error.

For every subject I have 6 conditions and I want to average all subjects per condition.
After preprocessing I calculate the covariance matrix and then  I use the MUSIC algorithm for my sources.
For  the grid calculation I use a default MRI a default VOL and a default electrodes' positions.
However  for every subject the grid is not identical since  cfg.channel in ft_prepare_leadfield is dependent on the channels I've discarded as noisy during the preprocessing.
By the way for the grid calculation I had to change the order  of cfg.elec because it didn't agree with the order of cfg,channel in my data.
So apparently I end up with a different grid for every subject but still I want to average all of them per condition.

Do I have to use another function to average my sources in this case?
Because the grid would never be identical among subjects.


I hope somebody out there experienced that before and can probably help me.
Thank you.

Konstantina [Nadia] Kalogianni
PhD candidate, TU Delft


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From elisa at csl.psychol.cam.ac.uk  Fri Aug  9 11:25:15 2013
From: elisa at csl.psychol.cam.ac.uk (Elisa Carrus)
Date: Fri, 09 Aug 2013 10:25:15 +0100
Subject: [FieldTrip] question about virtual electrode MNI coordinates
In-Reply-To: <520384C5.80703@donders.ru.nl>
References: <CAFN2X+fdvTW8jkx1EPS8C+J_FGRTQgTtYL38aYw7Gv6BbLtsxg@mail.gmail.com>
	<52024310.1020109@donders.ru.nl>
	<520371B9.8060101@csl.psychol.cam.ac.uk>
	<520384C5.80703@donders.ru.nl>
Message-ID: <5204B57B.6040004@csl.psychol.cam.ac.uk>

Dear Jorn,

ah, I apologise for not writing a complete email! The good news is that 
I've done things correctly so far,  as I do have the same number of grid 
points in both the subject-specific and template, as expected :) I gave 
you the wrong indices because I thought that in your previous email you 
referred to the MRI rather than the sourcemodel. My bad. Sorry for the 
misunderstanding and thanks a lot for explaining this again!

Best,
Elisa


On 08/08/2013 12:45, "Jörn M. Horschig" wrote:
> Dear Elisa,
>
> hard to tell, because you are not telling us exactly what you are 
> doing :)
> The idea in the extended beamforming tutorial is that you first create 
> an MNI template sourcemodel (or grid). Subsequently, you use exactly 
> this grid and spatially transform it such that it fits to the 
> subject-specific brain, based on the MRI. After following these steps, 
> by definition, the number of grid points in the subject-specific grid 
> and the MNI grid are the same - just the place where the grid points 
> end up did change. (Otherwise, it would also not be possible to 
> replace the .pos field from the source-reconstructed data by the 
> template grid, as being done in the plotting part of the tutorial). 
> The problem in the tutorial was exactly this replacement of the 
> position description (which iself can be a perfectly fine step as e.g. 
> earlier in the tutorial). Since we provide a sourcemodel based on the 
> subject's mri, we need to specify the position based on that 
> mri/sourcemodel and not based on the MNI template.
>
> You, obviously, do not have the same number of grid points for the 
> subject-specific sourcemodel as in the template sourcemodel. I cannot 
> guarantee that what you did is correct, but at least I can tell you 
> that what you did is not affects by this - else you would have had the 
> same number of elements for both sourcemodels. I cross my fingers that 
> you're doing the right thing :)
>
> Best,
> Jörn
>
> On 8/8/2013 12:23 PM, Elisa Carrus wrote:
>> Hi all,
>>
>> From the previous email it seems that I'm doing something wrong then. 
>> I have previously used the MNI-aligned subject grid (warped template) 
>> for the positions, hence I didn't encounter any problem. However, 
>> this seems to be wrong, as Jorn suggested. The question is the following:
>>
>> The sourcediff.avg.pow is produced using the warped MNI template, 
>> therefore the grid positions and indexes will be different from the 
>> subject-specific MRI. Specifically in my case, the warped template 
>> has 11000 x 3 pos, whereas the subject-specific has 2652 x 3.
>> My question is, when I therefore index the maxpos using:
>>
>> [maxval, maxind] = max(sourcediff.avg.pow), my index is 3171, which 
>> exceeds the matrix dimensions of the subject-specific MRI (2652).
>>
>> Which step am I missing?
>>
>> Thanks for your help in advance,
>> Elisa
>>
>>
>>
>>
>>
>>
>> On 07/08/2013 13:52, "Jörn M. Horschig" wrote:
>>> Dear Charidimos,
>>>
>>> thanks very much for pointing to this, it is indeed an error in the 
>>> appendix of the tutorial. cfg.grid.pos should be based on the 
>>> subject-specific MRI or sourcemodel. So, correctly it should say 
>>> that you need to load sourcemodel.mat (i.e. subject specific grid) 
>>> and then use sourcemodel.pos(maxpowindx, :)
>>> The rationale in principle is that the warped grid has the same size 
>>> and is indexed the same as the original grid; that is why you can 
>>> use the index variable obtained from the MNI-warped source 
>>> reconstructed data. The virtual channel reconstruction should 
>>> however still be done in whatever coordinate system the subject's 
>>> anatomical data is in. I will update the appendix accordingly.
>>>
>>> Best,
>>> Jörn
>>>
>>> On 8/6/2013 8:24 PM, Charidimos Tzagarakis wrote:
>>>> Hi there,
>>>> I have a question regarding virtual electrodes: How can I double 
>>>> check that the MNI coordinates that I enter are correctly interpreted?
>>>> More specifically:
>>>> I have followed the the extended beamforming tutorial in the 
>>>> "Appendix" and have been able to transpose it to my data (I have 
>>>> 4D/BTi MEG files and Dicom mri volumes).The part I am not certain 
>>>> about is the call to the LCMV beamformer.
>>>> Here it is in my case ( I just want to get the voxel were the power 
>>>> is max in the previous analysis):
>>>> cfg              = [];
>>>> cfg.method       = 'lcmv';
>>>> cfg.vol          = volfcm;
>>>> cfg.grid.pos     = source_diff.pos(maxpowindx, :);
>>>> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
>>>> cfg.grid.outside = [];
>>>> cfg.grad=senscm
>>>> source_idx       = ft_sourceanalysis(cfg, tlock);
>>>> My headmodel does not include MEG channel information so I need to 
>>>> also define the cfg.grad parameter. What I don't understand is how 
>>>> cfg.grid.pos (which is in MNI coordinates as per the previous part 
>>>> of the tutorial) can be correctly applied to the coordinates of the 
>>>> headmodel and the channels since these 2 are not in MNI coordinates 
>>>> (in my case they are in 4d/Bti coordinates and rescaled to cm).In 
>>>> the previous part of the tutorial this is (if I understand 
>>>> correctly) accomplished because the leadfield used when calling 
>>>> ft_sourceanalysis was created using and MNI-warped template. I 
>>>> don't see where the equivalent part is when estimating the virtual 
>>>> electrode though.
>>>> Any advice you may have would be much appreciated.
>>>> Best,
>>>> Haris
>>>>
>>>>
>>>> Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
>>>> University of Minnesota Dept of Neuroscience and Brain Sciences Center
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>
>>> -- 
>>> Jörn M. Horschig
>>> PhD Student
>>> Donders Institute for Brain, Cognition and Behaviour
>>> Centre for Cognitive Neuroimaging
>>> Radboud University Nijmegen
>>> Neuronal Oscillations Group
>>> FieldTrip Development Team
>>>
>>> P.O. Box 9101
>>> NL-6500 HB Nijmegen
>>> The Netherlands
>>>
>>> Contact:
>>> E-Mail:jm.horschig at donders.ru.nl
>>> Tel:    +31-(0)24-36-68493
>>> Web:http://www.ru.nl/donders
>>>
>>> Visiting address:
>>> Trigon, room 2.30
>>> Kapittelweg 29
>>> NL-6525 EN Nijmegen
>>> The Netherlands
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> -- 
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
> FieldTrip Development Team
>
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>
> Contact:
> E-Mail:jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web:http://www.ru.nl/donders
>
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From g.dimitriadis at donders.ru.nl  Fri Aug  9 17:22:50 2013
From: g.dimitriadis at donders.ru.nl (Dimitriadis, G. (George))
Date: Fri, 9 Aug 2013 17:22:50 +0200 (CEST)
Subject: [FieldTrip] Error from postamble
Message-ID: <1463263304.1956192.1376061770792.JavaMail.root@monoceros.zimbra.ru.nl>


Hello guys,

I seem to be getting an error relating to the generation of warnings withing the postamble. I am not doing anything that I haven't been doing for the past year.

I had problems with the preamble (due to large file sizes) before and I am doing the cfg.stackcallinfo = 'no' trick.

But now I am getting the following series of errors:

---------------------------------------------------
Warning:
'@(hObject,eventdata)mainRatAnalysisGUI('pushbutton_run_analysis_Callback',hObject,eventdata,guidata(hObject))'
 exceeds MATLAB's maximum name length of 63 characters and has
been truncated to
 '@(hObject,eventdata)mainRatAnalysisGUI('pushbutton_run_analysis'. 
> In utilities/private/warning_once>fieldnameFromStack at 196
  In utilities/private/warning_once at 123
  In utilities/private/ft_postamble_history at 55
  In ft_postamble at 55
  In ft_preprocessing at 611
  In gd_eri_preprocratdata at 71
  In gd_eri_getratdatasignals at 39
  In mainRatAnalysisGUI>pushbutton_run_analysis_Callback at 120
  In gui_mainfcn at 96
  In mainRatAnalysisGUI at 42
  In @(hObject,eventdata)mainRatAnalysisGUI('pushbutton_run_analysis_Callback',hObject,eventdata,guidata(hObject)) 
Invalid field name:
'@(hObject,eventdata)mainRatAnalysisGUI('pushbutton_run_analysis'.

Error in warning_once>fieldnameFromStack (line 196)
  ft_previous_warnings.(stack(end).name) = []; % iteratively
  build up structure fields

Error in warning_once (line 123)
  [tmpfname ft_default.warning.identifier line] =
  fieldnameFromStack(ft_default.warning.identifier);

Error in ft_postamble_history (line 55)
warning_once('-clear');

Error in ft_postamble (line 55)
  evalin('caller', ['ft_postamble_' cmd]);

Error in ft_preprocessing (line 611)
ft_postamble history data

Error in gd_eri_preprocratdata (line 71)
  datacell{datindx}=ft_preprocessing(cfg_pp);

Error in gd_eri_getratdatasignals (line 39)
data=gd_eri_preprocratdata(cfg);

Error in mainRatAnalysisGUI>pushbutton_run_analysis_Callback
(line 120)
        data =gd_eri_getratdatasignals(cfg);

Error in gui_mainfcn (line 96)
        feval(varargin{:});

Error in mainRatAnalysisGUI (line 42)
    gui_mainfcn(gui_State, varargin{:});

Error in
@(hObject,eventdata)mainRatAnalysisGUI('pushbutton_run_analysis_Callback',hObject,eventdata,guidata(hObject))

 
Error while evaluating uicontrol Callback
----------------------------------------

I am calling my original function from within a gui.

So it seems that in the postamble_history a warning gets generated which then throws an error for some reason I would really like not to have to find out by myself.


Thanks for your time


George Dimitriadis


From r.cox at uva.nl  Tue Aug 13 11:29:23 2013
From: r.cox at uva.nl (Roy Cox)
Date: Tue, 13 Aug 2013 11:29:23 +0200
Subject: [FieldTrip] ft_freqstatistics
Message-ID: <CABafTZcchaOGyh1PVvx0KZ6v5rd+Cj2=KVhmgwgMEPN2LnaFDw@mail.gmail.com>

Hi,

Can anyone tell me how fieldtrip selects freq bins when calling
ft_freqstatistics with cfg.frequency?

That is, if I'm interested in two freq bands from, say, 10 to 20, and from
20 to 30 Hz, and I don't want a freq bin to be used twice, do I use
cfg.frequency=[10 20] and cfg.frequency=[20 30]? Or would the freq bin
closest to 20 be used twice?

I guess I'm asking how precisely the find function (with arguments 'first',
'last') is applied.

Best,

Roy


-- 
Roy Cox, M.Sc. | Brain & Cognition Group | Department of Psychology |
University of Amsterdam | Weesperplein 4 | 1018 XA Amsterdam | the
Netherlands | room 3.21 | phone: +31 20 525 6847 | email: r.cox at uva.nl
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From hweeling.lee at gmail.com  Wed Aug 14 16:51:23 2013
From: hweeling.lee at gmail.com (Hwee Ling Lee)
Date: Wed, 14 Aug 2013 16:51:23 +0200
Subject: [FieldTrip] newbie
Message-ID: <CABG7z0SvaX134oFfEbhasgrWRLtea+8=AxfcJDdrjHwR7veg_g@mail.gmail.com>

Hi to all!

I'm new to fieldtrip! I have a dataset that has been corrected for scanner
artifacts and BC artifacts using Brainvision Analyser. I would like to
export the corrected data as a .eeg file so that I can load the data onto
Matlab and use fieldtrip to perform further analyses.

However, I kept getting error messages from Matlab that the sub-file format
is unsupported. I've been searching online the best way to export the
corrected data from Brainvision Analyser, however, I could not find any
solution at all.

Would anyone please kindly instruct me the settings that I should have when
I export the corrected data?

Thanks!

Best wishes,
Hweeling
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From elisa at csl.psychol.cam.ac.uk  Wed Aug 14 17:32:42 2013
From: elisa at csl.psychol.cam.ac.uk (Elisa Carrus)
Date: Wed, 14 Aug 2013 16:32:42 +0100
Subject: [FieldTrip] newbie
In-Reply-To: <CABG7z0SvaX134oFfEbhasgrWRLtea+8=AxfcJDdrjHwR7veg_g@mail.gmail.com>
References: <CABG7z0SvaX134oFfEbhasgrWRLtea+8=AxfcJDdrjHwR7veg_g@mail.gmail.com>
Message-ID: <520BA31A.9040803@csl.psychol.cam.ac.uk>

Hi Hweeling,

Welcome! Can you give us a bit more information about the script you 
used to load the data? I haven't used BrainVision before but you should 
be able to read the .eeg data directly from Fieldtrip 
http://fieldtrip.fcdonders.nl/dataformat 
<http://fieldtrip.fcdonders.nl/dataformat>

Best,
Elisa



On 14/08/2013 15:51, Hwee Ling Lee wrote:
> Hi to all!
>
> I'm new to fieldtrip! I have a dataset that has been corrected for 
> scanner artifacts and BC artifacts using Brainvision Analyser. I would 
> like to export the corrected data as a .eeg file so that I can load 
> the data onto Matlab and use fieldtrip to perform further analyses.
>
> However, I kept getting error messages from Matlab that the sub-file 
> format is unsupported. I've been searching online the best way to 
> export the corrected data from Brainvision Analyser, however, I could 
> not find any solution at all.
>
> Would anyone please kindly instruct me the settings that I should have 
> when I export the corrected data?
>
> Thanks!
>
> Best wishes,
> Hweeling
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From r.oostenveld at donders.ru.nl  Wed Aug 14 21:34:02 2013
From: r.oostenveld at donders.ru.nl (Robert Oostenveld)
Date: Wed, 14 Aug 2013 21:34:02 +0200
Subject: [FieldTrip] newbie
In-Reply-To: <CABG7z0SvaX134oFfEbhasgrWRLtea+8=AxfcJDdrjHwR7veg_g@mail.gmail.com>
References: <CABG7z0SvaX134oFfEbhasgrWRLtea+8=AxfcJDdrjHwR7veg_g@mail.gmail.com>
Message-ID: <CA0DCF09-96E0-4D29-9CFE-9EE2C1B7EBFF@donders.ru.nl>

Hi Hweeling

The channel level data in the BrainVision data file can be represented in ascii and binary format. Furthermore, the order can be one channel at a time or sample-by-sample. Finally there are different numeric precisions (integer, float, etc).

This is something that you cannot see from the outside of the file, but if you open the *.vhdr file in a text editor you can see these details. Since there are so many possible combinations of these three factors, it is not difficult easy to support all possible variants. 

You could try storing the data as multiplexed and in single- or double-precision, which is the most common format. Otherwise, you can report it as feature request on http://bugzilla.fcdonders.nl and attach a small piece of data (with vhdr and vmrk file) there.

best regards,
Robert
 


On 14 Aug 2013, at 16:51, Hwee Ling Lee wrote:

> Hi to all!
> 
> I'm new to fieldtrip! I have a dataset that has been corrected for scanner artifacts and BC artifacts using Brainvision Analyser. I would like to export the corrected data as a .eeg file so that I can load the data onto Matlab and use fieldtrip to perform further analyses.
> 
> However, I kept getting error messages from Matlab that the sub-file format is unsupported. I've been searching online the best way to export the corrected data from Brainvision Analyser, however, I could not find any solution at all.
> 
> Would anyone please kindly instruct me the settings that I should have when I export the corrected data?
> 
> Thanks!
> 
> Best wishes,
> Hweeling
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip




From gopalar.ccf at gmail.com  Wed Aug 14 22:58:34 2013
From: gopalar.ccf at gmail.com (Raghavan Gopalakrishnan)
Date: Wed, 14 Aug 2013 16:58:34 -0400
Subject: [FieldTrip] Reading multiple NEX files
Message-ID: <CAHz=SkUQRqKD1reF53o4gL5Lw0mmW6FTzkAhd4T-x=JA2hfK6A@mail.gmail.com>

I have multiple nex files that have LFP and spike data. I would like to
read them and plot one raster, since the multple nex files are from same
subject. ft_appendspike does not append data structures with same channel
label. All my data structures from different nex files have same channel
label. Any ideas?
Thanks.
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From hweeling.lee at gmail.com  Thu Aug 15 11:34:33 2013
From: hweeling.lee at gmail.com (Hwee Ling Lee)
Date: Thu, 15 Aug 2013 11:34:33 +0200
Subject: [FieldTrip] EEG sensor position layout
Message-ID: <CABG7z0QLsEDt2O9Pth3Xe4aQOBtbHhGnROtCeGHqRHN4goUAtQ@mail.gmail.com>

Hi all!

After performing ICA, I used the command to browse the data in component
mode.

However, I got a warning message:

Warning: No layout specified - will try to construct one using sensor
positions
> In ft_databrowser at 217
Error using ft_databrowser (line 223)
cannot infer sensor type

I understand that one can manually create the layout, however, I was not
sure how I can do it. Could someone please help?

Thank you.

Best regards,
Hweeling
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From johanna.zumer at donders.ru.nl  Thu Aug 15 12:45:51 2013
From: johanna.zumer at donders.ru.nl (Johanna Zumer)
Date: Thu, 15 Aug 2013 12:45:51 +0200
Subject: [FieldTrip] EEG sensor position layout
In-Reply-To: <CABG7z0QLsEDt2O9Pth3Xe4aQOBtbHhGnROtCeGHqRHN4goUAtQ@mail.gmail.com>
References: <CABG7z0QLsEDt2O9Pth3Xe4aQOBtbHhGnROtCeGHqRHN4goUAtQ@mail.gmail.com>
Message-ID: <CAL4kA6d9A90HfXRErt5SxhDF4dTVhQzUWaU8Vvg=q1S2D=J=+g@mail.gmail.com>

Dear Hweeling,

You should indeed specify cfg.layout, naming the layout file for the data
that you have.
You can first check in the folder fieldtrip/template/layout to see if there
is already an existing template that you can use.
If not, please see ft_prepare_layout for more details.

If you're still stuck, please ask again with more specific details on your
layout.

Best,
Johanna



2013/8/15 Hwee Ling Lee <hweeling.lee at gmail.com>

> Hi all!
>
> After performing ICA, I used the command to browse the data in component
> mode.
>
> However, I got a warning message:
>
> Warning: No layout specified - will try to construct one using sensor
> positions
> > In ft_databrowser at 217
> Error using ft_databrowser (line 223)
> cannot infer sensor type
>
> I understand that one can manually create the layout, however, I was not
> sure how I can do it. Could someone please help?
>
> Thank you.
>
> Best regards,
> Hweeling
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From hweeling.lee at gmail.com  Thu Aug 15 13:21:19 2013
From: hweeling.lee at gmail.com (Hwee Ling Lee)
Date: Thu, 15 Aug 2013 13:21:19 +0200
Subject: [FieldTrip] EEG sensor position layout again
Message-ID: <CABG7z0TdTBH=c0e4szgPsSLnDgnmZvN6gh1Q6yTSAD6rDDnoWw@mail.gmail.com>

Hi,

A bit more details about my setup.

I'm using a Easycap MRI compatible 128 channels cap. I tried to search for
a layout on the templates/layout, and I found one that might closest fit to
my needs ('QuikCap_NSL_128').
To view my components, I tried these series of commands:

cfg = [];
cfg.viewmode = 'component';
cfg.continuous = 'yes';
cfg.layout = ft_prepare_layout('QuikCap_NSL_128');
ft_databrowser(cfg,ic_data);

However, I was prompted with error messages:
Warning: Struct field assignment overwrites a value with class "char". See
MATLAB R14SP2 Release Notes, Assigning Nonstructure
Variables As Structures Displays Warning, for details.
> In utilities\private\ft_preamble_provenance at 49
  In ft_preamble at 54
  In ft_prepare_layout at 91
Error using ft_prepare_layout (line 582)
no layout detected, please specify cfg.layout

Also when I tried the command,

cfg = [];
cfg.viewmode = 'component';
cfg.continuous = 'yes';
cfg.layout = 'QuikCap_NSL_128';
ft_databrowser(cfg,ic_data);

I get this error message:
Warning: could not open QuikCap_NSL_128
> In fileio\private\warning_once at 116
  In fileio\private\filetype_check_header at 54
  In ft_filetype at 328
  In ft_prepare_layout at 253
  In ft_databrowser at 226
Warning: could not determine filetype of QuikCap_NSL_128
> In fileio\private\warning_once at 116
  In ft_filetype at 1115
  In ft_prepare_layout at 253
  In ft_databrowser at 226
creating layout from electrode file QuikCap_NSL_128
Error using ft_read_sens (line 68)
file 'QuikCap_NSL_128' does not exist

Error in ft_prepare_layout (line 275)
  lay = sens2lay(ft_read_sens(cfg.layout), cfg.rotate, cfg.projection,
cfg.style, cfg.overlap);

Error in ft_databrowser (line 226)
  cfg.layout = ft_prepare_layout(tmpcfg);


Would anyone please help?

Cheers,
Hweeling
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From johanna.zumer at gmail.com  Thu Aug 15 13:33:57 2013
From: johanna.zumer at gmail.com (Johanna Zumer)
Date: Thu, 15 Aug 2013 13:33:57 +0200
Subject: [FieldTrip] EEG sensor position layout again
In-Reply-To: <CABG7z0TdTBH=c0e4szgPsSLnDgnmZvN6gh1Q6yTSAD6rDDnoWw@mail.gmail.com>
References: <CABG7z0TdTBH=c0e4szgPsSLnDgnmZvN6gh1Q6yTSAD6rDDnoWw@mail.gmail.com>
Message-ID: <CAL4kA6dXMDNUMcpiqi_1aaFYXmEHt2mTLgoT=dGH+c3L78miXQ@mail.gmail.com>

Hi Hweeling,

Since it says that it cannot find the Quikcap file, it sounds like it's not
on your path.    Run  ft_defaults on your Matlab command, then test if the
file is on your path:
>> ft_defaults
>> which QuikCap_NSL_128.mat

Assuming it finds the file on your path, then do you still get the browser
error?

Best,
Johanna


2013/8/15 Hwee Ling Lee <hweeling.lee at gmail.com>

> Hi,
>
> A bit more details about my setup.
>
> I'm using a Easycap MRI compatible 128 channels cap. I tried to search for
> a layout on the templates/layout, and I found one that might closest fit to
> my needs ('QuikCap_NSL_128').
> To view my components, I tried these series of commands:
>
> cfg = [];
> cfg.viewmode = 'component';
> cfg.continuous = 'yes';
> cfg.layout = ft_prepare_layout('QuikCap_NSL_128');
> ft_databrowser(cfg,ic_data);
>
> However, I was prompted with error messages:
> Warning: Struct field assignment overwrites a value with class "char". See
> MATLAB R14SP2 Release Notes, Assigning Nonstructure
> Variables As Structures Displays Warning, for details.
> > In utilities\private\ft_preamble_provenance at 49
>   In ft_preamble at 54
>   In ft_prepare_layout at 91
> Error using ft_prepare_layout (line 582)
> no layout detected, please specify cfg.layout
>
> Also when I tried the command,
>
> cfg = [];
> cfg.viewmode = 'component';
> cfg.continuous = 'yes';
> cfg.layout = 'QuikCap_NSL_128';
> ft_databrowser(cfg,ic_data);
>
> I get this error message:
> Warning: could not open QuikCap_NSL_128
> > In fileio\private\warning_once at 116
>   In fileio\private\filetype_check_header at 54
>   In ft_filetype at 328
>   In ft_prepare_layout at 253
>   In ft_databrowser at 226
> Warning: could not determine filetype of QuikCap_NSL_128
> > In fileio\private\warning_once at 116
>   In ft_filetype at 1115
>   In ft_prepare_layout at 253
>   In ft_databrowser at 226
> creating layout from electrode file QuikCap_NSL_128
> Error using ft_read_sens (line 68)
> file 'QuikCap_NSL_128' does not exist
>
> Error in ft_prepare_layout (line 275)
>   lay = sens2lay(ft_read_sens(cfg.layout), cfg.rotate, cfg.projection,
> cfg.style, cfg.overlap);
>
> Error in ft_databrowser (line 226)
>   cfg.layout = ft_prepare_layout(tmpcfg);
>
>
> Would anyone please help?
>
> Cheers,
> Hweeling
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From hweeling.lee at gmail.com  Thu Aug 15 13:59:17 2013
From: hweeling.lee at gmail.com (Hwee Ling Lee)
Date: Thu, 15 Aug 2013 13:59:17 +0200
Subject: [FieldTrip] EEG sensor position layout again
In-Reply-To: <CAL4kA6dXMDNUMcpiqi_1aaFYXmEHt2mTLgoT=dGH+c3L78miXQ@mail.gmail.com>
References: <CABG7z0TdTBH=c0e4szgPsSLnDgnmZvN6gh1Q6yTSAD6rDDnoWw@mail.gmail.com>
	<CAL4kA6dXMDNUMcpiqi_1aaFYXmEHt2mTLgoT=dGH+c3L78miXQ@mail.gmail.com>
Message-ID: <CABG7z0TQFuakrpr4zJDkP2TnfPvw0FwL+qqp9K_6o3owDsXFaw@mail.gmail.com>

Hi,

It states that:
'QuikCap_NSL_128.mat' not found.

However, when I checked fieldtrip/templates/layout, the mat file is stored
in this folder.

Cheers,
Hweeling



On 15 August 2013 13:33, Johanna Zumer <johanna.zumer at gmail.com> wrote:

> Hi Hweeling,
>
> Since it says that it cannot find the Quikcap file, it sounds like it's
> not on your path.    Run  ft_defaults on your Matlab command, then test if
> the file is on your path:
> >> ft_defaults
> >> which QuikCap_NSL_128.mat
>
> Assuming it finds the file on your path, then do you still get the browser
> error?
>
> Best,
> Johanna
>
>
> 2013/8/15 Hwee Ling Lee <hweeling.lee at gmail.com>
>
>> Hi,
>>
>> A bit more details about my setup.
>>
>> I'm using a Easycap MRI compatible 128 channels cap. I tried to search
>> for a layout on the templates/layout, and I found one that might closest
>> fit to my needs ('QuikCap_NSL_128').
>> To view my components, I tried these series of commands:
>>
>> cfg = [];
>> cfg.viewmode = 'component';
>> cfg.continuous = 'yes';
>> cfg.layout = ft_prepare_layout('QuikCap_NSL_128');
>> ft_databrowser(cfg,ic_data);
>>
>> However, I was prompted with error messages:
>> Warning: Struct field assignment overwrites a value with class "char".
>> See MATLAB R14SP2 Release Notes, Assigning Nonstructure
>> Variables As Structures Displays Warning, for details.
>> > In utilities\private\ft_preamble_provenance at 49
>>   In ft_preamble at 54
>>   In ft_prepare_layout at 91
>> Error using ft_prepare_layout (line 582)
>> no layout detected, please specify cfg.layout
>>
>> Also when I tried the command,
>>
>> cfg = [];
>> cfg.viewmode = 'component';
>> cfg.continuous = 'yes';
>> cfg.layout = 'QuikCap_NSL_128';
>> ft_databrowser(cfg,ic_data);
>>
>> I get this error message:
>> Warning: could not open QuikCap_NSL_128
>> > In fileio\private\warning_once at 116
>>   In fileio\private\filetype_check_header at 54
>>   In ft_filetype at 328
>>   In ft_prepare_layout at 253
>>   In ft_databrowser at 226
>> Warning: could not determine filetype of QuikCap_NSL_128
>> > In fileio\private\warning_once at 116
>>   In ft_filetype at 1115
>>   In ft_prepare_layout at 253
>>   In ft_databrowser at 226
>> creating layout from electrode file QuikCap_NSL_128
>> Error using ft_read_sens (line 68)
>> file 'QuikCap_NSL_128' does not exist
>>
>> Error in ft_prepare_layout (line 275)
>>   lay = sens2lay(ft_read_sens(cfg.layout), cfg.rotate, cfg.projection,
>> cfg.style, cfg.overlap);
>>
>> Error in ft_databrowser (line 226)
>>   cfg.layout = ft_prepare_layout(tmpcfg);
>>
>>
>> Would anyone please help?
>>
>> Cheers,
>> Hweeling
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>


-- 
=================================================
Dr. rer. nat. Lee, Hwee Ling
Postdoc
German Center for Neurodegenerative Diseases (DZNE) Bonn

Email 1: hwee-ling.lee<at>dzne.de
Email 2: hweeling.lee<at>gmail.com

https://sites.google.com/site/hweelinglee/home

Correspondence Address:
Ernst-Robert-Curtius Strasse 12, 53117, Bonn, Germany
=================================================
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From johanna.zumer at gmail.com  Thu Aug 15 14:01:39 2013
From: johanna.zumer at gmail.com (Johanna Zumer)
Date: Thu, 15 Aug 2013 14:01:39 +0200
Subject: [FieldTrip] EEG sensor position layout again
In-Reply-To: <CABG7z0TQFuakrpr4zJDkP2TnfPvw0FwL+qqp9K_6o3owDsXFaw@mail.gmail.com>
References: <CABG7z0TdTBH=c0e4szgPsSLnDgnmZvN6gh1Q6yTSAD6rDDnoWw@mail.gmail.com>
	<CAL4kA6dXMDNUMcpiqi_1aaFYXmEHt2mTLgoT=dGH+c3L78miXQ@mail.gmail.com>
	<CABG7z0TQFuakrpr4zJDkP2TnfPvw0FwL+qqp9K_6o3owDsXFaw@mail.gmail.com>
Message-ID: <CAL4kA6ddn8MoCfigmDq7nWnXy-UOBRJ842yBmucehOLoDFRw4Q@mail.gmail.com>

Hi Hweeling,

I just checked on my computer, and it helped to restart matlab and try
again.  Maybe there is something strange if ft_defaults is called (again)
during an already open session with previous calls to FT functions?

Best,
Johanna


2013/8/15 Hwee Ling Lee <hweeling.lee at gmail.com>

> Hi,
>
> It states that:
> 'QuikCap_NSL_128.mat' not found.
>
> However, when I checked fieldtrip/templates/layout, the mat file is stored
> in this folder.
>
> Cheers,
> Hweeling
>
>
>
> On 15 August 2013 13:33, Johanna Zumer <johanna.zumer at gmail.com> wrote:
>
>> Hi Hweeling,
>>
>> Since it says that it cannot find the Quikcap file, it sounds like it's
>> not on your path.    Run  ft_defaults on your Matlab command, then test if
>> the file is on your path:
>> >> ft_defaults
>> >> which QuikCap_NSL_128.mat
>>
>> Assuming it finds the file on your path, then do you still get the
>> browser error?
>>
>> Best,
>> Johanna
>>
>>
>> 2013/8/15 Hwee Ling Lee <hweeling.lee at gmail.com>
>>
>>> Hi,
>>>
>>> A bit more details about my setup.
>>>
>>> I'm using a Easycap MRI compatible 128 channels cap. I tried to search
>>> for a layout on the templates/layout, and I found one that might closest
>>> fit to my needs ('QuikCap_NSL_128').
>>> To view my components, I tried these series of commands:
>>>
>>> cfg = [];
>>> cfg.viewmode = 'component';
>>> cfg.continuous = 'yes';
>>> cfg.layout = ft_prepare_layout('QuikCap_NSL_128');
>>> ft_databrowser(cfg,ic_data);
>>>
>>> However, I was prompted with error messages:
>>> Warning: Struct field assignment overwrites a value with class "char".
>>> See MATLAB R14SP2 Release Notes, Assigning Nonstructure
>>> Variables As Structures Displays Warning, for details.
>>> > In utilities\private\ft_preamble_provenance at 49
>>>   In ft_preamble at 54
>>>   In ft_prepare_layout at 91
>>> Error using ft_prepare_layout (line 582)
>>> no layout detected, please specify cfg.layout
>>>
>>> Also when I tried the command,
>>>
>>> cfg = [];
>>> cfg.viewmode = 'component';
>>> cfg.continuous = 'yes';
>>> cfg.layout = 'QuikCap_NSL_128';
>>> ft_databrowser(cfg,ic_data);
>>>
>>> I get this error message:
>>> Warning: could not open QuikCap_NSL_128
>>> > In fileio\private\warning_once at 116
>>>   In fileio\private\filetype_check_header at 54
>>>   In ft_filetype at 328
>>>   In ft_prepare_layout at 253
>>>   In ft_databrowser at 226
>>> Warning: could not determine filetype of QuikCap_NSL_128
>>> > In fileio\private\warning_once at 116
>>>   In ft_filetype at 1115
>>>   In ft_prepare_layout at 253
>>>   In ft_databrowser at 226
>>> creating layout from electrode file QuikCap_NSL_128
>>> Error using ft_read_sens (line 68)
>>> file 'QuikCap_NSL_128' does not exist
>>>
>>> Error in ft_prepare_layout (line 275)
>>>   lay = sens2lay(ft_read_sens(cfg.layout), cfg.rotate, cfg.projection,
>>> cfg.style, cfg.overlap);
>>>
>>> Error in ft_databrowser (line 226)
>>>   cfg.layout = ft_prepare_layout(tmpcfg);
>>>
>>>
>>> Would anyone please help?
>>>
>>> Cheers,
>>> Hweeling
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>
>
> --
> =================================================
> Dr. rer. nat. Lee, Hwee Ling
> Postdoc
> German Center for Neurodegenerative Diseases (DZNE) Bonn
>
> Email 1: hwee-ling.lee<at>dzne.de
> Email 2: hweeling.lee<at>gmail.com
>
> https://sites.google.com/site/hweelinglee/home
>
> Correspondence Address:
> Ernst-Robert-Curtius Strasse 12, 53117, Bonn, Germany
> =================================================
>
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From hweeling.lee at gmail.com  Thu Aug 15 14:13:04 2013
From: hweeling.lee at gmail.com (Hwee Ling Lee)
Date: Thu, 15 Aug 2013 14:13:04 +0200
Subject: [FieldTrip] EEG sensor position layout again
In-Reply-To: <CAL4kA6ddn8MoCfigmDq7nWnXy-UOBRJ842yBmucehOLoDFRw4Q@mail.gmail.com>
References: <CABG7z0TdTBH=c0e4szgPsSLnDgnmZvN6gh1Q6yTSAD6rDDnoWw@mail.gmail.com>
	<CAL4kA6dXMDNUMcpiqi_1aaFYXmEHt2mTLgoT=dGH+c3L78miXQ@mail.gmail.com>
	<CABG7z0TQFuakrpr4zJDkP2TnfPvw0FwL+qqp9K_6o3owDsXFaw@mail.gmail.com>
	<CAL4kA6ddn8MoCfigmDq7nWnXy-UOBRJ842yBmucehOLoDFRw4Q@mail.gmail.com>
Message-ID: <CABG7z0SjsY7WSjM=PP5mfNq8oHY4NCv1pzRSjqV2FVVyVw92-Q@mail.gmail.com>

Hi,

Thanks for your advice. I restarted Matlab, and call for ft_defaults and
which QuikCap_NSL_128.mat, and I still get the same error message.

Also, is this the right layout file to use for my data?

Cheers,
Hweeling



On 15 August 2013 14:01, Johanna Zumer <johanna.zumer at gmail.com> wrote:

> Hi Hweeling,
>
> I just checked on my computer, and it helped to restart matlab and try
> again.  Maybe there is something strange if ft_defaults is called (again)
> during an already open session with previous calls to FT functions?
>
> Best,
> Johanna
>
>
> 2013/8/15 Hwee Ling Lee <hweeling.lee at gmail.com>
>
>> Hi,
>>
>> It states that:
>> 'QuikCap_NSL_128.mat' not found.
>>
>> However, when I checked fieldtrip/templates/layout, the mat file is
>> stored in this folder.
>>
>> Cheers,
>> Hweeling
>>
>>
>>
>> On 15 August 2013 13:33, Johanna Zumer <johanna.zumer at gmail.com> wrote:
>>
>>> Hi Hweeling,
>>>
>>> Since it says that it cannot find the Quikcap file, it sounds like it's
>>> not on your path.    Run  ft_defaults on your Matlab command, then test if
>>> the file is on your path:
>>> >> ft_defaults
>>> >> which QuikCap_NSL_128.mat
>>>
>>> Assuming it finds the file on your path, then do you still get the
>>> browser error?
>>>
>>> Best,
>>> Johanna
>>>
>>>
>>> 2013/8/15 Hwee Ling Lee <hweeling.lee at gmail.com>
>>>
>>>> Hi,
>>>>
>>>> A bit more details about my setup.
>>>>
>>>> I'm using a Easycap MRI compatible 128 channels cap. I tried to search
>>>> for a layout on the templates/layout, and I found one that might closest
>>>> fit to my needs ('QuikCap_NSL_128').
>>>> To view my components, I tried these series of commands:
>>>>
>>>> cfg = [];
>>>> cfg.viewmode = 'component';
>>>> cfg.continuous = 'yes';
>>>> cfg.layout = ft_prepare_layout('QuikCap_NSL_128');
>>>> ft_databrowser(cfg,ic_data);
>>>>
>>>> However, I was prompted with error messages:
>>>> Warning: Struct field assignment overwrites a value with class "char".
>>>> See MATLAB R14SP2 Release Notes, Assigning Nonstructure
>>>> Variables As Structures Displays Warning, for details.
>>>> > In utilities\private\ft_preamble_provenance at 49
>>>>   In ft_preamble at 54
>>>>   In ft_prepare_layout at 91
>>>> Error using ft_prepare_layout (line 582)
>>>> no layout detected, please specify cfg.layout
>>>>
>>>> Also when I tried the command,
>>>>
>>>> cfg = [];
>>>> cfg.viewmode = 'component';
>>>> cfg.continuous = 'yes';
>>>> cfg.layout = 'QuikCap_NSL_128';
>>>> ft_databrowser(cfg,ic_data);
>>>>
>>>> I get this error message:
>>>> Warning: could not open QuikCap_NSL_128
>>>> > In fileio\private\warning_once at 116
>>>>   In fileio\private\filetype_check_header at 54
>>>>   In ft_filetype at 328
>>>>   In ft_prepare_layout at 253
>>>>   In ft_databrowser at 226
>>>> Warning: could not determine filetype of QuikCap_NSL_128
>>>> > In fileio\private\warning_once at 116
>>>>   In ft_filetype at 1115
>>>>   In ft_prepare_layout at 253
>>>>   In ft_databrowser at 226
>>>> creating layout from electrode file QuikCap_NSL_128
>>>> Error using ft_read_sens (line 68)
>>>> file 'QuikCap_NSL_128' does not exist
>>>>
>>>> Error in ft_prepare_layout (line 275)
>>>>   lay = sens2lay(ft_read_sens(cfg.layout), cfg.rotate, cfg.projection,
>>>> cfg.style, cfg.overlap);
>>>>
>>>> Error in ft_databrowser (line 226)
>>>>   cfg.layout = ft_prepare_layout(tmpcfg);
>>>>
>>>>
>>>> Would anyone please help?
>>>>
>>>> Cheers,
>>>> Hweeling
>>>>
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>
>>>
>>>
>>
>>
>> --
>> =================================================
>> Dr. rer. nat. Lee, Hwee Ling
>> Postdoc
>> German Center for Neurodegenerative Diseases (DZNE) Bonn
>>
>> Email 1: hwee-ling.lee<at>dzne.de
>> Email 2: hweeling.lee<at>gmail.com
>>
>> https://sites.google.com/site/hweelinglee/home
>>
>> Correspondence Address:
>> Ernst-Robert-Curtius Strasse 12, 53117, Bonn, Germany
>> =================================================
>>
>
>


-- 
=================================================
Dr. rer. nat. Lee, Hwee Ling
Postdoc
German Center for Neurodegenerative Diseases (DZNE) Bonn

Email 1: hwee-ling.lee<at>dzne.de
Email 2: hweeling.lee<at>gmail.com

https://sites.google.com/site/hweelinglee/home

Correspondence Address:
Ernst-Robert-Curtius Strasse 12, 53117, Bonn, Germany
=================================================
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From m.kandula at uu.nl  Thu Aug 15 18:02:33 2013
From: m.kandula at uu.nl (Manasa Kandula)
Date: Thu, 15 Aug 2013 18:02:33 +0200
Subject: [FieldTrip] ft_databrowser No artifact.sampleinfo
Message-ID: <520CFB99.4060709@uu.nl>

I've been trying to use /ft_databrowser/ on segmented EEG data right 
after /ft_preprocessing/. However, at the subfunction /redraw_cb/, it's 
crashing as a call to /ft_fetch_data/ is resulting in an error as 
/opt.artdata.sampleinfo/ is not a field present in the /opt.artdata/ struct
(Error using ==> ft_fetch_data at 60 data does not contain a consistent 
trial definition, fetching data is not possible).
As far as I can tell, there is no point in the code that actually sets 
the /sampleinfo/ field for the /artifact/ struct.
Has anyone else encountered this problem?

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From pattersons076 at gmail.com  Thu Aug 15 20:01:32 2013
From: pattersons076 at gmail.com (Samantha Patterson)
Date: Thu, 15 Aug 2013 11:01:32 -0700
Subject: [FieldTrip] Fwd: error using freqdescriptives
In-Reply-To: <CACZDhUvHh-BRvcaPhKX7KXYMrSLX+fuEVqvDKZfUt7izwxBGjg@mail.gmail.com>
References: <CACZDhUvHh-BRvcaPhKX7KXYMrSLX+fuEVqvDKZfUt7izwxBGjg@mail.gmail.com>
Message-ID: <CACZDhUsnY6U5do=C0C3eJpX7sguUGJ1+Otbg-uybiZt3WpFEfg@mail.gmail.com>

Dear Fieldtrippers,


l am trying to use ft_freqdescriptives on freq data but i get an error
saying

Error using ft_checkdata (line 366)
This function requires freq or freqmvar data as input.

Error in ft_freqdescriptives (line 103)
freq = ft_checkdata(freq, 'datatype', {'freq', 'freqmvar'},
'feedback', 'yes');

Specfied cfg for freqdescriptives is

cfg = [];
cfg.foilim = [10 35];
cfg.toilim = [1.0 2.5];
cfg.keeptrials = 'yes';

test = ft_freqdescriptives(cfg,freq1);

output for freq1:

freq1

ans =

         label: {202x1 cell}
         dimord: 'rpt_chan_freq_time'
         freq: [1x22 double]
         time: [1x201 double]
         powspctrm: [4-D double]
         cumtapcnt: [26x18 double]
         grad: [1x1 struct]
         cfg: [1x1 struct]
         trialinfo: [26x3 double]

Any thoughts?

Thanks!!!!!

Samantha
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From M.Kandula at uu.nl  Thu Aug 15 22:26:54 2013
From: M.Kandula at uu.nl (Kandula, M. (Manasa))
Date: Thu, 15 Aug 2013 20:26:54 +0000
Subject: [FieldTrip] ft_databrowser No artifact.sampleinfo
In-Reply-To: <520CFB99.4060709@uu.nl>
References: <520CFB99.4060709@uu.nl>
Message-ID: <48A0B9F7F9A4BD4C836E1CC21805EB7E191D0BFC@ICTSC-W-S203.soliscom.uu.nl>

Hey all,
A minor correction.. I meant the artdata struct , not the artifact struct.
Thanks!!
Manasa
________________________________
From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Manasa Kandula [m.kandula at uu.nl]
Sent: Thursday, August 15, 2013 6:02 PM
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] ft_databrowser No artifact.sampleinfo

I've been trying to use ft_databrowser on segmented EEG data right after ft_preprocessing. However, at the subfunction redraw_cb, it's crashing as a call to ft_fetch_data is resulting in an error as opt.artdata.sampleinfo is not a field present in the opt.artdata struct
(Error using ==> ft_fetch_data at 60 data does not contain a consistent trial definition, fetching data is not possible).
As far as I can tell, there is no point in the code that actually sets the sampleinfo field for the artifact struct.
Has anyone else encountered this problem?

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From mbj0310 at gmail.com  Sun Aug 18 14:31:53 2013
From: mbj0310 at gmail.com (Beom Jun Min)
Date: Sun, 18 Aug 2013 21:31:53 +0900
Subject: [FieldTrip] Visualizing grand-averaged ERPs with different channels
Message-ID: <CA+v9jv+02_xb8sd-rQR14nqf5iA9Rs3HxYfbVgVx1=q+50YKkw@mail.gmail.com>

Dear all.

Hello

What I want to do is visualizing ERPs in different channels, simultaneously
in a single figure window.
For example, CZ, CPZ, & PZ or P4 & P5 in a group.

I use ft_singleplotER like below

*figure; *
*cfg = [];*
*cfg.ylim = [-8 8];*
*cfg.baseline = [-0.2 0];*
*cfg.linewidth = [2];*
*ft_singleplotER(cfg, group1_CP4, group1_CP3)*

I succeeded visualizing 3 different groups simultaneously with certain same
channel using the same manner above. (cfg, group1_CZ, group2_CZ)
However, when I try the same code with different channels, the result only
to show mean value (e.g. mean(CP4).

I do not know how to solve it.
Please help me.

With regards.

-- 
BeomJun Min, M.D.

Department of Medical System Engineering (DMSE)
Gwangju Institute of Science and Technology (GIST)
261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
500-712, Republic of Korea (South)
Phone: +82-62-715-3266 / Fax: +82-62-715-3244
E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
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From Sara.Bogels at mpi.nl  Mon Aug 19 11:39:54 2013
From: Sara.Bogels at mpi.nl (=?ISO-8859-1?Q?Sara_B=F6gels?=)
Date: Mon, 19 Aug 2013 11:39:54 +0200
Subject: [FieldTrip] problem with ft_multiplotER
In-Reply-To: <51E6838F.3050302@donders.ru.nl>
References: <CAPjpx=wTC727vv5fzqX_DdP-7wZi968TC13mkQR-bx80Faa-Zw@mail.gmail.com>
	<51E67229.8040001@mpi.nl> <51E6838F.3050302@donders.ru.nl>
Message-ID: <5211E7EA.8090907@mpi.nl>

Hi Jörn and others,

Some time ago, I posted the question below to the mailinglist. I now 
have had this error many times for both ft_timelockgrandaverage and 
ft_multiplotER. It happens for some datasets but not others and this 
appears quite random to me. The error message is:

"Subscripted assignment dimension mismatch"
Error in ft_timelockgrandaverage (line 182).
avgmat(s,:,:) = varargin{s}.(cfg.parameter{k});


It appears to have something to do with the different time limits of the 
different data I want to average or plot. I use cfg.latency to make sure 
the latency falls within the time limits of all files but this sometimes 
still does not help.

Any ideas?

Thank you,
Sara

"Jörn M. Horschig" wrote:
> Dear Sara,
>
> What you describe sounds like a bug to me. It looks like that in these
> lines the averages of the two conditions should be concatenated into one
> matrix, and apparently something goes wrong. However, you truncated the
> error message a bit (you pasted the line where the error occurs, but not
> the error message itself). If one of us developers should look into this
> further, it would be great if you register and create a bugreport on
> bugzilla.fconders.nl. Preferably would be to upload a snippet of your
> data, e.g. timelockstructures of one participant, and some lines of code
> which reproduce the error. We can then look into this further and fix
> this as soon as possible :)
>
> Best,
> Jörn
>
> On 7/17/2013 12:30 PM, Sara Bögels wrote:
>> Hi all,
>>
>> I have a very specific problem with the ft_multiplotER function. For 2
>> of my 24 participants, the function gives an error-message when I try
>> to plot the averages of two conditions at the same time. Plotting them
>> one by one is not a problem. There appears to be a specific point in
>> time (different for the two participants) when this goes wrong. If I
>> avoid that time (by using cfg.xlim) it works fine. My trials have
>> different lengths and I used "cfg.vartrllength = 2;" when calling
>> ft_timelockanalysis (not sure whether this is relevant).
>>
>> The error message I get is
>> "Error in ft_multiplotER (line 616)
>> yval(i,:) = datamatrix{i}(m,:);"
>>
>> I cannot find out what happens in this line. Can anyone tell me what
>> this might be referring to?
>>
>> Thank you,
>> Sara
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>


From frank.ye.mei at gmail.com  Mon Aug 19 22:18:39 2013
From: frank.ye.mei at gmail.com (Ye Mei)
Date: Mon, 19 Aug 2013 16:18:39 -0400
Subject: [FieldTrip] Can beamformer give both the location and the
 orientation of the source?
Message-ID: <52127D9F.3090102@gmail.com>

Hi all,

Can beamformer give both the location and the orientation of the source? 
If yes, how to do it in fieldtrip?

thanks ahead,
Ye




From arr at uvic.ca  Mon Aug 19 22:47:27 2013
From: arr at uvic.ca (Ashley Rose)
Date: Mon, 19 Aug 2013 13:47:27 -0700
Subject: [FieldTrip] fieldtrip question
Message-ID: <314d3147c1b422e458d033e10d7a6b17.squirrel@wm3.uvic.ca>


Hi there,

I'm having an issue running Fieldtrip.  I keep getting this warning:
"Warning: Dimensions of AlphaData must be 1x1, or must match CData."
But I haven't done anything to AlphaData or CData that would make them
inconsistent.  Has anyone had this problem before?

Thank you,
Ashley Rose




From imponderabilion at gmail.com  Tue Aug 20 00:54:49 2013
From: imponderabilion at gmail.com (=?ISO-8859-2?Q?Miko=B3aj_Magnuski?=)
Date: Tue, 20 Aug 2013 00:54:49 +0200
Subject: [FieldTrip] ft_neighbourplot does not plot new connections in 3D
Message-ID: <CAOb=78enLVbZZcApNNBGJALm=rZAtHH7CqiUqSSAimiDJYbmzw@mail.gmail.com>

Hi FieldTrippers!

just a short note in case it wasn'r reported before:
ft_neighbourplot with option .enableedit = 'on' (the bleeding option)
plots new connections (new - that means click-created) only as 2D
projections even if everything else is plotted in 3D.

changing lines 286 - 287 to something like:
    if size(proj,2) == 2
        Coord = {X, Y};
    elseif size(proj,2) > 2
        Z = [proj(curSensId,3) proj(lastSensId,3)];
        Coord = {X, Y, Z};
    end
    hl(curSensId, lastSensId) = line(Coord{:}, 'color', 'r');
    hl(lastSensId, curSensId) = line(Coord{:}, 'color', 'r');

fixes this problem.


Regards,
Mikołaj Magnuski
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From jm.horschig at donders.ru.nl  Fri Aug 23 09:28:18 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Fri, 23 Aug 2013 09:28:18 +0200
Subject: [FieldTrip] ft_neighbourplot does not plot new connections in 3D
In-Reply-To: <CAOb=78enLVbZZcApNNBGJALm=rZAtHH7CqiUqSSAimiDJYbmzw@mail.gmail.com>
References: <CAOb=78enLVbZZcApNNBGJALm=rZAtHH7CqiUqSSAimiDJYbmzw@mail.gmail.com>
Message-ID: <52170F12.9020107@donders.ru.nl>

Dear Miko?aj,

thanks very much for reporting this. I fixed it and the fix should be 
available inthe next FieldTrip release (i.e. tomorrow).

Best,
Jörn

On 8/20/2013 12:54 AM, Miko?aj Magnuski wrote:
> Hi FieldTrippers!
>
> just a short note in case it wasn'r reported before:
> ft_neighbourplot with option .enableedit = 'on' (the bleeding option)
> plots new connections (new - that means click-created) only as 2D
> projections even if everything else is plotted in 3D.
>
> changing lines 286 - 287 to something like:
>     if size(proj,2) == 2
>         Coord = {X, Y};
>     elseif size(proj,2) > 2
>         Z = [proj(curSensId,3) proj(lastSensId,3)];
>         Coord = {X, Y, Z};
>     end
>     hl(curSensId, lastSensId) = line(Coord{:}, 'color', 'r');
>     hl(lastSensId, curSensId) = line(Coord{:}, 'color', 'r');
>
> fixes this problem.
>
>
> Regards,
> Miko?aj Magnuski
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From narayan.ps at tut.fi  Fri Aug 23 12:37:20 2013
From: narayan.ps at tut.fi (Narayan Puthanmadam Subramaniyam)
Date: Fri, 23 Aug 2013 13:37:20 +0300
Subject: [FieldTrip] simulation of EOG
Message-ID: <001501ce9fec$bee80ce0$3cb826a0$@tut.fi>

Dear FT experts

I am not sure if I should be asking this question here. I want to simulate
'pure' EOG signal by placing rotating dipole in the eye. Can I use FT to
compute the lead field matrix from eye to  all scalp electrodes ? Has anyone
used a BEM model where eyes are segmented ?

Many Thanks
Narayan



From ingenieureniso at gmail.com  Fri Aug 23 19:40:14 2013
From: ingenieureniso at gmail.com (ingenieur eniso)
Date: Fri, 23 Aug 2013 18:40:14 +0100
Subject: [FieldTrip] how to open bdf and rdf files
Message-ID: <CAPjpx=yj73grOv58wwiLF4Ec2fLGzAiNpy7ziDZGpb+Lphynsg@mail.gmail.com>

Dear all,


I have EEG record files in rdf and bdf formats. but I do not know how to
open them.

Please can anyone send me a matlab function to open these files?

I hope you will send me positive and helpful response.

Thanks a lot in advance!

Best,

ahmed
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From johanna.zumer at gmail.com  Sun Aug 25 07:18:14 2013
From: johanna.zumer at gmail.com (Johanna Zumer)
Date: Sun, 25 Aug 2013 07:18:14 +0200
Subject: [FieldTrip] how to open bdf and rdf files
In-Reply-To: <CAPjpx=yj73grOv58wwiLF4Ec2fLGzAiNpy7ziDZGpb+Lphynsg@mail.gmail.com>
References: <CAPjpx=yj73grOv58wwiLF4Ec2fLGzAiNpy7ziDZGpb+Lphynsg@mail.gmail.com>
Message-ID: <CAL4kA6dwgo31sL43OMwpruHyOnF5O8MZW0Ha-Z682HfNs8gc=A@mail.gmail.com>

Dear Ahmed,

Does this help?  (http://fieldtrip.fcdonders.nl/getting_started/bdf )

If you are still stuck, maybe try EEGlab
import<http://sccn.ucsd.edu/wiki/A01:_Importing_Continuous_and_Epoched_Data>
and
then convert EEGlab format to FieldTrip format (
http://fieldtrip.fcdonders.nl/integrating_with/integrating_with_eeglab)

Best,
Johanna


2013/8/23 ingenieur eniso <ingenieureniso at gmail.com>

> Dear all,
>
>
> I have EEG record files in rdf and bdf formats. but I do not know how to
> open them.
>
> Please can anyone send me a matlab function to open these files?
>
> I hope you will send me positive and helpful response.
>
> Thanks a lot in advance!
>
> Best,
>
> ahmed
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From roeysc at gmail.com  Mon Aug 26 00:08:19 2013
From: roeysc at gmail.com (Roey Schurr)
Date: Mon, 26 Aug 2013 01:08:19 +0300
Subject: [FieldTrip] Source Analysis Normalisation in-subject and in-group
Message-ID: <CAHm4wZAWwHisWEPd41qxe6EiNAgkh_vqv2eMWvaGpNWdRQ1xww@mail.gmail.com>

Hi all,

We have a question regarding normalisation of EEG signals for source
reconstruction analysis.

We have EEG records (not ERP) of a few patients in two different conditions
(each condition consists of several 2 seconds segments/trials). Each
recording was done over a period of a few days, and in different sessions.
We also have anatomycal MRI scans for each patient (subject).

We would like to make two statistic comparisons:

1.    Compare the source analysis of the two conditions in each subject.

2.    Compare the source analysis of the two conditions, based upon all
subjects.

For the first comparison, we are puzzled about the appropriate way to
normalise and standardize our data, since each EEG segment was recorded at
a different time, and hence may be affected by different electrode
conductivity, for example. How would you normalise the data?

For the second comparison, of course, we would like to normalise the source
analysis results in the anatomycal level using ft_volumenormalise.

However, we are puzzled about the appropriate way to normalise and
standardize our data, since subjects differ from each other (for example,
anatomycally, resulting in changes of power spectrum).

How would you standartize the data between subjects?



Thank you very much,

best regards,

Aia and Roey
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From polomacnenad at gmail.com  Tue Aug 27 20:44:39 2013
From: polomacnenad at gmail.com (Nenad Polomac)
Date: Tue, 27 Aug 2013 20:44:39 +0200
Subject: [FieldTrip] ICA on highpass filtered MEG data
Message-ID: <CAEk4EpFExFt8U85CfTjz0MPQPQhOrV7R4LdCqLkVRjvahywiUQ@mail.gmail.com>

Dear Fieldtrip users,

I have CTF 275 channels MEG data and I am interested in gamma band. For
this purpose I would like to remove microsaccade artifacts from the data
using the ICA. In order to obtain the microsacade components I have
filtered data ( highpass and lowpass; 30-150 Hz) and than I've wanted to
run ICA calculation. However, I've read here
http://sccn.ucsd.edu/pipermail/eeglablist/2013/006710.html that after
filtering data are more dependent and that is a big problem for ICA
calculation. And I also experienced that ICA takes very long time and
sometimes doesn't converge. So, to overcome this problem, the data
dimensionality has to be reduced. I have found two different solutions from
different sources.

One solution might be to estimate variance with PCA and than choose the
amount of variance that should stay in the data. e.g.
[COEFF,SCORE,eigenvalues ] = princomp(data_matrix);
A= cumsum(eigenvalues);
num_of_comp=find(A/A(end)>0.98,1); % 98% is the percentage of variance that
will be used for the ICA, 2% will be discarded
This percentage will be the same for all subjects.

The second option might be to use the same eigenvalue cutoff value for all
subjects:
[COEFF,SCORE,eigenvalues ] = princomp(data_matrix);
A=(find(eigenvalues>0.005));  %0.005 here is just for example
num_of_comp=A(end);

The variable num_of_comp represents the number of component to which
filtered data will be reduced before ICA.
e.g.
    cfg = [];
    cfg.method = 'runica';
    cfg.runica.pca = num_of_comp;
    cfg.runica.maxsteps = 600;
    cfg.runica.stop = 1e-7;
    cfg.runica.extended = 1;
    ica_comp = ft_componentanalysis(cfg, data);



Finally, my question is which of this two methods is more objective? And is
there any other possibility I should consider?
I would like to add that in my case second calculation gives me less
variant number of components among 22 subjects.

Thank you in advance!

All the best!
Nenad
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From aaron.schurger at gmail.com  Tue Aug 27 21:49:21 2013
From: aaron.schurger at gmail.com (Aaron Schurger)
Date: Tue, 27 Aug 2013 21:49:21 +0200
Subject: [FieldTrip] ICA on highpass filtered MEG data
In-Reply-To: <CAEk4EpFExFt8U85CfTjz0MPQPQhOrV7R4LdCqLkVRjvahywiUQ@mail.gmail.com>
References: <CAEk4EpFExFt8U85CfTjz0MPQPQhOrV7R4LdCqLkVRjvahywiUQ@mail.gmail.com>
Message-ID: <CALeeyASWNx4+ZMfZuDqY-cfvrXma-0BquHNsbWUFrcE2xpjvCw@mail.gmail.com>

I am not aware of any good way to remove microsaccade artifacts from
EEG or MEG data. ICA might find a microsaccade component if you have
sufficient data, but you will have to hunt through the components to
find the "right" one. The difficult question is how to know which is
the right component, or whether or not microsaccades are incorporated
into two or more components (or not at all). Having an MEG-compatible
eye tracker with a high sampling rate is what I would want.
Best wishes,
Aaron

On Tue, Aug 27, 2013 at 8:44 PM, Nenad Polomac <polomacnenad at gmail.com> wrote:
> Dear Fieldtrip users,
>
> I have CTF 275 channels MEG data and I am interested in gamma band. For this
> purpose I would like to remove microsaccade artifacts from the data using
> the ICA. In order to obtain the microsacade components I have filtered data
> ( highpass and lowpass; 30-150 Hz) and than I've wanted to run ICA
> calculation. However, I've read here
> http://sccn.ucsd.edu/pipermail/eeglablist/2013/006710.html that after
> filtering data are more dependent and that is a big problem for ICA
> calculation. And I also experienced that ICA takes very long time and
> sometimes doesn't converge. So, to overcome this problem, the data
> dimensionality has to be reduced. I have found two different solutions from
> different sources.
>
> One solution might be to estimate variance with PCA and than choose the
> amount of variance that should stay in the data. e.g.
> [COEFF,SCORE,eigenvalues ] = princomp(data_matrix);
> A= cumsum(eigenvalues);
> num_of_comp=find(A/A(end)>0.98,1); % 98% is the percentage of variance that
> will be used for the ICA, 2% will be discarded
> This percentage will be the same for all subjects.
>
> The second option might be to use the same eigenvalue cutoff value for all
> subjects:
> [COEFF,SCORE,eigenvalues ] = princomp(data_matrix);
> A=(find(eigenvalues>0.005));  %0.005 here is just for example
> num_of_comp=A(end);
>
> The variable num_of_comp represents the number of component to which
> filtered data will be reduced before ICA.
> e.g.
>     cfg = [];
>     cfg.method = 'runica';
>     cfg.runica.pca = num_of_comp;
>     cfg.runica.maxsteps = 600;
>     cfg.runica.stop = 1e-7;
>     cfg.runica.extended = 1;
>     ica_comp = ft_componentanalysis(cfg, data);
>
>
>
> Finally, my question is which of this two methods is more objective? And is
> there any other possibility I should consider?
> I would like to add that in my case second calculation gives me less variant
> number of components among 22 subjects.
>
> Thank you in advance!
>
> All the best!
> Nenad
>
>
>
>
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



-- 
Aaron Schurger, PhD
Post-doctoral researcher
INSERM U992 / NeuroSpin
CEA - Saclay, France
+33-1-69-08-66-47
aaron.schurger at gmail.com
http://www.unicog.org


From sreenivasan.r.nadar at gmail.com  Tue Aug 27 22:17:03 2013
From: sreenivasan.r.nadar at gmail.com (Sreenivasan R. Nadar, Ph.D.)
Date: Tue, 27 Aug 2013 16:17:03 -0400
Subject: [FieldTrip] 19 channel EEG for source modeling of epileptic focus
Message-ID: <CAL+KoxgGx-BfL77H2VNL3dssfuB2FNAO5wFOB6p-gEKFLdNVFg@mail.gmail.com>

Hi All,

I have a 19 channel Nihon - Kohden EEG for epilepsy monitoring and I use
the following file for channel locations in
ftp://sccn.ucsd.edu/pub/locfiles/eeglab/Standard-10-20-Cap19.ced for data
analysis in EEGLab.

Please let me know if anybody has pre-processing script to import the data
in Fieldtrip and also for source localisation of epileptic focus.

Thank you.

Sreenivasan
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From jm.horschig at donders.ru.nl  Thu Aug 29 10:02:45 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Thu, 29 Aug 2013 10:02:45 +0200
Subject: [FieldTrip] 19 channel EEG for source modeling of epileptic
	focus
In-Reply-To: <CAL+KoxgGx-BfL77H2VNL3dssfuB2FNAO5wFOB6p-gEKFLdNVFg@mail.gmail.com>
References: <CAL+KoxgGx-BfL77H2VNL3dssfuB2FNAO5wFOB6p-gEKFLdNVFg@mail.gmail.com>
Message-ID: <521F0025.8090104@donders.ru.nl>

Dear Sreenivasan,

I am not sure whether you can read in .ced files with the ft_read_sens 
function. You could give it a try though by specifying cfg.elecfile = 
'PATH_TO_FILE/Standard-10-20-Cap19.ced'

Otherwise, I can see two ways how you can make this work.
First, you could change the content of the file to match the format of 
the other sensor-templates. For this, you can best have a look in 
fieldtrip/template/elec and have a look at one of these files. Then, you 
would need to rearrange the values of your .ced file to match the order 
of the .elc-format.
Alternatively, you could write your own wrapper function, which reads in 
the x-, y- and z-position of the electrodes from the .ced file and 
stores them in a matrix. Also, you need to store the corresponding 
channel label. Using these, you can create an elec-structure that you 
can use as cfg.elec for whatever function you want to do.

Maybe someone else here has worked with .ced files before and can thus 
can help with either of the two solutions. Good luck :)

Best,
Jörn

On 8/27/2013 10:17 PM, Sreenivasan R. Nadar, Ph.D. wrote:
> Hi All,
>
> I have a 19 channel Nihon - Kohden EEG for epilepsy monitoring and I 
> use the following file for channel locations in 
> ftp://sccn.ucsd.edu/pub/locfiles/eeglab/Standard-10-20-Cap19.ced for 
> data analysis in EEGLab.
>
> Please let me know if anybody has pre-processing script to import the 
> data in Fieldtrip and also for source localisation of epileptic focus.
>
> Thank you.
>
> Sreenivasan
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From ben.vanlier at bsse.ethz.ch  Thu Aug 29 13:53:26 2013
From: ben.vanlier at bsse.ethz.ch (van Lier  Ben)
Date: Thu, 29 Aug 2013 11:53:26 +0000
Subject: [FieldTrip] slow reading with ft_preprocessing of a fcdc_matbin
	file?
Message-ID: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A7B87E@MBX13.d.ethz.ch>

Hi all,

I have a pretty big data file of 120 channels for 20min continuous at 20khz. clearly i need to downsample. to do so, i convert the original file to fcdc_matbin, creating a 22gb bin file with all the data.

then its time for downsampling as shown on http://fieldtrip.fcdonders.nl/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory

this is very slow. ft_preprocessing takes 230 seconds per channel (using 380 mb), doing nothing but just reading 1 channel. the subsequent downsampling with ft_resample to 1khz is surprisingly fast with only 4 seconds.

does that make any sense? it seems like a very long time to read in 380mb... :(

Best,
Ben



From jan.schoffelen at donders.ru.nl  Thu Aug 29 14:01:59 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 29 Aug 2013 14:01:59 +0200
Subject: [FieldTrip] slow reading with ft_preprocessing of a fcdc_matbin
	file?
In-Reply-To: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A7B87E@MBX13.d.ethz.ch>
References: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A7B87E@MBX13.d.ethz.ch>
Message-ID: <264BF553-0691-4AC9-95B8-D78000F0CA6B@donders.ru.nl>

Hi Ben,

I guess MATLAB needs to read in the whole datafile each time (for each channel). What about creating separate files for each channel?

JM


On Aug 29, 2013, at 1:53 PM, van Lier Ben wrote:

> Hi all,
> 
> I have a pretty big data file of 120 channels for 20min continuous at 20khz. clearly i need to downsample. to do so, i convert the original file to fcdc_matbin, creating a 22gb bin file with all the data.
> 
> then its time for downsampling as shown on http://fieldtrip.fcdonders.nl/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory
> 
> this is very slow. ft_preprocessing takes 230 seconds per channel (using 380 mb), doing nothing but just reading 1 channel. the subsequent downsampling with ft_resample to 1khz is surprisingly fast with only 4 seconds.
> 
> does that make any sense? it seems like a very long time to read in 380mb... :(
> 
> Best,
> Ben
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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From jm.horschig at donders.ru.nl  Thu Aug  1 12:37:08 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Thu, 01 Aug 2013 12:37:08 +0200
Subject: [FieldTrip] ancova for sources analysis
In-Reply-To: <2264a36963356fbe.51f8fb71@upo.es>
References: <167095db43e3fd69.51f8d35e@upo.es>
	<1763660954.2174368.1375257362812.JavaMail.root@sculptor.zimbra.ru.nl>
	<2264a36963356fbe.51f8fb71@upo.es>
Message-ID: <51FA3A54.8020001@donders.ru.nl>

Dear Gabriel,

if you have a .stat field, you did already run statistics on your data. 
I wouldn't regress anything out of e.g. t-values. Rather, the idea is to 
regress out confounding factors before doing statistics, so that you 
reduce variance across trials and subsequently maximize sensitivity of 
your statistical test. I could really advise you to read the paper I 
suggested, the rationale is explained there.
Moreover, if you are interested in a covariate like 'age', a simple 
correlational analysis might make more sense. As stated, the idea of 
regressconfound is to explain and remove variance across observations, 
but depending on what you want, a correlation might make more sense.
Want to improve your stats? Then go for regressconfound. Find out if 
there is age explains neural effects? Then go for a simple correlation.

Best,
Jörn

On 7/31/2013 11:56 AM, Gabriel Gonzalez Escamilla wrote:
> Thank you all for your responses.
>
> The last problem I did wrote is now solved, see below.
>
> I had a field called 'stat' instead of the 'pow', I'm guessing this 
> field was set before, so, now i'm using this field as if it was the 
> 'pow' I needed and it's working, Is that OK?
>
> Now it takes me to the next question, my data has the avg field, and 
> it says that will update the descriptives but that the 'method' is 
> missing, is this update necessary? or can I just skeep it?
>
>
> Many thanks in advanced,
> Gabriel
>
>
> ----- Mensaje original -----
> De: "Stolk, A." <a.stolk at fcdonders.ru.nl>
> Fecha: Miércoles, 31 de Julio de 2013, 10:04 am
> Asunto: Re: [FieldTrip] ancova for sources analysis
> A: FieldTrip discussion list <fieldtrip at science.ru.nl>
>
> >Dear Gabriel,
> >
> > This page demonstrates how to remove contributions to the data 
> originating from head movement, but one could as well follow the same 
> principle for any other type of covariate (e.g. eye movement related 
> activity).
> >
> > http://fieldtrip.fcdonders.nl/example/how_to_incorporate_head_movements_in_meg_analysis?
> >
> > Yours,
> > Arjen
> >
> ------------------------------------------------------------------------
>
>     *> Van: *"Gabriel Gonzalez Escamilla" <ggonesc at upo.es>
>     *> Aan: *"fieFieldTrip discussion list" <fieldtrip at science.ru.nl>
>     *> Verzonden: *Woensdag 31 juli 2013 09:05:34
>     *> Onderwerp: *[FieldTrip] ancova for sources analysis
>     >
>     > Dear fieldtrip experts,
>     >
>     > I'm wondering if it is possible to perform an ancova or to remove
>     the effect of a covariate in a source analysis?
>     >
>     > Many thanks in advanced,
>     > Gabriel
>     > _______________________________________________
>     > fieldtrip mailing list
>     > fieldtrip at donders.ru.nl
>     > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> <font size="3">--------------------------<br />PhD. student Gabriel 
> González-Escamilla<br />Laboratory of Functional Neuroscience<br 
> />Department of Physiology, Anatomy, and Cell Biology<br />University 
> Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br 
> />- Spain -<br /><br />Email: ggonesc at upo.es<br 
> />http://www.upo.es/neuroaging/es/</font>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From lzyang at ustc.edu.cn  Sat Aug  3 10:49:59 2013
From: lzyang at ustc.edu.cn (lzyang)
Date: Sat, 03 Aug 2013 16:49:59 +0800
Subject: [FieldTrip] units of data sample read from neuroscan avg file is
	incorrect
Message-ID: <51FCC437.5070409@ustc.edu.cn>

Dear fieldtrip list,
I used ft_read_data to read in .avg files (neuroscan format) to do some
advanced analysis.
data=ft_read_data('sham.avg', 'dataformat', 'ns_avg');
I noticed that the unit of data sample read by this function is incorrect.
Values of samples ranged from -0.1 to 0.1.
I will appreciate if anyone can give me some hints on how to import avg
files correctly using fieldtrip.

Thanks very much!

Best Regards,
-Lizhuang




From politzerahless at gmail.com  Sat Aug  3 13:48:58 2013
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Sat, 3 Aug 2013 07:48:58 -0400
Subject: [FieldTrip] fieldtrip Digest, Vol 33, Issue 3
In-Reply-To: <mailman.1.1375524018.6192.fieldtrip@science.ru.nl>
References: <mailman.1.1375524018.6192.fieldtrip@science.ru.nl>
Message-ID: <CAJT2k__JuKQth_DrjFDn39rJBMsNSAx1wsg=RAiq-mOq+D0N9g@mail.gmail.com>

Hi Lizhuang,

I haven't used Fieldtrip to import .avg files so I'm not sure about this,
but I wonder if this is related to the same problem in EEGLAB. EEGLAB also
scales .avg files like this when importing them, for some reason, so if the
Fieldtrip function is based on EEGLAB code these issues may be related.
(However, I just looked at read_ns_avg.m, which is what ft_read_data calls,
and it doesn't say it's copied from EEGLAB). If you have EEGLAB, you can
add the custom function loadavg_bcl.m to your path (it is available at
http://sccn.ucsd.edu/pipermail/eeglablist/2011/003986.html, as one of the
attachments near the bottom), use that to import the .avg file, and then
use the EEGLAB function eeglab2fieldtrip() to get the data into FieldTrip.

Also, have you tried reading the data with ft_preprocessing() instead of
ft_read_data? ft_read_data is kind of a low-level function; in the past I
think I've had better luck just using ft_preprocessing.

Best,
Steve


Stephen Politzer-Ahles
New York University, Abu Dhabi
Psychology Department


> Message: 1
> Date: Sat, 03 Aug 2013 16:49:59 +0800
> From: lzyang <lzyang at ustc.edu.cn>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] units of data sample read from neuroscan avg file
>         is      incorrect
> Message-ID: <51FCC437.5070409 at ustc.edu.cn>
> Content-Type: text/plain; charset=GB2312
>
> Dear fieldtrip list,
> I used ft_read_data to read in .avg files (neuroscan format) to do some
> advanced analysis.
> data=ft_read_data('sham.avg', 'dataformat', 'ns_avg');
> I noticed that the unit of data sample read by this function is incorrect.
> Values of samples ranged from -0.1 to 0.1.
> I will appreciate if anyone can give me some hints on how to import avg
> files correctly using fieldtrip.
>
> Thanks very much!
>
> Best Regards,
> -Lizhuang
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From politzerahless at gmail.com  Sat Aug  3 13:50:40 2013
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Sat, 3 Aug 2013 07:50:40 -0400
Subject: [FieldTrip] units of data sample read from neuroscan avg file
	is incorrect
Message-ID: <CAJT2k_8z9nv4YnX8AKYhUAwSv4cHnaPDDH7KqrjQ-T=f1RAAdg@mail.gmail.com>

Hi Lizhuang,

I haven't used Fieldtrip to import .avg files so I'm not sure about this,
but I wonder if this is related to the same problem in EEGLAB. EEGLAB also
scales .avg files like this when importing them, for some reason, so if the
Fieldtrip function is based on EEGLAB code these issues may be related.
(However, I just looked at read_ns_avg.m, which is what ft_read_data calls,
and it doesn't say it's copied from EEGLAB). If you have EEGLAB, you can
add the custom function loadavg_bcl.m to your path (it is available at
http://sccn.ucsd.edu/pipermail/eeglablist/2011/003986.html, as one of the
attachments near the bottom), use that to import the .avg file, and then
use the EEGLAB function eeglab2fieldtrip() to get the data into FieldTrip.

Also, have you tried reading the data with ft_preprocessing() instead of
ft_read_data? ft_read_data is kind of a low-level function; in the past I
think I've had better luck just using ft_preprocessing.

Best,
Steve



Stephen Politzer-Ahles
New York University, Abu Dhabi
Psychology Department


> Message: 1
> Date: Sat, 03 Aug 2013 16:49:59 +0800
> From: lzyang <lzyang at ustc.edu.cn>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] units of data sample read from neuroscan avg file
>         is      incorrect
> Message-ID: <51FCC437.5070409 at ustc.edu.cn>
> Content-Type: text/plain; charset=GB2312
>
> Dear fieldtrip list,
> I used ft_read_data to read in .avg files (neuroscan format) to do some
> advanced analysis.
> data=ft_read_data('sham.avg', 'dataformat', 'ns_avg');
> I noticed that the unit of data sample read by this function is incorrect.
> Values of samples ranged from -0.1 to 0.1.
> I will appreciate if anyone can give me some hints on how to import avg
> files correctly using fieldtrip.
>
> Thanks very much!
>
> Best Regards,
> -Lizhuang
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From Izabela.Mikula at mpi.nl  Tue Aug  6 12:10:32 2013
From: Izabela.Mikula at mpi.nl (Izabela Mikula)
Date: Tue, 6 Aug 2013 12:10:32 +0200
Subject: [FieldTrip] Error in ft_rejectartifact for the newest fieldtrip
	version
Message-ID: <9532B831-AB8E-4EBC-A984-5A3783E5313D@mpi.nl>

Dear all,
I was wondering if any of you have ever encountered similar problem and might know if I'm doing something wrong or it is a bug..

I have tried using (my old scripts for preprocessing) ft_rejectartifact(cfg, data) but I get an error:

evaluating artifact_jump
??? Error using ==> feval
Undefined function or method 'artifact_jump' for input arguments of type 'struct'.

Error in ==> ft_rejectartifact at 257
    cfg = feval(sprintf('artifact_%s', cfg.artfctdef.type{type}), cfg, data);

It is important to note that this error only occurs when using the newest fieldtrip version. For previous versions it works without any problems. I have also tried multiple datasets, but the problem remains.
 
data = 

       fsample: 1200
          grad: [1x1 struct]
    sampleinfo: [180x2 double]
     trialinfo: [180x1 double]
         trial: {1x180 cell}
          time: {1x180 cell}
         label: {273x1 cell}
           cfg: [1x1 struct]

and

cfg.artfctdef = 

          reject: 'complete'
            jump: [1x1 struct]
          muscle: [1x1 struct]
            type: {2x1 cell}
    minaccepttim: 0.1000
      crittoilim: []
        feedback: 'no'

Thanks in advance!

Best,
Izabela




From jan.schoffelen at donders.ru.nl  Tue Aug  6 13:13:09 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Tue, 6 Aug 2013 13:13:09 +0200
Subject: [FieldTrip] Error in ft_rejectartifact for the newest fieldtrip
	version
In-Reply-To: <9532B831-AB8E-4EBC-A984-5A3783E5313D@mpi.nl>
References: <9532B831-AB8E-4EBC-A984-5A3783E5313D@mpi.nl>
Message-ID: <C671E708-23FB-40E2-9094-1DFD80CAED92@donders.ru.nl>

Hi Izabela,

This is indeed a bug. We reorganized our compat-directory, that is dealing with backward compatibility issues. One of these issues was to support backward compatibility for calling ft-functions without the ft_prefix. E.g. calling freqanalysis should redirect to a call to ft_freqanalysis. With this feature removed, ft_rejectartifact cannot execute artifact_xxx, because it is not redirected anymore to ft_artifact_xxx.
I have fixed this. It should be available within 15 minutes on the DCCN Fieldtrip version, and in the download version as of tonight.

Thanks for reporting,
Jan-Mathijs

 
On Aug 6, 2013, at 12:10 PM, Izabela Mikula wrote:

> Dear all,
> I was wondering if any of you have ever encountered similar problem and might know if I'm doing something wrong or it is a bug..
> 
> I have tried using (my old scripts for preprocessing) ft_rejectartifact(cfg, data) but I get an error:
> 
> evaluating artifact_jump
> ??? Error using ==> feval
> Undefined function or method 'artifact_jump' for input arguments of type 'struct'.
> 
> Error in ==> ft_rejectartifact at 257
>    cfg = feval(sprintf('artifact_%s', cfg.artfctdef.type{type}), cfg, data);
> 
> It is important to note that this error only occurs when using the newest fieldtrip version. For previous versions it works without any problems. I have also tried multiple datasets, but the problem remains.
> 
> data = 
> 
>       fsample: 1200
>          grad: [1x1 struct]
>    sampleinfo: [180x2 double]
>     trialinfo: [180x1 double]
>         trial: {1x180 cell}
>          time: {1x180 cell}
>         label: {273x1 cell}
>           cfg: [1x1 struct]
> 
> and
> 
> cfg.artfctdef = 
> 
>          reject: 'complete'
>            jump: [1x1 struct]
>          muscle: [1x1 struct]
>            type: {2x1 cell}
>    minaccepttim: 0.1000
>      crittoilim: []
>        feedback: 'no'
> 
> Thanks in advance!
> 
> Best,
> Izabela
> 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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From ben.vanlier at bsse.ethz.ch  Tue Aug  6 17:56:55 2013
From: ben.vanlier at bsse.ethz.ch (van Lier  Ben)
Date: Tue, 6 Aug 2013 15:56:55 +0000
Subject: [FieldTrip] from trials to continuous and an error in selfromraw
Message-ID: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A6CBB0@MBX23.d.ethz.ch>

Hi guys,

for testing purposes im trying to use data in trials as one continuous piece of data. when i do freqanalysis with cfg.trials = 'all' and then singleplotTFR, i get to see only 1 trial. it should plot the spectra of all of them right? i do use cfg.continuous = yes
i can tell it is processing all the trials in the command window feedback and databrowser is putting them together fine.

i guess related, when i do cfg.trials = '1' (or any) and then freqanalysis it gives me the following error:

--------------------------
Error using selfromraw (line 13)
incorrect specification of requested repetitions

Error in ft_selectdata_old (line 547)
    data = selfromraw(data, 'rpt', selrpt);

Error in ft_selectdata (line 45)
  [varargout{1:nargout}] = ft_selectdata_old(varargin{:});

Error in ft_freqanalysis (line 225)
  data = ft_selectdata(data, 'rpt', cfg.trials);
----------------------------

i tried with data coming from ft_appendata (2 copies of the same file) and also with ft_definetrial from one continuous file.

i am using the version of 5 aug 13

anyone knows whats going wrong?

cheers
Ben




From eelke.spaak at donders.ru.nl  Tue Aug  6 19:44:33 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Tue, 6 Aug 2013 19:44:33 +0200
Subject: [FieldTrip] from trials to continuous and an error in selfromraw
In-Reply-To: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A6CBB0@MBX23.d.ethz.ch>
References: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A6CBB0@MBX23.d.ethz.ch>
Message-ID: <CABPNLUrc3FRn5V9h+kmsqDgoDPQBc26k+5kvfj_1OpzrSNDAqg@mail.gmail.com>

Hi Ben,

The cfg.trials option for ft_freqanalysis refers to which trials
should be used in the computation of the output. By default,
ft_freqanalysis returns the average over all those trials. If you want
to get estimates for each individual trial, you should specify
cfg.keeptrials = 'yes'. (See also
http://fieldtrip.fcdonders.nl/reference/ft_freqanalysis .) I am not
sure if ft_singleplotTFR will give you plots for individual trials,
though; I think it will do the averaging anyway. To get individual
trial plots, you probably have to call the plotting function several
times with cfg.trials = 1, 2, 3, etc.

Regarding cfg.trials = '1', it is important to use just a regular
scalar quantity, and not a string, so cfg.trials = 1.

Best,
Eelke

On 6 August 2013 17:56, van Lier  Ben <ben.vanlier at bsse.ethz.ch> wrote:
> Hi guys,
>
> for testing purposes im trying to use data in trials as one continuous piece of data. when i do freqanalysis with cfg.trials = 'all' and then singleplotTFR, i get to see only 1 trial. it should plot the spectra of all of them right? i do use cfg.continuous = yes
> i can tell it is processing all the trials in the command window feedback and databrowser is putting them together fine.
>
> i guess related, when i do cfg.trials = '1' (or any) and then freqanalysis it gives me the following error:
>
> --------------------------
> Error using selfromraw (line 13)
> incorrect specification of requested repetitions
>
> Error in ft_selectdata_old (line 547)
>     data = selfromraw(data, 'rpt', selrpt);
>
> Error in ft_selectdata (line 45)
>   [varargout{1:nargout}] = ft_selectdata_old(varargin{:});
>
> Error in ft_freqanalysis (line 225)
>   data = ft_selectdata(data, 'rpt', cfg.trials);
> ----------------------------
>
> i tried with data coming from ft_appendata (2 copies of the same file) and also with ft_definetrial from one continuous file.
>
> i am using the version of 5 aug 13
>
> anyone knows whats going wrong?
>
> cheers
> Ben
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From haristz at gmail.com  Tue Aug  6 20:24:55 2013
From: haristz at gmail.com (Charidimos Tzagarakis)
Date: Tue, 6 Aug 2013 13:24:55 -0500
Subject: [FieldTrip] question about virtual electrode MNI coordinates
Message-ID: <CAFN2X+fdvTW8jkx1EPS8C+J_FGRTQgTtYL38aYw7Gv6BbLtsxg@mail.gmail.com>

Hi there,
I have a question regarding virtual electrodes: How can I double check that
the MNI coordinates that I enter are correctly interpreted?
More specifically:
I have followed the the extended beamforming tutorial in the "Appendix" and
have been able to transpose it to my data (I have 4D/BTi MEG files and
Dicom mri volumes).The part I am not certain about is the call to the LCMV
beamformer.
Here it is in my case ( I just want to get the voxel were the power is max
in the previous analysis):
cfg              = [];
cfg.method       = 'lcmv';
cfg.vol          = volfcm;
cfg.grid.pos     = source_diff.pos(maxpowindx, :);
cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
cfg.grid.outside = [];
cfg.grad=senscm
source_idx       = ft_sourceanalysis(cfg, tlock);
My headmodel does not include MEG channel information so I need to also
define the cfg.grad parameter. What I don't understand is how cfg.grid.pos
(which is in MNI coordinates as per the previous part of the tutorial) can
be correctly applied to the coordinates of the headmodel and the channels
since these 2 are not in MNI coordinates (in my case they are in 4d/Bti
coordinates and rescaled to cm).In the previous part of the tutorial this
is (if I understand correctly) accomplished because the leadfield used when
calling ft_sourceanalysis was created using and MNI-warped template. I
don't see where the equivalent part is when estimating the virtual
electrode though.
Any advice you may have would be much appreciated.
Best,
Haris


Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
University of Minnesota Dept of Neuroscience and Brain Sciences Center
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From franziska.bilger at uni-ulm.de  Wed Aug  7 11:23:50 2013
From: franziska.bilger at uni-ulm.de (franziska.bilger at uni-ulm.de)
Date: Wed, 07 Aug 2013 11:23:50 +0200
Subject: [FieldTrip] topoplotER - how to plot a selection of channels ?
Message-ID: <20130807112350.i24h5npq80sgscws@imap.uni-ulm.de>

Dear subscribers,

I´m using fieldtrip to analyze the data for my bachelor thesis (topic:  
motor imagery in patientens in vegetative state) and I would be happy  
to get some help concerning the function ft_topoplotER.

Originally, my data derives from a 256-channel system, but I only like  
to plot a selection of 60 channels above the motor cortex.
This is my Region of Interest.
When I´m now plotting the data from these 60 channels with  
ft_topoplotER I receive a figure, which shows the plotted activation  
over the whole cortex.

My Question: Is there a possibility to plot only the activation in my  
Region of Interest/over the selected 60 channels above the motor cortex?

This would result in a figure where there´s only activation shown over  
the motor cortex and the rest of the plot is blank/white.

Thank you very much!

Kind regards,
Franziska





From jm.horschig at donders.ru.nl  Wed Aug  7 11:41:26 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 07 Aug 2013 11:41:26 +0200
Subject: [FieldTrip] topoplotER - how to plot a selection of channels ?
In-Reply-To: <20130807112350.i24h5npq80sgscws@imap.uni-ulm.de>
References: <20130807112350.i24h5npq80sgscws@imap.uni-ulm.de>
Message-ID: <52021646.4050203@donders.ru.nl>

Hi Franziska,

check out the help of ft_topoplotER and what options there are for 
cfg.interpolation, one of these does what you want (afair 'cubic'). An 
alternative would be to set datapoints of all irrelevant channels to nan 
and then use cfg.interpolatenan = 'no', but the former suggestion is 
cleaner/better/easier than the latter.

Good luck with writing your thesis!
Best,
Jörm

On 8/7/2013 11:23 AM, franziska.bilger at uni-ulm.de wrote:
> Dear subscribers,
>
> I´m using fieldtrip to analyze the data for my bachelor thesis (topic: 
> motor imagery in patientens in vegetative state) and I would be happy 
> to get some help concerning the function ft_topoplotER.
>
> Originally, my data derives from a 256-channel system, but I only like 
> to plot a selection of 60 channels above the motor cortex.
> This is my Region of Interest.
> When I´m now plotting the data from these 60 channels with 
> ft_topoplotER I receive a figure, which shows the plotted activation 
> over the whole cortex.
>
> My Question: Is there a possibility to plot only the activation in my 
> Region of Interest/over the selected 60 channels above the motor cortex?
>
> This would result in a figure where there´s only activation shown over 
> the motor cortex and the rest of the plot is blank/white.
>
> Thank you very much!
>
> Kind regards,
> Franziska
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands



From ben.vanlier at bsse.ethz.ch  Wed Aug  7 13:00:31 2013
From: ben.vanlier at bsse.ethz.ch (van Lier  Ben)
Date: Wed, 7 Aug 2013 11:00:31 +0000
Subject: [FieldTrip] from trials to continuous and an error in selfromraw
In-Reply-To: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A6CBB0@MBX23.d.ethz.ch>
References: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A6CBB0@MBX23.d.ethz.ch>
Message-ID: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A6CC10@MBX23.d.ethz.ch>

Hi Eelke,

thanks. its the little things you miss so cfg.trials = 1 works ofcourse :)

for plotting all the trials in a continuous spectrum i just merge them into 1 big trial first

cfg = [];
cfg.trl = [1 max(max(data.sampleinfo)) 0];
data = ft_redefinetrial(cfg, data);

perfect for my purposes, im trying to reanalyze old recordings chopped into several files but ft_append puts them in separate trials.

liking fieldtrip alot so far, very flexible :)

cheers
Ben



From jm.horschig at donders.ru.nl  Wed Aug  7 14:52:32 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 07 Aug 2013 14:52:32 +0200
Subject: [FieldTrip] question about virtual electrode MNI coordinates
In-Reply-To: <CAFN2X+fdvTW8jkx1EPS8C+J_FGRTQgTtYL38aYw7Gv6BbLtsxg@mail.gmail.com>
References: <CAFN2X+fdvTW8jkx1EPS8C+J_FGRTQgTtYL38aYw7Gv6BbLtsxg@mail.gmail.com>
Message-ID: <52024310.1020109@donders.ru.nl>

Dear Charidimos,

thanks very much for pointing to this, it is indeed an error in the 
appendix of the tutorial. cfg.grid.pos should be based on the 
subject-specific MRI or sourcemodel. So, correctly it should say that 
you need to load sourcemodel.mat (i.e. subject specific grid) and then 
use sourcemodel.pos(maxpowindx, :)
The rationale in principle is that the warped grid has the same size and 
is indexed the same as the original grid; that is why you can use the 
index variable obtained from the MNI-warped source reconstructed data. 
The virtual channel reconstruction should however still be done in 
whatever coordinate system the subject's anatomical data is in. I will 
update the appendix accordingly.

Best,
Jörn

On 8/6/2013 8:24 PM, Charidimos Tzagarakis wrote:
> Hi there,
> I have a question regarding virtual electrodes: How can I double check 
> that the MNI coordinates that I enter are correctly interpreted?
> More specifically:
> I have followed the the extended beamforming tutorial in the 
> "Appendix" and have been able to transpose it to my data (I have 
> 4D/BTi MEG files and Dicom mri volumes).The part I am not certain 
> about is the call to the LCMV beamformer.
> Here it is in my case ( I just want to get the voxel were the power is 
> max in the previous analysis):
> cfg              = [];
> cfg.method       = 'lcmv';
> cfg.vol          = volfcm;
> cfg.grid.pos     = source_diff.pos(maxpowindx, :);
> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
> cfg.grid.outside = [];
> cfg.grad=senscm
> source_idx       = ft_sourceanalysis(cfg, tlock);
> My headmodel does not include MEG channel information so I need to 
> also define the cfg.grad parameter. What I don't understand is how 
> cfg.grid.pos (which is in MNI coordinates as per the previous part of 
> the tutorial) can be correctly applied to the coordinates of the 
> headmodel and the channels since these 2 are not in MNI coordinates 
> (in my case they are in 4d/Bti coordinates and rescaled to cm).In the 
> previous part of the tutorial this is (if I understand correctly) 
> accomplished because the leadfield used when calling ft_sourceanalysis 
> was created using and MNI-warped template. I don't see where the 
> equivalent part is when estimating the virtual electrode though.
> Any advice you may have would be much appreciated.
> Best,
> Haris
>
>
> Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
> University of Minnesota Dept of Neuroscience and Brain Sciences Center
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From annevanhoogmoed at email.arizona.edu  Thu Aug  8 05:51:47 2013
From: annevanhoogmoed at email.arizona.edu (van Hoogmoed, Anne H - (annevanhoogmoed))
Date: Thu, 8 Aug 2013 03:51:47 +0000
Subject: [FieldTrip] reading in and segmenting Netstation data
Message-ID: <B4002ED52EC6814D8B6E1FF85B6AFBB30A198EA7@SPACEMT.catnet.arizona.edu>

Dear all,



I'm using Fieldtrip to analyze my Netstation data. The problem is that the segmented data (incl triggers) are shifted in Fieldtrip as compared to the Netstation analysis.

I've checked several things:

- The events are the same in Netstation and Fieldtrip

- The raw data look the same in both programs

- Fieldtrip produces the right trl based on the triggers.



The script I'm using is this:

cfg = [];

cfg.dataset = 'c007_raw';

cfg.continuous = 'yes';

data_eeg = ft_preprocessing(cfg);



hdr = ft_read_header('c007_raw');

event = ft_read_event('c007_raw');



cfg = [];

cfg.trialfun = 'trialfun_first_enc';

cfg_trials = ft_definetrial(cfg);

data_trials = ft_redefinetrial(cfg_trials, data_eeg);





The trialfun I'm using is this:

function [trl, event] = trialfun_first(cfg)

load event;

load hdr;





value = [event.value];

sample = [event.sample];

% determine the number of samples before and after the trigger

pretrig = -100; % = 200 ms

posttrig = 400; % = 800 ms

% for each trigger

trl = [];

for j = 1:length(event)

if (strcmp(event(1,j).value, '+Lrt') || strcmp(event(1,j).value, '+OOt')) || strcmp(event(1,j).value, '+SOt')

trlbegin = event(1,j).sample + pretrig;

trlend = event(1,j).sample + posttrig;

offset = pretrig;

newtrl = [trlbegin trlend offset];

trl = [trl; newtrl];

end

j = j + 1;

end





Does anyone know what I'm doing wrong here?



Thank you very much for your help!



Kind regards,



Anne



Anne van Hoogmoed

Down Syndrome Research Group

Department of Psychology, University of Arizona
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From d.lozanosoldevilla at fcdonders.ru.nl  Thu Aug  8 08:12:42 2013
From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego))
Date: Thu, 8 Aug 2013 08:12:42 +0200 (CEST)
Subject: [FieldTrip] reading in and segmenting Netstation data
In-Reply-To: <B4002ED52EC6814D8B6E1FF85B6AFBB30A198EA7@SPACEMT.catnet.arizona.edu>
Message-ID: <1178733115.2232641.1375942362693.JavaMail.root@sculptor.zimbra.ru.nl>

Hi Anne, What do you mean by "shifted"? Time samples mismatch might be? I don't see what's going wrong with the code you pasted but it'd be nice if you could file a bug (I'll assign to me) with a piece of preprocessed data with fieldtrip and a plot about how data looks like with Netstation to have a bit more info. best, Diego ps : do you have a non-integer eeg sampling rate, like 511.3Hz? ----- Original Message -----
> From: "van Hoogmoed , Anne H - ( annevanhoogmoed )" < annevanhoogmoed
> @email. arizona . edu >
> To: fieldtrip @science. ru . nl
> Sent: Thursday, 8 August, 2013 5:51:47 AM
> Subject: [ FieldTrip ] reading in and segmenting Netstation data
> Dear all,
> I'm using Fieldtrip to analyze my Netstation data. The problem is that
> the segmented data (incl triggers) are shifted in Fieldtrip as
> compared to the Netstation analysis.
> I've checked several things:
> - The events are the same in Netstation and Fieldtrip
> - The raw data look the same in both programs
> - Fieldtrip produces the right trl based on the triggers.
> The script I'm using is this:
> cfg = [];
> cfg . dataset = 'c007_ raw' ;
> cfg .continuous = 'yes' ;
> data_ eeg = ft_ preprocessing ( cfg );
> hdr = ft_read_header( 'c007_ raw' );
> event = ft_read_event( 'c007_ raw' );
> cfg = [];
> cfg . trialfun = 'trialfun _first_ enc' ;
> cfg _trials = ft_ definetrial ( cfg );
> data_trials = ft_ redefinetrial ( cfg _trials, data_ eeg );
> The trialfun I'm using is this:
> function [ trl , event] = trialfun _first( cfg )
> load event ;
> load hdr ;
> value = [event.value];
> sample = [event.sample];
> % determine the number of samples before and after the trigger
> pretrig = -100; % = 200 ms
> posttrig = 400; % = 800 ms
> % for each trigger
> trl = [];
> for j = 1:length(event)
> if ( strcmp (event(1,j).value, '+ Lrt' ) || strcmp (event(1,j).value,
> '+ OOt' )) || strcmp (event(1,j).value, '+ SOt' )
> trlbegin = event(1,j).sample + pretrig ;
> trlend = event(1,j).sample + posttrig ;
> offset = pretrig ;
> newtrl = [ trlbegin trlend offset];
> trl = [ trl ; newtrl ];
> end
> j = j + 1;
> end
> Does anyone know what I'm doing wrong here?
> Thank you very much for your help!
> Kind regards,
> Anne
> Anne van Hoogmoed
> Down Syndrome Research Group
> Department of Psychology, University of Arizona
> _______________________________________________
> fieldtrip mailing list
> fieldtrip @ donders . ru . nl
> http ://mailman.science. ru . nl /mailman/ listinfo / fieldtrip
-- PhD Student Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen NL-6525 EN Nijmegen The Netherlands http :// www . ru . nl /people/ donders /lozano-soldevilla-d/ 
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From elisa at csl.psychol.cam.ac.uk  Thu Aug  8 12:23:53 2013
From: elisa at csl.psychol.cam.ac.uk (Elisa Carrus)
Date: Thu, 08 Aug 2013 11:23:53 +0100
Subject: [FieldTrip] question about virtual electrode MNI coordinates
In-Reply-To: <52024310.1020109@donders.ru.nl>
References: <CAFN2X+fdvTW8jkx1EPS8C+J_FGRTQgTtYL38aYw7Gv6BbLtsxg@mail.gmail.com>
	<52024310.1020109@donders.ru.nl>
Message-ID: <520371B9.8060101@csl.psychol.cam.ac.uk>

Hi all,

 From the previous email it seems that I'm doing something wrong then. I 
have previously used the MNI-aligned subject grid (warped template) for 
the positions, hence I didn't encounter any problem. However, this seems 
to be wrong, as Jorn suggested. The question is the following:

The sourcediff.avg.pow is produced using the warped MNI template, 
therefore the grid positions and indexes will be different from the 
subject-specific MRI. Specifically in my case, the warped template has 
11000 x 3 pos, whereas the subject-specific has 2652 x 3.
My question is, when I therefore index the maxpos using:

[maxval, maxind] = max(sourcediff.avg.pow), my index is 3171, which 
exceeds the matrix dimensions of the subject-specific MRI (2652).

Which step am I missing?

Thanks for your help in advance,
Elisa






On 07/08/2013 13:52, "Jörn M. Horschig" wrote:
> Dear Charidimos,
>
> thanks very much for pointing to this, it is indeed an error in the 
> appendix of the tutorial. cfg.grid.pos should be based on the 
> subject-specific MRI or sourcemodel. So, correctly it should say that 
> you need to load sourcemodel.mat (i.e. subject specific grid) and then 
> use sourcemodel.pos(maxpowindx, :)
> The rationale in principle is that the warped grid has the same size 
> and is indexed the same as the original grid; that is why you can use 
> the index variable obtained from the MNI-warped source reconstructed 
> data. The virtual channel reconstruction should however still be done 
> in whatever coordinate system the subject's anatomical data is in. I 
> will update the appendix accordingly.
>
> Best,
> Jörn
>
> On 8/6/2013 8:24 PM, Charidimos Tzagarakis wrote:
>> Hi there,
>> I have a question regarding virtual electrodes: How can I double 
>> check that the MNI coordinates that I enter are correctly interpreted?
>> More specifically:
>> I have followed the the extended beamforming tutorial in the 
>> "Appendix" and have been able to transpose it to my data (I have 
>> 4D/BTi MEG files and Dicom mri volumes).The part I am not certain 
>> about is the call to the LCMV beamformer.
>> Here it is in my case ( I just want to get the voxel were the power 
>> is max in the previous analysis):
>> cfg              = [];
>> cfg.method       = 'lcmv';
>> cfg.vol          = volfcm;
>> cfg.grid.pos     = source_diff.pos(maxpowindx, :);
>> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
>> cfg.grid.outside = [];
>> cfg.grad=senscm
>> source_idx       = ft_sourceanalysis(cfg, tlock);
>> My headmodel does not include MEG channel information so I need to 
>> also define the cfg.grad parameter. What I don't understand is how 
>> cfg.grid.pos (which is in MNI coordinates as per the previous part of 
>> the tutorial) can be correctly applied to the coordinates of the 
>> headmodel and the channels since these 2 are not in MNI coordinates 
>> (in my case they are in 4d/Bti coordinates and rescaled to cm).In the 
>> previous part of the tutorial this is (if I understand correctly) 
>> accomplished because the leadfield used when calling 
>> ft_sourceanalysis was created using and MNI-warped template. I don't 
>> see where the equivalent part is when estimating the virtual 
>> electrode though.
>> Any advice you may have would be much appreciated.
>> Best,
>> Haris
>>
>>
>> Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
>> University of Minnesota Dept of Neuroscience and Brain Sciences Center
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> -- 
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
> FieldTrip Development Team
>
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>
> Contact:
> E-Mail:jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web:http://www.ru.nl/donders
>
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From jm.horschig at donders.ru.nl  Thu Aug  8 13:45:09 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Thu, 08 Aug 2013 13:45:09 +0200
Subject: [FieldTrip] question about virtual electrode MNI coordinates
In-Reply-To: <520371B9.8060101@csl.psychol.cam.ac.uk>
References: <CAFN2X+fdvTW8jkx1EPS8C+J_FGRTQgTtYL38aYw7Gv6BbLtsxg@mail.gmail.com>
	<52024310.1020109@donders.ru.nl>
	<520371B9.8060101@csl.psychol.cam.ac.uk>
Message-ID: <520384C5.80703@donders.ru.nl>

Dear Elisa,

hard to tell, because you are not telling us exactly what you are doing :)
The idea in the extended beamforming tutorial is that you first create 
an MNI template sourcemodel (or grid). Subsequently, you use exactly 
this grid and spatially transform it such that it fits to the 
subject-specific brain, based on the MRI. After following these steps, 
by definition, the number of grid points in the subject-specific grid 
and the MNI grid are the same - just the place where the grid points end 
up did change. (Otherwise, it would also not be possible to replace the 
.pos field from the source-reconstructed data by the template grid, as 
being done in the plotting part of the tutorial). The problem in the 
tutorial was exactly this replacement of the position description (which 
iself can be a perfectly fine step as e.g. earlier in the tutorial). 
Since we provide a sourcemodel based on the subject's mri, we need to 
specify the position based on that mri/sourcemodel and not based on the 
MNI template.

You, obviously, do not have the same number of grid points for the 
subject-specific sourcemodel as in the template sourcemodel. I cannot 
guarantee that what you did is correct, but at least I can tell you that 
what you did is not affects by this - else you would have had the same 
number of elements for both sourcemodels. I cross my fingers that you're 
doing the right thing :)

Best,
Jörn

On 8/8/2013 12:23 PM, Elisa Carrus wrote:
> Hi all,
>
> From the previous email it seems that I'm doing something wrong then. 
> I have previously used the MNI-aligned subject grid (warped template) 
> for the positions, hence I didn't encounter any problem. However, this 
> seems to be wrong, as Jorn suggested. The question is the following:
>
> The sourcediff.avg.pow is produced using the warped MNI template, 
> therefore the grid positions and indexes will be different from the 
> subject-specific MRI. Specifically in my case, the warped template has 
> 11000 x 3 pos, whereas the subject-specific has 2652 x 3.
> My question is, when I therefore index the maxpos using:
>
> [maxval, maxind] = max(sourcediff.avg.pow), my index is 3171, which 
> exceeds the matrix dimensions of the subject-specific MRI (2652).
>
> Which step am I missing?
>
> Thanks for your help in advance,
> Elisa
>
>
>
>
>
>
> On 07/08/2013 13:52, "Jörn M. Horschig" wrote:
>> Dear Charidimos,
>>
>> thanks very much for pointing to this, it is indeed an error in the 
>> appendix of the tutorial. cfg.grid.pos should be based on the 
>> subject-specific MRI or sourcemodel. So, correctly it should say that 
>> you need to load sourcemodel.mat (i.e. subject specific grid) and 
>> then use sourcemodel.pos(maxpowindx, :)
>> The rationale in principle is that the warped grid has the same size 
>> and is indexed the same as the original grid; that is why you can use 
>> the index variable obtained from the MNI-warped source reconstructed 
>> data. The virtual channel reconstruction should however still be done 
>> in whatever coordinate system the subject's anatomical data is in. I 
>> will update the appendix accordingly.
>>
>> Best,
>> Jörn
>>
>> On 8/6/2013 8:24 PM, Charidimos Tzagarakis wrote:
>>> Hi there,
>>> I have a question regarding virtual electrodes: How can I double 
>>> check that the MNI coordinates that I enter are correctly interpreted?
>>> More specifically:
>>> I have followed the the extended beamforming tutorial in the 
>>> "Appendix" and have been able to transpose it to my data (I have 
>>> 4D/BTi MEG files and Dicom mri volumes).The part I am not certain 
>>> about is the call to the LCMV beamformer.
>>> Here it is in my case ( I just want to get the voxel were the power 
>>> is max in the previous analysis):
>>> cfg              = [];
>>> cfg.method       = 'lcmv';
>>> cfg.vol          = volfcm;
>>> cfg.grid.pos     = source_diff.pos(maxpowindx, :);
>>> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
>>> cfg.grid.outside = [];
>>> cfg.grad=senscm
>>> source_idx       = ft_sourceanalysis(cfg, tlock);
>>> My headmodel does not include MEG channel information so I need to 
>>> also define the cfg.grad parameter. What I don't understand is how 
>>> cfg.grid.pos (which is in MNI coordinates as per the previous part 
>>> of the tutorial) can be correctly applied to the coordinates of the 
>>> headmodel and the channels since these 2 are not in MNI coordinates 
>>> (in my case they are in 4d/Bti coordinates and rescaled to cm).In 
>>> the previous part of the tutorial this is (if I understand 
>>> correctly) accomplished because the leadfield used when calling 
>>> ft_sourceanalysis was created using and MNI-warped template. I don't 
>>> see where the equivalent part is when estimating the virtual 
>>> electrode though.
>>> Any advice you may have would be much appreciated.
>>> Best,
>>> Haris
>>>
>>>
>>> Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
>>> University of Minnesota Dept of Neuroscience and Brain Sciences Center
>>>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>> -- 
>> Jörn M. Horschig
>> PhD Student
>> Donders Institute for Brain, Cognition and Behaviour
>> Centre for Cognitive Neuroimaging
>> Radboud University Nijmegen
>> Neuronal Oscillations Group
>> FieldTrip Development Team
>>
>> P.O. Box 9101
>> NL-6500 HB Nijmegen
>> The Netherlands
>>
>> Contact:
>> E-Mail:jm.horschig at donders.ru.nl
>> Tel:    +31-(0)24-36-68493
>> Web:http://www.ru.nl/donders
>>
>> Visiting address:
>> Trigon, room 2.30
>> Kapittelweg 29
>> NL-6525 EN Nijmegen
>> The Netherlands
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From K.Kalogianni at tudelft.nl  Fri Aug  9 09:59:18 2013
From: K.Kalogianni at tudelft.nl (Konstantina Kalogianni)
Date: Fri, 9 Aug 2013 07:59:18 +0000
Subject: [FieldTrip] ft_sourcegrandaverage & grid computation
Message-ID: <4DF682D3A10EAC46B462A46E16F0B049128EE308@SRV364.tudelft.net>

Dear fieldtripers,
I have experienced a problem with ft_sourcegrandaverage and the calculation of my grid and I want to ask for help.
The error I get is the following :different grid locations in source reconstructions.

I will describe briefly the processing to give you a better idea about my error.

For every subject I have 6 conditions and I want to average all subjects per condition.
After preprocessing I calculate the covariance matrix and then  I use the MUSIC algorithm for my sources.
For  the grid calculation I use a default MRI a default VOL and a default electrodes' positions.
However  for every subject the grid is not identical since  cfg.channel in ft_prepare_leadfield is dependent on the channels I've discarded as noisy during the preprocessing.
By the way for the grid calculation I had to change the order  of cfg.elec because it didn't agree with the order of cfg,channel in my data.
So apparently I end up with a different grid for every subject but still I want to average all of them per condition.

Do I have to use another function to average my sources in this case?
Because the grid would never be identical among subjects.


I hope somebody out there experienced that before and can probably help me.
Thank you.

Konstantina [Nadia] Kalogianni
PhD candidate, TU Delft


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From elisa at csl.psychol.cam.ac.uk  Fri Aug  9 11:25:15 2013
From: elisa at csl.psychol.cam.ac.uk (Elisa Carrus)
Date: Fri, 09 Aug 2013 10:25:15 +0100
Subject: [FieldTrip] question about virtual electrode MNI coordinates
In-Reply-To: <520384C5.80703@donders.ru.nl>
References: <CAFN2X+fdvTW8jkx1EPS8C+J_FGRTQgTtYL38aYw7Gv6BbLtsxg@mail.gmail.com>
	<52024310.1020109@donders.ru.nl>
	<520371B9.8060101@csl.psychol.cam.ac.uk>
	<520384C5.80703@donders.ru.nl>
Message-ID: <5204B57B.6040004@csl.psychol.cam.ac.uk>

Dear Jorn,

ah, I apologise for not writing a complete email! The good news is that 
I've done things correctly so far,  as I do have the same number of grid 
points in both the subject-specific and template, as expected :) I gave 
you the wrong indices because I thought that in your previous email you 
referred to the MRI rather than the sourcemodel. My bad. Sorry for the 
misunderstanding and thanks a lot for explaining this again!

Best,
Elisa


On 08/08/2013 12:45, "Jörn M. Horschig" wrote:
> Dear Elisa,
>
> hard to tell, because you are not telling us exactly what you are 
> doing :)
> The idea in the extended beamforming tutorial is that you first create 
> an MNI template sourcemodel (or grid). Subsequently, you use exactly 
> this grid and spatially transform it such that it fits to the 
> subject-specific brain, based on the MRI. After following these steps, 
> by definition, the number of grid points in the subject-specific grid 
> and the MNI grid are the same - just the place where the grid points 
> end up did change. (Otherwise, it would also not be possible to 
> replace the .pos field from the source-reconstructed data by the 
> template grid, as being done in the plotting part of the tutorial). 
> The problem in the tutorial was exactly this replacement of the 
> position description (which iself can be a perfectly fine step as e.g. 
> earlier in the tutorial). Since we provide a sourcemodel based on the 
> subject's mri, we need to specify the position based on that 
> mri/sourcemodel and not based on the MNI template.
>
> You, obviously, do not have the same number of grid points for the 
> subject-specific sourcemodel as in the template sourcemodel. I cannot 
> guarantee that what you did is correct, but at least I can tell you 
> that what you did is not affects by this - else you would have had the 
> same number of elements for both sourcemodels. I cross my fingers that 
> you're doing the right thing :)
>
> Best,
> Jörn
>
> On 8/8/2013 12:23 PM, Elisa Carrus wrote:
>> Hi all,
>>
>> From the previous email it seems that I'm doing something wrong then. 
>> I have previously used the MNI-aligned subject grid (warped template) 
>> for the positions, hence I didn't encounter any problem. However, 
>> this seems to be wrong, as Jorn suggested. The question is the following:
>>
>> The sourcediff.avg.pow is produced using the warped MNI template, 
>> therefore the grid positions and indexes will be different from the 
>> subject-specific MRI. Specifically in my case, the warped template 
>> has 11000 x 3 pos, whereas the subject-specific has 2652 x 3.
>> My question is, when I therefore index the maxpos using:
>>
>> [maxval, maxind] = max(sourcediff.avg.pow), my index is 3171, which 
>> exceeds the matrix dimensions of the subject-specific MRI (2652).
>>
>> Which step am I missing?
>>
>> Thanks for your help in advance,
>> Elisa
>>
>>
>>
>>
>>
>>
>> On 07/08/2013 13:52, "Jörn M. Horschig" wrote:
>>> Dear Charidimos,
>>>
>>> thanks very much for pointing to this, it is indeed an error in the 
>>> appendix of the tutorial. cfg.grid.pos should be based on the 
>>> subject-specific MRI or sourcemodel. So, correctly it should say 
>>> that you need to load sourcemodel.mat (i.e. subject specific grid) 
>>> and then use sourcemodel.pos(maxpowindx, :)
>>> The rationale in principle is that the warped grid has the same size 
>>> and is indexed the same as the original grid; that is why you can 
>>> use the index variable obtained from the MNI-warped source 
>>> reconstructed data. The virtual channel reconstruction should 
>>> however still be done in whatever coordinate system the subject's 
>>> anatomical data is in. I will update the appendix accordingly.
>>>
>>> Best,
>>> Jörn
>>>
>>> On 8/6/2013 8:24 PM, Charidimos Tzagarakis wrote:
>>>> Hi there,
>>>> I have a question regarding virtual electrodes: How can I double 
>>>> check that the MNI coordinates that I enter are correctly interpreted?
>>>> More specifically:
>>>> I have followed the the extended beamforming tutorial in the 
>>>> "Appendix" and have been able to transpose it to my data (I have 
>>>> 4D/BTi MEG files and Dicom mri volumes).The part I am not certain 
>>>> about is the call to the LCMV beamformer.
>>>> Here it is in my case ( I just want to get the voxel were the power 
>>>> is max in the previous analysis):
>>>> cfg              = [];
>>>> cfg.method       = 'lcmv';
>>>> cfg.vol          = volfcm;
>>>> cfg.grid.pos     = source_diff.pos(maxpowindx, :);
>>>> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
>>>> cfg.grid.outside = [];
>>>> cfg.grad=senscm
>>>> source_idx       = ft_sourceanalysis(cfg, tlock);
>>>> My headmodel does not include MEG channel information so I need to 
>>>> also define the cfg.grad parameter. What I don't understand is how 
>>>> cfg.grid.pos (which is in MNI coordinates as per the previous part 
>>>> of the tutorial) can be correctly applied to the coordinates of the 
>>>> headmodel and the channels since these 2 are not in MNI coordinates 
>>>> (in my case they are in 4d/Bti coordinates and rescaled to cm).In 
>>>> the previous part of the tutorial this is (if I understand 
>>>> correctly) accomplished because the leadfield used when calling 
>>>> ft_sourceanalysis was created using and MNI-warped template. I 
>>>> don't see where the equivalent part is when estimating the virtual 
>>>> electrode though.
>>>> Any advice you may have would be much appreciated.
>>>> Best,
>>>> Haris
>>>>
>>>>
>>>> Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
>>>> University of Minnesota Dept of Neuroscience and Brain Sciences Center
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>
>>> -- 
>>> Jörn M. Horschig
>>> PhD Student
>>> Donders Institute for Brain, Cognition and Behaviour
>>> Centre for Cognitive Neuroimaging
>>> Radboud University Nijmegen
>>> Neuronal Oscillations Group
>>> FieldTrip Development Team
>>>
>>> P.O. Box 9101
>>> NL-6500 HB Nijmegen
>>> The Netherlands
>>>
>>> Contact:
>>> E-Mail:jm.horschig at donders.ru.nl
>>> Tel:    +31-(0)24-36-68493
>>> Web:http://www.ru.nl/donders
>>>
>>> Visiting address:
>>> Trigon, room 2.30
>>> Kapittelweg 29
>>> NL-6525 EN Nijmegen
>>> The Netherlands
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> -- 
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
> FieldTrip Development Team
>
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>
> Contact:
> E-Mail:jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web:http://www.ru.nl/donders
>
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From g.dimitriadis at donders.ru.nl  Fri Aug  9 17:22:50 2013
From: g.dimitriadis at donders.ru.nl (Dimitriadis, G. (George))
Date: Fri, 9 Aug 2013 17:22:50 +0200 (CEST)
Subject: [FieldTrip] Error from postamble
Message-ID: <1463263304.1956192.1376061770792.JavaMail.root@monoceros.zimbra.ru.nl>


Hello guys,

I seem to be getting an error relating to the generation of warnings withing the postamble. I am not doing anything that I haven't been doing for the past year.

I had problems with the preamble (due to large file sizes) before and I am doing the cfg.stackcallinfo = 'no' trick.

But now I am getting the following series of errors:

---------------------------------------------------
Warning:
'@(hObject,eventdata)mainRatAnalysisGUI('pushbutton_run_analysis_Callback',hObject,eventdata,guidata(hObject))'
 exceeds MATLAB's maximum name length of 63 characters and has
been truncated to
 '@(hObject,eventdata)mainRatAnalysisGUI('pushbutton_run_analysis'. 
> In utilities/private/warning_once>fieldnameFromStack at 196
  In utilities/private/warning_once at 123
  In utilities/private/ft_postamble_history at 55
  In ft_postamble at 55
  In ft_preprocessing at 611
  In gd_eri_preprocratdata at 71
  In gd_eri_getratdatasignals at 39
  In mainRatAnalysisGUI>pushbutton_run_analysis_Callback at 120
  In gui_mainfcn at 96
  In mainRatAnalysisGUI at 42
  In @(hObject,eventdata)mainRatAnalysisGUI('pushbutton_run_analysis_Callback',hObject,eventdata,guidata(hObject)) 
Invalid field name:
'@(hObject,eventdata)mainRatAnalysisGUI('pushbutton_run_analysis'.

Error in warning_once>fieldnameFromStack (line 196)
  ft_previous_warnings.(stack(end).name) = []; % iteratively
  build up structure fields

Error in warning_once (line 123)
  [tmpfname ft_default.warning.identifier line] =
  fieldnameFromStack(ft_default.warning.identifier);

Error in ft_postamble_history (line 55)
warning_once('-clear');

Error in ft_postamble (line 55)
  evalin('caller', ['ft_postamble_' cmd]);

Error in ft_preprocessing (line 611)
ft_postamble history data

Error in gd_eri_preprocratdata (line 71)
  datacell{datindx}=ft_preprocessing(cfg_pp);

Error in gd_eri_getratdatasignals (line 39)
data=gd_eri_preprocratdata(cfg);

Error in mainRatAnalysisGUI>pushbutton_run_analysis_Callback
(line 120)
        data =gd_eri_getratdatasignals(cfg);

Error in gui_mainfcn (line 96)
        feval(varargin{:});

Error in mainRatAnalysisGUI (line 42)
    gui_mainfcn(gui_State, varargin{:});

Error in
@(hObject,eventdata)mainRatAnalysisGUI('pushbutton_run_analysis_Callback',hObject,eventdata,guidata(hObject))

 
Error while evaluating uicontrol Callback
----------------------------------------

I am calling my original function from within a gui.

So it seems that in the postamble_history a warning gets generated which then throws an error for some reason I would really like not to have to find out by myself.


Thanks for your time


George Dimitriadis


From r.cox at uva.nl  Tue Aug 13 11:29:23 2013
From: r.cox at uva.nl (Roy Cox)
Date: Tue, 13 Aug 2013 11:29:23 +0200
Subject: [FieldTrip] ft_freqstatistics
Message-ID: <CABafTZcchaOGyh1PVvx0KZ6v5rd+Cj2=KVhmgwgMEPN2LnaFDw@mail.gmail.com>

Hi,

Can anyone tell me how fieldtrip selects freq bins when calling
ft_freqstatistics with cfg.frequency?

That is, if I'm interested in two freq bands from, say, 10 to 20, and from
20 to 30 Hz, and I don't want a freq bin to be used twice, do I use
cfg.frequency=[10 20] and cfg.frequency=[20 30]? Or would the freq bin
closest to 20 be used twice?

I guess I'm asking how precisely the find function (with arguments 'first',
'last') is applied.

Best,

Roy


-- 
Roy Cox, M.Sc. | Brain & Cognition Group | Department of Psychology |
University of Amsterdam | Weesperplein 4 | 1018 XA Amsterdam | the
Netherlands | room 3.21 | phone: +31 20 525 6847 | email: r.cox at uva.nl
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From hweeling.lee at gmail.com  Wed Aug 14 16:51:23 2013
From: hweeling.lee at gmail.com (Hwee Ling Lee)
Date: Wed, 14 Aug 2013 16:51:23 +0200
Subject: [FieldTrip] newbie
Message-ID: <CABG7z0SvaX134oFfEbhasgrWRLtea+8=AxfcJDdrjHwR7veg_g@mail.gmail.com>

Hi to all!

I'm new to fieldtrip! I have a dataset that has been corrected for scanner
artifacts and BC artifacts using Brainvision Analyser. I would like to
export the corrected data as a .eeg file so that I can load the data onto
Matlab and use fieldtrip to perform further analyses.

However, I kept getting error messages from Matlab that the sub-file format
is unsupported. I've been searching online the best way to export the
corrected data from Brainvision Analyser, however, I could not find any
solution at all.

Would anyone please kindly instruct me the settings that I should have when
I export the corrected data?

Thanks!

Best wishes,
Hweeling
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From elisa at csl.psychol.cam.ac.uk  Wed Aug 14 17:32:42 2013
From: elisa at csl.psychol.cam.ac.uk (Elisa Carrus)
Date: Wed, 14 Aug 2013 16:32:42 +0100
Subject: [FieldTrip] newbie
In-Reply-To: <CABG7z0SvaX134oFfEbhasgrWRLtea+8=AxfcJDdrjHwR7veg_g@mail.gmail.com>
References: <CABG7z0SvaX134oFfEbhasgrWRLtea+8=AxfcJDdrjHwR7veg_g@mail.gmail.com>
Message-ID: <520BA31A.9040803@csl.psychol.cam.ac.uk>

Hi Hweeling,

Welcome! Can you give us a bit more information about the script you 
used to load the data? I haven't used BrainVision before but you should 
be able to read the .eeg data directly from Fieldtrip 
http://fieldtrip.fcdonders.nl/dataformat 
<http://fieldtrip.fcdonders.nl/dataformat>

Best,
Elisa



On 14/08/2013 15:51, Hwee Ling Lee wrote:
> Hi to all!
>
> I'm new to fieldtrip! I have a dataset that has been corrected for 
> scanner artifacts and BC artifacts using Brainvision Analyser. I would 
> like to export the corrected data as a .eeg file so that I can load 
> the data onto Matlab and use fieldtrip to perform further analyses.
>
> However, I kept getting error messages from Matlab that the sub-file 
> format is unsupported. I've been searching online the best way to 
> export the corrected data from Brainvision Analyser, however, I could 
> not find any solution at all.
>
> Would anyone please kindly instruct me the settings that I should have 
> when I export the corrected data?
>
> Thanks!
>
> Best wishes,
> Hweeling
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From r.oostenveld at donders.ru.nl  Wed Aug 14 21:34:02 2013
From: r.oostenveld at donders.ru.nl (Robert Oostenveld)
Date: Wed, 14 Aug 2013 21:34:02 +0200
Subject: [FieldTrip] newbie
In-Reply-To: <CABG7z0SvaX134oFfEbhasgrWRLtea+8=AxfcJDdrjHwR7veg_g@mail.gmail.com>
References: <CABG7z0SvaX134oFfEbhasgrWRLtea+8=AxfcJDdrjHwR7veg_g@mail.gmail.com>
Message-ID: <CA0DCF09-96E0-4D29-9CFE-9EE2C1B7EBFF@donders.ru.nl>

Hi Hweeling

The channel level data in the BrainVision data file can be represented in ascii and binary format. Furthermore, the order can be one channel at a time or sample-by-sample. Finally there are different numeric precisions (integer, float, etc).

This is something that you cannot see from the outside of the file, but if you open the *.vhdr file in a text editor you can see these details. Since there are so many possible combinations of these three factors, it is not difficult easy to support all possible variants. 

You could try storing the data as multiplexed and in single- or double-precision, which is the most common format. Otherwise, you can report it as feature request on http://bugzilla.fcdonders.nl and attach a small piece of data (with vhdr and vmrk file) there.

best regards,
Robert
 


On 14 Aug 2013, at 16:51, Hwee Ling Lee wrote:

> Hi to all!
> 
> I'm new to fieldtrip! I have a dataset that has been corrected for scanner artifacts and BC artifacts using Brainvision Analyser. I would like to export the corrected data as a .eeg file so that I can load the data onto Matlab and use fieldtrip to perform further analyses.
> 
> However, I kept getting error messages from Matlab that the sub-file format is unsupported. I've been searching online the best way to export the corrected data from Brainvision Analyser, however, I could not find any solution at all.
> 
> Would anyone please kindly instruct me the settings that I should have when I export the corrected data?
> 
> Thanks!
> 
> Best wishes,
> Hweeling
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip




From gopalar.ccf at gmail.com  Wed Aug 14 22:58:34 2013
From: gopalar.ccf at gmail.com (Raghavan Gopalakrishnan)
Date: Wed, 14 Aug 2013 16:58:34 -0400
Subject: [FieldTrip] Reading multiple NEX files
Message-ID: <CAHz=SkUQRqKD1reF53o4gL5Lw0mmW6FTzkAhd4T-x=JA2hfK6A@mail.gmail.com>

I have multiple nex files that have LFP and spike data. I would like to
read them and plot one raster, since the multple nex files are from same
subject. ft_appendspike does not append data structures with same channel
label. All my data structures from different nex files have same channel
label. Any ideas?
Thanks.
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From hweeling.lee at gmail.com  Thu Aug 15 11:34:33 2013
From: hweeling.lee at gmail.com (Hwee Ling Lee)
Date: Thu, 15 Aug 2013 11:34:33 +0200
Subject: [FieldTrip] EEG sensor position layout
Message-ID: <CABG7z0QLsEDt2O9Pth3Xe4aQOBtbHhGnROtCeGHqRHN4goUAtQ@mail.gmail.com>

Hi all!

After performing ICA, I used the command to browse the data in component
mode.

However, I got a warning message:

Warning: No layout specified - will try to construct one using sensor
positions
> In ft_databrowser at 217
Error using ft_databrowser (line 223)
cannot infer sensor type

I understand that one can manually create the layout, however, I was not
sure how I can do it. Could someone please help?

Thank you.

Best regards,
Hweeling
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From johanna.zumer at donders.ru.nl  Thu Aug 15 12:45:51 2013
From: johanna.zumer at donders.ru.nl (Johanna Zumer)
Date: Thu, 15 Aug 2013 12:45:51 +0200
Subject: [FieldTrip] EEG sensor position layout
In-Reply-To: <CABG7z0QLsEDt2O9Pth3Xe4aQOBtbHhGnROtCeGHqRHN4goUAtQ@mail.gmail.com>
References: <CABG7z0QLsEDt2O9Pth3Xe4aQOBtbHhGnROtCeGHqRHN4goUAtQ@mail.gmail.com>
Message-ID: <CAL4kA6d9A90HfXRErt5SxhDF4dTVhQzUWaU8Vvg=q1S2D=J=+g@mail.gmail.com>

Dear Hweeling,

You should indeed specify cfg.layout, naming the layout file for the data
that you have.
You can first check in the folder fieldtrip/template/layout to see if there
is already an existing template that you can use.
If not, please see ft_prepare_layout for more details.

If you're still stuck, please ask again with more specific details on your
layout.

Best,
Johanna



2013/8/15 Hwee Ling Lee <hweeling.lee at gmail.com>

> Hi all!
>
> After performing ICA, I used the command to browse the data in component
> mode.
>
> However, I got a warning message:
>
> Warning: No layout specified - will try to construct one using sensor
> positions
> > In ft_databrowser at 217
> Error using ft_databrowser (line 223)
> cannot infer sensor type
>
> I understand that one can manually create the layout, however, I was not
> sure how I can do it. Could someone please help?
>
> Thank you.
>
> Best regards,
> Hweeling
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From hweeling.lee at gmail.com  Thu Aug 15 13:21:19 2013
From: hweeling.lee at gmail.com (Hwee Ling Lee)
Date: Thu, 15 Aug 2013 13:21:19 +0200
Subject: [FieldTrip] EEG sensor position layout again
Message-ID: <CABG7z0TdTBH=c0e4szgPsSLnDgnmZvN6gh1Q6yTSAD6rDDnoWw@mail.gmail.com>

Hi,

A bit more details about my setup.

I'm using a Easycap MRI compatible 128 channels cap. I tried to search for
a layout on the templates/layout, and I found one that might closest fit to
my needs ('QuikCap_NSL_128').
To view my components, I tried these series of commands:

cfg = [];
cfg.viewmode = 'component';
cfg.continuous = 'yes';
cfg.layout = ft_prepare_layout('QuikCap_NSL_128');
ft_databrowser(cfg,ic_data);

However, I was prompted with error messages:
Warning: Struct field assignment overwrites a value with class "char". See
MATLAB R14SP2 Release Notes, Assigning Nonstructure
Variables As Structures Displays Warning, for details.
> In utilities\private\ft_preamble_provenance at 49
  In ft_preamble at 54
  In ft_prepare_layout at 91
Error using ft_prepare_layout (line 582)
no layout detected, please specify cfg.layout

Also when I tried the command,

cfg = [];
cfg.viewmode = 'component';
cfg.continuous = 'yes';
cfg.layout = 'QuikCap_NSL_128';
ft_databrowser(cfg,ic_data);

I get this error message:
Warning: could not open QuikCap_NSL_128
> In fileio\private\warning_once at 116
  In fileio\private\filetype_check_header at 54
  In ft_filetype at 328
  In ft_prepare_layout at 253
  In ft_databrowser at 226
Warning: could not determine filetype of QuikCap_NSL_128
> In fileio\private\warning_once at 116
  In ft_filetype at 1115
  In ft_prepare_layout at 253
  In ft_databrowser at 226
creating layout from electrode file QuikCap_NSL_128
Error using ft_read_sens (line 68)
file 'QuikCap_NSL_128' does not exist

Error in ft_prepare_layout (line 275)
  lay = sens2lay(ft_read_sens(cfg.layout), cfg.rotate, cfg.projection,
cfg.style, cfg.overlap);

Error in ft_databrowser (line 226)
  cfg.layout = ft_prepare_layout(tmpcfg);


Would anyone please help?

Cheers,
Hweeling
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From johanna.zumer at gmail.com  Thu Aug 15 13:33:57 2013
From: johanna.zumer at gmail.com (Johanna Zumer)
Date: Thu, 15 Aug 2013 13:33:57 +0200
Subject: [FieldTrip] EEG sensor position layout again
In-Reply-To: <CABG7z0TdTBH=c0e4szgPsSLnDgnmZvN6gh1Q6yTSAD6rDDnoWw@mail.gmail.com>
References: <CABG7z0TdTBH=c0e4szgPsSLnDgnmZvN6gh1Q6yTSAD6rDDnoWw@mail.gmail.com>
Message-ID: <CAL4kA6dXMDNUMcpiqi_1aaFYXmEHt2mTLgoT=dGH+c3L78miXQ@mail.gmail.com>

Hi Hweeling,

Since it says that it cannot find the Quikcap file, it sounds like it's not
on your path.    Run  ft_defaults on your Matlab command, then test if the
file is on your path:
>> ft_defaults
>> which QuikCap_NSL_128.mat

Assuming it finds the file on your path, then do you still get the browser
error?

Best,
Johanna


2013/8/15 Hwee Ling Lee <hweeling.lee at gmail.com>

> Hi,
>
> A bit more details about my setup.
>
> I'm using a Easycap MRI compatible 128 channels cap. I tried to search for
> a layout on the templates/layout, and I found one that might closest fit to
> my needs ('QuikCap_NSL_128').
> To view my components, I tried these series of commands:
>
> cfg = [];
> cfg.viewmode = 'component';
> cfg.continuous = 'yes';
> cfg.layout = ft_prepare_layout('QuikCap_NSL_128');
> ft_databrowser(cfg,ic_data);
>
> However, I was prompted with error messages:
> Warning: Struct field assignment overwrites a value with class "char". See
> MATLAB R14SP2 Release Notes, Assigning Nonstructure
> Variables As Structures Displays Warning, for details.
> > In utilities\private\ft_preamble_provenance at 49
>   In ft_preamble at 54
>   In ft_prepare_layout at 91
> Error using ft_prepare_layout (line 582)
> no layout detected, please specify cfg.layout
>
> Also when I tried the command,
>
> cfg = [];
> cfg.viewmode = 'component';
> cfg.continuous = 'yes';
> cfg.layout = 'QuikCap_NSL_128';
> ft_databrowser(cfg,ic_data);
>
> I get this error message:
> Warning: could not open QuikCap_NSL_128
> > In fileio\private\warning_once at 116
>   In fileio\private\filetype_check_header at 54
>   In ft_filetype at 328
>   In ft_prepare_layout at 253
>   In ft_databrowser at 226
> Warning: could not determine filetype of QuikCap_NSL_128
> > In fileio\private\warning_once at 116
>   In ft_filetype at 1115
>   In ft_prepare_layout at 253
>   In ft_databrowser at 226
> creating layout from electrode file QuikCap_NSL_128
> Error using ft_read_sens (line 68)
> file 'QuikCap_NSL_128' does not exist
>
> Error in ft_prepare_layout (line 275)
>   lay = sens2lay(ft_read_sens(cfg.layout), cfg.rotate, cfg.projection,
> cfg.style, cfg.overlap);
>
> Error in ft_databrowser (line 226)
>   cfg.layout = ft_prepare_layout(tmpcfg);
>
>
> Would anyone please help?
>
> Cheers,
> Hweeling
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From hweeling.lee at gmail.com  Thu Aug 15 13:59:17 2013
From: hweeling.lee at gmail.com (Hwee Ling Lee)
Date: Thu, 15 Aug 2013 13:59:17 +0200
Subject: [FieldTrip] EEG sensor position layout again
In-Reply-To: <CAL4kA6dXMDNUMcpiqi_1aaFYXmEHt2mTLgoT=dGH+c3L78miXQ@mail.gmail.com>
References: <CABG7z0TdTBH=c0e4szgPsSLnDgnmZvN6gh1Q6yTSAD6rDDnoWw@mail.gmail.com>
	<CAL4kA6dXMDNUMcpiqi_1aaFYXmEHt2mTLgoT=dGH+c3L78miXQ@mail.gmail.com>
Message-ID: <CABG7z0TQFuakrpr4zJDkP2TnfPvw0FwL+qqp9K_6o3owDsXFaw@mail.gmail.com>

Hi,

It states that:
'QuikCap_NSL_128.mat' not found.

However, when I checked fieldtrip/templates/layout, the mat file is stored
in this folder.

Cheers,
Hweeling



On 15 August 2013 13:33, Johanna Zumer <johanna.zumer at gmail.com> wrote:

> Hi Hweeling,
>
> Since it says that it cannot find the Quikcap file, it sounds like it's
> not on your path.    Run  ft_defaults on your Matlab command, then test if
> the file is on your path:
> >> ft_defaults
> >> which QuikCap_NSL_128.mat
>
> Assuming it finds the file on your path, then do you still get the browser
> error?
>
> Best,
> Johanna
>
>
> 2013/8/15 Hwee Ling Lee <hweeling.lee at gmail.com>
>
>> Hi,
>>
>> A bit more details about my setup.
>>
>> I'm using a Easycap MRI compatible 128 channels cap. I tried to search
>> for a layout on the templates/layout, and I found one that might closest
>> fit to my needs ('QuikCap_NSL_128').
>> To view my components, I tried these series of commands:
>>
>> cfg = [];
>> cfg.viewmode = 'component';
>> cfg.continuous = 'yes';
>> cfg.layout = ft_prepare_layout('QuikCap_NSL_128');
>> ft_databrowser(cfg,ic_data);
>>
>> However, I was prompted with error messages:
>> Warning: Struct field assignment overwrites a value with class "char".
>> See MATLAB R14SP2 Release Notes, Assigning Nonstructure
>> Variables As Structures Displays Warning, for details.
>> > In utilities\private\ft_preamble_provenance at 49
>>   In ft_preamble at 54
>>   In ft_prepare_layout at 91
>> Error using ft_prepare_layout (line 582)
>> no layout detected, please specify cfg.layout
>>
>> Also when I tried the command,
>>
>> cfg = [];
>> cfg.viewmode = 'component';
>> cfg.continuous = 'yes';
>> cfg.layout = 'QuikCap_NSL_128';
>> ft_databrowser(cfg,ic_data);
>>
>> I get this error message:
>> Warning: could not open QuikCap_NSL_128
>> > In fileio\private\warning_once at 116
>>   In fileio\private\filetype_check_header at 54
>>   In ft_filetype at 328
>>   In ft_prepare_layout at 253
>>   In ft_databrowser at 226
>> Warning: could not determine filetype of QuikCap_NSL_128
>> > In fileio\private\warning_once at 116
>>   In ft_filetype at 1115
>>   In ft_prepare_layout at 253
>>   In ft_databrowser at 226
>> creating layout from electrode file QuikCap_NSL_128
>> Error using ft_read_sens (line 68)
>> file 'QuikCap_NSL_128' does not exist
>>
>> Error in ft_prepare_layout (line 275)
>>   lay = sens2lay(ft_read_sens(cfg.layout), cfg.rotate, cfg.projection,
>> cfg.style, cfg.overlap);
>>
>> Error in ft_databrowser (line 226)
>>   cfg.layout = ft_prepare_layout(tmpcfg);
>>
>>
>> Would anyone please help?
>>
>> Cheers,
>> Hweeling
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>


-- 
=================================================
Dr. rer. nat. Lee, Hwee Ling
Postdoc
German Center for Neurodegenerative Diseases (DZNE) Bonn

Email 1: hwee-ling.lee<at>dzne.de
Email 2: hweeling.lee<at>gmail.com

https://sites.google.com/site/hweelinglee/home

Correspondence Address:
Ernst-Robert-Curtius Strasse 12, 53117, Bonn, Germany
=================================================
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From johanna.zumer at gmail.com  Thu Aug 15 14:01:39 2013
From: johanna.zumer at gmail.com (Johanna Zumer)
Date: Thu, 15 Aug 2013 14:01:39 +0200
Subject: [FieldTrip] EEG sensor position layout again
In-Reply-To: <CABG7z0TQFuakrpr4zJDkP2TnfPvw0FwL+qqp9K_6o3owDsXFaw@mail.gmail.com>
References: <CABG7z0TdTBH=c0e4szgPsSLnDgnmZvN6gh1Q6yTSAD6rDDnoWw@mail.gmail.com>
	<CAL4kA6dXMDNUMcpiqi_1aaFYXmEHt2mTLgoT=dGH+c3L78miXQ@mail.gmail.com>
	<CABG7z0TQFuakrpr4zJDkP2TnfPvw0FwL+qqp9K_6o3owDsXFaw@mail.gmail.com>
Message-ID: <CAL4kA6ddn8MoCfigmDq7nWnXy-UOBRJ842yBmucehOLoDFRw4Q@mail.gmail.com>

Hi Hweeling,

I just checked on my computer, and it helped to restart matlab and try
again.  Maybe there is something strange if ft_defaults is called (again)
during an already open session with previous calls to FT functions?

Best,
Johanna


2013/8/15 Hwee Ling Lee <hweeling.lee at gmail.com>

> Hi,
>
> It states that:
> 'QuikCap_NSL_128.mat' not found.
>
> However, when I checked fieldtrip/templates/layout, the mat file is stored
> in this folder.
>
> Cheers,
> Hweeling
>
>
>
> On 15 August 2013 13:33, Johanna Zumer <johanna.zumer at gmail.com> wrote:
>
>> Hi Hweeling,
>>
>> Since it says that it cannot find the Quikcap file, it sounds like it's
>> not on your path.    Run  ft_defaults on your Matlab command, then test if
>> the file is on your path:
>> >> ft_defaults
>> >> which QuikCap_NSL_128.mat
>>
>> Assuming it finds the file on your path, then do you still get the
>> browser error?
>>
>> Best,
>> Johanna
>>
>>
>> 2013/8/15 Hwee Ling Lee <hweeling.lee at gmail.com>
>>
>>> Hi,
>>>
>>> A bit more details about my setup.
>>>
>>> I'm using a Easycap MRI compatible 128 channels cap. I tried to search
>>> for a layout on the templates/layout, and I found one that might closest
>>> fit to my needs ('QuikCap_NSL_128').
>>> To view my components, I tried these series of commands:
>>>
>>> cfg = [];
>>> cfg.viewmode = 'component';
>>> cfg.continuous = 'yes';
>>> cfg.layout = ft_prepare_layout('QuikCap_NSL_128');
>>> ft_databrowser(cfg,ic_data);
>>>
>>> However, I was prompted with error messages:
>>> Warning: Struct field assignment overwrites a value with class "char".
>>> See MATLAB R14SP2 Release Notes, Assigning Nonstructure
>>> Variables As Structures Displays Warning, for details.
>>> > In utilities\private\ft_preamble_provenance at 49
>>>   In ft_preamble at 54
>>>   In ft_prepare_layout at 91
>>> Error using ft_prepare_layout (line 582)
>>> no layout detected, please specify cfg.layout
>>>
>>> Also when I tried the command,
>>>
>>> cfg = [];
>>> cfg.viewmode = 'component';
>>> cfg.continuous = 'yes';
>>> cfg.layout = 'QuikCap_NSL_128';
>>> ft_databrowser(cfg,ic_data);
>>>
>>> I get this error message:
>>> Warning: could not open QuikCap_NSL_128
>>> > In fileio\private\warning_once at 116
>>>   In fileio\private\filetype_check_header at 54
>>>   In ft_filetype at 328
>>>   In ft_prepare_layout at 253
>>>   In ft_databrowser at 226
>>> Warning: could not determine filetype of QuikCap_NSL_128
>>> > In fileio\private\warning_once at 116
>>>   In ft_filetype at 1115
>>>   In ft_prepare_layout at 253
>>>   In ft_databrowser at 226
>>> creating layout from electrode file QuikCap_NSL_128
>>> Error using ft_read_sens (line 68)
>>> file 'QuikCap_NSL_128' does not exist
>>>
>>> Error in ft_prepare_layout (line 275)
>>>   lay = sens2lay(ft_read_sens(cfg.layout), cfg.rotate, cfg.projection,
>>> cfg.style, cfg.overlap);
>>>
>>> Error in ft_databrowser (line 226)
>>>   cfg.layout = ft_prepare_layout(tmpcfg);
>>>
>>>
>>> Would anyone please help?
>>>
>>> Cheers,
>>> Hweeling
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>
>
> --
> =================================================
> Dr. rer. nat. Lee, Hwee Ling
> Postdoc
> German Center for Neurodegenerative Diseases (DZNE) Bonn
>
> Email 1: hwee-ling.lee<at>dzne.de
> Email 2: hweeling.lee<at>gmail.com
>
> https://sites.google.com/site/hweelinglee/home
>
> Correspondence Address:
> Ernst-Robert-Curtius Strasse 12, 53117, Bonn, Germany
> =================================================
>
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From hweeling.lee at gmail.com  Thu Aug 15 14:13:04 2013
From: hweeling.lee at gmail.com (Hwee Ling Lee)
Date: Thu, 15 Aug 2013 14:13:04 +0200
Subject: [FieldTrip] EEG sensor position layout again
In-Reply-To: <CAL4kA6ddn8MoCfigmDq7nWnXy-UOBRJ842yBmucehOLoDFRw4Q@mail.gmail.com>
References: <CABG7z0TdTBH=c0e4szgPsSLnDgnmZvN6gh1Q6yTSAD6rDDnoWw@mail.gmail.com>
	<CAL4kA6dXMDNUMcpiqi_1aaFYXmEHt2mTLgoT=dGH+c3L78miXQ@mail.gmail.com>
	<CABG7z0TQFuakrpr4zJDkP2TnfPvw0FwL+qqp9K_6o3owDsXFaw@mail.gmail.com>
	<CAL4kA6ddn8MoCfigmDq7nWnXy-UOBRJ842yBmucehOLoDFRw4Q@mail.gmail.com>
Message-ID: <CABG7z0SjsY7WSjM=PP5mfNq8oHY4NCv1pzRSjqV2FVVyVw92-Q@mail.gmail.com>

Hi,

Thanks for your advice. I restarted Matlab, and call for ft_defaults and
which QuikCap_NSL_128.mat, and I still get the same error message.

Also, is this the right layout file to use for my data?

Cheers,
Hweeling



On 15 August 2013 14:01, Johanna Zumer <johanna.zumer at gmail.com> wrote:

> Hi Hweeling,
>
> I just checked on my computer, and it helped to restart matlab and try
> again.  Maybe there is something strange if ft_defaults is called (again)
> during an already open session with previous calls to FT functions?
>
> Best,
> Johanna
>
>
> 2013/8/15 Hwee Ling Lee <hweeling.lee at gmail.com>
>
>> Hi,
>>
>> It states that:
>> 'QuikCap_NSL_128.mat' not found.
>>
>> However, when I checked fieldtrip/templates/layout, the mat file is
>> stored in this folder.
>>
>> Cheers,
>> Hweeling
>>
>>
>>
>> On 15 August 2013 13:33, Johanna Zumer <johanna.zumer at gmail.com> wrote:
>>
>>> Hi Hweeling,
>>>
>>> Since it says that it cannot find the Quikcap file, it sounds like it's
>>> not on your path.    Run  ft_defaults on your Matlab command, then test if
>>> the file is on your path:
>>> >> ft_defaults
>>> >> which QuikCap_NSL_128.mat
>>>
>>> Assuming it finds the file on your path, then do you still get the
>>> browser error?
>>>
>>> Best,
>>> Johanna
>>>
>>>
>>> 2013/8/15 Hwee Ling Lee <hweeling.lee at gmail.com>
>>>
>>>> Hi,
>>>>
>>>> A bit more details about my setup.
>>>>
>>>> I'm using a Easycap MRI compatible 128 channels cap. I tried to search
>>>> for a layout on the templates/layout, and I found one that might closest
>>>> fit to my needs ('QuikCap_NSL_128').
>>>> To view my components, I tried these series of commands:
>>>>
>>>> cfg = [];
>>>> cfg.viewmode = 'component';
>>>> cfg.continuous = 'yes';
>>>> cfg.layout = ft_prepare_layout('QuikCap_NSL_128');
>>>> ft_databrowser(cfg,ic_data);
>>>>
>>>> However, I was prompted with error messages:
>>>> Warning: Struct field assignment overwrites a value with class "char".
>>>> See MATLAB R14SP2 Release Notes, Assigning Nonstructure
>>>> Variables As Structures Displays Warning, for details.
>>>> > In utilities\private\ft_preamble_provenance at 49
>>>>   In ft_preamble at 54
>>>>   In ft_prepare_layout at 91
>>>> Error using ft_prepare_layout (line 582)
>>>> no layout detected, please specify cfg.layout
>>>>
>>>> Also when I tried the command,
>>>>
>>>> cfg = [];
>>>> cfg.viewmode = 'component';
>>>> cfg.continuous = 'yes';
>>>> cfg.layout = 'QuikCap_NSL_128';
>>>> ft_databrowser(cfg,ic_data);
>>>>
>>>> I get this error message:
>>>> Warning: could not open QuikCap_NSL_128
>>>> > In fileio\private\warning_once at 116
>>>>   In fileio\private\filetype_check_header at 54
>>>>   In ft_filetype at 328
>>>>   In ft_prepare_layout at 253
>>>>   In ft_databrowser at 226
>>>> Warning: could not determine filetype of QuikCap_NSL_128
>>>> > In fileio\private\warning_once at 116
>>>>   In ft_filetype at 1115
>>>>   In ft_prepare_layout at 253
>>>>   In ft_databrowser at 226
>>>> creating layout from electrode file QuikCap_NSL_128
>>>> Error using ft_read_sens (line 68)
>>>> file 'QuikCap_NSL_128' does not exist
>>>>
>>>> Error in ft_prepare_layout (line 275)
>>>>   lay = sens2lay(ft_read_sens(cfg.layout), cfg.rotate, cfg.projection,
>>>> cfg.style, cfg.overlap);
>>>>
>>>> Error in ft_databrowser (line 226)
>>>>   cfg.layout = ft_prepare_layout(tmpcfg);
>>>>
>>>>
>>>> Would anyone please help?
>>>>
>>>> Cheers,
>>>> Hweeling
>>>>
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>
>>>
>>>
>>
>>
>> --
>> =================================================
>> Dr. rer. nat. Lee, Hwee Ling
>> Postdoc
>> German Center for Neurodegenerative Diseases (DZNE) Bonn
>>
>> Email 1: hwee-ling.lee<at>dzne.de
>> Email 2: hweeling.lee<at>gmail.com
>>
>> https://sites.google.com/site/hweelinglee/home
>>
>> Correspondence Address:
>> Ernst-Robert-Curtius Strasse 12, 53117, Bonn, Germany
>> =================================================
>>
>
>


-- 
=================================================
Dr. rer. nat. Lee, Hwee Ling
Postdoc
German Center for Neurodegenerative Diseases (DZNE) Bonn

Email 1: hwee-ling.lee<at>dzne.de
Email 2: hweeling.lee<at>gmail.com

https://sites.google.com/site/hweelinglee/home

Correspondence Address:
Ernst-Robert-Curtius Strasse 12, 53117, Bonn, Germany
=================================================
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From m.kandula at uu.nl  Thu Aug 15 18:02:33 2013
From: m.kandula at uu.nl (Manasa Kandula)
Date: Thu, 15 Aug 2013 18:02:33 +0200
Subject: [FieldTrip] ft_databrowser No artifact.sampleinfo
Message-ID: <520CFB99.4060709@uu.nl>

I've been trying to use /ft_databrowser/ on segmented EEG data right 
after /ft_preprocessing/. However, at the subfunction /redraw_cb/, it's 
crashing as a call to /ft_fetch_data/ is resulting in an error as 
/opt.artdata.sampleinfo/ is not a field present in the /opt.artdata/ struct
(Error using ==> ft_fetch_data at 60 data does not contain a consistent 
trial definition, fetching data is not possible).
As far as I can tell, there is no point in the code that actually sets 
the /sampleinfo/ field for the /artifact/ struct.
Has anyone else encountered this problem?

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From pattersons076 at gmail.com  Thu Aug 15 20:01:32 2013
From: pattersons076 at gmail.com (Samantha Patterson)
Date: Thu, 15 Aug 2013 11:01:32 -0700
Subject: [FieldTrip] Fwd: error using freqdescriptives
In-Reply-To: <CACZDhUvHh-BRvcaPhKX7KXYMrSLX+fuEVqvDKZfUt7izwxBGjg@mail.gmail.com>
References: <CACZDhUvHh-BRvcaPhKX7KXYMrSLX+fuEVqvDKZfUt7izwxBGjg@mail.gmail.com>
Message-ID: <CACZDhUsnY6U5do=C0C3eJpX7sguUGJ1+Otbg-uybiZt3WpFEfg@mail.gmail.com>

Dear Fieldtrippers,


l am trying to use ft_freqdescriptives on freq data but i get an error
saying

Error using ft_checkdata (line 366)
This function requires freq or freqmvar data as input.

Error in ft_freqdescriptives (line 103)
freq = ft_checkdata(freq, 'datatype', {'freq', 'freqmvar'},
'feedback', 'yes');

Specfied cfg for freqdescriptives is

cfg = [];
cfg.foilim = [10 35];
cfg.toilim = [1.0 2.5];
cfg.keeptrials = 'yes';

test = ft_freqdescriptives(cfg,freq1);

output for freq1:

freq1

ans =

         label: {202x1 cell}
         dimord: 'rpt_chan_freq_time'
         freq: [1x22 double]
         time: [1x201 double]
         powspctrm: [4-D double]
         cumtapcnt: [26x18 double]
         grad: [1x1 struct]
         cfg: [1x1 struct]
         trialinfo: [26x3 double]

Any thoughts?

Thanks!!!!!

Samantha
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From M.Kandula at uu.nl  Thu Aug 15 22:26:54 2013
From: M.Kandula at uu.nl (Kandula, M. (Manasa))
Date: Thu, 15 Aug 2013 20:26:54 +0000
Subject: [FieldTrip] ft_databrowser No artifact.sampleinfo
In-Reply-To: <520CFB99.4060709@uu.nl>
References: <520CFB99.4060709@uu.nl>
Message-ID: <48A0B9F7F9A4BD4C836E1CC21805EB7E191D0BFC@ICTSC-W-S203.soliscom.uu.nl>

Hey all,
A minor correction.. I meant the artdata struct , not the artifact struct.
Thanks!!
Manasa
________________________________
From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Manasa Kandula [m.kandula at uu.nl]
Sent: Thursday, August 15, 2013 6:02 PM
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] ft_databrowser No artifact.sampleinfo

I've been trying to use ft_databrowser on segmented EEG data right after ft_preprocessing. However, at the subfunction redraw_cb, it's crashing as a call to ft_fetch_data is resulting in an error as opt.artdata.sampleinfo is not a field present in the opt.artdata struct
(Error using ==> ft_fetch_data at 60 data does not contain a consistent trial definition, fetching data is not possible).
As far as I can tell, there is no point in the code that actually sets the sampleinfo field for the artifact struct.
Has anyone else encountered this problem?

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From mbj0310 at gmail.com  Sun Aug 18 14:31:53 2013
From: mbj0310 at gmail.com (Beom Jun Min)
Date: Sun, 18 Aug 2013 21:31:53 +0900
Subject: [FieldTrip] Visualizing grand-averaged ERPs with different channels
Message-ID: <CA+v9jv+02_xb8sd-rQR14nqf5iA9Rs3HxYfbVgVx1=q+50YKkw@mail.gmail.com>

Dear all.

Hello

What I want to do is visualizing ERPs in different channels, simultaneously
in a single figure window.
For example, CZ, CPZ, & PZ or P4 & P5 in a group.

I use ft_singleplotER like below

*figure; *
*cfg = [];*
*cfg.ylim = [-8 8];*
*cfg.baseline = [-0.2 0];*
*cfg.linewidth = [2];*
*ft_singleplotER(cfg, group1_CP4, group1_CP3)*

I succeeded visualizing 3 different groups simultaneously with certain same
channel using the same manner above. (cfg, group1_CZ, group2_CZ)
However, when I try the same code with different channels, the result only
to show mean value (e.g. mean(CP4).

I do not know how to solve it.
Please help me.

With regards.

-- 
BeomJun Min, M.D.

Department of Medical System Engineering (DMSE)
Gwangju Institute of Science and Technology (GIST)
261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
500-712, Republic of Korea (South)
Phone: +82-62-715-3266 / Fax: +82-62-715-3244
E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
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From Sara.Bogels at mpi.nl  Mon Aug 19 11:39:54 2013
From: Sara.Bogels at mpi.nl (=?ISO-8859-1?Q?Sara_B=F6gels?=)
Date: Mon, 19 Aug 2013 11:39:54 +0200
Subject: [FieldTrip] problem with ft_multiplotER
In-Reply-To: <51E6838F.3050302@donders.ru.nl>
References: <CAPjpx=wTC727vv5fzqX_DdP-7wZi968TC13mkQR-bx80Faa-Zw@mail.gmail.com>
	<51E67229.8040001@mpi.nl> <51E6838F.3050302@donders.ru.nl>
Message-ID: <5211E7EA.8090907@mpi.nl>

Hi Jörn and others,

Some time ago, I posted the question below to the mailinglist. I now 
have had this error many times for both ft_timelockgrandaverage and 
ft_multiplotER. It happens for some datasets but not others and this 
appears quite random to me. The error message is:

"Subscripted assignment dimension mismatch"
Error in ft_timelockgrandaverage (line 182).
avgmat(s,:,:) = varargin{s}.(cfg.parameter{k});


It appears to have something to do with the different time limits of the 
different data I want to average or plot. I use cfg.latency to make sure 
the latency falls within the time limits of all files but this sometimes 
still does not help.

Any ideas?

Thank you,
Sara

"Jörn M. Horschig" wrote:
> Dear Sara,
>
> What you describe sounds like a bug to me. It looks like that in these
> lines the averages of the two conditions should be concatenated into one
> matrix, and apparently something goes wrong. However, you truncated the
> error message a bit (you pasted the line where the error occurs, but not
> the error message itself). If one of us developers should look into this
> further, it would be great if you register and create a bugreport on
> bugzilla.fconders.nl. Preferably would be to upload a snippet of your
> data, e.g. timelockstructures of one participant, and some lines of code
> which reproduce the error. We can then look into this further and fix
> this as soon as possible :)
>
> Best,
> Jörn
>
> On 7/17/2013 12:30 PM, Sara Bögels wrote:
>> Hi all,
>>
>> I have a very specific problem with the ft_multiplotER function. For 2
>> of my 24 participants, the function gives an error-message when I try
>> to plot the averages of two conditions at the same time. Plotting them
>> one by one is not a problem. There appears to be a specific point in
>> time (different for the two participants) when this goes wrong. If I
>> avoid that time (by using cfg.xlim) it works fine. My trials have
>> different lengths and I used "cfg.vartrllength = 2;" when calling
>> ft_timelockanalysis (not sure whether this is relevant).
>>
>> The error message I get is
>> "Error in ft_multiplotER (line 616)
>> yval(i,:) = datamatrix{i}(m,:);"
>>
>> I cannot find out what happens in this line. Can anyone tell me what
>> this might be referring to?
>>
>> Thank you,
>> Sara
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>


From frank.ye.mei at gmail.com  Mon Aug 19 22:18:39 2013
From: frank.ye.mei at gmail.com (Ye Mei)
Date: Mon, 19 Aug 2013 16:18:39 -0400
Subject: [FieldTrip] Can beamformer give both the location and the
 orientation of the source?
Message-ID: <52127D9F.3090102@gmail.com>

Hi all,

Can beamformer give both the location and the orientation of the source? 
If yes, how to do it in fieldtrip?

thanks ahead,
Ye




From arr at uvic.ca  Mon Aug 19 22:47:27 2013
From: arr at uvic.ca (Ashley Rose)
Date: Mon, 19 Aug 2013 13:47:27 -0700
Subject: [FieldTrip] fieldtrip question
Message-ID: <314d3147c1b422e458d033e10d7a6b17.squirrel@wm3.uvic.ca>


Hi there,

I'm having an issue running Fieldtrip.  I keep getting this warning:
"Warning: Dimensions of AlphaData must be 1x1, or must match CData."
But I haven't done anything to AlphaData or CData that would make them
inconsistent.  Has anyone had this problem before?

Thank you,
Ashley Rose




From imponderabilion at gmail.com  Tue Aug 20 00:54:49 2013
From: imponderabilion at gmail.com (=?ISO-8859-2?Q?Miko=B3aj_Magnuski?=)
Date: Tue, 20 Aug 2013 00:54:49 +0200
Subject: [FieldTrip] ft_neighbourplot does not plot new connections in 3D
Message-ID: <CAOb=78enLVbZZcApNNBGJALm=rZAtHH7CqiUqSSAimiDJYbmzw@mail.gmail.com>

Hi FieldTrippers!

just a short note in case it wasn'r reported before:
ft_neighbourplot with option .enableedit = 'on' (the bleeding option)
plots new connections (new - that means click-created) only as 2D
projections even if everything else is plotted in 3D.

changing lines 286 - 287 to something like:
    if size(proj,2) == 2
        Coord = {X, Y};
    elseif size(proj,2) > 2
        Z = [proj(curSensId,3) proj(lastSensId,3)];
        Coord = {X, Y, Z};
    end
    hl(curSensId, lastSensId) = line(Coord{:}, 'color', 'r');
    hl(lastSensId, curSensId) = line(Coord{:}, 'color', 'r');

fixes this problem.


Regards,
Mikołaj Magnuski
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From jm.horschig at donders.ru.nl  Fri Aug 23 09:28:18 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Fri, 23 Aug 2013 09:28:18 +0200
Subject: [FieldTrip] ft_neighbourplot does not plot new connections in 3D
In-Reply-To: <CAOb=78enLVbZZcApNNBGJALm=rZAtHH7CqiUqSSAimiDJYbmzw@mail.gmail.com>
References: <CAOb=78enLVbZZcApNNBGJALm=rZAtHH7CqiUqSSAimiDJYbmzw@mail.gmail.com>
Message-ID: <52170F12.9020107@donders.ru.nl>

Dear Miko?aj,

thanks very much for reporting this. I fixed it and the fix should be 
available inthe next FieldTrip release (i.e. tomorrow).

Best,
Jörn

On 8/20/2013 12:54 AM, Miko?aj Magnuski wrote:
> Hi FieldTrippers!
>
> just a short note in case it wasn'r reported before:
> ft_neighbourplot with option .enableedit = 'on' (the bleeding option)
> plots new connections (new - that means click-created) only as 2D
> projections even if everything else is plotted in 3D.
>
> changing lines 286 - 287 to something like:
>     if size(proj,2) == 2
>         Coord = {X, Y};
>     elseif size(proj,2) > 2
>         Z = [proj(curSensId,3) proj(lastSensId,3)];
>         Coord = {X, Y, Z};
>     end
>     hl(curSensId, lastSensId) = line(Coord{:}, 'color', 'r');
>     hl(lastSensId, curSensId) = line(Coord{:}, 'color', 'r');
>
> fixes this problem.
>
>
> Regards,
> Miko?aj Magnuski
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From narayan.ps at tut.fi  Fri Aug 23 12:37:20 2013
From: narayan.ps at tut.fi (Narayan Puthanmadam Subramaniyam)
Date: Fri, 23 Aug 2013 13:37:20 +0300
Subject: [FieldTrip] simulation of EOG
Message-ID: <001501ce9fec$bee80ce0$3cb826a0$@tut.fi>

Dear FT experts

I am not sure if I should be asking this question here. I want to simulate
'pure' EOG signal by placing rotating dipole in the eye. Can I use FT to
compute the lead field matrix from eye to  all scalp electrodes ? Has anyone
used a BEM model where eyes are segmented ?

Many Thanks
Narayan



From ingenieureniso at gmail.com  Fri Aug 23 19:40:14 2013
From: ingenieureniso at gmail.com (ingenieur eniso)
Date: Fri, 23 Aug 2013 18:40:14 +0100
Subject: [FieldTrip] how to open bdf and rdf files
Message-ID: <CAPjpx=yj73grOv58wwiLF4Ec2fLGzAiNpy7ziDZGpb+Lphynsg@mail.gmail.com>

Dear all,


I have EEG record files in rdf and bdf formats. but I do not know how to
open them.

Please can anyone send me a matlab function to open these files?

I hope you will send me positive and helpful response.

Thanks a lot in advance!

Best,

ahmed
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From johanna.zumer at gmail.com  Sun Aug 25 07:18:14 2013
From: johanna.zumer at gmail.com (Johanna Zumer)
Date: Sun, 25 Aug 2013 07:18:14 +0200
Subject: [FieldTrip] how to open bdf and rdf files
In-Reply-To: <CAPjpx=yj73grOv58wwiLF4Ec2fLGzAiNpy7ziDZGpb+Lphynsg@mail.gmail.com>
References: <CAPjpx=yj73grOv58wwiLF4Ec2fLGzAiNpy7ziDZGpb+Lphynsg@mail.gmail.com>
Message-ID: <CAL4kA6dwgo31sL43OMwpruHyOnF5O8MZW0Ha-Z682HfNs8gc=A@mail.gmail.com>

Dear Ahmed,

Does this help?  (http://fieldtrip.fcdonders.nl/getting_started/bdf )

If you are still stuck, maybe try EEGlab
import<http://sccn.ucsd.edu/wiki/A01:_Importing_Continuous_and_Epoched_Data>
and
then convert EEGlab format to FieldTrip format (
http://fieldtrip.fcdonders.nl/integrating_with/integrating_with_eeglab)

Best,
Johanna


2013/8/23 ingenieur eniso <ingenieureniso at gmail.com>

> Dear all,
>
>
> I have EEG record files in rdf and bdf formats. but I do not know how to
> open them.
>
> Please can anyone send me a matlab function to open these files?
>
> I hope you will send me positive and helpful response.
>
> Thanks a lot in advance!
>
> Best,
>
> ahmed
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From roeysc at gmail.com  Mon Aug 26 00:08:19 2013
From: roeysc at gmail.com (Roey Schurr)
Date: Mon, 26 Aug 2013 01:08:19 +0300
Subject: [FieldTrip] Source Analysis Normalisation in-subject and in-group
Message-ID: <CAHm4wZAWwHisWEPd41qxe6EiNAgkh_vqv2eMWvaGpNWdRQ1xww@mail.gmail.com>

Hi all,

We have a question regarding normalisation of EEG signals for source
reconstruction analysis.

We have EEG records (not ERP) of a few patients in two different conditions
(each condition consists of several 2 seconds segments/trials). Each
recording was done over a period of a few days, and in different sessions.
We also have anatomycal MRI scans for each patient (subject).

We would like to make two statistic comparisons:

1.    Compare the source analysis of the two conditions in each subject.

2.    Compare the source analysis of the two conditions, based upon all
subjects.

For the first comparison, we are puzzled about the appropriate way to
normalise and standardize our data, since each EEG segment was recorded at
a different time, and hence may be affected by different electrode
conductivity, for example. How would you normalise the data?

For the second comparison, of course, we would like to normalise the source
analysis results in the anatomycal level using ft_volumenormalise.

However, we are puzzled about the appropriate way to normalise and
standardize our data, since subjects differ from each other (for example,
anatomycally, resulting in changes of power spectrum).

How would you standartize the data between subjects?



Thank you very much,

best regards,

Aia and Roey
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From polomacnenad at gmail.com  Tue Aug 27 20:44:39 2013
From: polomacnenad at gmail.com (Nenad Polomac)
Date: Tue, 27 Aug 2013 20:44:39 +0200
Subject: [FieldTrip] ICA on highpass filtered MEG data
Message-ID: <CAEk4EpFExFt8U85CfTjz0MPQPQhOrV7R4LdCqLkVRjvahywiUQ@mail.gmail.com>

Dear Fieldtrip users,

I have CTF 275 channels MEG data and I am interested in gamma band. For
this purpose I would like to remove microsaccade artifacts from the data
using the ICA. In order to obtain the microsacade components I have
filtered data ( highpass and lowpass; 30-150 Hz) and than I've wanted to
run ICA calculation. However, I've read here
http://sccn.ucsd.edu/pipermail/eeglablist/2013/006710.html that after
filtering data are more dependent and that is a big problem for ICA
calculation. And I also experienced that ICA takes very long time and
sometimes doesn't converge. So, to overcome this problem, the data
dimensionality has to be reduced. I have found two different solutions from
different sources.

One solution might be to estimate variance with PCA and than choose the
amount of variance that should stay in the data. e.g.
[COEFF,SCORE,eigenvalues ] = princomp(data_matrix);
A= cumsum(eigenvalues);
num_of_comp=find(A/A(end)>0.98,1); % 98% is the percentage of variance that
will be used for the ICA, 2% will be discarded
This percentage will be the same for all subjects.

The second option might be to use the same eigenvalue cutoff value for all
subjects:
[COEFF,SCORE,eigenvalues ] = princomp(data_matrix);
A=(find(eigenvalues>0.005));  %0.005 here is just for example
num_of_comp=A(end);

The variable num_of_comp represents the number of component to which
filtered data will be reduced before ICA.
e.g.
    cfg = [];
    cfg.method = 'runica';
    cfg.runica.pca = num_of_comp;
    cfg.runica.maxsteps = 600;
    cfg.runica.stop = 1e-7;
    cfg.runica.extended = 1;
    ica_comp = ft_componentanalysis(cfg, data);



Finally, my question is which of this two methods is more objective? And is
there any other possibility I should consider?
I would like to add that in my case second calculation gives me less
variant number of components among 22 subjects.

Thank you in advance!

All the best!
Nenad
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From aaron.schurger at gmail.com  Tue Aug 27 21:49:21 2013
From: aaron.schurger at gmail.com (Aaron Schurger)
Date: Tue, 27 Aug 2013 21:49:21 +0200
Subject: [FieldTrip] ICA on highpass filtered MEG data
In-Reply-To: <CAEk4EpFExFt8U85CfTjz0MPQPQhOrV7R4LdCqLkVRjvahywiUQ@mail.gmail.com>
References: <CAEk4EpFExFt8U85CfTjz0MPQPQhOrV7R4LdCqLkVRjvahywiUQ@mail.gmail.com>
Message-ID: <CALeeyASWNx4+ZMfZuDqY-cfvrXma-0BquHNsbWUFrcE2xpjvCw@mail.gmail.com>

I am not aware of any good way to remove microsaccade artifacts from
EEG or MEG data. ICA might find a microsaccade component if you have
sufficient data, but you will have to hunt through the components to
find the "right" one. The difficult question is how to know which is
the right component, or whether or not microsaccades are incorporated
into two or more components (or not at all). Having an MEG-compatible
eye tracker with a high sampling rate is what I would want.
Best wishes,
Aaron

On Tue, Aug 27, 2013 at 8:44 PM, Nenad Polomac <polomacnenad at gmail.com> wrote:
> Dear Fieldtrip users,
>
> I have CTF 275 channels MEG data and I am interested in gamma band. For this
> purpose I would like to remove microsaccade artifacts from the data using
> the ICA. In order to obtain the microsacade components I have filtered data
> ( highpass and lowpass; 30-150 Hz) and than I've wanted to run ICA
> calculation. However, I've read here
> http://sccn.ucsd.edu/pipermail/eeglablist/2013/006710.html that after
> filtering data are more dependent and that is a big problem for ICA
> calculation. And I also experienced that ICA takes very long time and
> sometimes doesn't converge. So, to overcome this problem, the data
> dimensionality has to be reduced. I have found two different solutions from
> different sources.
>
> One solution might be to estimate variance with PCA and than choose the
> amount of variance that should stay in the data. e.g.
> [COEFF,SCORE,eigenvalues ] = princomp(data_matrix);
> A= cumsum(eigenvalues);
> num_of_comp=find(A/A(end)>0.98,1); % 98% is the percentage of variance that
> will be used for the ICA, 2% will be discarded
> This percentage will be the same for all subjects.
>
> The second option might be to use the same eigenvalue cutoff value for all
> subjects:
> [COEFF,SCORE,eigenvalues ] = princomp(data_matrix);
> A=(find(eigenvalues>0.005));  %0.005 here is just for example
> num_of_comp=A(end);
>
> The variable num_of_comp represents the number of component to which
> filtered data will be reduced before ICA.
> e.g.
>     cfg = [];
>     cfg.method = 'runica';
>     cfg.runica.pca = num_of_comp;
>     cfg.runica.maxsteps = 600;
>     cfg.runica.stop = 1e-7;
>     cfg.runica.extended = 1;
>     ica_comp = ft_componentanalysis(cfg, data);
>
>
>
> Finally, my question is which of this two methods is more objective? And is
> there any other possibility I should consider?
> I would like to add that in my case second calculation gives me less variant
> number of components among 22 subjects.
>
> Thank you in advance!
>
> All the best!
> Nenad
>
>
>
>
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



-- 
Aaron Schurger, PhD
Post-doctoral researcher
INSERM U992 / NeuroSpin
CEA - Saclay, France
+33-1-69-08-66-47
aaron.schurger at gmail.com
http://www.unicog.org


From sreenivasan.r.nadar at gmail.com  Tue Aug 27 22:17:03 2013
From: sreenivasan.r.nadar at gmail.com (Sreenivasan R. Nadar, Ph.D.)
Date: Tue, 27 Aug 2013 16:17:03 -0400
Subject: [FieldTrip] 19 channel EEG for source modeling of epileptic focus
Message-ID: <CAL+KoxgGx-BfL77H2VNL3dssfuB2FNAO5wFOB6p-gEKFLdNVFg@mail.gmail.com>

Hi All,

I have a 19 channel Nihon - Kohden EEG for epilepsy monitoring and I use
the following file for channel locations in
ftp://sccn.ucsd.edu/pub/locfiles/eeglab/Standard-10-20-Cap19.ced for data
analysis in EEGLab.

Please let me know if anybody has pre-processing script to import the data
in Fieldtrip and also for source localisation of epileptic focus.

Thank you.

Sreenivasan
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From jm.horschig at donders.ru.nl  Thu Aug 29 10:02:45 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Thu, 29 Aug 2013 10:02:45 +0200
Subject: [FieldTrip] 19 channel EEG for source modeling of epileptic
	focus
In-Reply-To: <CAL+KoxgGx-BfL77H2VNL3dssfuB2FNAO5wFOB6p-gEKFLdNVFg@mail.gmail.com>
References: <CAL+KoxgGx-BfL77H2VNL3dssfuB2FNAO5wFOB6p-gEKFLdNVFg@mail.gmail.com>
Message-ID: <521F0025.8090104@donders.ru.nl>

Dear Sreenivasan,

I am not sure whether you can read in .ced files with the ft_read_sens 
function. You could give it a try though by specifying cfg.elecfile = 
'PATH_TO_FILE/Standard-10-20-Cap19.ced'

Otherwise, I can see two ways how you can make this work.
First, you could change the content of the file to match the format of 
the other sensor-templates. For this, you can best have a look in 
fieldtrip/template/elec and have a look at one of these files. Then, you 
would need to rearrange the values of your .ced file to match the order 
of the .elc-format.
Alternatively, you could write your own wrapper function, which reads in 
the x-, y- and z-position of the electrodes from the .ced file and 
stores them in a matrix. Also, you need to store the corresponding 
channel label. Using these, you can create an elec-structure that you 
can use as cfg.elec for whatever function you want to do.

Maybe someone else here has worked with .ced files before and can thus 
can help with either of the two solutions. Good luck :)

Best,
Jörn

On 8/27/2013 10:17 PM, Sreenivasan R. Nadar, Ph.D. wrote:
> Hi All,
>
> I have a 19 channel Nihon - Kohden EEG for epilepsy monitoring and I 
> use the following file for channel locations in 
> ftp://sccn.ucsd.edu/pub/locfiles/eeglab/Standard-10-20-Cap19.ced for 
> data analysis in EEGLab.
>
> Please let me know if anybody has pre-processing script to import the 
> data in Fieldtrip and also for source localisation of epileptic focus.
>
> Thank you.
>
> Sreenivasan
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From ben.vanlier at bsse.ethz.ch  Thu Aug 29 13:53:26 2013
From: ben.vanlier at bsse.ethz.ch (van Lier  Ben)
Date: Thu, 29 Aug 2013 11:53:26 +0000
Subject: [FieldTrip] slow reading with ft_preprocessing of a fcdc_matbin
	file?
Message-ID: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A7B87E@MBX13.d.ethz.ch>

Hi all,

I have a pretty big data file of 120 channels for 20min continuous at 20khz. clearly i need to downsample. to do so, i convert the original file to fcdc_matbin, creating a 22gb bin file with all the data.

then its time for downsampling as shown on http://fieldtrip.fcdonders.nl/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory

this is very slow. ft_preprocessing takes 230 seconds per channel (using 380 mb), doing nothing but just reading 1 channel. the subsequent downsampling with ft_resample to 1khz is surprisingly fast with only 4 seconds.

does that make any sense? it seems like a very long time to read in 380mb... :(

Best,
Ben



From jan.schoffelen at donders.ru.nl  Thu Aug 29 14:01:59 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 29 Aug 2013 14:01:59 +0200
Subject: [FieldTrip] slow reading with ft_preprocessing of a fcdc_matbin
	file?
In-Reply-To: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A7B87E@MBX13.d.ethz.ch>
References: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A7B87E@MBX13.d.ethz.ch>
Message-ID: <264BF553-0691-4AC9-95B8-D78000F0CA6B@donders.ru.nl>

Hi Ben,

I guess MATLAB needs to read in the whole datafile each time (for each channel). What about creating separate files for each channel?

JM


On Aug 29, 2013, at 1:53 PM, van Lier Ben wrote:

> Hi all,
> 
> I have a pretty big data file of 120 channels for 20min continuous at 20khz. clearly i need to downsample. to do so, i convert the original file to fcdc_matbin, creating a 22gb bin file with all the data.
> 
> then its time for downsampling as shown on http://fieldtrip.fcdonders.nl/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory
> 
> this is very slow. ft_preprocessing takes 230 seconds per channel (using 380 mb), doing nothing but just reading 1 channel. the subsequent downsampling with ft_resample to 1khz is surprisingly fast with only 4 seconds.
> 
> does that make any sense? it seems like a very long time to read in 380mb... :(
> 
> Best,
> Ben
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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